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Trinh IV, Desai SP, Ley SH, Mo Z, Satou R, Pridjian GC, Longo SA, Shaffer JG, Robinson JE, Norton EB, Piedimonte G. Prenatal Infection by Respiratory Viruses Is Associated with Immunoinflammatory Responses in the Fetus. Am J Respir Crit Care Med 2024; 209:693-702. [PMID: 38051928 PMCID: PMC10945055 DOI: 10.1164/rccm.202308-1461oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023] Open
Abstract
Rationale: Respiratory viral infections can be transmitted from pregnant women to their offspring, but frequency, mechanisms, and postnatal outcomes remain unclear. Objectives: The aims of this prospective cohort study were to compare the frequencies of transplacental transmission of respiratory syncytial virus (RSV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), analyze the concentrations of inflammatory mediators in maternal and fetal blood, and assess clinical consequences. Methods: We recruited pregnant women who developed upper respiratory infections or tested positive for SARS-CoV-2. Maternal and cord blood samples were collected at delivery. Study questionnaires and electronic medical records were used to document demographic and medical information. Measurements and Main Results: From October 2020 to June 2022, droplet digital PCR was used to test blood mononuclear cells from 103 mother-baby dyads. Twice more newborns in our sample were vertically infected with RSV compared with SARS-CoV-2 (25.2% [26 of 103] vs. 11.9% [12 of 101]; P = 0.019). Multiplex ELISA measured significantly increased concentrations of several inflammatory cytokines and chemokines in maternal and cord blood from newborns, with evidence of viral exposure in utero compared with control dyads. Prenatal infection was associated with significantly lower birth weight and postnatal weight growth. Conclusions: Data suggest a higher frequency of vertical transmission for RSV than SARS-CoV-2. Intrauterine exposure is associated with fetal inflammation driven by soluble inflammatory mediators, with expression profiles dependent on the virus type and affecting the rate of viral transmission. Virus-induced inflammation may have pathological consequences already in the first days of life, as shown by its effects on birth weight and postnatal weight growth.
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Affiliation(s)
| | | | | | | | | | | | - Sherri A. Longo
- Department of Pediatrics, Ochsner Medical Center, New Orleans, Louisiana
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana; and
| | | | | | - Giovanni Piedimonte
- Department of Pediatrics
- Department of Biochemistry and Molecular Biology, School of Medicine, and
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2
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Tea K, Zu Y, Chung CH, Pagliaro J, Espinoza-Barrera D, Mehta P, Grewal H, Douglas IS, Khan YA, Shaffer JG, Denson JL. The Relationship Between Metabolic Syndrome and Mortality Among Patients With Acute Respiratory Distress Syndrome in Acute Respiratory Distress Syndrome Network and Prevention and Early Treatment of Acute Lung Injury Network Trials. Crit Care Med 2024; 52:407-419. [PMID: 37909824 PMCID: PMC10922467 DOI: 10.1097/ccm.0000000000006092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
OBJECTIVES Metabolic syndrome is known to predict outcomes in COVID-19 acute respiratory distress syndrome (ARDS) but has never been studied in non-COVID-19 ARDS. We therefore aimed to determine the association of metabolic syndrome with mortality among ARDS trial subjects. DESIGN Retrospective cohort study of ARDS trials' data. SETTING An ancillary analysis was conducted using data from seven ARDS Network and Prevention and Early Treatment of Acute Lung Injury Network randomized trials within the Biologic Specimen and Data Repository Information Coordinating Center database. PATIENTS Hospitalized patients with ARDS and metabolic syndrome (defined by obesity, diabetes, and hypertension) were compared with similar patients without metabolic syndrome (those with less than three criteria). INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS The primary outcome was 28-day mortality. Among 4288 ARDS trial participants, 454 (10.6%) with metabolic syndrome were compared with 3834 controls (89.4%). In adjusted analyses, the metabolic syndrome group was associated with lower 28-day and 90-day mortality when compared with control (adjusted odds ratio [aOR], 0.70 [95% CI, 0.55-0.89] and 0.75 [95% CI, 0.60-0.95], respectively). With each additional metabolic criterion from 0 to 3, adjusted 28-day mortality was reduced by 18%, 22%, and 40%, respectively. In subgroup analyses stratifying by ARDS etiology, mortality was lower for metabolic syndrome vs. control in ARDS caused by sepsis or pneumonia (at 28 d, aOR 0.64 [95% CI, 0.48-0.84] and 90 d, aOR 0.69 [95% CI, 0.53-0.89]), but not in ARDS from noninfectious causes (at 28 d, aOR 1.18 [95% CI, 0.70-1.99] and 90 d, aOR 1.26 [95% CI, 0.77-2.06]). Interaction p = 0.04 and p = 0.02 for 28- and 90-day comparisons, respectively. CONCLUSIONS Metabolic syndrome in ARDS was associated with a lower risk of mortality in non-COVID-19 ARDS. The relationship between metabolic inflammation and ARDS may provide a novel biological pathway to be explored in precision medicine-based trials.
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Affiliation(s)
- Kevin Tea
- Section of Pulmonary Diseases, Critical Care, and Environmental Medicine, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA
| | - Yuanhao Zu
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA
| | - Cheng Han Chung
- Section of Pulmonary Diseases, Critical Care, and Environmental Medicine, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA
| | - Jaclyn Pagliaro
- Section of Pulmonary Diseases, Critical Care, and Environmental Medicine, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA
| | - Diana Espinoza-Barrera
- Section of Pulmonary Diseases, Critical Care, and Environmental Medicine, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA
| | - Prakriti Mehta
- Section of Pulmonary Diseases, Critical Care, and Environmental Medicine, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA
| | - Himmat Grewal
- Section of Pulmonary Diseases, Critical Care, and Environmental Medicine, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA
| | - Ivor S Douglas
- Division of Pulmonary Sciences and Critical Care Medicine, Denver Health Medical Center, Denver, CO
| | - Yasin A Khan
- Section of Pulmonary Diseases, Critical Care, and Environmental Medicine, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Jeffrey G Shaffer
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA
| | - Joshua L Denson
- Section of Pulmonary Diseases, Critical Care, and Environmental Medicine, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA
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3
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Toure M, Shaffer JG, Sanogo D, Keita S, Keita M, Kane F, Traore B, Dabitao D, Kone A, Doumbia CO, Keating J, Yukich J, Hansson HH, Barry AE, Diakité M, Alifrangis M, Doumbia S. Seasonal Malaria Chemoprevention Therapy in Children Up To 9 Years of Age: Protocol for a Cluster-Randomized Trial Study. JMIR Res Protoc 2024; 13:e51660. [PMID: 38252481 PMCID: PMC10845024 DOI: 10.2196/51660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND Seasonal malaria chemoprevention (SMC) is recommended by the World Health Organization for the sub-Sahel region in sub-Saharan Africa for preventing malaria in children 3 months old to younger than 5 years. Since 2016, the Malian National Malaria Control Program has deployed SMC countrywide during its high malaria transmission season at a rate of 4 monthly cycles annually. The standard SMC regimen includes sulfadoxine-pyrimethamine (SP) plus amodiaquine (AQ). Resistance against SP is suspected to be rising across West Africa; therefore, assessing the effectiveness of an alternative antimalarial drug for SMC is needed to provide a second-line regimen when it is ultimately needed. It is not well understood whether SMC effectively prevents malaria in children aged 5 years or older. OBJECTIVE The primary goal of the study is to compare 2 SMC regimens (SP-AQ and dihydroartemisinin-piperaquine [DHA-PQ]) in preventing uncomplicated Plasmodium falciparum malaria in children 3 months to 9 years old. Secondly, we will assess the possible use of DHA-PQ as an alternative SMC drug in areas where resistance to SP or AQ may increase following intensive use. METHODS The study design is a 3-arm cluster-randomized design comparing the SP-AQ and DHA-PQ arms in 2 age groups (younger than 5 years and 5-9 years) and a control group for children aged 5-9 years. Standard SMC (SP-AQ) for children younger than 5 years was provided to the control arm, while SMC with SP-AQ was delivered to children aged 3 months to 9 years (arm 2), and SMC with DHA-PQ will be implemented in study arm 3 for children up to 9 years of age. The study was performed in Mali's Koulikoro District, a rural area in southwest Mali with historically high malaria transmission rates. The study's primary outcome is P falciparum incidence for 2 SMC regimens in children up to 9 years of age. Should DHA-PQ provide an acceptable alternative to SP-AQ, a plausible second-line prevention option would be available in the event of SP resistance or drug supply shortages. A significant byproduct of this effort included bolstering district health information systems for rapid identification of severe malaria cases. RESULTS The study began on July 1, 2019. Through November 2022, a total of 4556 children 3 months old to younger than 5 years were enrolled. Data collection ended in spring 2023, and the findings are expected to be published later in early 2024. CONCLUSIONS Routine evaluation of antimalarial drugs is needed to establish appropriate SMC age targets. The study goals here may impact public health policy and provide alternative therapies in the event of drug shortages or resistance. TRIAL REGISTRATION ClinicalTrials.gov NCT04149106, https://clinicaltrials.gov/ct2/show/NCT04149106. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/51660.
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Affiliation(s)
- Mahamoudou Toure
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| | - Jeffrey G Shaffer
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Daouda Sanogo
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| | - Soumba Keita
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| | - Moussa Keita
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| | - Fousseyni Kane
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| | - Bourama Traore
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| | - Djeneba Dabitao
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| | - Aissata Kone
- Mali National Malaria Control Program, Bamako, Mali
| | - Cheick Oumar Doumbia
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| | - Joseph Keating
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Joshua Yukich
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Helle H Hansson
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Alyssa E Barry
- Institute for Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, Melbourne, Australia
- Life Sciences Discipline, Burnet Institute, Melbourne, Australia
| | - Mahamadou Diakité
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
| | - Michael Alifrangis
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Seydou Doumbia
- University Clinical Research Center, Universite des Sciences, des Techniques et des Technologies, Bamako, Mali
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Howell MM, Olajiga OM, Cardenas JC, Parada-Higuera CA, Gonzales-Pabon MU, Gutierrez-Silva LY, Jaimes-Villamizar L, Werner BM, Shaffer JG, Manuzak JA, Londono-Renteria B. Mosquito Salivary Antigens and Their Relationship to Dengue and P. vivax Malaria. Pathogens 2024; 13:52. [PMID: 38251359 PMCID: PMC10818852 DOI: 10.3390/pathogens13010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/10/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024] Open
Abstract
In tropical areas, the simultaneous transmission of multiple vector-borne diseases is common due to ecological factors shared by arthropod vectors. Malaria and dengue virus, transmitted by Anopheles and Aedes mosquitoes, respectively, are among the top vector-borne diseases that cause significant morbidity and mortality in endemic areas. Notably, tropical areas often have suitable conditions for the co-existence of these mosquito species, highlighting the importance of identifying markers that accurately indicate the risk of acquiring each specific disease entity. Aedes are daytime-biting mosquitoes, while Anopheles preferentially bite during the night. These biting patterns raise the possibility of concurrent exposure to bites from both species. This is important because mosquito saliva, deposited in the skin during blood feeding, induces immune responses that modulate pathogen establishment and infection. Previous studies have focused on characterizing such effects on the vector-pathogen interface for an individual pathogen and its mosquito vector. In this study, we evaluated associations between immune responses to salivary proteins from non-dengue and non-malaria vector mosquito species with clinical characteristics of malaria and dengue, respectively. Surprisingly, antibody responses against Anopheles antigens in dengue patients correlated with red blood cell count and hematocrit, while antibody responses against Aedes proteins were associated with platelet count in malaria patients. Our data indicate that concurrent exposure to multiple disease-carrying mosquito vectors and their salivary proteins with differing immunomodulatory properties could influence the transmission, pathogenesis, and clinical presentation of malaria, dengue fever, and other vector-borne illnesses.
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Affiliation(s)
- McKenna M. Howell
- Arbovirology Laboratory, Department of Tropical Medicine and Infectious Disease, Tulane University, New Orleans, LA 70112, USA; (M.M.H.); (J.C.C.)
| | - Olayinka M. Olajiga
- Arbovirology Laboratory, Department of Tropical Medicine and Infectious Disease, Tulane University, New Orleans, LA 70112, USA; (M.M.H.); (J.C.C.)
| | - Jenny C. Cardenas
- Arbovirology Laboratory, Department of Tropical Medicine and Infectious Disease, Tulane University, New Orleans, LA 70112, USA; (M.M.H.); (J.C.C.)
| | | | | | | | | | - Brett M. Werner
- College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA;
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA;
| | - Jennifer A. Manuzak
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA;
| | - Berlin Londono-Renteria
- Arbovirology Laboratory, Department of Tropical Medicine and Infectious Disease, Tulane University, New Orleans, LA 70112, USA; (M.M.H.); (J.C.C.)
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5
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Pan K, Jukic AM, Mishra GD, Mumford SL, Wise LA, Schisterman EF, Ley SH, Charlton BM, Chavarro JE, Hart JE, Sidney S, Xiong X, Barbosa-Leiker C, Schliep K, Shaffer JG, Bazzano LA, Harville EW. The association between preconception cannabis use and gestational diabetes mellitus: The Preconception Period Analysis of Risks and Exposures Influencing health and Development (PrePARED) consortium. Paediatr Perinat Epidemiol 2024; 38:69-85. [PMID: 37751914 PMCID: PMC11000150 DOI: 10.1111/ppe.13008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/28/2023]
Abstract
BACKGROUND The metabolic changes that ultimately lead to gestational diabetes mellitus (GDM) likely begin before pregnancy. Cannabis use might increase the risk of GDM by increasing appetite or promoting fat deposition and adipogenesis. OBJECTIVES We aimed to assess the association between preconception cannabis use and GDM incidence. METHODS We analysed individual-level data from eight prospective cohort studies. We identified the first, or index, pregnancy (lasting ≥20 weeks of gestation with GDM status) after cannabis use. In analyses of pooled individual-level data, we used logistic regression to estimate study-type-specific odds ratios (OR) and 95% confidence intervals (CI), adjusting for potential confounders using random effect meta-analysis to combine study-type-specific ORs and 95% CIs. Stratified analyses assessed potential effect modification by preconception tobacco use and pre-pregnancy body mass index (BMI). RESULTS Of 17,880 participants with an index pregnancy, 1198 (6.7%) were diagnosed with GDM. Before the index pregnancy, 12.5% of participants used cannabis in the past year. Overall, there was no association between preconception cannabis use in the past year and GDM (OR 0.97, 95% CI 0.79, 1.18). Among participants who never used tobacco, however, those who used cannabis more than weekly had a higher risk of developing GDM than those who did not use cannabis in the past year (OR 2.65, 95% CI 1.15, 6.09). This association was not present among former or current tobacco users. Results were similar across all preconception BMI groups. CONCLUSIONS In this pooled analysis of preconception cohort studies, preconception cannabis use was associated with a higher risk of developing GDM among individuals who never used tobacco but not among individuals who formerly or currently used tobacco. Future studies with more detailed measurements are needed to investigate the influence of preconception cannabis use on pregnancy complications.
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Affiliation(s)
- Ke Pan
- Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Anne Marie Jukic
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Gita D. Mishra
- School of Public Health, University of Queensland, Herston, QLD, Australia
| | - Sunni L. Mumford
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lauren A. Wise
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Enrique F. Schisterman
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sylvia H. Ley
- Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Brittany M. Charlton
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Jorge E. Chavarro
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Departments of Nutrition and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jaime E. Hart
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stephen Sidney
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Xu Xiong
- Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | | | - Karen Schliep
- Division of Public Health, Department of Family and Preventive Medicine, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Lydia A. Bazzano
- Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Emily W. Harville
- Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA, USA
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6
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Pan K, Bazzano LA, Betha K, Charlton BM, Chavarro JE, Cordero C, Gunderson EP, Haggerty CL, Hart JE, Jukic AM, Ley SH, Mishra GD, Mumford SL, Schisterman EF, Schliep K, Shaffer JG, Sotres-Alvarez D, Stanford JB, Wilcox AJ, Wise LA, Yeung E, Harville EW. Large-Scale Data Harmonization Across Prospective Studies. Am J Epidemiol 2023; 192:2033-2049. [PMID: 37403415 PMCID: PMC10988223 DOI: 10.1093/aje/kwad153] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 04/11/2023] [Accepted: 06/29/2023] [Indexed: 07/06/2023] Open
Abstract
The Preconception Period Analysis of Risks and Exposures Influencing Health and Development (PrePARED) Consortium creates a novel resource for addressing preconception health by merging data from numerous cohort studies. In this paper, we describe our data harmonization methods and results. Individual-level data from 12 prospective studies were pooled. The crosswalk-cataloging-harmonization procedure was used. The index pregnancy was defined as the first postbaseline pregnancy lasting more than 20 weeks. We assessed heterogeneity across studies by comparing preconception characteristics in different types of studies. The pooled data set included 114,762 women, and 25,531 (22%) reported at least 1 pregnancy of more than 20 weeks' gestation during the study period. Babies from the index pregnancies were delivered between 1976 and 2021 (median, 2008), at a mean maternal age of 29.7 (standard deviation, 4.6) years. Before the index pregnancy, 60% of women were nulligravid, 58% had a college degree or more, and 37% were overweight or obese. Other harmonized variables included race/ethnicity, household income, substance use, chronic conditions, and perinatal outcomes. Participants from pregnancy-planning studies had more education and were healthier. The prevalence of preexisting medical conditions did not vary substantially based on whether studies relied on self-reported data. Use of harmonized data presents opportunities to study uncommon preconception risk factors and pregnancy-related events. This harmonization effort laid the groundwork for future analyses and additional data harmonization.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Emily W Harville
- Correspondence to Dr. Emily W. Harville, Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, New Orleans, LA 70112 (e-mail: )
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7
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Monk CH, Youngquist BM, Brady AD, Shaffer JG, Hu TY, Ning B, Zwezdaryk KJ. Development of a CRISPR-Cas12a rapid diagnostic for human cytomegalovirus. Antiviral Res 2023; 215:105624. [PMID: 37150408 DOI: 10.1016/j.antiviral.2023.105624] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
Despite decades of research, human cytomegalovirus (CMV) continues to contribute to significant morbidity and mortality in transplant settings and remains the leading cause of viral congenital infections. Clinical diagnosis of CMV infection and/or reactivation under these settings is completed using real time quantitative polymerase chain reaction (RT-qPCR). This assay performs well but is hampered by poor sensitivity and a lack of standardization among testing facilities. A point-of-care rapid diagnostic to determine CMV viremia could address these issues and improve patient care. In this manuscript, we introduce clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a technology to design and validate a rapid diagnostic for CMV. This system was tested using CMV spiked human saliva and urine samples. Sensitivity of the assay was ∼10 infectious units (IU)/mL. Specificity of the assay was robust and failed to detect other herpesviruses. Collectively, we have designed and validated a rapid diagnostic for CMV that overcomes limitations of the current standard diagnostic. This assay has the potential to be used as a point-of-care screening tool in transplant and neonatal settings.
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Affiliation(s)
- Chandler H Monk
- Bioinnovation Program, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Brady M Youngquist
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Alyson D Brady
- Neurosceince Program, Tulane University, New Orleans, LA, 70112, United States
| | - Jeffrey G Shaffer
- Department of Biostatistics and Data Science, Tulane School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Tony Y Hu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Bo Ning
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Kevin J Zwezdaryk
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Tulane Brain Institute, Tulane University School of Medicine, New Orleans, LA, 70112, USA; Tulane Center for Aging, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
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8
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Diabate O, Cisse C, Sangare M, Soremekun O, Fatumo S, Shaffer JG, Doumbia S, Wele M. Identification of promising high-affinity inhibitors of SARS-CoV-2 main protease from African Natural Products Databases by Virtual Screening. Res Sq 2023:rs.3.rs-2673755. [PMID: 36993208 PMCID: PMC10055610 DOI: 10.21203/rs.3.rs-2673755/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
With the rapid spread of the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen agent of COVID-19 pandemic created a serious threat to global public health, requiring the most urgent research for potential therapeutic agents. The availability of genomic data of SARS-CoV-2 and efforts to determine the protein structure of the virus facilitated the identification of potent inhibitors by using structure-based approach and bioinformatics tools. Many pharmaceuticals have been proposed for the treatment of COVID-19, although their effectiveness has not been assessed yet. However, it is important to find out new-targeted drugs to overcome the resistance concern. Several viral proteins such as proteases, polymerases or structural proteins have been considered as potential therapeutic targets. But the virus target must be essential for host invasion match some drugability criterion. In this Work, we selected the highly validated pharmacological target main protease Mpro and we performed high throughput virtual screening of African Natural Products Databases such as NANPDB, EANPDB, AfroDb, and SANCDB to identify the most potent inhibitors with the best pharmacological properties. In total, 8753 natural compounds were virtually screened by AutoDock vina against the main protease of SARS-CoV-2. Two hundred and five (205) compounds showed high-affinity scores (less than - 10.0 Kcal/mol), while fifty-eight (58) filtered through Lipinski's rules showed better affinity than known Mpro inhibitors (i.e., ABBV-744, Onalespib, Daunorubicin, Alpha-ketoamide, Perampanel, Carprefen, Celecoxib, Alprazolam, Trovafloxacin, Sarafloxacin, Ethyl biscoumacetate…). Those promising compounds could be considered for further investigations toward the developpement of SARS-CoV-2 drug development.
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Affiliation(s)
- Oudou Diabate
- University of Sciences, Technics and Technologies of Bamako (USTTB)
| | - Cheickna Cisse
- University of Sciences, Technics and Technologies of Bamako (USTTB)
| | | | | | - Segun Fatumo
- University of Sciences, Technics and Technologies of Bamako (USTTB)
| | | | - Seydou Doumbia
- University of Sciences, Technics and Technologies of Bamako (USTTB)
| | - Mamadou Wele
- University of Sciences, Technics and Technologies of Bamako (USTTB)
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9
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Chandra PK, Braun SE, Maity S, Castorena-Gonzalez JA, Kim H, Shaffer JG, Cikic S, Rutkai I, Fan J, Guidry JJ, Worthylake DK, Li C, Abdel-Mageed AB, Busija DW. Circulating Plasma Exosomal Proteins of Either SHIV-Infected Rhesus Macaque or HIV-Infected Patient Indicates a Link to Neuropathogenesis. Viruses 2023; 15:794. [PMID: 36992502 PMCID: PMC10058833 DOI: 10.3390/v15030794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
Despite the suppression of human immunodeficiency virus (HIV) replication by combined antiretroviral therapy (cART), 50-60% of HIV-infected patients suffer from HIV-associated neurocognitive disorders (HAND). Studies are uncovering the role of extracellular vesicles (EVs), especially exosomes, in the central nervous system (CNS) due to HIV infection. We investigated links among circulating plasma exosomal (crExo) proteins and neuropathogenesis in simian/human immunodeficiency virus (SHIV)-infected rhesus macaques (RM) and HIV-infected and cART treated patients (Patient-Exo). Isolated EVs from SHIV-infected (SHIV-Exo) and uninfected (CTL-Exo) RM were predominantly exosomes (particle size < 150 nm). Proteomic analysis quantified 5654 proteins, of which 236 proteins (~4%) were significantly, differentially expressed (DE) between SHIV-/CTL-Exo. Interestingly, different CNS cell specific markers were abundantly expressed in crExo. Proteins involved in latent viral reactivation, neuroinflammation, neuropathology-associated interactive as well as signaling molecules were expressed at significantly higher levels in SHIV-Exo than CTL-Exo. However, proteins involved in mitochondrial biogenesis, ATP production, autophagy, endocytosis, exocytosis, and cytoskeleton organization were significantly less expressed in SHIV-Exo than CTL-Exo. Interestingly, proteins involved in oxidative stress, mitochondrial biogenesis, ATP production, and autophagy were significantly downregulated in primary human brain microvascular endothelial cells exposed with HIV+/cART+ Patient-Exo. We showed that Patient-Exo significantly increased blood-brain barrier permeability, possibly due to loss of platelet endothelial cell adhesion molecule-1 protein and actin cytoskeleton structure. Our novel findings suggest that circulating exosomal proteins expressed CNS cell markers-possibly associated with viral reactivation and neuropathogenesis-that may elucidate the etiology of HAND.
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Affiliation(s)
- Partha K. Chandra
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Stephen E. Braun
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Sudipa Maity
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | | | - Hogyoung Kim
- Department of Urology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, Tulane University, New Orleans, LA 70112, USA
| | - Sinisa Cikic
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Ibolya Rutkai
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jia Fan
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jessie J. Guidry
- Proteomics Core Facility, Louisiana State University, New Orleans, LA 70112, USA
| | - David K. Worthylake
- Proteomics Core Facility, Louisiana State University, New Orleans, LA 70112, USA
| | - Chenzhong Li
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Asim B. Abdel-Mageed
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Department of Urology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - David W. Busija
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112, USA
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10
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Smither AR, Koninga J, Kanneh FB, Foday M, Boisen ML, Bond NG, Momoh M, Sandi JD, Kanneh L, Alhasan F, Kanneh IM, Yillah MS, Grant DS, Bush DJ, Nelson DKS, Cruz KM, Klitting R, Pauthner M, Andersen KG, Shaffer JG, Cross RW, Schieffelin JS, Garry RF. Novel Tools for Lassa Virus Surveillance in Peri-domestic Rodents. medRxiv 2023:2023.03.17.23287380. [PMID: 36993465 PMCID: PMC10055574 DOI: 10.1101/2023.03.17.23287380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Background Lassa fever (LF) is a rodent-borne disease endemic to West Africa. In the absence of licensed therapeutics or vaccines, rodent exclusion from living spaces remains the primary method of preventing LF. Zoonotic surveillance of Lassa virus (LASV), the etiologic agent of LF, can assess the burden of LASV in a region and guide public health measures against LF. Methods In this study, we adapted commercially available LASV human diagnostics to assess the prevalence of LASV in peri-domestic rodents in Eastern Sierra Leone. Small mammal trapping was conducted in Kenema district, Sierra Leone between November 2018-July 2019. LASV antigen was detected using a commercially available LASV NP antigen rapid diagnostic test. LASV IgG antibodies against LASV nucleoprotein (NP) and glycoprotein (GP) were tested by adapting a commercially available semi-quantitative enzyme linked immunosorbent assay (ELISA) for detection of mouse-related and rat-related species IgG. Findings Of the 373 tested specimens, 74 (20%) tested positive for LASV antigen. 40 (11%) specimens tested positive for LASV NP IgG, while an additional 12 (3%) specimens only tested positive for LASV GP IgG. Simultaneous antigen presence and IgG antibody presence was linked in Mastomys sp. specimens (p < 0.01), but not Rattus sp. specimens (p = 1). Despite the link between antigen presence and IgG antibody presence in Mastomys sp., the strength of antigen response did not correlate with the strength of IgG response to either GP IgG or NP IgG. Interpretation The tools developed in this study can aid in the generation of valuable public health data for rapid field assessment of LASV burden during outbreak investigations and general LASV surveillance. Funding Funding for this work was supported by the National Institute of Allergy and Infectious Diseases National Institute of Health, Department of Health and Human Services under the following grants: International Collaboration in Infectious Disease Research on Lassa fever and Ebola - ICIDR - U19 AI115589, Consortium for Viral Systems Biology - CViSB - 5U19AI135995, West African Emerging Infectious Disease Research Center - WARN-ID - U01AI151812, West African Center for Emerging Infectious Diseases: U01AI151801.
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Affiliation(s)
- Allison R. Smither
- Tulane University School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA
- University of Texas Medical Branch, Galveston National Laboratory, Galveston, TX, USA
| | - James Koninga
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Franklyn B. Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Momoh Foday
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | | | - Nell G. Bond
- Tulane University School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA
| | - Mambu Momoh
- Tulane University School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - John Demby Sandi
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Foday Alhasan
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Ibrahim Mustapha Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Mohamed S. Yillah
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Donald S. Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
- College of Medicine and Allied Health Sciences, University of Sierra Leone
| | | | | | - Kaitlin M. Cruz
- Tulane University School of Medicine, Department of Pediatrics, Section of Infectious Disease, New Orleans, LA, USA
| | - Raphaëlle Klitting
- The Scripps Research Institute, Department of Microbiology and Immunology, La Jolla, CA, USA
| | - Matthias Pauthner
- The Scripps Research Institute, Department of Microbiology and Immunology, La Jolla, CA, USA
| | - Kristian G. Andersen
- The Scripps Research Institute, Department of Microbiology and Immunology, La Jolla, CA, USA
| | - Jeffrey G. Shaffer
- Tulane University School of Public Health and Tropical Medicine, Department of Biostatistics, New Orleans, LA, USA
| | - Robert W. Cross
- University of Texas Medical Branch, Galveston National Laboratory, Galveston, TX, USA
| | - John S. Schieffelin
- Tulane University School of Medicine, Department of Pediatrics, Section of Infectious Disease, New Orleans, LA, USA
| | - Robert F. Garry
- Tulane University School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA
- Zalgen Labs, LLC, Frederick, MD, USA
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11
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Diawara A, Coulibaly DM, Hussain TYA, Cisse C, Li J, Wele M, Diakite M, Traore K, Doumbia SO, Shaffer JG. Type 2 diabetes prevalence, awareness, and risk factors in rural Mali: a cross-sectional study. Sci Rep 2023; 13:3718. [PMID: 36878951 PMCID: PMC9987397 DOI: 10.1038/s41598-023-29743-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
Diabetes is currently a crisis in sub-Saharan West Africa (SSWA) with dramatic implications for public health and national budgets prioritizing infectious diseases. There is limited recent literature about the prevalence, awareness, and risk factors for type 2 diabetes (T2D) in rural parts of SSWA. This study characterized T2D prevalence and risk factors for the rural Malian community of Nièna, which is situated in Mali's second-largest province of Sikasso. Between December 2020 and July 2021, a cross-sectional study of 412 participants was conducted in the Nièna community using clinical questionnaires and rapid diagnostic tests. Among 412 participants, there were 143 (34.7%) and 269 (65.3%) males and females, respectively. The overall prevalence of T2D in Nièna was 7.5% (31/412), and prevalence rates were 8.6% (23/269) and 5.6% (8/143) for females and males, respectively. Age, family history of diabetes, hypertension, waist circumference, and fetal macrosomia were significantly associated with T2D (p = 0.007, p < 0.001, p = 0.003, p = 0.013, and p < 0.001, respectively). Notably, 61.3% (19/31) of T2D subjects were unaware of their diabetic status before the study. Field surveys have considerable utility in driving T2D awareness in rural African settings.
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Affiliation(s)
- Abdoulaye Diawara
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
| | | | | | - Cheickna Cisse
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Jian Li
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Mamadou Wele
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamadou Diakite
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Seydou O Doumbia
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
| | - Jeffrey G Shaffer
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA.
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12
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Grant DS, Engel EJ, Roberts Yerkes N, Kanneh L, Koninga J, Gbakie MA, Alhasan F, Kanneh FB, Kanneh IM, Kamara FK, Momoh M, Yillah MS, Foday M, Okoli A, Zeoli A, Weldon C, Bishop CM, Zheng C, Hartnett J, Chao K, Shore K, Melnik LI, Mucci M, Bond NG, Doyle P, Yenni R, Podgorski R, Ficenec SC, Moses L, Shaffer JG, Garry RF, Schieffelin JS. Seroprevalence of anti-Lassa Virus IgG antibodies in three districts of Sierra Leone: A cross-sectional, population-based study. PLoS Negl Trop Dis 2023; 17:e0010938. [PMID: 36758101 PMCID: PMC9946222 DOI: 10.1371/journal.pntd.0010938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 02/22/2023] [Accepted: 11/09/2022] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND Lassa virus (LASV), the cause of the acute viral hemorrhagic illness Lassa fever (LF), is endemic in West Africa. Infections in humans occur mainly after exposure to infected excrement or urine of the rodent-host, Mastomys natalensis. The prevalence of exposure to LASV in Sierra Leone is crudely estimated and largely unknown. This cross-sectional study aimed to establish a baseline point seroprevalence of IgG antibodies to LASV in three administrative districts of Sierra Leone and identify potential risk factors for seropositivity and LASV exposure. METHODOLOGY AND PRINCIPAL FINDINGS Between 2015 and 2018, over 10,642 participants from Kenema, Tonkolili, and Port Loko Districts were enrolled in this cross-sectional study. Previous LASV and LF epidemiological studies support classification of these districts as "endemic," "emerging," and "non-endemic", respectively. Dried blood spot samples were tested for LASV antibodies by ELISA to determine the seropositivity of participants, indicating previous exposure to LASV. Surveys were administered to each participant to assess demographic and environmental factors associated with a higher risk of exposure to LASV. Overall seroprevalence for antibodies to LASV was 16.0%. In Kenema, Port Loko, and Tonkolili Districts, seroprevalences were 20.1%, 14.1%, and 10.6%, respectively. In a multivariate analysis, individuals were more likely to be LASV seropositive if they were living in Kenema District, regardless of sex, age, or occupation. Environmental factors contributed to an increased risk of LASV exposure, including poor housing construction and proximity to bushland, forested areas, and refuse. CONCLUSIONS AND SIGNIFICANCE In this study we determine a baseline LASV seroprevalence in three districts which will inform future epidemiological, ecological, and clinical studies on LF and the LASV in Sierra Leone. The heterogeneity of the distribution of LASV and LF over both space, and time, can make the design of efficacy trials and intervention programs difficult. Having more studies on the prevalence of LASV and identifying potential hyper-endemic areas will greatly increase the awareness of LF and improve targeted control programs related to LASV.
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Affiliation(s)
- Donald S. Grant
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Emily J. Engel
- Department of Pediatrics, Sections of Pediatric Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Nicole Roberts Yerkes
- Department of Pediatrics, Sections of Pediatric Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Lansana Kanneh
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - James Koninga
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Michael A. Gbakie
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Foday Alhasan
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Franklyn B. Kanneh
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Ibrahim Mustapha Kanneh
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Fatima K. Kamara
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Mambu Momoh
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
- Eastern Technical University of Sierra Leone, Kenema, Sierra Leone
| | - Mohamed S. Yillah
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Momoh Foday
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Adaora Okoli
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Ashley Zeoli
- Department of Pediatrics, Sections of Pediatric Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Caroline Weldon
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Christopher M. Bishop
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Crystal Zheng
- Department of Internal Medicine, Section of Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Jessica Hartnett
- Department of Pediatrics, Sections of Pediatric Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Karissa Chao
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Kayla Shore
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Lilia I. Melnik
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Mallory Mucci
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Nell G. Bond
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Philip Doyle
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Rachael Yenni
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Rachel Podgorski
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Samuel C. Ficenec
- Department of Internal Medicine, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Lina Moses
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
| | - Robert F. Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - John S. Schieffelin
- Department of Pediatrics, Sections of Pediatric Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
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13
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Chiosi JJ, Schieffelin JS, Shaffer JG, Grant DS. Evaluation of Three Clinical Prediction Tools to Predict Mortality in Hospitalized Patients with Lassa Fever. Am J Trop Med Hyg 2022; 107:856-862. [PMID: 35895416 PMCID: PMC9651537 DOI: 10.4269/ajtmh.20-1624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/14/2022] [Indexed: 10/03/2023] Open
Abstract
Lassa fever is a viral hemorrhagic illness with a case fatality rate for hospitalized patients as high as 69%. Identifying cases before they progress to serious illness can lead to earlier treatment and improved clinical outcomes. Three existing clinical prediction tools were evaluated on their ability to predict the in-hospital mortality in Lassa fever: the quick Sequential Organ Failure Assessment (qSOFA), the Modified Early Warning System (MEWS), and the Universal Vital Assessment (UVA). This was a retrospective cohort study of patients admitted to the dedicated Lassa fever ward of the Kenema Government Hospital in Sierra Leone between May 2013 and December 2019. Data among three serology groups were analyzed: Lassa antigen-positive (Ag+) regardless of IgM status, Lassa Ag- and IgM+, and Lassa Ag- and IgM- cases. There were 123 cases of suspected Lassa fever included in this study. Abnormalities in respiratory rate, oxygenation status, mental status, and serum markers of kidney and liver dysfunction were more likely seen in the Ag+ group, which had an in-hospital mortality of 85.7%. For the Lassa Ag+ group, the sensitivity and positive predictive value of qSOFA ≥ 2 was 70.6% and 92.3%, MEWS ≥ 5 was 96.9% and 86.1%, and UVA ≥ 5 was 60.0% and 100.0%. The MEWS and UVA scores show potential for use in Lassa fever, but there is opportunity for future development of a tool that includes the clinical and laboratory markers specific to Lassa fever.
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Affiliation(s)
- John J. Chiosi
- Medical Practice Evaluation Center, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - John S. Schieffelin
- Section of Infectious Diseases, Department of Pediatrics, Tulane University School of Medicine, New Orleans, Louisiana
| | - Jeffrey G. Shaffer
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - Donald S. Grant
- Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
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14
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Doumbia S, Toure M, Sogoba N, Alifrangis M, Diakite M, Diarra A, Keita M, Konaté D, Diawara SI, Thiam SM, Keita S, Tounkara M, Cissé I, Sanogo V, Magassa MH, Barry AE, Winch PJ, Marker HC, Shaffer JG, Traoré SF, Müller GC, Cui L, Beier JC, Mihigo J. The West Africa ICEMR Partnerships for Guiding Policy to Improve the Malaria Prevention and Control. Am J Trop Med Hyg 2022; 107:84-89. [PMID: 36228908 PMCID: PMC9662222 DOI: 10.4269/ajtmh.21-1330] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 07/06/2022] [Indexed: 12/01/2022] Open
Abstract
The Mali National Malaria Control Program (NMCP) recently established a phased set of goals for eliminating malaria in Mali by 2030. Over the past decade, the scale-up of NMCP-led malaria control interventions has led to considerable progress, as evidenced by multiple malariometric indicators. The West Africa International Center of Excellence in Malaria Research (WA-ICEMR) is a multidisciplinary research program that works closely with the NMCP and its partners to address critical research needs for malaria control. This coordinated effort includes assessing the effectiveness of control interventions based on key malaria research topics, including immune status, parasite genetic diversity, insecticide and drug resistance, diagnostic accuracy, malaria vector populations and biting behaviors, and vectorial capacity. Several signature accomplishments of the WA-ICEMR include identifying changing malaria age demographic profiles, testing innovative approaches to improve control strategies, and providing regular reporting on drug and insecticide resistance status. The NMCP and WA-ICEMR partnership between the WA-ICEMR and the NMCP offers a comprehensive research platform that informs the design and implementation of malaria prevention and control research programs. These efforts build local expertise and capacity for the next generation of malaria researchers and guide local policy, which is crucial in sustaining efforts toward eliminating malaria in West Africa.
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Affiliation(s)
- Seydou Doumbia
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamoudou Toure
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nafomon Sogoba
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Mahamadou Diakite
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Ayouba Diarra
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Moussa Keita
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Drissa Konaté
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sory I. Diawara
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sidibé M’Baye Thiam
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Soumba Keita
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Moctar Tounkara
- Department of Public Health, Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Idrissa Cissé
- National Malaria Control Program, Ministry of Health, Bamako, Mali
| | - Vincent Sanogo
- National Malaria Control Program, Ministry of Health, Bamako, Mali
| | | | | | - Peter J. Winch
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Hannah C. Marker
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Jeffrey G. Shaffer
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana
| | - Sékou F. Traoré
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Günter C. Müller
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Liwang Cui
- Division of Infectious Diseases and Internal Medicine, Department of Internal Medicine, University of South Florida, Tampa, Florida
| | - John C. Beier
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, Florida
| | - Jules Mihigo
- U.S. President’s Malaria Initiative, United States Agency for International Development Office, Bamako, Mali
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Doumbia S, Sogoba N, Diakite M, Toure M, Keita M, Konaté D, Diawara SI, Diarra A, Sanogo D, Kane F, Diakite SAS, Traore K, Thiam SM, Traoré SF, Cisse I, Mihigo J, Coulibaly MB, Dabitao D, Alifrangis M, Barry AE, Müller GC, Beier JC, Shaffer JG. A Decade of Progress Accelerating Malaria Control in Mali: Evidence from the West Africa International Center of Excellence for Malaria Research. Am J Trop Med Hyg 2022; 107:75-83. [PMID: 36228923 PMCID: PMC9662231 DOI: 10.4269/ajtmh.21-1309] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/06/2022] [Indexed: 11/07/2022] Open
Abstract
This article highlights over a decade of signature achievements by the West Africa International Centers for Excellence in Malaria Research (WA-ICEMR) and its partners toward guiding malaria prevention and control strategies. Since 2010, the WA-ICEMR has performed longitudinal studies to monitor and assess malaria control interventions with respect to space-time patterns, vector transmission indicators, and drug resistance markers. These activities were facilitated and supported by the Mali National Malaria Control Program. Research activities included large-scale active and passive surveillance and expanded coverage of universal long-lasting insecticide-treated bed nets and seasonal malaria chemoprevention (SMC). The findings revealed substantial declines in malaria occurrence after the scale-up of control interventions in WA-ICEMR study sites. WA-ICEMR studies showed that SMC using sulfadoxine-pyrimethamine plus amodiaquine was highly effective in preventing malaria among children under 5 years of age. An alternative SMC regimen (dihydroartemisinin plus piperaquine) was shown to be potentially more effective and provided advantages for acceptability and compliance over the standard SMC regimen. Other findings discussed in this article include higher observed multiplicity of infection rates for malaria in historically high-endemic areas, continued antimalarial drug sensitivity to Plasmodium falciparum, high outdoor malaria transmission rates, and increased insecticide resistance over the past decade. The progress achieved by the WA-ICEMR and its partners highlights the critical need for maintaining current malaria control interventions while developing novel strategies to disrupt malaria transmission. Enhanced evaluation of these strategies through research partnerships is particularly needed in the wake of reported artemisinin resistance in Southeast Asia and East Africa.
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Affiliation(s)
- Seydou Doumbia
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nafomon Sogoba
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamadou Diakite
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamoudou Toure
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Moussa Keita
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Drissa Konaté
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sory I. Diawara
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Ayouba Diarra
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Daouda Sanogo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Fousseyni Kane
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Seidina A. S. Diakite
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Karim Traore
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sidibé M’Baye Thiam
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sékou F. Traoré
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Idrissa Cisse
- National Malaria Control Program, Ministry of Health, Bamako, Mali
| | - Jules Mihigo
- U.S. President’s Malaria Initiative, United States Agency for International Development Office, Bamako, Mali
| | - Mamadou B. Coulibaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Djeneba Dabitao
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | | | - Günter C. Müller
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - John C. Beier
- Miller School of Medicine, University of Miami, Miami, Florida
| | - Jeffrey G. Shaffer
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana
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Tegally H, San JE, Cotten M, Moir M, Tegomoh B, Mboowa G, Martin DP, Baxter C, Lambisia AW, Diallo A, Amoako DG, Diagne MM, Sisay A, Zekri ARN, Gueye AS, Sangare AK, Ouedraogo AS, Sow A, Musa AO, Sesay AK, Abias AG, Elzagheid AI, Lagare A, Kemi AS, Abar AE, Johnson AA, Fowotade A, Oluwapelumi AO, Amuri AA, Juru A, Kandeil A, Mostafa A, Rebai A, Sayed A, Kazeem A, Balde A, Christoffels A, Trotter AJ, Campbell A, Keita AK, Kone A, Bouzid A, Souissi A, Agweyu A, Naguib A, Gutierrez AV, Nkeshimana A, Page AJ, Yadouleton A, Vinze A, Happi AN, Chouikha A, Iranzadeh A, Maharaj A, Batchi-Bouyou AL, Ismail A, Sylverken AA, Goba A, Femi A, Sijuwola AE, Marycelin B, Salako BL, Oderinde BS, Bolajoko B, Diarra B, Herring BL, Tsofa B, Lekana-Douki B, Mvula B, Njanpop-Lafourcade BM, Marondera BT, Khaireh BA, Kouriba B, Adu B, Pool B, McInnis B, Brook C, Williamson C, Nduwimana C, Anscombe C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Mapanguy CM, Loucoubar C, Onwuamah CK, Ihekweazu C, Malaka CN, Peyrefitte C, Grace C, Omoruyi CE, Rafaï CD, Morang’a CM, Erameh C, Lule DB, Bridges DJ, Mukadi-Bamuleka D, Park D, Rasmussen DA, Baker D, Nokes DJ, Ssemwanga D, Tshiabuila D, Amuzu DSY, Goedhals D, Grant DS, Omuoyo DO, Maruapula D, Wanjohi DW, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong’era EM, Ngabana EN, Abworo EO, Otieno E, Shumba E, Barasa E, Ahmed EB, Ahmed EA, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Manuel E, Leendertz F, Taweh FM, Wasfi F, Abdelmoula F, Takawira FT, Derrar F, Ajogbasile FV, Treurnicht F, Onikepe F, Ntoumi F, Muyembe FM, Ragomzingba FEZ, Dratibi FA, Iyanu FA, Mbunsu GK, Thilliez G, Kay GL, Akpede GO, van Zyl GU, Awandare GA, Kpeli GS, Schubert G, Maphalala GP, Ranaivoson HC, Omunakwe HE, Onywera H, Abe H, Karray H, Nansumba H, Triki H, Kadjo HAA, Elgahzaly H, Gumbo H, Mathieu H, Kavunga-Membo H, Smeti I, Olawoye IB, Adetifa IMO, Odia I, Ben Boubaker IB, Mohammad IA, Ssewanyana I, Wurie I, Konstantinus IS, Halatoko JWA, Ayei J, Sonoo J, Makangara JCC, Tamfum JJM, Heraud JM, Shaffer JG, Giandhari J, Musyoki J, Nkurunziza J, Uwanibe JN, Bhiman JN, Yasuda J, Morais J, Kiconco J, Sandi JD, Huddleston J, Odoom JK, Morobe JM, Gyapong JO, Kayiwa JT, Okolie JC, Xavier JS, Gyamfi J, Wamala JF, Bonney JHK, Nyandwi J, Everatt J, Nakaseegu J, Ngoi JM, Namulondo J, Oguzie JU, Andeko JC, Lutwama JJ, Mogga JJH, O’Grady J, Siddle KJ, Victoir K, Adeyemi KT, Tumedi KA, Carvalho KS, Mohammed KS, Dellagi K, Musonda KG, Duedu KO, Fki-Berrajah L, Singh L, Kepler LM, Biscornet L, de Oliveira Martins L, Chabuka L, Olubayo L, Ojok LD, Deng LL, Ochola-Oyier LI, Tyers L, Mine M, Ramuth M, Mastouri M, ElHefnawi M, Mbanne M, Matsheka MI, Kebabonye M, Diop M, Momoh M, Lima Mendonça MDL, Venter M, Paye MF, Faye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina MG, Owusu M, Wiley MR, Tatfeng MY, Ayekaba MO, Abouelhoda M, Beloufa MA, Seadawy MG, Khalifa MK, Matobo MM, Kane M, Salou M, Mbulawa MB, Mwenda M, Allam M, Phan MVT, Abid N, Rujeni N, Abuzaid N, Ismael N, Elguindy N, Top NM, Dia N, Mabunda N, Hsiao NY, Silochi NB, Francisco NM, Saasa N, Bbosa N, Murunga N, Gumede N, Wolter N, Sitharam N, Ndodo N, Ajayi NA, Tordo N, Mbhele N, Razanajatovo NH, Iguosadolo N, Mba N, Kingsley OC, Sylvanus O, Femi O, Adewumi OM, Testimony O, Ogunsanya OA, Fakayode O, Ogah OE, Oludayo OE, Faye O, Smith-Lawrence P, Ondoa P, Combe P, Nabisubi P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Okokhere PO, Bejon P, Dussart P, Bester PA, Mbala PK, Kaleebu P, Abechi P, El-Shesheny R, Joseph R, Aziz RK, Essomba RG, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Neto Rodrigues RMDESA, Audu RA, Carr RAA, Gargouri S, Masmoudi S, Bootsma S, Sankhe S, Mohamed SI, Femi S, Mhalla S, Hosch S, Kassim SK, Metha S, Trabelsi S, Agwa SH, Mwangi SW, Doumbia S, Makiala-Mandanda S, Aryeetey S, Ahmed SS, Ahmed SM, Elhamoumi S, Moyo S, Lutucuta S, Gaseitsiwe S, Jalloh S, Andriamandimby SF, Oguntope S, Grayo S, Lekana-Douki S, Prosolek S, Ouangraoua S, van Wyk S, Schaffner SF, Kanyerezi S, Ahuka-Mundeke S, Rudder S, Pillay S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Mohale T, Le-Viet T, Velavan TP, Schindler T, Maponga TG, Bedford T, Anyaneji UJ, Chinedu U, Ramphal U, George UE, Enouf V, Nene V, Gorova V, Roshdy WH, Karim WA, Ampofo WK, Preiser W, Choga WT, Ahmed YA, Ramphal Y, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR, Ouma AEO, von Gottberg A, Githinji G, Moeti M, Tomori O, Sabeti PC, Sall AA, Oyola SO, Tebeje YK, Tessema SK, de Oliveira T, Happi C, Lessells R, Nkengasong J, Wilkinson E. The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. Science 2022; 378:eabq5358. [PMID: 36108049 PMCID: PMC9529057 DOI: 10.1126/science.abq5358] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022]
Abstract
Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.
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Affiliation(s)
- Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James E. San
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Matthew Cotten
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Bryan Tegomoh
- The Biotechnology Centre of the University of Yaoundé I, Yaoundé, Cameroon
- CDC Foundation, Atlanta, Georgia, Nebraska Department of Health and Human Services, Lincoln, NE, USA
| | - Gerald Mboowa
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | | | - Amadou Diallo
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Daniel G. Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
| | | | - Abay Sisay
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abdel-Rahman N. Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Abdou Salam Gueye
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Abdoul K. Sangare
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
| | - Abdoul-Salam Ouedraogo
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | | | - Abdualmoniem O. Musa
- Faculty of Medicine and Health Sciences, Kassala University, Kassala City, Sudan
- Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Gezira, Gezira, Sudan
- General Administration of Laboratories and Blood Banks, Ministry of Health, Kassala State, Sudan
| | | | - Abe G. Abias
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | | | - Adamou Lagare
- Center for Medical and Sanitary Research (CERMES), Niamey, Niger
| | | | - Aden Elmi Abar
- Laboratoire de la Caisse Nationale de Sécurité Sociale, Djibouti, Republic of Djibouti
| | - Adeniji A. Johnson
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeola Fowotade
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeyemi O. Oluwapelumi
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
- The Pirbright Institute, Woking, UK
| | - Adrienne A. Amuri
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Agnes Juru
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Ahmed Kandeil
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ahmed Sayed
- Genomics and Epigenomics Program, Research Department CCHE57357, Cairo, Egypt
| | - Akano Kazeem
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Aladje Balde
- Laboratório de Biologia Molecular Jean Piaget, Bissau, Guinea-Bissau
- University Jean Piaget in Guinea-Bissau, Bissau, Guinea-Bissau
| | - Alan Christoffels
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
- SAMRC Bioinformatics Unit, SA Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | | | - Allan Campbell
- Central Public Health Reference Laboratories, Freetown, Sierra Leone
| | - Alpha K. Keita
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier University, 34090, Montpellier, France
| | - Amadou Kone
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Amal Bouzid
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Amel Naguib
- Central Public Health Laboratories (CPHL), Cairo, Egypt
| | | | | | | | - Anges Yadouleton
- Laboratoire des Fièvres Hémorragiques Virales du Benin, Cotonou, Benin
| | - Anika Vinze
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Anise N. Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Anissa Chouikha
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Apporach and Technological Innovation for a Better Health”, LR20IPT02, Pasteur Institute, Tunis 1002, Tunisia
| | - Arash Iranzadeh
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arisha Maharaj
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Armel L. Batchi-Bouyou
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Marien Ngouabi, Brazzaville, Republic of the Congo
| | - Arshad Ismail
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Augustina A. Sylverken
- Kwame Nkrumah University of Science and Technology, Department of Theoretical and Applied Biology, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Augustine Goba
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Ayoade Femi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Ayotunde E. Sijuwola
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Baba Marycelin
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
- Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Borno State, Nigeria
| | - Babatunde L. Salako
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Bamidele S. Oderinde
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bankole Bolajoko
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Bassirou Diarra
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Belinda L. Herring
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | | | - Bernard Lekana-Douki
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
- Département de Parasitologie-Mycologie Université des Sciences de la Santé (USS), Libreville, Gabon
| | - Bernard Mvula
- National HIV Reference Laboratory, Community Health Sciences Unit, Ministry of Health, Lilongwe, Malawi
| | | | | | - Bouh Abdi Khaireh
- National Medical and Molecular Biology Laboratory, Ministry of Health, Djibouti, Republic of Djibouti
- Africa CDC, Rapid Responder, Team Djibouti, Djibouti, Djibouti
| | - Bourema Kouriba
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
| | - Bright Adu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Brigitte Pool
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health Seychelles, Victoria, Seychelles
| | - Bronwyn McInnis
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Cara Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Carolyn Williamson
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | - Catherine Anscombe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- SAMRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Chantal G. Akoua-Koffi
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
- UFR Sciences Médicales, Universite Alassane Ouattara, Bouaké, Côte d’Ivoire
| | - Charles N. Agoti
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Public Health, Pwani University, Kilifi, Kenya
| | - Chastel M. Mapanguy
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Faculty of Science and Techniques, University Marien Ngouabi, Brazzaville, Republic of the Congo
| | | | - Chika K. Onwuamah
- Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Chikwe Ihekweazu
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Christian N. Malaka
- Laboratoire des Arbovirus, Fièvres Hémorragiques virales, Virus Emergents et Zoonoses, Institut Pasteur de Bangui, Bangui, Central African Republic
| | | | - Chukwa Grace
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Chukwuma E. Omoruyi
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Clotaire D. Rafaï
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
| | - Collins M. Morang’a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Cyril Erameh
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Daniel B. Lule
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | | | - Daniel Mukadi-Bamuleka
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
| | - Danny Park
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - David A. Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | | | - David J. Nokes
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Deogratius Ssemwanga
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Dominic S. Y. Amuzu
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Dominique Goedhals
- PathCare Vermaak, Pretoria, South Africa and Division of Virology, University of the Free State, Bloemfontein, South Africa
| | - Donald S. Grant
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | | | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Dorcas W. Wanjohi
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | | | - Eddy K. Lusamaki
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier University, 34090, Montpellier, France
| | | | | | - Edith N. Ngabana
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Edward O. Abworo
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Edward Otieno
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Edwin Shumba
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | - Edwine Barasa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - El Bara Ahmed
- INRSP, Nouakchott, Mauritania
- Faculté de Médecine de Nouakchott, Nouakchott, Mauritani
| | - Elhadi A. Ahmed
- Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Gezira, Gezira, Sudan
| | - Emmanuel Lokilo
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
| | | | - Eromon Philomena
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Etilé A. Anoh
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | - Eusebio Manuel
- Direcção Nacional da Saúde Pública, Ministério da Saúde, Luanda, Angola
| | | | - Fahn M. Taweh
- National Public Health Reference Laboratory–National Public Health Institute of Liberia, Monrovia, Liberia
| | - Fares Wasfi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
| | - Fatma Abdelmoula
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | | | - Fawzi Derrar
- National Influenza Centre, Institut Pasteur d’Algérie, Algiers, Algeria
| | - Fehintola V. Ajogbasile
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Florette Treurnicht
- Department of Virology, National Health Laboratory Service (NHLS), Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Folarin Onikepe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Francine Ntoumi
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Francisca M. Muyembe
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | | | - Fred A. Dratibi
- WHO Int Comoros, Moroni, Union of Comoros
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Fred-Akintunwa Iyanu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Gabriel K. Mbunsu
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | | | | | - George O. Akpede
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Gert U. van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Grace S. Kpeli
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | | | - Gugu P. Maphalala
- Ministry of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini
| | | | - Hannah E. Omunakwe
- Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Nigeria
| | - Harris Onywera
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Hela Karray
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Henda Triki
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
| | | | - Hesham Elgahzaly
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Hlanai Gumbo
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Hota Mathieu
- Doctoral School of Technical and Environmental Sciences, Department of Biology and Human Health, N’Djamena, Chad
| | - Hugo Kavunga-Membo
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
| | - Ibtihel Smeti
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Idowu B. Olawoye
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Ifedayo M. O. Adetifa
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Ikponmwosa Odia
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Ilhem Boutiba Ben Boubaker
- Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Research Laboratory LR99ES09, Tunis, Tunisia
| | - Iluoreh Ahmed Mohammad
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | - Isatta Wurie
- College of Medicine and Allied Health Science, University of Sierra Leone, Freetown, Sierra Leone
| | | | | | - James Ayei
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | - Janaki Sonoo
- Virology/Molecular Biology Department, Central Health Laboratory, Victoria Hospital, Ministry of Health and Wellness, Port Louis, Mauritius
| | - Jean-Claude C. Makangara
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Jean-Jacques M. Tamfum
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Jean-Michel Heraud
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | | | - Jessica N. Uwanibe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Jinal N. Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Joana Morais
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
- Departamento de Bioquímica, Faculdade de Medicina, Universidade Agostinho Neto, Luanda, Angola
| | | | - John D. Sandi
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - John K. Odoom
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - John O. Gyapong
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - John T. Kayiwa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Johnson C. Okolie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Joicymara S. Xavier
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
| | - Jones Gyamfi
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | - Joseph H. K. Bonney
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Joseph Nyandwi
- National Institute of Public Health, Bujumbura, Burundi
- Faculty of Medicine, University of Burundi, Bujumbura, Burundi
| | - Josie Everatt
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Joyce M. Ngoi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | | | - Judith U. Oguzie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Julia C. Andeko
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | | | | | - Katherine J. Siddle
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Kayode T. Adeyemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Kefentse A. Tumedi
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
| | | | | | | | | | - Kwabena O. Duedu
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | - Lamia Fki-Berrajah
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Lenora M. Kepler
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Leon Biscornet
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health Seychelles, Victoria, Seychelles
| | | | | | - Luicer Olubayo
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
| | - Lul Deng Ojok
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | - Lul Lojok Deng
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | | | - Lynn Tyers
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Magalutcheemee Ramuth
- Virology/Molecular Biology Department, Central Health Laboratory, Victoria Hospital, Ministry of Health and Wellness, Port Louis, Mauritius
| | - Maha Mastouri
- Laboratory of Transmissible Diseases and Biologically Active Substances (LR99ES27), Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Mahmoud ElHefnawi
- Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, Cairo, Egypt
| | - Maimouna Mbanne
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | | | - Mamadou Diop
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mambu Momoh
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- Eastern Technical University of Sierra Leone, Kenema, Sierra Leone
| | | | - Marietjie Venter
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Marietou F. Paye
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Martin Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | | | - Matoke-Muhia Damaris
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Maximillian G. Mpina
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- Ifakara Health Insitute, Ifakara, Tanzania
| | - Michael Owusu
- Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Michael R. Wiley
- University of Nebraska Medical Center (UNMC), Omaha, NE, USA
- PraesensBio, Lincoln, NE, USA
| | - Mirabeau Y. Tatfeng
- Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria
| | | | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo, Egypt
- King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | | | - Mohamed G. Seadawy
- Biological Prevention Department, Ministry of Defence, Cairo, Egypt
- Faculty of Science, Fayoum University, Fayoum, Egypt
| | | | | | - Mouhamed Kane
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | | | | | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - My V. T. Phan
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biologically Active Substances (LR99ES27), Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- High Institute of Biotechnology of Monastir, University of Monastir, Rue Taher Haddad 5000, Monastir, Tunisia
| | - Nadine Rujeni
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Nadir Abuzaid
- Department of Microbiology, Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Sudan
| | - Nalia Ismael
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | | | | | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Nédio Mabunda
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Nei-yuan Hsiao
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | - Ngiambudulu M. Francisco
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
| | - Ngonda Saasa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Nicholas Bbosa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | | | - Nicksy Gumede
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Nicole Wolter
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Nikita Sitharam
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Nnaemeka Ndodo
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Nnennaya A. Ajayi
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Noël Tordo
- Institut Pasteur de Guinée, Conarky, Guinea
| | - Nokuzola Mbhele
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Nosamiefan Iguosadolo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Nwando Mba
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Ojide C. Kingsley
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Okogbenin Sylvanus
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Oladiji Femi
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences. College of Health Sciences. University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Olubusuyi M. Adewumi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olumade Testimony
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Olusola A. Ogunsanya
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Oluwatosin Fakayode
- Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria
| | - Onwe E. Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Ope-Ewe Oludayo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Pascale Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | | | - Patricia Nabisubi
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | | | - Paul E. Oluniyi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Paulo Arnaldo
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Peter Kojo Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Peter O. Okokhere
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- Department of Medicine, Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Edo State, Nigeria
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Phillip A. Bester
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | - Placide K. Mbala
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Pontiano Kaleebu
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Priscilla Abechi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Rabeh El-Shesheny
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
- Infectious Hazards Preparedness, World Health Organization, Eastern Mediterranean Regional Office, Cairo, Egypt
| | - Rageema Joseph
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Ramy Karam Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Microbiology and Immunology Research Program, Children’s Cancer Hospital Egypt, Cairo, Egypt
| | - René G. Essomba
- National Public Health Laboratory, Ministry of Public Health of Cameroon, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon
| | - Reuben Ayivor-Djanie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | - Richard Njouom
- Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon
| | - Richard O. Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richmond Gorman
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Rosa Maria D. E. S. A. Neto Rodrigues
- Coordenadora da rede do Diagnóstico Tuberculose/HIV/COVID-19 na Instituição - Laboratório Nacional de Referência da Tuberculose em São Tomé e Príncipe, São Tomé, São Tomé and Principe
- Ponto focal para Melhoria da qualidade dos Laboratórios (SLIPTA) ao nível de São Tomé e Príncipe, São Tomé, São Tomé and Principe
| | - Rosemary A. Audu
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Rosina A. A. Carr
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | - Saba Gargouri
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Safietou Sankhe
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Saibu Femi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Salma Mhalla
- University of Tunis El Manar, Faculty of Medicine of Tunis, Research Laboratory LR99ES09, Tunis, Tunisia
- Faculty of Medicine of Monastir, University of Monastir, Monastir, Tunisia
| | - Salome Hosch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Samar Kamal Kassim
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Samar Metha
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sameh Trabelsi
- Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia
| | - Sara Hassan Agwa
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Sarah Wambui Mwangi
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Seydou Doumbia
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Sheila Makiala-Mandanda
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Sherihane Aryeetey
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | | | - Siham Elhamoumi
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Silvia Lutucuta
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simbirie Jalloh
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | | | - Sobajo Oguntope
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | - Sonia Lekana-Douki
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Soumeya Ouangraoua
- Centre MURAZ, Ouagadougou, Burkina Faso
- National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso
| | - Stephanie van Wyk
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Stephen F. Schaffner
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Stephen Kanyerezi
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | - Steve Ahuka-Mundeke
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | | | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Susan Nabadda
- Central Public Health Laboratories (CPHL), Kampala, Uganda
| | - Sylvie Behillil
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
| | | | - Sylvie van der Werf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
| | - Tapfumanei Mashe
- National Microbiology Reference Laboratory, Harare, Zimbabwe
- World Health Organization, Harare, Zimbabwe
| | - Thabo Mohale
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Thirumalaisamy P. Velavan
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
| | - Tobias Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- University of Basel, Basel, Switzerland
| | - Tongai G. Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ugwu Chinedu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa
| | - Uwem E. George
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Vincent Enouf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
| | - Vishvanath Nene
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Vivianne Gorova
- World Health Organization, WHO Lesotho, Maseru, Lesotho
- Med24 Medical Centre, Ruwa, Zimbabwe
| | | | - Wasim Abdul Karim
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - William K. Ampofo
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Wonderful T. Choga
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Yahaya Ali Ahmed
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Yajna Ramphal
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Yemaachi Biotech, Accra, Ghana
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Yvan Butera
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
| | | | - Africa Pathogen Genomics Initiative (Africa PGI)
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- The Biotechnology Centre of the University of Yaoundé I, Yaoundé, Cameroon
- CDC Foundation, Atlanta, Georgia, Nebraska Department of Health and Human Services, Lincoln, NE, USA
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
- West African Health Organisation, Bobo-Dioulasso, Burkina Faso
- Faculty of Medicine and Health Sciences, Kassala University, Kassala City, Sudan
- Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Gezira, Gezira, Sudan
- General Administration of Laboratories and Blood Banks, Ministry of Health, Kassala State, Sudan
- MRC Unit The Gambia at LSHTM, Fajara, Gambia
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
- Libyan Biotechnology Research Center, Tripoli, Libya
- Center for Medical and Sanitary Research (CERMES), Niamey, Niger
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Laboratoire de la Caisse Nationale de Sécurité Sociale, Djibouti, Republic of Djibouti
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
- The Pirbright Institute, Woking, UK
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
- National Microbiology Reference Laboratory, Harare, Zimbabwe
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Genomics and Epigenomics Program, Research Department CCHE57357, Cairo, Egypt
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- Laboratório de Biologia Molecular Jean Piaget, Bissau, Guinea-Bissau
- University Jean Piaget in Guinea-Bissau, Bissau, Guinea-Bissau
- SAMRC Bioinformatics Unit, SA Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
- Quadram Institute Bioscience, Norwich, UK
- Central Public Health Reference Laboratories, Freetown, Sierra Leone
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier University, 34090, Montpellier, France
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Central Public Health Laboratories (CPHL), Cairo, Egypt
- National Institute of Public Health, Bujumbura, Burundi
- Laboratoire des Fièvres Hémorragiques Virales du Benin, Cotonou, Benin
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Apporach and Technological Innovation for a Better Health”, LR20IPT02, Pasteur Institute, Tunis 1002, Tunisia
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Marien Ngouabi, Brazzaville, Republic of the Congo
- Kwame Nkrumah University of Science and Technology, Department of Theoretical and Applied Biology, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
- Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Borno State, Nigeria
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
- Département de Parasitologie-Mycologie Université des Sciences de la Santé (USS), Libreville, Gabon
- National HIV Reference Laboratory, Community Health Sciences Unit, Ministry of Health, Lilongwe, Malawi
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
- National Medical and Molecular Biology Laboratory, Ministry of Health, Djibouti, Republic of Djibouti
- Africa CDC, Rapid Responder, Team Djibouti, Djibouti, Djibouti
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health Seychelles, Victoria, Seychelles
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- National Health Laboratory Service (NHLS), Cape Town, South Africa
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
- University of Nebraska Medical Center (UNMC), Omaha, NE, USA
- SAMRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
- UFR Sciences Médicales, Universite Alassane Ouattara, Bouaké, Côte d’Ivoire
- School of Public Health, Pwani University, Kilifi, Kenya
- Faculty of Science and Techniques, University Marien Ngouabi, Brazzaville, Republic of the Congo
- Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
- Laboratoire des Arbovirus, Fièvres Hémorragiques virales, Virus Emergents et Zoonoses, Institut Pasteur de Bangui, Bangui, Central African Republic
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- PATH, Lusaka, Zambia
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
- Uganda Virus Research Institute, Entebbe, Uganda
- PathCare Vermaak, Pretoria, South Africa and Division of Virology, University of the Free State, Bloemfontein, South Africa
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Macha Research Trust, Choma, Zambia
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- INRSP, Nouakchott, Mauritania
- Faculté de Médecine de Nouakchott, Nouakchott, Mauritani
- Rwanda National Reference Laboratory, Kigali, Rwanda
- Robert Koch-Institute, Berlin, Germany
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Paris, France
- Direcção Nacional da Saúde Pública, Ministério da Saúde, Luanda, Angola
- National Public Health Reference Laboratory–National Public Health Institute of Liberia, Monrovia, Liberia
- Faculty of Pharmacy of Monastir, Monastir, Tunisia
- National Influenza Centre, Institut Pasteur d’Algérie, Algiers, Algeria
- Department of Virology, National Health Laboratory Service (NHLS), Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
- Ministère de Santé Publique et de la Solidarité Nationale, Ndjamena, Chad
- WHO Int Comoros, Moroni, Union of Comoros
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
- Ministry of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini
- Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Nigeria
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
- Central Public Health Laboratories (CPHL), Kampala, Uganda
- Institut Pasteur de Côte d’Ivoire, Departement des Virus Epidemiques, Abidjan, Côte d’Ivoire
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
- Doctoral School of Technical and Environmental Sciences, Department of Biology and Human Health, N’Djamena, Chad
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
- Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Research Laboratory LR99ES09, Tunis, Tunisia
- College of Medicine and Allied Health Science, University of Sierra Leone, Freetown, Sierra Leone
- Namibia Institute of Pathology, Windhoek, Namibia
- National Institute of Hygiene, Lomé, Togo
- Virology/Molecular Biology Department, Central Health Laboratory, Victoria Hospital, Ministry of Health and Wellness, Port Louis, Mauritius
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
- WHO Burundi, Gitega, Burundi
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
- Departamento de Bioquímica, Faculdade de Medicina, Universidade Agostinho Neto, Luanda, Angola
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
- WHO South Sudan, Juba, South Sudan
- Faculty of Medicine, University of Burundi, Bujumbura, Burundi
- Pasteur Network, Institut Pasteur, Paris, France
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- Instituto Nacional de Saúde Pública, Praia, Cape Verde
- Zambia National Public Health Institute, Lusaka, Zambia
- Public Health Institute of Malawi, Lilongwe, Malawi
- National Health Laboratory, Gaborone, Botswana
- Laboratory of Transmissible Diseases and Biologically Active Substances (LR99ES27), Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
- Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, Cairo, Egypt
- Ministry of Health and Wellness, Gaborone, Botswana
- Eastern Technical University of Sierra Leone, Kenema, Sierra Leone
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
- National Reference Laboratory Lesotho, Maseru, Lesotho
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- Ifakara Health Insitute, Ifakara, Tanzania
- Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- PraesensBio, Lincoln, NE, USA
- Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo, Egypt
- King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
- Biological Prevention Department, Ministry of Defence, Cairo, Egypt
- Faculty of Science, Fayoum University, Fayoum, Egypt
- Molecular Pathology Lab, Children’s Cancer Hospital, Cairo, Egypt
- Laboratoire Biolim FSS/Université de Lomé, Lomé, Togo
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
- High Institute of Biotechnology of Monastir, University of Monastir, Rue Taher Haddad 5000, Monastir, Tunisia
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Department of Microbiology, Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Sudan
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
- Institut Pasteur de Guinée, Conarky, Guinea
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences. College of Health Sciences. University of Ilorin, Ilorin, Kwara State, Nigeria
- Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
- Mayotte Hospital Center, Mayotte, France
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
- Department of Medicine, Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Edo State, Nigeria
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
- Infectious Hazards Preparedness, World Health Organization, Eastern Mediterranean Regional Office, Cairo, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Microbiology and Immunology Research Program, Children’s Cancer Hospital Egypt, Cairo, Egypt
- National Public Health Laboratory, Ministry of Public Health of Cameroon, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon
- Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon
- Coordenadora da rede do Diagnóstico Tuberculose/HIV/COVID-19 na Instituição - Laboratório Nacional de Referência da Tuberculose em São Tomé e Príncipe, São Tomé, São Tomé and Principe
- Ponto focal para Melhoria da qualidade dos Laboratórios (SLIPTA) ao nível de São Tomé e Príncipe, São Tomé, São Tomé and Principe
- National Public Health Reference Laboratory (NPHRL), Mogadishu, Somalia
- Faculty of Medicine of Monastir, University of Monastir, Monastir, Tunisia
- University of Basel, Basel, Switzerland
- Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre MURAZ, Ouagadougou, Burkina Faso
- National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
- World Health Organization, Harare, Zimbabwe
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa
- World Health Organization, WHO Lesotho, Maseru, Lesotho
- Med24 Medical Centre, Ruwa, Zimbabwe
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Yemaachi Biotech, Accra, Ghana
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Ahmed E. O. Ouma
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Matshidiso Moeti
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Pardis C. Sabeti
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Amadou A. Sall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Samuel O. Oyola
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Yenew K. Tebeje
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Sofonias K. Tessema
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - John Nkengasong
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
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17
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Ficenec SC, Grant DS, Sumah I, Alhasan F, Yillah MS, Brima J, Konuwa E, Gbakie MA, Kamara FK, Bond NG, Engel EJ, Shaffer JG, Fischer WA, Wohl DA, Emmett SD, Schieffelin JS. The prevalence of Post-Ebola Syndrome hearing loss, Sierra Leone. BMC Infect Dis 2022; 22:624. [PMID: 35850699 PMCID: PMC9290210 DOI: 10.1186/s12879-022-07604-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Globally, hearing loss is the second leading cause of disability, affecting approximately 18.7% of the world's population. However, the burden of hearing loss is unequally distributed, with the majority of affected individuals located in Asia or Sub-Saharan Africa. Following the 2014 West African Ebola Outbreak, disease survivors began to describe hearing loss as part of the constellation of symptoms known as Post-Ebola Syndrome. The goal of this study was to more fully characterize hearing loss among Ebola Virus Disease (EVD) survivors. METHODOLOGY AND PRINCIPAL FINDINGS EVD survivors and their household contacts were recruited (n = 1,12) from Eastern Sierra Leone. Each individual completed a symptom questionnaire, physical exam, and a two-step audiometry process measuring both air and bone conduction thresholds. In comparison to contacts, EVD survivors were more likely to have complaints or abnormal findings affecting every organ system. A significantly greater percentage of EVD survivors were found to have hearing loss in comparison to contacts (23% vs. 9%, p < 0.001). Additionally, survivors were more likely to have bilateral hearing loss of a mixed etiology. Logistic regression revealed that the presence of any symptoms of middle or inner ear (p < 0.001), eye (p = 0.005), psychiatric (p = 0.019), and nervous system (p = 0.037) increased the odds of developing hearing loss. CONCLUSIONS AND SIGNIFICANCE This study is the first to use an objective and standardized measurement to report hearing loss among EVD survivors in a clinically meaningful manner. In this study it was found that greater than 1/5th of EVD survivors develop hearing loss. The association between hearing impairment and symptoms affecting the eye and nervous system may indicate a similar mechanism of pathogenesis, which should be investigated further. Due to the quality of life and socioeconomic detriments associated with untreated hearing loss, a greater emphasis must be placed on understanding and mitigating hearing loss following survival to aid in economic recovery following infectious disease epidemics.
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Affiliation(s)
- Samuel C Ficenec
- Department of Internal Medicine, Tulane University School of Medicine, New Orleans, LA, USA.
| | - Donald S Grant
- Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Ibrahim Sumah
- Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Foday Alhasan
- Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Mohamed S Yillah
- Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Jenneh Brima
- Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Edwin Konuwa
- Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Michael A Gbakie
- Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Fatima K Kamara
- Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Nell G Bond
- Department of Immunology and Microbiology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Emily J Engel
- Department of Pediatrics, Section of Infectious Diseases, Tulane University School of Medicine, New Orleans, LA, USA
| | - Jeffrey G Shaffer
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - William A Fischer
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - David A Wohl
- Department of Internal Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Susan D Emmett
- Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Otolaryngology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - John S Schieffelin
- Department of Pediatrics, Section of Infectious Diseases, Tulane University School of Medicine, New Orleans, LA, USA
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18
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Touré M, Keita M, Kané F, Sanogo D, Kanté S, Konaté D, Diarra A, Sogoba N, Coulibaly MB, Traoré SF, Alifrangis M, Diakité M, Shaffer JG, Krogstad DJ, Doumbia S. Trends in malaria epidemiological factors following the implementation of current control strategies in Dangassa, Mali. Malar J 2022; 21:65. [PMID: 35197053 PMCID: PMC8867639 DOI: 10.1186/s12936-022-04058-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 01/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Over the past decade, three strategies have reduced severe malaria cases and deaths in endemic regions of Africa, Asia and the Americas, specifically: (1) artemisinin-based combination therapy (ACT); (2) insecticide-treated bed nets (ITNs); and, (3) intermittent preventive treatment with sulfadoxine-pyrimethamine in pregnancy (IPTp). The rationale for this study was to examine communities in Dangassa, Mali where, in 2015, two additional control strategies were implemented: ITN universal coverage and seasonal malaria chemoprevention (SMC) among children under 5 years old. METHODS This was a prospective study based on a rolling longitudinal cohort of 1401 subjects participating in bi-annual smear surveys for the prevalence of asymptomatic Plasmodium falciparum infection and continuous surveillance for the incidence of human disease (uncomplicated malaria), performed in the years from 2012 to 2020. Entomological collections were performed to examine the intensity of transmission based on pyrethroid spray catches, human landing catches and enzyme-linked immunosorbent assay (ELISA) testing for circumsporozoite antigen. RESULTS A total of 1401 participants of all ages were enrolled in the study in 2012 after random sampling of households from the community census list. Prevalence of infection was extremely high in Dangassa, varying from 9.5 to 62.8% at the start of the rainy season and from 15.1 to 66.7% at the end of the rainy season. Likewise, the number of vectors per house, biting rates, sporozoites rates, and entomological inoculation rates (EIRs) were substantially greater in Dangassa. DISCUSSION The findings for this study are consistent with the progressive implementation of effective malaria control strategies in Dangassa. At baseline (2012-2014), prevalence of P. falciparum was above 60% followed by a significant year-to-year decease starting in 2015. Incidence of uncomplicated infection was greater among children < 5 years old, while asymptomatic infection was more frequent among the 5-14 years old. A significant decrease in EIR was also observed from 2015 to 2020. Likewise, vector density, sporozoite rates, and EIRs decreased substantially during the study period. CONCLUSION Efficient implementation of two main malaria prevention strategies in Dangassa substantially contribute to a reduction of both asymptomatic and symptomatic malaria from 2015 to 2020.
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Affiliation(s)
- Mahamoudou Touré
- West African International Center of Excellence for Malaria Research, Bamako, Mali. .,Faculté de Médecine et d'Odonto-Stomatologie (FMOS), Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali.
| | - Moussa Keita
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Faculté de Médecine et d'Odonto-Stomatologie (FMOS), Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Fousseyni Kané
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Faculté de Médecine et d'Odonto-Stomatologie (FMOS), Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Daouda Sanogo
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Faculté de Médecine et d'Odonto-Stomatologie (FMOS), Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Salim Kanté
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Faculté de Médecine et d'Odonto-Stomatologie (FMOS), Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Drissa Konaté
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Faculté de Médecine et d'Odonto-Stomatologie (FMOS), Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Ayouba Diarra
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Faculté de Médecine et d'Odonto-Stomatologie (FMOS), Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Nafomon Sogoba
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Faculté de Médecine et d'Odonto-Stomatologie (FMOS), Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Mamadou B Coulibaly
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Faculté de Médecine et d'Odonto-Stomatologie (FMOS), Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Sekou F Traoré
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Faculté de Pharmacie (FAPH), Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Michael Alifrangis
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Department of Immunology and Microbiology, Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mahamadou Diakité
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Faculté de Pharmacie (FAPH), Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Jeffrey G Shaffer
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Departments of Tropical Medicine and Biostatistics, Tulane School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Donald J Krogstad
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Departments of Tropical Medicine and Biostatistics, Tulane School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Seydou Doumbia
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Faculté de Médecine et d'Odonto-Stomatologie (FMOS), Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
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19
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Denson JL, Gillet AS, Zu Y, Brown M, Pham T, Yoshida Y, Mauvais-Jarvis F, Douglas IS, Moore M, Tea K, Wetherbie A, Stevens R, Lefante J, Shaffer JG, Armaignac DL, Belden KA, Kaufman M, Heavner SF, Danesh VC, Cheruku SR, St Hill CA, Boman K, Deo N, Bansal V, Kumar VK, Walkey AJ, Kashyap R. Metabolic Syndrome and Acute Respiratory Distress Syndrome in Hospitalized Patients With COVID-19. JAMA Netw Open 2021; 4:e2140568. [PMID: 34935924 PMCID: PMC8696573 DOI: 10.1001/jamanetworkopen.2021.40568] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
IMPORTANCE Obesity, diabetes, and hypertension are common comorbidities in patients with severe COVID-19, yet little is known about the risk of acute respiratory distress syndrome (ARDS) or death in patients with COVID-19 and metabolic syndrome. OBJECTIVE To determine whether metabolic syndrome is associated with an increased risk of ARDS and death from COVID-19. DESIGN, SETTING, AND PARTICIPANTS This multicenter cohort study used data from the Society of Critical Care Medicine Discovery Viral Respiratory Illness Universal Study collected from 181 hospitals across 26 countries from February 15, 2020, to February 18, 2021. Outcomes were compared between patients with metabolic syndrome (defined as ≥3 of the following criteria: obesity, prediabetes or diabetes, hypertension, and dyslipidemia) and a control population without metabolic syndrome. Participants included adult patients hospitalized for COVID-19 during the study period who had a completed discharge status. Data were analyzed from February 22 to October 5, 2021. EXPOSURES Exposures were SARS-CoV-2 infection, metabolic syndrome, obesity, prediabetes or diabetes, hypertension, and/or dyslipidemia. MAIN OUTCOMES AND MEASURES The primary outcome was in-hospital mortality. Secondary outcomes included ARDS, intensive care unit (ICU) admission, need for invasive mechanical ventilation, and length of stay (LOS). RESULTS Among 46 441 patients hospitalized with COVID-19, 29 040 patients (mean [SD] age, 61.2 [17.8] years; 13 059 [45.0%] women and 15713 [54.1%] men; 6797 Black patients [23.4%], 5325 Hispanic patients [18.3%], and 16 507 White patients [57.8%]) met inclusion criteria. A total of 5069 patients (17.5%) with metabolic syndrome were compared with 23 971 control patients (82.5%) without metabolic syndrome. In adjusted analyses, metabolic syndrome was associated with increased risk of ICU admission (adjusted odds ratio [aOR], 1.32 [95% CI, 1.14-1.53]), invasive mechanical ventilation (aOR, 1.45 [95% CI, 1.28-1.65]), ARDS (aOR, 1.36 [95% CI, 1.12-1.66]), and mortality (aOR, 1.19 [95% CI, 1.08-1.31]) and prolonged hospital LOS (median [IQR], 8.0 [4.2-15.8] days vs 6.8 [3.4-13.0] days; P < .001) and ICU LOS (median [IQR], 7.0 [2.8-15.0] days vs 6.4 [2.7-13.0] days; P < .001). Each additional metabolic syndrome criterion was associated with increased risk of ARDS in an additive fashion (1 criterion: 1147 patients with ARDS [10.4%]; P = .83; 2 criteria: 1191 patients with ARDS [15.3%]; P < .001; 3 criteria: 817 patients with ARDS [19.3%]; P < .001; 4 criteria: 203 patients with ARDS [24.3%]; P < .001). CONCLUSIONS AND RELEVANCE These findings suggest that metabolic syndrome was associated with increased risks of ARDS and death in patients hospitalized with COVID-19. The association with ARDS was cumulative for each metabolic syndrome criteria present.
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Affiliation(s)
- Joshua L Denson
- Section of Pulmonary Diseases, Critical Care, and Environmental Medicine, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | | | - Yuanhao Zu
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - Margo Brown
- Section of Pulmonary Diseases, Critical Care, and Environmental Medicine, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Thaidan Pham
- Section of Pulmonary Diseases, Critical Care, and Environmental Medicine, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Yilin Yoshida
- Section of Endocrinology and Metabolism, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana
- Southeast Louisiana Veterans Affairs Healthcare System, New Orleans
| | - Franck Mauvais-Jarvis
- Section of Endocrinology and Metabolism, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana
- Southeast Louisiana Veterans Affairs Healthcare System, New Orleans
| | - Ivor S Douglas
- Division of Pulmonary Sciences & Critical Care Medicine, Denver Health Medical Center, Denver, Colorado
- University of Colorado, Anschutz School of Medicine, Aurora
| | - Mathew Moore
- Section of Pulmonary Diseases, Critical Care, and Environmental Medicine, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Kevin Tea
- Section of Pulmonary Diseases, Critical Care, and Environmental Medicine, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Andrew Wetherbie
- Section of Pulmonary Diseases, Critical Care, and Environmental Medicine, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Rachael Stevens
- Section of Pulmonary Diseases, Critical Care, and Environmental Medicine, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - John Lefante
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - Jeffrey G Shaffer
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | | | - Katherine A Belden
- Division of Infectious Diseases, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | | | - Smith F Heavner
- Prisma Health Department of Medicine, Prisma Health Upstate, Greenville, South Carolina
| | - Valerie C Danesh
- Baylor Scott & White Health, Department of Nursing, Dallas, Texas
| | - Sreekanth R Cheruku
- Divisions of Cardiothoracic Anesthesiology and Critical Care Medicine, Department of Anesthesiology and Pain Management, UT Southwestern Medical Center, Dallas, Texas
| | | | - Karen Boman
- Society of Critical Care Medicine, Mount Prospect, Illinois
| | - Neha Deo
- Department of Anesthesia and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota
| | - Vikas Bansal
- Department of Anesthesia and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Allan J Walkey
- The Pulmonary Center, Division of Pulmonary, Allergy, Sleep and Critical Care; Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Rahul Kashyap
- Department of Anesthesia and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota
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20
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Borrega R, Nelson DKS, Koval AP, Bond NG, Heinrich ML, Rowland MM, Lathigra R, Bush DJ, Aimukanova I, Phinney WN, Koval SA, Hoffmann AR, Smither AR, Bell-Kareem AR, Melnik LI, Genemaras KJ, Chao K, Snarski P, Melton AB, Harrell JE, Smira AA, Elliott DH, Rouelle JA, Sabino-Santos G, Drouin AC, Momoh M, Sandi JD, Goba A, Samuels RJ, Kanneh L, Gbakie M, Branco ZL, Shaffer JG, Schieffelin JS, Robinson JE, Fusco DN, Sabeti PC, Andersen KG, Grant DS, Boisen ML, Branco LM, Garry RF. Cross-Reactive Antibodies to SARS-CoV-2 and MERS-CoV in Pre-COVID-19 Blood Samples from Sierra Leoneans. Viruses 2021; 13:2325. [PMID: 34835131 PMCID: PMC8625389 DOI: 10.3390/v13112325] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/14/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
Many countries in sub-Saharan Africa have experienced lower COVID-19 caseloads and fewer deaths than countries in other regions worldwide. Under-reporting of cases and a younger population could partly account for these differences, but pre-existing immunity to coronaviruses is another potential factor. Blood samples from Sierra Leonean Lassa fever and Ebola survivors and their contacts collected before the first reported COVID-19 cases were assessed using enzyme-linked immunosorbent assays for the presence of antibodies binding to proteins of coronaviruses that infect humans. Results were compared to COVID-19 subjects and healthy blood donors from the United States. Prior to the pandemic, Sierra Leoneans had more frequent exposures than Americans to coronaviruses with epitopes that cross-react with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), SARS-CoV, and Middle Eastern respiratory syndrome coronavirus (MERS-CoV). The percentage of Sierra Leoneans with antibodies reacting to seasonal coronaviruses was also higher than for American blood donors. Serological responses to coronaviruses by Sierra Leoneans did not differ by age or sex. Approximately a quarter of Sierra Leonian pre-pandemic blood samples had neutralizing antibodies against SARS-CoV-2 pseudovirus, while about a third neutralized MERS-CoV pseudovirus. Prior exposures to coronaviruses that induce cross-protective immunity may contribute to reduced COVID-19 cases and deaths in Sierra Leone.
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Affiliation(s)
- Rodrigo Borrega
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Diana K. S. Nelson
- Zalgen Labs, LCC, Broomfield, CO 80045, USA; (D.K.S.N.); (D.J.B.); (I.A.); (W.N.P.)
| | - Anatoliy P. Koval
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Nell G. Bond
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
| | - Megan L. Heinrich
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Megan M. Rowland
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Raju Lathigra
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Duane J. Bush
- Zalgen Labs, LCC, Broomfield, CO 80045, USA; (D.K.S.N.); (D.J.B.); (I.A.); (W.N.P.)
| | - Irina Aimukanova
- Zalgen Labs, LCC, Broomfield, CO 80045, USA; (D.K.S.N.); (D.J.B.); (I.A.); (W.N.P.)
| | - Whitney N. Phinney
- Zalgen Labs, LCC, Broomfield, CO 80045, USA; (D.K.S.N.); (D.J.B.); (I.A.); (W.N.P.)
| | - Sophia A. Koval
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Andrew R. Hoffmann
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
| | - Allison R. Smither
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
| | - Antoinette R. Bell-Kareem
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
| | - Lilia I. Melnik
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
| | - Kaylynn J. Genemaras
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
- Bioinnovation Program, Tulane University, New Orleans, LA 70118, USA
| | - Karissa Chao
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
- Bioinnovation Program, Tulane University, New Orleans, LA 70118, USA
| | - Patricia Snarski
- Heart and Vascular Institute, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA;
- Department of Physiology, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Alexandra B. Melton
- Department of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA;
| | - Jaikin E. Harrell
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
| | - Ashley A. Smira
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.A.S.); (D.H.E.); (J.A.R.); (J.S.S.); (J.E.R.)
| | - Debra H. Elliott
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.A.S.); (D.H.E.); (J.A.R.); (J.S.S.); (J.E.R.)
| | - Julie A. Rouelle
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.A.S.); (D.H.E.); (J.A.R.); (J.S.S.); (J.E.R.)
| | - Gilberto Sabino-Santos
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA;
- Centre for Virology Research, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirao Preto 14049-900, SP, Brazil
| | - Arnaud C. Drouin
- Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.C.D.); (D.N.F.)
| | - Mambu Momoh
- Eastern Polytechnic Institute, Kenema, Sierra Leone;
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - John Demby Sandi
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
| | - Augustine Goba
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
| | - Robert J. Samuels
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
| | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
| | - Michael Gbakie
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
| | - Zoe L. Branco
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA;
| | - John S. Schieffelin
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.A.S.); (D.H.E.); (J.A.R.); (J.S.S.); (J.E.R.)
- Department of Internal Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - James E. Robinson
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.A.S.); (D.H.E.); (J.A.R.); (J.S.S.); (J.E.R.)
| | - Dahlene N. Fusco
- Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (A.C.D.); (D.N.F.)
| | - Pardis C. Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA;
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Kristian G. Andersen
- Department of Immunology and Microbial Science, Scripps Research, La Jolla, CA 92037, USA;
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Donald S. Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (J.D.S.); (A.G.); (R.J.S.); (L.K.); (M.G.)
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Matthew L. Boisen
- Zalgen Labs, LCC, Broomfield, CO 80045, USA; (D.K.S.N.); (D.J.B.); (I.A.); (W.N.P.)
| | - Luis M. Branco
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
| | - Robert F. Garry
- Zalgen Labs, LCC, Germantown, MD 20876, USA; (R.B.); (A.P.K.); (M.L.H.); (M.M.R.); (R.L.); (S.A.K.); (Z.L.B.)
- Zalgen Labs, LCC, Broomfield, CO 80045, USA; (D.K.S.N.); (D.J.B.); (I.A.); (W.N.P.)
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (N.G.B.); (A.R.H.); (A.R.S.); (A.R.B.-K.); (L.I.M.); (K.J.G.); (K.C.); (J.E.H.)
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21
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Konaté D, Diawara SI, Keita B, Sogoba N, Fayiçal M, Guindo A, Thiam S, Traoré SF, Shaffer JG, Doumbia S, Diakité M. Effectiveness and Community Acceptance of Extending Seasonal Malaria Chemoprevention to Children 5 to 14 Years of Age in Dangassa, Mali. Am J Trop Med Hyg 2021; 106:648-654. [PMID: 34781256 PMCID: PMC8832934 DOI: 10.4269/ajtmh.21-0046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 09/13/2021] [Indexed: 11/12/2022] Open
Abstract
Seasonal malaria chemoprevention (SMC) was adopted in Mali in 2012 for preventing malaria in children younger than 5 years. Although this strategy has been highly effective in reducing childhood malaria, an uptick in malaria occurrence has occurred in children 5 to 15 years of age. This study aimed to investigate the feasibility of providing SMC to older children. A cohort of 350 children age 5 to 14 years were monitored during the 2019 transmission season in Dangassa, Mali. The intervention group received five monthly rounds of sulfadoxine–pyrimethamine plus amodiaquine, whereas the control group consisted of untreated children. Community acceptance for extending SMC was assessed during the final round. Logistic regression models were applied to compare the risk of Plasmodium falciparum malaria infection, anemia, and fever between the intervention and control groups. Kaplan-Meier survival analyses were used to compare the time to P. falciparum parasitemia infection between the groups. The community acceptance rate was 96.5% (139 of 144). Significant declines were observed in the prevalence of P. falciparum parasitemia (adjusted odds ratio, 0.22; 95% CI, 0.11–0.42) and anemia (adjusted odds ratio, 0.15; 95% CI, 0.07–0.28) in the intervention group compared with the control group. The cumulative incidence of P. falciparum infections was significantly greater (75.4%, 104 of 138) in the control group compared with the intervention group (40.7%, 61 of 143, P = 0.001). This study reveals that expanding SMC to older children is likely feasible, has high community acceptance, and is in reducing uncomplicated malaria and anemia in older children.
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Affiliation(s)
- Drissa Konaté
- West African International Center for Excellence in Malaria Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sory Ibrahim Diawara
- West African International Center for Excellence in Malaria Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Bourama Keita
- West African International Center for Excellence in Malaria Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nafomon Sogoba
- West African International Center for Excellence in Malaria Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamadou Fayiçal
- West African International Center for Excellence in Malaria Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Agnès Guindo
- West African International Center for Excellence in Malaria Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sibe Thiam
- West African International Center for Excellence in Malaria Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sékou Fantamady Traoré
- West African International Center for Excellence in Malaria Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.,University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Jeffrey G Shaffer
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana
| | - Seydou Doumbia
- West African International Center for Excellence in Malaria Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.,University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamadou Diakité
- West African International Center for Excellence in Malaria Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.,University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
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22
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Wilkinson E, Giovanetti M, Tegally H, San JE, Lessells R, Cuadros D, Martin DP, Rasmussen DA, Zekri ARN, Sangare AK, Ouedraogo AS, Sesay AK, Priscilla A, Kemi AS, Olubusuyi AM, Oluwapelumi AOO, Hammami A, Amuri AA, Sayed A, Ouma AEO, Elargoubi A, Ajayi NA, Victoria AF, Kazeem A, George A, Trotter AJ, Yahaya AA, Keita AK, Diallo A, Kone A, Souissi A, Chtourou A, Gutierrez AV, Page AJ, Vinze A, Iranzadeh A, Lambisia A, Ismail A, Rosemary A, Sylverken A, Femi A, Ibrahimi A, Marycelin B, Oderinde BS, Bolajoko B, Dhaala B, Herring BL, Njanpop-Lafourcade BM, Kleinhans B, McInnis B, Tegomoh B, Brook C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Peyrefitte C, Daubenberger C, Morang’a CM, Nokes DJ, Amoako DG, Bugembe DL, Park D, Baker D, Doolabh D, Ssemwanga D, Tshiabuila D, Bassirou D, Amuzu DSY, Goedhals D, Omuoyo DO, Maruapula D, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong’era EM, Ngabana EN, Shumba E, El Fahime E, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Leendertz F, Ajili F, Enoch FO, Wasfi F, Abdelmoula F, Mosha FS, Takawira FT, Derrar F, Bouzid F, Onikepe F, Adeola F, Muyembe FM, Tanser F, Dratibi FA, Mbunsu GK, Thilliez G, Kay GL, Githinji G, van Zyl G, Awandare GA, Schubert G, Maphalala GP, Ranaivoson HC, Lemriss H, Anise H, Abe H, Karray HH, Nansumba H, Elgahzaly HA, Gumbo H, Smeti I, Ayed IB, Odia I, Ben Boubaker IB, Gaaloul I, Gazy I, Mudau I, Ssewanyana I, Konstantinus I, Lekana-Douk JB, Makangara JCC, Tamfum JJM, Heraud JM, Shaffer JG, Giandhari J, Li J, Yasuda J, Mends JQ, Kiconco J, Morobe JM, Gyapong JO, Okolie JC, Kayiwa JT, Edwards JA, Gyamfi J, Farah J, Nakaseegu J, Ngoi JM, Namulondo J, Andeko JC, Lutwama JJ, O’Grady J, Siddle K, Adeyemi KT, Tumedi KA, Said KM, Hae-Young K, Duedu KO, Belyamani L, Fki-Berrajah L, Singh L, Martins LDO, Tyers L, Ramuth M, Mastouri M, Aouni M, el Hefnawi M, Matsheka MI, Kebabonye M, Diop M, Turki M, Paye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina M, Nwando M, Owusu M, Wiley MR, Youtchou MT, Ayekaba MO, Abouelhoda M, Seadawy MG, Khalifa MK, Sekhele M, Ouadghiri M, Diagne MM, Mwenda M, Allam M, Phan MVT, Abid N, Touil N, Rujeni N, Kharrat N, Ismael N, Dia N, Mabunda N, Hsiao NY, Silochi NB, Nsenga N, Gumede N, Mulder N, Ndodo N, Razanajatovo NH, Iguosadolo N, Judith O, Kingsley OC, Sylvanus O, Peter O, Femi O, Idowu O, Testimony O, Chukwuma OE, Ogah OE, Onwuamah CK, Cyril O, Faye O, Tomori O, Ondoa P, Combe P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Dussart P, Bester PA, Mbala PK, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Carr RAA, El Kabbaj S, Gargouri S, Masmoudi S, Sankhe S, Lawal SB, Kassim S, Trabelsi S, Metha S, Kammoun S, Lemriss S, Agwa SHA, Calvignac-Spencer S, Schaffner SF, Doumbia S, Mandanda SM, Aryeetey S, Ahmed SS, Elhamoumi S, Andriamandimby S, Tope S, Lekana-Douki S, Prosolek S, Ouangraoua S, Mundeke SA, Rudder S, Panji S, Pillay S, Engelbrecht S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Aanniz T, Mohale T, Le-Viet T, Schindler T, Anyaneji UJ, Chinedu U, Ramphal U, Jessica U, George U, Fonseca V, Enouf V, Gorova V, Roshdy WH, Ampofo WK, Preiser W, Choga WT, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR, Sall AA, Rebai A, von Gottberg A, Kouriba B, Williamson C, Bridges DJ, Chikwe I, Bhiman JN, Mine M, Cotten M, Moyo S, Gaseitsiwe S, Saasa N, Sabeti PC, Kaleebu P, Tebeje YK, Tessema SK, Happi C, Nkengasong J, de Oliveira T. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science 2021; 374:423-431. [PMID: 34672751 PMCID: PMC7613315 DOI: 10.1126/science.abj4336] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/03/2021] [Indexed: 01/05/2023]
Abstract
The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants.
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Affiliation(s)
- Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James E. San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Diego Cuadros
- Department of Geography and GIS, University of Cincinnati, Cincinnati, OH, USA
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - David A. Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Abdel-Rahman N. Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Abdoul K. Sangare
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
| | - Abdoul-Salam Ouedraogo
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | | | - Abechi Priscilla
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Adedotun-Sulaiman Kemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | - Adeyemi O. O. Oluwapelumi
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Adnène Hammami
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Adrienne A. Amuri
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Ahmad Sayed
- Genomics Research Program, Children’s Cancer Hospital, Cairo, Egypt
| | - Ahmed E. O. Ouma
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Aida Elargoubi
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Nnennaya A. Ajayi
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Ajogbasile F. Victoria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Akano Kazeem
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Ali A. Yahaya
- World Health Organization, Africa Region, Brazzaville Congo
| | - Alpha K. Keita
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea
- TransVIHMI, Montpellier University/IRD/INSERM, Montpellier, France
| | - Amadou Diallo
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou Kone
- Mali-University Clinical Research Center (UCRC), Bamako, Mali
| | - Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Amel Chtourou
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | | | | | - Anika Vinze
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Arash Iranzadeh
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arnold Lambisia
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Arshad Ismail
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Audu Rosemary
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | | | - Ayoade Femi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Baba Marycelin
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bamidele S. Oderinde
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bankole Bolajoko
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | | | - Bronwyn Kleinhans
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Bronwyn McInnis
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Bryan Tegomoh
- The Biotechnology Center of the University of Yaoundé I, Cameroon and CDC Foundation, Yaounde, Cameroon
| | - Cara Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | | | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Chantal G. Akoua-Koffi
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | - Charles N. Agoti
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- School of Public Health, Pwani University, Kilifi, Kenya
| | | | | | - Collins M. Morang’a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - D. James Nokes
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Daniel G. Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Danny Park
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | | | - Deelan Doolabh
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Deogratius Ssemwanga
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Diarra Bassirou
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Dominic S. Y. Amuzu
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Dominique Goedhals
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | | | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | | | - Eddy K. Lusamaki
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Edgar Simulundu
- University of Zambia, School of Veterinary Medicine, Department of Disease Control, Lusaka, Zambia
| | | | - Edith N. Ngabana
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Edwin Shumba
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | - Elmostafa El Fahime
- Functional Genomic Platform/National Centre for Scientific and Technical Research (CNRST), Rabat, Morocco
| | - Emmanuel Lokilo
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
| | | | - Eromon Philomena
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Etilé A. Anoh
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | | | - Faida Ajili
- Research Unit of Autoimmune Diseases UR17DN02, Military Hospital of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Fakayode O. Enoch
- Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria
| | - Fares Wasfi
- Laboratory of Clinical Virology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Fatma Abdelmoula
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | | | | | - Fawzi Derrar
- National Influenza Centre, Viral Respiratory Laboratory, Algiers, Algeria
| | - Feriel Bouzid
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Folarin Onikepe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Fowotade Adeola
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Francisca M. Muyembe
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Frank Tanser
- Lincoln International Institute for Rural Health, University of Lincoln, Lincoln, UK
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
| | | | - Gabriel K. Mbunsu
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | | | - George Githinji
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Gert van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | | | - Gugu P. Maphalala
- Institution and Department, Ministry Of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini
| | | | - Hajar Lemriss
- Laboratory of Health Sciences and Technologies, High Institute of Health Sciences, Hassan 1st University, Settat, Morocco
| | - Happi Anise
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Hela H. Karray
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | | | - Hesham A. Elgahzaly
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Hlanai Gumbo
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Ibtihel Smeti
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ikhlas B. Ayed
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Ilhem Boutiba Ben Boubaker
- Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, 1006 Tunis, Tunisia
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Imed Gaaloul
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | - Inbal Gazy
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Innocent Mudau
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Jean B. Lekana-Douk
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | - Jean-Claude C. Makangara
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Jean-Jacques M. Tamfum
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Jean-Michel Heraud
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jingjing Li
- Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, PA, USA
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Joana Q. Mends
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | - John M. Morobe
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - John O. Gyapong
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Johnson C. Okolie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - John T. Kayiwa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Johnathan A. Edwards
- Lincoln International Institute for Rural Health, University of Lincoln, Lincoln, UK
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jones Gyamfi
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | | | - Joyce M. Ngoi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | | | - Julia C. Andeko
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | | | | | - Kayode T. Adeyemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Kefentse A. Tumedi
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
| | - Khadija M. Said
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Kim Hae-Young
- New York University Grossman School of Medicine, New York City, NY, USA
| | - Kwabena O. Duedu
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Lahcen Belyamani
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Lamia Fki-Berrajah
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Lynn Tyers
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Magalutcheemee Ramuth
- Virology/Molecular Biology Department, Central Health Laboratory, Ministry of Health and Wellness, Mauritius
| | - Maha Mastouri
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Mahjoub Aouni
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | - Mahmoud el Hefnawi
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo Egypt
| | | | | | - Mamadou Diop
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Manel Turki
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Marietou Paye
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | | | - Matoke-Muhia Damaris
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | - Maureen W. Mburu
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Maximillian Mpina
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- Ifakara Health Institute, Dar-es-Salaam, Tanzania
| | - Mba Nwando
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Michael Owusu
- Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Mirabeau T. Youtchou
- Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria
| | | | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo 12613, Egypt
- King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Mohamed G. Seadawy
- Biological Prevention Department, Main Chemical Laboratories, Egypt Army, Cairo, Egypt
| | | | - Mooko Sekhele
- National Reference Laboratory Lesotho, Maseru, Lesotho
| | - Mouna Ouadghiri
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | | | | | - Mushal Allam
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - My V. T. Phan
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
- Department of Biotechnology, High Institute of Biotechnology of Sidi Thabet, University of Manouba, BP-66, 2020 Ariana-Tunis, Tunisia
| | - Nadia Touil
- Genomic Center for Human Pathologies (GENOPATH), Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Nadine Rujeni
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Najla Kharrat
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Nalia Ismael
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Nedio Mabunda
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Nei-yuan Hsiao
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | - Ngoy Nsenga
- World Health Organization, Africa Region, Brazzaville Congo
| | - Nicksy Gumede
- World Health Organization, Africa Region, Brazzaville Congo
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa
| | | | | | - Nosamiefan Iguosadolo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Oguzie Judith
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Ojide C. Kingsley
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | | | | | - Oladiji Femi
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Olawoye Idowu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Olumade Testimony
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Omoruyi E. Chukwuma
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Onwe E. Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Chika K. Onwuamah
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | | | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Pascale Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | | | | | - Paul E. Oluniyi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Paulo Arnaldo
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Peter K. Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Phillip A. Bester
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | - Placide K. Mbala
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Reuben Ayivor-Djanie
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Richard Njouom
- Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon
| | - Richard O. Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richmond Gorman
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Rosina A. A. Carr
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Saâd El Kabbaj
- Laboratoire de Recherche et d’Analyses Médicales de la Gendarmerie Royale, Rabat, Morocco
| | - Saba Gargouri
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Safietou Sankhe
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Salako B. Lawal
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Samar Kassim
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Sameh Trabelsi
- Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia
| | - Samar Metha
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Sami Kammoun
- CHU Hedi Chaker Sfax, Service de Pneumologie, Tunis, Tunisia
| | - Sanaâ Lemriss
- Laboratoire de Recherche et d’Analyses Médicales de la Gendarmerie Royale, Rabat, Morocco
| | - Sara H. A. Agwa
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | | | | | - Seydou Doumbia
- Mali-University Clinical Research Center (UCRC), Bamako, Mali
| | - Sheila M. Mandanda
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | | | | | | | - Sobajo Tope
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Sonia Lekana-Douki
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Soumeya Ouangraoua
- Centre MURAZ, Ouagadougou, Burkina Faso
- National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso
| | - Steve A. Mundeke
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | - Sumir Panji
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Susan Nabadda
- Central Public Health Laboratories (CPHL), Kampala, Uganda
| | - Sylvie Behillil
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | | | - Sylvie van der Werf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | | | - Tarik Aanniz
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Thabo Mohale
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Tobias Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ugwu Chinedu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa
| | - Uwanibe Jessica
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Uwem George
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Coordenação Geral de Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - Vincent Enouf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | - Vivianne Gorova
- World Health Organization, WHO Lesotho, Maseru, Lesotho
- Med24 Medical Centre, Ruwa, Zimbabwe
| | | | - William K. Ampofo
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Wonderful T. Choga
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Yvan Butera
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
| | | | - Amadou A. Sall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Bourema Kouriba
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | - Carolyn Williamson
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | | | - Jinal N. Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Matthew Cotten
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ngonda Saasa
- University of Zambia, School of Veterinary Medicine, Department of Disease Control, Lusaka, Zambia
| | | | | | - Yenew K. Tebeje
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Sofonias K. Tessema
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - John Nkengasong
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
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23
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Bond NG, Grant DS, Himmelfarb ST, Engel EJ, Al-Hasan F, Gbakie M, Kamara F, Kanneh L, Mustapha I, Okoli A, Fischer W, Wohl D, Garry RF, Samuels R, Shaffer JG, Schieffelin JS. Post-Ebola Syndrome Presents With Multiple Overlapping Symptom Clusters: Evidence From an Ongoing Cohort Study in Eastern Sierra Leone. Clin Infect Dis 2021; 73:1046-1054. [PMID: 33822010 PMCID: PMC8442780 DOI: 10.1093/cid/ciab267] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/25/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Following the 2013-2016 West African Ebola outbreak, distinct, persistent health complaints were recognized in Ebola virus disease (EVD) survivors. Here we provide an in-depth characterization of post-Ebola syndrome >2.5 years after resolution of disease. Additionally, we report subphenotypes of post-Ebola syndrome with overlapping symptom clusters in survivors from Eastern Sierra Leone. METHODS Participants in Eastern Sierra Leone were identified by the Sierra Leone Association of Ebola survivors. Survivors and their contacts were administered a questionnaire assessing self-reported symptoms and a physical examination. Comparisons between survivors and contacts were conducted using conditional logistic regression. Symptom groupings were identified using hierarchical clustering approaches. Simplified presentation of incredibly complex evaluations (SPICE), correlation analysis, logistic regression, and principal component analysis (PCA) were performed to explore the relationships between symptom clusters. RESULTS Three hundred seventy-five EVD survivors and 1040 contacts were enrolled into the study. At enrollment, EVD survivors reported significantly more symptoms than their contacts in all categories (P < .001). Symptom clusters representing distinct organ systems were identified. Correlation and logistic regression analysis identified relationships between symptom clusters, including stronger relationships between clusters including musculoskeletal symptoms (r = 0.63, P < .001; and P < .001 for correlation and logistic regression, respectively). SPICE and PCA further highlighted subphenotypes with or without musculoskeletal symptoms. CONCLUSIONS This study presents an in-depth characterization of post-Ebola syndrome in Sierra Leonean survivors >2.5 years after disease. The interrelationship between symptom clusters indicates that post-Ebola syndrome is a heterogeneous disease. The distinct musculoskeletal and non-musculoskeletal phenotypes identified likely require targeted therapies to optimize long-term treatment for EVD survivors.
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Affiliation(s)
- Nell G Bond
- Tulane University, New Orleans, Louisiana, USA
| | | | | | | | | | | | | | | | | | | | - William Fischer
- University of North Carolina, Chapel Hill, North Carolina, USA
| | - David Wohl
- University of North Carolina, Chapel Hill, North Carolina, USA
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24
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Maiga FO, Wele M, Toure SM, Keita M, Tangara CO, Refeld RR, Thiero O, Kayentao K, Diakite M, Dara A, Li J, Toure M, Sagara I, Djimdé A, Mather FJ, Doumbia SO, Shaffer JG. Artemisinin-based combination therapy for uncomplicated Plasmodium falciparum malaria in Mali: a systematic review and meta-analysis. Malar J 2021; 20:356. [PMID: 34461901 PMCID: PMC8404312 DOI: 10.1186/s12936-021-03890-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Artemisinin-based combination therapy (ACT) was deployed in 2005 as an alternative to chloroquine and is considered the most efficacious treatment currently available for uncomplicated falciparum malaria. While widespread artemisinin resistance has not been reported to date in Africa, recent studies have reported partial resistance in Rwanda. The purpose of this study is to provide a current systematic review and meta-analysis on ACT at Mali study sites, where falciparum malaria is highly endemic. METHODS A systematic review of the literature maintained in the bibliographic databases accessible through the PubMed, ScienceDirect and Web of Science search engines was performed to identify research studies on ACT occurring at Mali study sites. Selected studies included trials occurring at Mali study sites with reported polymerase chain reaction (PCR)-corrected adequate clinical and parasite response rates (ACPRcs) at 28 days. Data were stratified by treatment arm (artemether-lumefantrine (AL), the first-line treatment for falciparum malaria in Mali and non-AL arms) and analysed using random-effects, meta-analysis approaches. RESULTS A total of 11 studies met the inclusion criteria, and a risk of bias assessment carried out by two independent reviewers determined low risk of bias among all assessed criteria. The ACPRc for the first-line AL at Mali sites was 99.0% (95% CI (98.3%, 99.8%)), while the ACPRc among non-AL treatment arms was 98.9% (95% CI (98.3%, 99.5%)). The difference in ACPRcs between non-AL treatment arms and AL treatment arms was not statistically significant (p = .752), suggesting that there are potential treatment alternatives beyond the first-line of AL in Mali. CONCLUSIONS ACT remains highly efficacious in treating uncomplicated falciparum malaria in Mali. Country-specific meta-analyses on ACT are needed on an ongoing basis for monitoring and evaluating drug efficacy patterns to guide local malaria treatment policies, particularly in the wake of observed artemisinin resistance in Southeast Asia and partial resistance in Rwanda.
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Affiliation(s)
- Fatoumata O Maiga
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
| | - Mamadou Wele
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sounkou M Toure
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Makan Keita
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Randi R Refeld
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, 1440 Canal Street #8310, Suite 1610, New Orleans, LA, 70112-2703, USA
| | - Oumar Thiero
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Kassoum Kayentao
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamadou Diakite
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Antoine Dara
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Jian Li
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, 1440 Canal Street #8310, Suite 1610, New Orleans, LA, 70112-2703, USA
| | - Mahamoudou Toure
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Issaka Sagara
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye Djimdé
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Frances J Mather
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, 1440 Canal Street #8310, Suite 1610, New Orleans, LA, 70112-2703, USA
| | - Seydou O Doumbia
- University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
| | - Jeffrey G Shaffer
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, 1440 Canal Street #8310, Suite 1610, New Orleans, LA, 70112-2703, USA.
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Koch MR, Kanneh L, Wise PH, Kurina LM, Alhasan F, Garry RF, Schieffelin JS, Shaffer JG, Grant DS. Health seeking behavior after the 2013-16 Ebola epidemic: Lassa fever as a metric of persistent changes in Kenema District, Sierra Leone. PLoS Negl Trop Dis 2021; 15:e0009576. [PMID: 34260615 PMCID: PMC8312964 DOI: 10.1371/journal.pntd.0009576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/26/2021] [Accepted: 06/19/2021] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The West African Ebola epidemic of 2013-2016 killed nearly 4,000 Sierra Leoneans and devastated health infrastructure across West Africa. Changes in health seeking behavior (HSB) during the outbreak resulted in dramatic underreporting and substantial declines in hospital presentations to public health facilities, resulting in an estimated tens of thousands of additional maternal, infant, and adult deaths per year. Sierra Leone's Kenema District, a major Ebola hotspot, is also endemic for Lassa fever (LF), another often-fatal hemorrhagic disease. Here we assess the impact of the West African Ebola epidemic on health seeking behaviors with respect to presentations to the Kenema Government Hospital (KGH) Lassa Ward, which serves as the primary health care referral center for suspected Lassa fever cases in the Eastern Province of Sierra Leone. METHODOLOGY/PRINCIPAL FINDINGS Presentation frequencies for suspected Lassa fever presenting to KGH or one of its referral centers from 2011-2019 were analyzed to consider the potential impact of the West African Ebola epidemic on presentation patterns. There was a significant decline in suspected LF cases presenting to KGH following the epidemic, and a lower percentage of subjects were admitted to the KGH Lassa Ward following the epidemic. To assess general HSB, a questionnaire was developed and administered to 200 residents from 8 villages in Kenema District. Among 194 completed interviews, 151 (78%) of respondents stated they felt hospitals were safer post-epidemic with no significant differences noted among subjects according to religious background, age, gender, or education. However, 37 (19%) subjects reported decreased attendance at hospitals since the epidemic, which suggests that trust in the healthcare system has not fully rebounded. Cost was identified as a major deterrent to seeking healthcare. CONCLUSIONS/SIGNIFICANCE Analysis of patient demographic data suggests that fewer individuals sought care for Lassa fever and other febrile illnesses in Kenema District after the West African Ebola epidemic. Re-establishing trust in health care services will require efforts beyond rebuilding infrastructure and require concerted efforts to rebuild the trust of local residents who may be wary of seeking healthcare post epidemic.
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Affiliation(s)
- Mikaela R. Koch
- Program in Human Biology, Stanford University, Stanford, California, United States of America
- * E-mail: (MRK); (JGS); (DSG)
| | - Lansana Kanneh
- Pediatrics–Neonatal and Developmental Medicine, Stanford University, Stanford, California, United States of America
| | - Paul H. Wise
- Pediatrics–Neonatal and Developmental Medicine, Stanford University, Stanford, California, United States of America
| | - Lianne M. Kurina
- Program in Human Biology, Stanford University, Stanford, California, United States of America
| | - Foday Alhasan
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
| | - Robert F. Garry
- Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, Louisiana, United States of America
- Zalgen Labs, LCC, Germantown, MD, United States of America
| | - John S. Schieffelin
- Sections of Infectious Disease, Department of Pediatrics, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Bioinformatics, Tulane School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
- * E-mail: (MRK); (JGS); (DSG)
| | - Donald S. Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- * E-mail: (MRK); (JGS); (DSG)
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26
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Shaffer JG, Schieffelin JS, Momoh M, Goba A, Kanneh L, Alhasan F, Gbakie M, Engel EJ, Bond NG, Hartnett JN, Nelson DKS, Bush DJ, Boisen ML, Heinrich ML, Rowland MM, Branco LM, Samuels RJ, Garry RF, Grant DS. Space-Time Trends in Lassa Fever in Sierra Leone by ELISA Serostatus, 2012-2019. Microorganisms 2021; 9:microorganisms9030586. [PMID: 33809204 PMCID: PMC8000031 DOI: 10.3390/microorganisms9030586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 01/03/2023] Open
Abstract
Lassa fever (LF) is a viral hemorrhagic disease found in Sub-Saharan Africa and is responsible for up to 300,000 cases and 5000 deaths annually. LF is highly endemic in Sierra Leone, particularly in its Eastern Province. Kenema Government Hospital (KGH) maintains one of only a few LF isolation facilities in the world with year-round diagnostic testing. Here we focus on space-time trends for LF occurring in Sierra Leone between 2012 and 2019 to provide a current account of LF in the wake of the 2014–2016 Ebola epidemic. Data were analyzed for 3277 suspected LF cases and classified as acute, recent, and non-LF or prior LF exposure using enzyme-linked immunosorbent assays (ELISAs). Presentation rates for acute, recent, and non-LF or prior LF exposure were 6.0% (195/3277), 25.6% (838/3277), and 68.4% (2244/3277), respectively. Among 2051 non-LF or prior LF exposures, 33.2% (682/2051) tested positive for convalescent LF exposure. The overall LF case-fatality rate (CFR) was 78.5% (106/135). Both clinical presentations and confirmed LF cases declined following the Ebola epidemic. These declines coincided with an increased duration between illness onset and clinical presentation, perhaps suggesting more severe disease or presentation at later stages of illness. Acute LF cases and their corresponding CFRs peaked during the dry season (November to April). Subjects with recent (but not acute) LF exposure were more likely to present during the rainy season (May to October) than the dry season (p < 0.001). The findings here suggest that LF remains endemic in Sierra Leone and that caseloads are likely to resume at levels observed prior to the Ebola epidemic. The results provide insight on the current epidemiological profile of LF in Sierra Leone to facilitate LF vaccine studies and accentuate the need for LF cohort studies and continued advancements in LF diagnostics.
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Affiliation(s)
- Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
- Correspondence: (J.G.S.); (J.S.S.); (D.S.G.); Tel.: +1-504-988-1142 (J.G.S.); +1-504-988-5117 (D.S.G.)
| | - John S. Schieffelin
- Sections of Infectious Disease, Departments of Pediatrics and Internal Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (E.J.E.); (N.G.B.)
- Correspondence: (J.G.S.); (J.S.S.); (D.S.G.); Tel.: +1-504-988-1142 (J.G.S.); +1-504-988-5117 (D.S.G.)
| | - Mambu Momoh
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
| | - Augustine Goba
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
| | - Lansana Kanneh
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
| | - Foday Alhasan
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
| | - Michael Gbakie
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
| | - Emily J. Engel
- Sections of Infectious Disease, Departments of Pediatrics and Internal Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (E.J.E.); (N.G.B.)
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA 70112, USA; (J.N.H.); (R.F.G.)
| | - Nell G. Bond
- Sections of Infectious Disease, Departments of Pediatrics and Internal Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (E.J.E.); (N.G.B.)
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA 70112, USA; (J.N.H.); (R.F.G.)
| | - Jessica N. Hartnett
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA 70112, USA; (J.N.H.); (R.F.G.)
| | - Diana K. S. Nelson
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Duane J. Bush
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Matthew L. Boisen
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Megan L. Heinrich
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Megan M. Rowland
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Luis M. Branco
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Robert J. Samuels
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, TE 37203, USA
| | - Robert F. Garry
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA 70112, USA; (J.N.H.); (R.F.G.)
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Donald S. Grant
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
- Correspondence: (J.G.S.); (J.S.S.); (D.S.G.); Tel.: +1-504-988-1142 (J.G.S.); +1-504-988-5117 (D.S.G.)
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27
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Keïta M, Doumbia S, Sissoko I, Touré M, Diawara SI, Konaté D, Sodio AB, Traoré SF, Diakité M, Doumbia SO, Sogoba N, Krogstad DJ, Shaffer JG, Coulibaly MB. Indoor and outdoor malaria transmission in two ecological settings in rural Mali: implications for vector control. Malar J 2021; 20:127. [PMID: 33663515 PMCID: PMC7931590 DOI: 10.1186/s12936-021-03650-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/15/2021] [Indexed: 11/17/2022] Open
Abstract
Background Implementation and upscale of effective malaria vector control strategies necessitates understanding the multi-factorial aspects of transmission patterns. The primary aims of this study are to determine the vector composition, biting rates, trophic preference, and the overall importance of distinguishing outdoor versus indoor malaria transmission through a study at two communities in rural Mali. Methods Mosquito collection was carried out between July 2012 and June 2016 at two rural Mali communities (Dangassa and Koïla Bamanan) using pyrethrum spray-catch and human landing catch approaches at both indoor and outdoor locations. Species of Anopheles gambiae complex were identified by polymerase chain reaction (PCR). Enzyme-Linked -Immuno-Sorbent Assay (ELISA) were used to determine the origin of mosquito blood meals and presence of Plasmodium falciparum sporozoite infections. Results A total of 11,237 An. gambiae sensu lato (s.l.) were collected during the study period (5239 and 5998 from the Dangassa and Koïla Bamanan sites, respectively). Of the 679 identified by PCR in Dangassa, Anopheles coluzzii was the predominant species with 91.4% of the catch followed by An. gambiae (8.0%) and Anopheles arabiensis (0.6%). At the same time in Koïla Bamanan, of the 623 An. gambiae s.l., An. coluzzii accounted for 99% of the catch, An. arabiensis 0.8% and An. gambiae 0.2%. Human Blood Index (HBI) measures were significantly higher in Dangassa (79.4%; 95% Bayesian credible interval (BCI) [77.4, 81.4]) than in Koïla Bamanan (15.9%; 95% BCI [14.7, 17.1]). The human biting rates were higher during the second half of the night at both sites. In Dangassa, the sporozoite rate was comparable between outdoor and indoor mosquito collections. For outdoor collections, the sporozoite positive rate was 3.6% (95% BCI [2.1–4.3]) and indoor collections were 3.1% (95% BCI [2.4–5.0]). In Koïla Bamanan, the sporozoite rate was higher indoors at 4.3% (95% BCI [2.7–6.3]) compared with outdoors at 2.4% (95% BCI [1.1–4.2]). In Dangassa, corrected entomological inoculation rates (cEIRs) using HBI were 13.74 [95% BCI 9.21–19.14] infective bites/person/month (ib/p/m) at indoor, and 18.66 [95% BCI 12.55–25.81] ib/p/m at outdoor. For Koïla Bamanan, cEIRs were 1.57 [95% BCI 2.34–2.72] ib/p/m and 0.94 [95% BCI 0.43–1.64] ib/p/m for indoor and outdoor, respectively. EIRs were significantly higher at the Dangassa site than the Koïla Bamanan site. Conclusion The findings in this work may indicate the occurrence of active, outdoor residual malaria transmission is comparable to indoor transmission in some geographic settings. The high outdoor transmission patterns observed here highlight the need for additional strategies to combat outdoor malaria transmission to complement traditional indoor preventive approaches such as long-lasting insecticidal nets (LLINs) and indoor residual spraying (IRS) which typically focus on resting mosquitoes.
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Affiliation(s)
- Moussa Keïta
- West African International Center of Excellence for Malaria Research, Bamako, Mali. .,Malaria Research and Training Center, Bamako, Mali. .,Faculty of Medicine and Odonto Stomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali. .,Faculty of Science and Techniques, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
| | - Sidy Doumbia
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Malaria Research and Training Center, Bamako, Mali
| | - Ibrahim Sissoko
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Malaria Research and Training Center, Bamako, Mali
| | - Mahamoudou Touré
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Malaria Research and Training Center, Bamako, Mali
| | - Sory Ibrahim Diawara
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Malaria Research and Training Center, Bamako, Mali
| | - Drissa Konaté
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Malaria Research and Training Center, Bamako, Mali
| | - Ambièlè Bernard Sodio
- Faculty of Science and Techniques, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sekou F Traoré
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Malaria Research and Training Center, Bamako, Mali
| | - Mahamadou Diakité
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Malaria Research and Training Center, Bamako, Mali
| | - Seydou O Doumbia
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Malaria Research and Training Center, Bamako, Mali.,Faculty of Medicine and Odonto Stomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nafomon Sogoba
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Malaria Research and Training Center, Bamako, Mali.,Faculty of Medicine and Odonto Stomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Donald J Krogstad
- School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, New Orleans, LA, 70112, USA
| | - Jeffrey G Shaffer
- School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, New Orleans, LA, 70112, USA
| | - Mamadou B Coulibaly
- West African International Center of Excellence for Malaria Research, Bamako, Mali.,Malaria Research and Training Center, Bamako, Mali
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28
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Samuels RJ, Moon TD, Starnes JR, Alhasan F, Gbakie M, Goba A, Koroma V, Momoh M, Sandi JD, Garry RF, Engel EJ, Shaffer JG, Schieffelin JS, Grant DS. Lassa Fever among Children in Eastern Province, Sierra Leone: A 7-year Retrospective Analysis (2012-2018). Am J Trop Med Hyg 2020; 104:585-592. [PMID: 33241780 PMCID: PMC7866338 DOI: 10.4269/ajtmh.20-0773] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/01/2020] [Indexed: 01/09/2023] Open
Abstract
Pediatric Lassa fever (LF) usually presents as a nonspecific febrile illness, similar to other endemic diseases in countries like Sierra Leone, where LF is considered to be hyperendemic. The nonspecificity of presentation and lack of research have made it difficult to fully understand best practices for pediatric management. We aim to describe clinical characteristics of hospitalized pediatric patients suspected or diagnosed with LF and assess factors associated with hospital outcomes among those with LF antigen-positive results. We conducted a 7-year retrospective cohort study using routine data for all children younger than 18 years admitted at the Kenema Government Hospital's LF ward. A total of 292 children with suspected or confirmed LF were analyzed. Overall, mortality was high (21%). Children with antigen-positive results had a high case fatality rate of 63% (P < 0.01). In univariate analyses, children who presented with unexplained bleeding (odds ratio [OR]: 3.58; 95% CI: 1.08-11.86; P = 0.040) and confusion (altered sensorium) (OR: 5.37; 95% CI: 1.34-21.48; P = 0.020) had increased odds of death. Abnormal serum levels of alanine aminotransferase (P = 0.001), creatinine (P = 0.004), and potassium (P = 0.003) were associated with increased likelihood of death in these children. Treatment with ribavirin was not significantly associated with survival (P = 0.916). Our findings provide insights into current pediatric LF clinical presentation and management. More evidence-based, high-quality research in creating predictive algorithms of antigen-positivity and hospital outcomes is needed in the management of pediatric LF.
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Affiliation(s)
- Robert J Samuels
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone.,Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Troy D Moon
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Joseph R Starnes
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Foday Alhasan
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Michael Gbakie
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Augustine Goba
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Veronica Koroma
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Mambu Momoh
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - John Demby Sandi
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Robert F Garry
- Department of Immunology and Microbiology, School of Medicine, Tulane University, New Orleans, Louisiana.,Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Emily J Engel
- Department of Pediatrics and Internal Medicine, Sections of Pediatric and Adult Infectious Diseases, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Jeffrey G Shaffer
- Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana
| | - John S Schieffelin
- Department of Pediatrics and Internal Medicine, Sections of Pediatric and Adult Infectious Diseases, School of Medicine, Tulane University, New Orleans, Louisiana.,Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Donald S Grant
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone.,Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
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29
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Ficenec SC, Percak J, Arguello S, Bays A, Goba A, Gbakie M, Shaffer JG, Emmett SD, Schieffelin JS, Bausch D. Lassa Fever Induced Hearing Loss: The Neglected Disability of Hemorrhagic Fever. Int J Infect Dis 2020; 100:82-87. [PMID: 32795603 PMCID: PMC7807889 DOI: 10.1016/j.ijid.2020.08.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/27/2020] [Accepted: 08/07/2020] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE Lassa fever (LF) a hemorrhagic fever endemic to Western has an incidence of approximately 500,000 cases per year. Here, we evaluate hearing loss and other sequelae following LF. METHODS This case-control study enrolled laboratory confirmed LF survivors, non-LF Febrile controls and Matched Community controls with no history of LF or recent hospitalization for a febrile illness. Study participants completed a symptom questionnaire. Pure-tone audiometry was completed by a subset of participants. RESULTS One hundred forty-seven subjects were enrolled aged from 3-66 years (mean = 23.3). LF survivors were significantly more likely to report balance difficulties (55% vs 20%, p < 0.001), hair loss (32% vs 7%, p < 0.001), difficulty speaking (19% vs 1%, p < 0.001), social isolation (50% vs 0%, p < 0.001), and hearing loss (17% vs 1%, p = 0.002) in comparison to Matched-Community Controls. Similar trends were noted in comparison to Febrile Controls, although these findings were non-significant. Fifty subjects completed audiometry. Audiometry found that LF survivors had significantly more bilateral hearing loss in comparison to Matched-Community Controls (30% vs 4%, p = 0.029). CONCLUSION This study characterizes the sequelae of LF and highlights the need for increased access to hearing care in West Africa.
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Affiliation(s)
| | - Jeffrey Percak
- Tulane University School of Medicine, New Orleans, LA, USA
| | - Sara Arguello
- Tulane University School of Medicine, New Orleans, LA, USA
| | - Alison Bays
- Division of Rheumatology, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | | | | | - Jeffrey G Shaffer
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Susan D Emmett
- Department of Head and Neck Surgery and Communication Sciences, Duke University School of Medicine, Durham, NC, USA; Duke Global Health Institute, Durham, NC, USA; Center for Health Policy and Inequalities Research, Duke University, Durham, NC, USA
| | | | - Daniel Bausch
- Tulane Viral Hemorrhagic Fever Research Program, Kenema Government Hospital, Kenema, Sierra Leone
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Ateba FF, Febrero-Bande M, Sagara I, Sogoba N, Touré M, Sanogo D, Diarra A, Magdalene Ngitah A, Winch PJ, Shaffer JG, Krogstad DJ, Marker HC, Gaudart J, Doumbia S. Predicting Malaria Transmission Dynamics in Dangassa, Mali: A Novel Approach Using Functional Generalized Additive Models. Int J Environ Res Public Health 2020; 17:E6339. [PMID: 32878174 PMCID: PMC7504016 DOI: 10.3390/ijerph17176339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 01/22/2023]
Abstract
Mali aims to reach the pre-elimination stage of malaria by the next decade. This study used functional regression models to predict the incidence of malaria as a function of past meteorological patterns to better prevent and to act proactively against impending malaria outbreaks. All data were collected over a five-year period (2012-2017) from 1400 persons who sought treatment at Dangassa's community health center. Rainfall, temperature, humidity, and wind speed variables were collected. Functional Generalized Spectral Additive Model (FGSAM), Functional Generalized Linear Model (FGLM), and Functional Generalized Kernel Additive Model (FGKAM) were used to predict malaria incidence as a function of the pattern of meteorological indicators over a continuum of the 18 weeks preceding the week of interest. Their respective outcomes were compared in terms of predictive abilities. The results showed that (1) the highest malaria incidence rate occurred in the village 10 to 12 weeks after we observed a pattern of air humidity levels >65%, combined with two or more consecutive rain episodes and a mean wind speed <1.8 m/s; (2) among the three models, the FGLM obtained the best results in terms of prediction; and (3) FGSAM was shown to be a good compromise between FGLM and FGKAM in terms of flexibility and simplicity. The models showed that some meteorological conditions may provide a basis for detection of future outbreaks of malaria. The models developed in this paper are useful for implementing preventive strategies using past meteorological and past malaria incidence.
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Affiliation(s)
- François Freddy Ateba
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.S.); (A.D.)
- Department of Mathematics, University of Quebec at Montreal (UQAM), Montréal, QC H2X 3Y7, Canada
- Faculty of Health Sciences, University of Buea, Buea BP 63, Cameroon;
| | - Manuel Febrero-Bande
- Department of Statistics, Mathematical Analysis and Optimization, University of Santiago de Compostela, Santiago de Compostela, 15782 Galicia, Spain;
| | - Issaka Sagara
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.S.); (A.D.)
- Department of Public Health Education and Research, Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako 1805, Mali
| | - Nafomon Sogoba
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.S.); (A.D.)
| | - Mahamoudou Touré
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.S.); (A.D.)
| | - Daouda Sanogo
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.S.); (A.D.)
| | - Ayouba Diarra
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.S.); (A.D.)
| | | | - Peter J. Winch
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (P.J.W.); (H.C.M.)
| | - Jeffrey G. Shaffer
- Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street New Orleans, New Orleans, Louisiana, LA 70112, USA; (J.G.S.); (D.J.K.)
| | - Donald J. Krogstad
- Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street New Orleans, New Orleans, Louisiana, LA 70112, USA; (J.G.S.); (D.J.K.)
| | - Hannah C. Marker
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; (P.J.W.); (H.C.M.)
| | - Jean Gaudart
- Aix Marseille University, APHM, INSERM, IRD, SESSTIM, Hop Timone, BioSTIC, Biostatistics & ICT, 13005 Marseille, France;
| | - Seydou Doumbia
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.S.); (A.D.)
- Department of Public Health Education and Research, Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako 1805, Mali
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Thompson TA, Touré MB, Sanogo D, Shaffer JG, Doumbia SO, Krogstad DJ. Template copy number and the sensitivity of quantitative PCR for Plasmodium falciparum in asymptomatic individuals. Malar J 2020; 19:295. [PMID: 32811534 PMCID: PMC7436962 DOI: 10.1186/s12936-020-03365-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/10/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The identification of asymptomatic individuals with Plasmodium falciparum infection is difficult because they do not seek medical treatment and often have too few asexual parasites detectable using microscopy or rapid diagnostic tests (≤ 200 parasites per μl). Quantitative PCR (qPCR) may provide greater sensitivity and permits estimation of the initial template DNA concentration. This study examined the hypothesis that qPCR assays using templates with higher copy numbers may be more sensitive for P. falciparum than assays based on templates with lower copy numbers. METHODS To test this hypothesis, ten qPCR assays for DNA sequences with template copy numbers from 1 to 160 were compared using parasite DNA standards (n = 2) and smear-positive filter paper blots from asymptomatic smear-positive subjects (n = 96). RESULTS Based on the testing of P. falciparum parasite DNA standards and filter paper blots, cycle threshold values decreased as the concentrations of template DNA and template copy numbers increased (p < 0.001). Likewise, the analytical and clinical sensitivities of qPCR assays for P. falciparum DNA (based on DNA standards and filter paper blots, respectively) increased with template copy number. Despite the gains in clinical sensitivity from increased template copy numbers, qPCR assays failed to detect more than half of the filter paper blots with low parasite densities (≤ 200 asexual parasites per μl). CONCLUSIONS These results confirm the hypothesis that the sensitivity of qPCR for P. falciparum in the blood of individuals with asymptomatic infection increases with template copy number. However, because even the most sensitive qPCR assays (with template copy numbers from 32 to 160) detected fewer than 50% of infections with ≤ 200 asexual parasites per μl, the sensitivity of qPCR must be increased further to identify all smear-positive, asymptomatic individuals in order to interrupt transmission.
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Affiliation(s)
- Trevor A Thompson
- West African International Center of Excellence for Malaria Research, Bamako, Mali.
- Tulane School of Public Health and Tropical Medicine, 1430 Tulane Avenue, #8317, J.B. Johnston Building, Room 510, New Orleans, LA, 70112-2699, USA.
| | - Mahamoudou B Touré
- West African International Center of Excellence for Malaria Research, Bamako, Mali
- University of the Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Daouda Sanogo
- West African International Center of Excellence for Malaria Research, Bamako, Mali
- University of the Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Jeffrey G Shaffer
- West African International Center of Excellence for Malaria Research, Bamako, Mali.
- Tulane School of Public Health and Tropical Medicine, 1430 Tulane Avenue, #8317, J.B. Johnston Building, Room 510, New Orleans, LA, 70112-2699, USA.
| | - Seydou O Doumbia
- West African International Center of Excellence for Malaria Research, Bamako, Mali
- University of the Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Donald J Krogstad
- West African International Center of Excellence for Malaria Research, Bamako, Mali.
- Tulane School of Public Health and Tropical Medicine, 1430 Tulane Avenue, #8317, J.B. Johnston Building, Room 510, New Orleans, LA, 70112-2699, USA.
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Gunn BM, Roy V, Karim MM, Hartnett JN, Suscovich TJ, Goba A, Momoh M, Sandi JD, Kanneh L, Andersen KG, Shaffer JG, Schieffelin JS, Garry RF, Grant DS, Alter G. Survivors of Ebola Virus Disease Develop Polyfunctional Antibody Responses. J Infect Dis 2020; 221:156-161. [PMID: 31301137 PMCID: PMC7184900 DOI: 10.1093/infdis/jiz364] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/11/2019] [Indexed: 11/21/2022] Open
Abstract
Monoclonal antibodies can mediate protection against Ebola virus (EBOV) infection through direct neutralization as well as through the recruitment of innate immune effector functions. However, the antibody functional response following survival of acute EBOV disease has not been well characterized. In this study, serum antibodies from Ebola virus disease (EVD) survivors from Sierra Leone were profiled to capture variation in overall subclass/isotype abundance, neutralizing activity, and innate immune effector functions. Antibodies from EVD survivors exhibited robust innate immune effector functions, mediated primarily by IgG1 and IgA1. In conclusion, development of functional antibodies follows survival of acute EVD.
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Affiliation(s)
- Bronwyn M Gunn
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts
| | - Vicky Roy
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts
| | - Marcus M Karim
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts
| | - Jessica N Hartnett
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Todd J Suscovich
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts
| | - Augustine Goba
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Mambu Momoh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital.,Eastern Polytechnic University, Kenema, Sierra Leone
| | | | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Kristian G Andersen
- Department of Immunology and Microbiology, Scripps Research Institute.,Scripps Research Translational Institute, La Jolla, California
| | - Jeffrey G Shaffer
- Department of Biostatistics and Bioinformatics, Tulane School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - John S Schieffelin
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Donald S Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital.,Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Galit Alter
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts
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Ateba FF, Sagara I, Sogoba N, Touré M, Konaté D, Diawara SI, Diakité SAS, Diarra A, Coulibaly MD, Dolo M, Dolo A, Sacko A, Thiam SM, Sissako A, Sangaré L, Diakité M, Koita OA, Cissoko M, Traore SF, Winch PJ, Febrero-Bande M, Shaffer JG, Krogtad DJ, Marker HC, Doumbia S, Gaudart J. Spatio-Temporal Dynamic of Malaria Incidence: A Comparison of Two Ecological Zones in Mali. Int J Environ Res Public Health 2020; 17:E4698. [PMID: 32629876 PMCID: PMC7370019 DOI: 10.3390/ijerph17134698] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023]
Abstract
Malaria transmission largely depends on environmental, climatic, and hydrological conditions. In Mali, malaria epidemiological patterns are nested within three ecological zones. This study aimed at assessing the relationship between those conditions and the incidence of malaria in Dangassa and Koila, Mali. Malaria data was collected through passive case detection at community health facilities of each study site from June 2015 to January 2017. Climate and environmental data were obtained over the same time period from the Goddard Earth Sciences (Giovanni) platform and hydrological data from Mali hydraulic services. A generalized additive model was used to determine the lagged time between each principal component analysis derived component and the incidence of malaria cases, and also used to analyze the relationship between malaria and the lagged components in a multivariate approach. Malaria transmission patterns were bimodal at both sites, but peak and lull periods were longer lasting for Koila study site. Temperatures were associated with malaria incidence in both sites. In Dangassa, the wind speed (p = 0.005) and river heights (p = 0.010) contributed to increasing malaria incidence, in contrast to Koila, where it was humidity (p < 0.001) and vegetation (p = 0.004). The relationships between environmental factors and malaria incidence differed between the two settings, implying different malaria dynamics and adjustments in the conception and plan of interventions.
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Affiliation(s)
- François Freddy Ateba
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.K.); (S.I.D.); (S.A.S.D.); (A.D.); (M.D.C.); (M.D.); (A.D.); (S.M.T.); (M.D.); (M.C.); (S.F.T.)
- Department of Mathematics, University of Quebec at Montreal (UQAM), Montréal, QC H2X 3Y7, Canada
| | - Issaka Sagara
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.K.); (S.I.D.); (S.A.S.D.); (A.D.); (M.D.C.); (M.D.); (A.D.); (S.M.T.); (M.D.); (M.C.); (S.F.T.)
- Department of Public Health Education and Research, Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali;
| | - Nafomon Sogoba
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.K.); (S.I.D.); (S.A.S.D.); (A.D.); (M.D.C.); (M.D.); (A.D.); (S.M.T.); (M.D.); (M.C.); (S.F.T.)
| | - Mahamoudou Touré
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.K.); (S.I.D.); (S.A.S.D.); (A.D.); (M.D.C.); (M.D.); (A.D.); (S.M.T.); (M.D.); (M.C.); (S.F.T.)
| | - Drissa Konaté
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.K.); (S.I.D.); (S.A.S.D.); (A.D.); (M.D.C.); (M.D.); (A.D.); (S.M.T.); (M.D.); (M.C.); (S.F.T.)
| | - Sory Ibrahim Diawara
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.K.); (S.I.D.); (S.A.S.D.); (A.D.); (M.D.C.); (M.D.); (A.D.); (S.M.T.); (M.D.); (M.C.); (S.F.T.)
| | - Séidina Aboubacar Samba Diakité
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.K.); (S.I.D.); (S.A.S.D.); (A.D.); (M.D.C.); (M.D.); (A.D.); (S.M.T.); (M.D.); (M.C.); (S.F.T.)
| | - Ayouba Diarra
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.K.); (S.I.D.); (S.A.S.D.); (A.D.); (M.D.C.); (M.D.); (A.D.); (S.M.T.); (M.D.); (M.C.); (S.F.T.)
| | - Mamadou D. Coulibaly
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.K.); (S.I.D.); (S.A.S.D.); (A.D.); (M.D.C.); (M.D.); (A.D.); (S.M.T.); (M.D.); (M.C.); (S.F.T.)
| | - Mathias Dolo
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.K.); (S.I.D.); (S.A.S.D.); (A.D.); (M.D.C.); (M.D.); (A.D.); (S.M.T.); (M.D.); (M.C.); (S.F.T.)
| | - Amagana Dolo
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.K.); (S.I.D.); (S.A.S.D.); (A.D.); (M.D.C.); (M.D.); (A.D.); (S.M.T.); (M.D.); (M.C.); (S.F.T.)
| | - Aissata Sacko
- Department of Public Health Education and Research, Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali;
| | - Sidibe M’baye Thiam
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.K.); (S.I.D.); (S.A.S.D.); (A.D.); (M.D.C.); (M.D.); (A.D.); (S.M.T.); (M.D.); (M.C.); (S.F.T.)
| | - Aliou Sissako
- Laboratory of Applied Molecular Biology (LBMA), Science and Technologies Faculty (FST), University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (A.S.); (L.S.); (O.A.K.)
| | - Lansana Sangaré
- Laboratory of Applied Molecular Biology (LBMA), Science and Technologies Faculty (FST), University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (A.S.); (L.S.); (O.A.K.)
| | - Mahamadou Diakité
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.K.); (S.I.D.); (S.A.S.D.); (A.D.); (M.D.C.); (M.D.); (A.D.); (S.M.T.); (M.D.); (M.C.); (S.F.T.)
| | - Ousmane A. Koita
- Laboratory of Applied Molecular Biology (LBMA), Science and Technologies Faculty (FST), University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (A.S.); (L.S.); (O.A.K.)
| | - Mady Cissoko
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.K.); (S.I.D.); (S.A.S.D.); (A.D.); (M.D.C.); (M.D.); (A.D.); (S.M.T.); (M.D.); (M.C.); (S.F.T.)
- APHM, INSERM, IRD, SESSTIM, Hop Timone, BioSTIC, Biostatistic & ICT, Aix Marseille Université, 13005 Marseille, France
| | - Sékou Fantamady Traore
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.K.); (S.I.D.); (S.A.S.D.); (A.D.); (M.D.C.); (M.D.); (A.D.); (S.M.T.); (M.D.); (M.C.); (S.F.T.)
| | - Peter John Winch
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; (P.J.W.); (H.C.M.)
| | - Manuel Febrero-Bande
- Department of Statistics, Mathematical Analysis and Optimization, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Jeffrey G. Shaffer
- Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America, 1440 Canal Street New Orleans, LA 70112, USA; (J.G.S.); (D.J.K.)
| | - Donald J. Krogtad
- Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America, 1440 Canal Street New Orleans, LA 70112, USA; (J.G.S.); (D.J.K.)
| | - Hannah Catherine Marker
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; (P.J.W.); (H.C.M.)
| | - Seydou Doumbia
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.K.); (S.I.D.); (S.A.S.D.); (A.D.); (M.D.C.); (M.D.); (A.D.); (S.M.T.); (M.D.); (M.C.); (S.F.T.)
- Department of Public Health Education and Research, Faculty of Medicine and Odonto-Stomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali;
| | - Jean Gaudart
- Malaria Research and Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako BP 1805, Mali; (F.F.A.); (I.S.); (N.S.); (M.T.); (D.K.); (S.I.D.); (S.A.S.D.); (A.D.); (M.D.C.); (M.D.); (A.D.); (S.M.T.); (M.D.); (M.C.); (S.F.T.)
- APHM, INSERM, IRD, SESSTIM, Hop Timone, BioSTIC, Biostatistic & ICT, Aix Marseille Université, 13005 Marseille, France
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Xiong X, Carter R, Lusamba-Dikassa PS, Kuburhanwa EC, Kimanuka F, Salumu F, Clarysse G, Tutu BK, Yuma S, Iyeti AM, Hernandez JH, Shaffer JG, Villeneuve S, Prual A, Pyne-Mercier L, Nigussie A, Buekens P. Improving the quality of maternal and newborn health outcomes through a clinical mentorship program in the Democratic Republic of the Congo: study protocol. Reprod Health 2019; 16:147. [PMID: 31601228 PMCID: PMC6785870 DOI: 10.1186/s12978-019-0796-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 08/26/2019] [Indexed: 11/10/2022] Open
Abstract
Background The Democratic Republic of the Congo (DRC) boasts one of the highest rates of institutional deliveries in sub-Saharan Africa (80%), with eight out of every ten births also assisted by a skilled provider. However, the maternal and neonatal mortality are still among the highest in the world, which demonstrates the poor in-facility quality of maternal and newborn care. The objective of this ongoing project is to design, implement, and evaluate a clinical mentorship program in 72 health facilities in two rural provinces of Kwango and Kwilu, DRC. Methods This is an ongoing quasi-experimental study. In the 72 facilities, 48 facilities were assigned to the group where the clinical mentorship program is being implemented (intervention group), and 24 facilities were assigned to the group where the clinical mentorship program is not being implemented (control group). The groups were selected and assigned based on administrative criteria, taking into account the number of deliveries in each facility, the coverage of health zones, accessibility, and ease of implementation of a clinical mentorship program. The main activities are organizing and training a national team of mentors (including senior midwives, obstetricians, and pediatricians) in clinical mentoring, deploying them to mentor all health providers (mentees) performing maternal and newborn health (MNH) services, and providing in-service training in routine and Emergency Obstetrical and Newborn Care (EmONC) to the mentees in health facilities over an 18-month period. Baseline and endline assessments are carried out to evaluate the effectiveness of the clinical mentorship program on the quality of MNH care and the effective coverage of key interventions to reduce maternal and neonatal mortality. Findings will be disseminated nationwide and internationally, as scientific evidence is scarce. A national strategy, guidelines, and tools for clinical mentorship in MNH will be developed for replication in other provinces, thus benefitting the entire country. Discussion This is the largest project on clinical mentorship aimed to improving the quality of MNH care in Africa. This program is expected to generate one of the first pieces of scientific evidence on the effectiveness of a clinical mentorship program in MNH on a scientifically designed and sustainable model.
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Affiliation(s)
- Xu Xiong
- Tulane University School of Public Health and Tropical Medicine, 1440 Canal St, Ste. 2000, New Orleans, LA, 70112, USA.
| | - Rebecca Carter
- Tulane University School of Public Health and Tropical Medicine, 1440 Canal St, Ste. 2000, New Orleans, LA, 70112, USA
| | - Paul-Samson Lusamba-Dikassa
- Tulane University School of Public Health and Tropical Medicine, 1440 Canal St, Ste. 2000, New Orleans, LA, 70112, USA.,Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Elvis C Kuburhanwa
- Tulane University School of Public Health and Tropical Medicine, 1440 Canal St, Ste. 2000, New Orleans, LA, 70112, USA.,Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Francine Kimanuka
- UNICEF, 372, avenue Colonel Mondjiba, Kinshasa-Ngaliema, Democratic Republic of the Congo
| | - Freddy Salumu
- UNICEF, 372, avenue Colonel Mondjiba, Kinshasa-Ngaliema, Democratic Republic of the Congo
| | - Guy Clarysse
- UNICEF, 372, avenue Colonel Mondjiba, Kinshasa-Ngaliema, Democratic Republic of the Congo
| | - Baudouin Kalume Tutu
- Ministère de la Santé, Secrétariat général, 36 Avenue de la Justice, Kinshasa - Gombe, Democratic Republic of the Congo
| | - Sylvain Yuma
- Ministère de la Santé, Secrétariat général, 36 Avenue de la Justice, Kinshasa - Gombe, Democratic Republic of the Congo
| | - Alain Mboko Iyeti
- Ministère de la Santé, Secrétariat général, 36 Avenue de la Justice, Kinshasa - Gombe, Democratic Republic of the Congo
| | - Julie H Hernandez
- Tulane University School of Public Health and Tropical Medicine, 1440 Canal St, Ste. 2000, New Orleans, LA, 70112, USA
| | - Jeffrey G Shaffer
- Tulane University School of Public Health and Tropical Medicine, 1440 Canal St, Ste. 2000, New Orleans, LA, 70112, USA
| | - Susie Villeneuve
- UNICEF Western & Central Africa Regional Office, PO Box 29720, Dakar-Yoff, Senegal
| | - Alain Prual
- UNICEF Western & Central Africa Regional Office, PO Box 29720, Dakar-Yoff, Senegal
| | | | - Assaye Nigussie
- Bill & Melinda Gates Foundation, PO Box 23350, Seattle, WA, USA
| | - Pierre Buekens
- Tulane University School of Public Health and Tropical Medicine, 1440 Canal St, Ste. 2000, New Orleans, LA, 70112, USA
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Carter R, Xiong X, Lusamba-Dikassa PS, Kuburhanwa EC, Kimanuka F, Salumu F, Clarysse G, Tutu BK, Yuma S, Iyeti AM, Hernandez JH, Shaffer JG, Bertrand JT, Villeneuve S, Prual A, Pyne-Mercier L, Nigussie A, Buekens P. Facility conditions, obstetric and neonatal care practices, and availability of emergency obstetric and neonatal care in 72 rural health facilities in the Democratic Republic of the Congo: A cross-sectional study. Gates Open Res 2019; 3:13. [PMID: 31410393 PMCID: PMC6676177 DOI: 10.12688/gatesopenres.12905.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 11/20/2022] Open
Abstract
Background: Current facility conditions, obstetric and neonatal care practices, and availability of emergency obstetric and neonatal care (EmONC) were assessed in the Kwango and Kwilu provinces of the Democratic Republic of the Congo (DRC). Methods: This is an analysis of the baseline survey data from an ongoing clinical mentoring program among 72 rural health facilities in the DRC. Data collectors visited each of the facilities and collected data through a pre-programmed smartphone. Frequencies of selected indicators were calculated by province and facility type-general referral hospital (GRH) and primary health centers (HC). Results: Facility conditions varied across province and facility type. Maternity wards and delivery rooms were available in the highest frequency of rooms assessed (>95% of all facilities). Drinking water was available in 25.0% of all facilities; electricity was available in 49.2% of labor rooms and 67.6% of delivery rooms in all facilities. Antenatal, delivery, and postnatal care services were available but varied across facilities. While the proportion of blood pressure measured during antenatal care was high (94.9%), the antenatal screening rate for proteinuria was low (14.7%). The use of uterotonics immediately after birth was observed in high numbers across both provinces (94.4% in Kwango and 75.6% in Kwilu) and facility type (91.3% in GRH and 81.4% in HC). The provision of immediate postnatal care to mothers every 15 minutes was provided in less than 50% of all facilities. GRH facilities generally had higher frequencies of available equipment and more services available than HC. GRH facilities provided an average of 6 EmONC signal functions (range: 2-9). Conclusions: Despite poor facility conditions and a lack of supplies, GRH and HC facilities were able to provide EmONC care in rural DRC. These findings could guide the provision of essential needs to the health facilities for better delivery of maternal and neonatal care.
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Affiliation(s)
- Rebecca Carter
- Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, 70112, USA
| | - Xu Xiong
- Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, 70112, USA
| | - Paul-Samson Lusamba-Dikassa
- Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, 70112, USA
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Elvis C. Kuburhanwa
- Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, 70112, USA
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | | | - Freddy Salumu
- UNICEF-DRC, Kinshasa-Ngaliema, Democratic Republic of the Congo
| | - Guy Clarysse
- UNICEF-DRC, Kinshasa-Ngaliema, Democratic Republic of the Congo
| | - Baudouin Kalume Tutu
- Ministère de la Santé, Secrétariat général, Kinshasa – Gombe, Democratic Republic of the Congo
| | - Sylvain Yuma
- Ministère de la Santé, Secrétariat général, Kinshasa – Gombe, Democratic Republic of the Congo
| | - Alain Mboko Iyeti
- Ministère de la Santé, Secrétariat général, Kinshasa – Gombe, Democratic Republic of the Congo
| | - Julie H. Hernandez
- Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, 70112, USA
| | - Jeffrey G. Shaffer
- Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, 70112, USA
| | - Jane T. Bertrand
- Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, 70112, USA
| | - Susie Villeneuve
- UNICEF Western & Central Africa Regional Office, Dakar-Yoff, Senegal
| | - Alain Prual
- UNICEF Western & Central Africa Regional Office, Dakar-Yoff, Senegal
| | | | | | - Pierre Buekens
- Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, 70112, USA
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Colubri A, Hartley MA, Siakor M, Wolfman V, Felix A, Sesay T, Shaffer JG, Garry RF, Grant DS, Levine AC, Sabeti PC. Machine-learning Prognostic Models from the 2014-16 Ebola Outbreak: Data-harmonization Challenges, Validation Strategies, and mHealth Applications. EClinicalMedicine 2019; 11:54-64. [PMID: 31312805 PMCID: PMC6610774 DOI: 10.1016/j.eclinm.2019.06.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 05/02/2019] [Accepted: 06/07/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Ebola virus disease (EVD) plagues low-resource and difficult-to-access settings. Machine learning prognostic models and mHealth tools could improve the understanding and use of evidence-based care guidelines in such settings. However, data incompleteness and lack of interoperability limit model generalizability. This study harmonizes diverse datasets from the 2014-16 EVD epidemic and generates several prognostic models incorporated into the novel Ebola Care Guidelines app that provides informed access to recommended evidence-based guidelines. METHODS Multivariate logistic regression was applied to investigate survival outcomes in 470 patients admitted to five Ebola treatment units in Liberia and Sierra Leone at various timepoints during 2014-16. We generated a parsimonious model (viral load, age, temperature, bleeding, jaundice, dyspnea, dysphagia, and time-to-presentation) and several fallback models for when these variables are unavailable. All were externally validated against two independent datasets and compared to further models including expert observational wellness assessments. Models were incorporated into an app highlighting the signs/symptoms with the largest contribution to prognosis. FINDINGS The parsimonious model approached the predictive power of observational assessments by experienced clinicians (Area-Under-the-Curve, AUC = 0.70-0.79, accuracy = 0.64-0.74) and maintained its performance across subcohorts with different healthcare seeking behaviors. Age and viral load contributed > 5-fold the weighting of other features and including them in a minimal model had a similar AUC, albeit at the cost of specificity. INTERPRETATION Clinically guided prognostic models can recapitulate clinical expertise and be useful when such expertise is unavailable. Incorporating these models into mHealth tools may facilitate their interpretation and provide informed access to comprehensive clinical guidelines. FUNDING Howard Hughes Medical Institute, US National Institutes of Health, Bill & Melinda Gates Foundation, International Medical Corps, UK Department for International Development, and GOAL Global.
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Affiliation(s)
- Andres Colubri
- Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Howard Hughes Medical Institute, Chevy Chase, USA
- Correspondence to: A. Colubri, Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, USA.
| | - Mary-Anne Hartley
- University of Lausanne, Faculty of Biology and Medicine, Lausanne, Switzerland
- GOAL Global, Dublin, Ireland
| | | | | | - August Felix
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Tom Sesay
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Jeffrey G. Shaffer
- Tulane University, School of Public Health and Tropical Medicine, New Orleans, USA
| | - Robert F. Garry
- Tulane University, Department of Microbiology and Immunology, New Orleans, USA
| | - Donald S. Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
| | - Adam C. Levine
- International Medical Corps, Los Angeles, USA
- Brown University, Warren Alpert School of Medicine, Providence, USA
- Correspondence to: A. C. Levine, International Medical Corps, Los Angeles, USA.
| | - Pardis C. Sabeti
- Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Howard Hughes Medical Institute, Chevy Chase, USA
- Harvard School of Public Health, Boston, USA
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Shaffer JG, Mather FJ, Wele M, Li J, Tangara CO, Kassogue Y, Srivastav SK, Thiero O, Diakite M, Sangare M, Dabitao D, Toure M, Djimde AA, Traore S, Diakite B, Coulibaly MB, Liu Y, Lacey M, Lefante JJ, Koita O, Schieffelin JS, Krogstad DJ, Doumbia SO. Expanding Research Capacity in Sub-Saharan Africa Through Informatics, Bioinformatics, and Data Science Training Programs in Mali. Front Genet 2019; 10:331. [PMID: 31031807 PMCID: PMC6473184 DOI: 10.3389/fgene.2019.00331] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/28/2019] [Indexed: 12/04/2022] Open
Abstract
Bioinformatics and data science research have boundless potential across Africa due to its high levels of genetic diversity and disproportionate burden of infectious diseases, including malaria, tuberculosis, HIV and AIDS, Ebola virus disease, and Lassa fever. This work lays out an incremental approach for reaching underserved countries in bioinformatics and data science research through a progression of capacity building, training, and research efforts. Two global health informatics training programs sponsored by the Fogarty International Center (FIC) were carried out at the University of Sciences, Techniques and Technologies of Bamako, Mali (USTTB) between 1999 and 2011. Together with capacity building efforts through the West Africa International Centers of Excellence in Malaria Research (ICEMR), this progress laid the groundwork for a bioinformatics and data science training program launched at USTTB as part of the Human Heredity and Health in Africa (H3Africa) initiative. Prior to the global health informatics training, its trainees published first or second authorship and third or higher authorship manuscripts at rates of 0.40 and 0.10 per year, respectively. Following the training, these rates increased to 0.70 and 1.23 per year, respectively, which was a statistically significant increase (p < 0.001). The bioinformatics and data science training program at USTTB commenced in 2017 focusing on student, faculty, and curriculum tiers of enhancement. The program's sustainable measures included institutional support for core elements, university tuition and fees, resource sharing and coordination with local research projects and companion training programs, increased student and faculty publication rates, and increased research proposal submissions. Challenges reliance of high-speed bandwidth availability on short-term funding, lack of a discounted software portal for basic software applications, protracted application processes for United States visas, lack of industry job positions, and low publication rates in the areas of bioinformatics and data science. Long-term, incremental processes are necessary for engaging historically underserved countries in bioinformatics and data science research. The multi-tiered enhancement approach laid out here provides a platform for generating bioinformatics and data science technicians, teachers, researchers, and program managers. Increased literature on bioinformatics and data science training approaches and progress is needed to provide a framework for establishing benchmarks on the topics.
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Affiliation(s)
- Jeffrey G. Shaffer
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Frances J. Mather
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Mamadou Wele
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Jian Li
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Cheick Oumar Tangara
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Yaya Kassogue
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sudesh K. Srivastav
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Oumar Thiero
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamadou Diakite
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Modibo Sangare
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Djeneba Dabitao
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamoudou Toure
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye A. Djimde
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sekou Traore
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Brehima Diakite
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mamadou B. Coulibaly
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Yaozhong Liu
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Michelle Lacey
- Department of Mathematics, Tulane University, New Orleans, LA, United States
| | - John J. Lefante
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Ousmane Koita
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - John S. Schieffelin
- Sections of Pediatric & Adult Infectious Diseases, School of Medicine, Tulane University, New Orleans, LA, United States
| | - Donald J. Krogstad
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Seydou O. Doumbia
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
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Godshaw BM, Mehl AE, Shaffer JG, Meyer MS, Thomas LC, Chimento GF. The Effects of Peri-Operative Dexamethasone on Patients Undergoing Total Hip or Knee Arthroplasty: Is It Safe for Diabetics? J Arthroplasty 2019; 34:645-649. [PMID: 30612830 DOI: 10.1016/j.arth.2018.12.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 11/24/2018] [Accepted: 12/11/2018] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Peri-operative dexamethasone has been shown to effectively reduce post-operative nausea and vomiting and aide in analgesia after total joint arthroplasty (TJA); however, systemic glucocorticoid therapy has many adverse effects. The purpose of this study is to determine the effects of dexamethasone on prosthetic joint infection (PJI) and blood glucose levels in patients undergoing TJA. METHODS A retrospective chart review of all patients receiving primary TJA from 2011 to 2015 (n = 2317) was conducted. Patients were divided into 2 cohorts: dexamethasone (n = 1426) and no dexamethasone (n = 891); these groups were subdivided into diabetic and non-diabetic patients. The primary outcome was PJI; secondary measures included glucose levels and pre-operative hemoglobin A1c (A1c) values. Statistics were carried out using logistic and regression models. RESULTS Of the 2317 joints, 1.12% developed PJI; this was not affected by dexamethasone (P = .166). Diabetics were found to have higher rate of infection (P < .001); however, diabetics who received dexamethasone were not found to have a significantly higher infection rate that non-diabetics (P = .646). Blood glucose levels were found to increase post-operatively, and dexamethasone did not increase this change (P = .537). Diabetes (P < .001) and increasing hemoglobin A1c (P < .001) were also associated with increased serum glucose levels; however, this was not influenced by dexamethasone (P = .595). CONCLUSION Although diabetic patients were found to have a higher infection rate overall, this was not affected by administration of intravenous dexamethasone, nor was the post-operative elevation in serum glucose levels. In this study population, peri-operative intravenous dexamethasone did not increase the rate of PJI and was safe to administer in patients undergoing TJA.
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Affiliation(s)
- Brian M Godshaw
- Department of Orthopaedic Surgery, Ochsner Medical Center, New Orleans, LA
| | - Ashley E Mehl
- Department of Orthopaedic Surgery, Ochsner Medical Center, New Orleans, LA
| | - Jeffrey G Shaffer
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Mark S Meyer
- Department of Orthopaedic Surgery, Ochsner Medical Center, New Orleans, LA
| | - Leslie C Thomas
- Department of Anesthesiology, Ochsner Medical Center, New Orleans, LA
| | - George F Chimento
- Department of Orthopaedic Surgery, Ochsner Medical Center, New Orleans, LA
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Shaffer JG, Schieffelin JS, Gbakie M, Alhasan F, Roberts NB, Goba A, Randazzo J, Momoh M, Moon TD, Kanneh L, Levy DC, Podgorski RM, Hartnett JN, Boisen ML, Branco LM, Samuels R, Grant DS, Garry RF. A medical records and data capture and management system for Lassa fever in Sierra Leone: Approach, implementation, and challenges. PLoS One 2019; 14:e0214284. [PMID: 30921383 PMCID: PMC6438490 DOI: 10.1371/journal.pone.0214284] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 03/11/2019] [Indexed: 12/17/2022] Open
Abstract
Situated in southeastern Sierra Leone, Kenema Government Hospital (KGH) maintains one of the world’s only Lassa fever isolation wards and was a strategic Ebola virus disease (EVD) treatment facility during the 2014 EVD outbreak. Since 2006, the Viral Hemorrhagic Fever Consortium (VHFC) has carried out research activities at KGH, capturing clinical and laboratory data for suspected cases of Lassa fever. Here we describe the approach, progress, and challenges in designing and maintaining a data capture and management system (DCMS) at KGH to assist infectious disease researchers in building and sustaining DCMS in low-resource environments. Results on screening patterns and case-fatality rates are provided to illustrate the context and scope of the DCMS covered in this study. A medical records system and DCMS was designed and implemented between 2010 and 2016 linking historical and prospective Lassa fever data sources across KGH Lassa fever units and its peripheral health units. Data were captured using a case report form (CRF) system, enzyme-linked immunosorbent assay (ELISA) plate readers, polymerase chain reaction (PCR) machines, blood chemistry analyzers, and data auditing procedures. Between 2008 and 2016, blood samples for 4,229 suspected Lassa fever cases were screened at KGH, ranging from 219 samples in 2008 to a peak of 760 samples in 2011. Lassa fever case-fatality rates before and following the Ebola outbreak were 65.5% (148/226) and 89.5% (17/19), respectively, suggesting that fewer, but more seriously ill subjects with Lassa fever presented to KGH following the 2014 EVD outbreak (p = .040). DCMS challenges included weak specificity of the Lassa fever suspected case definition, limited capture of patient survival outcome data, internet costs, lapses in internet connectivity, low bandwidth, equipment and software maintenance, lack of computer teaching laboratories, and workload fluctuations due to variable screening activity. DCMS are the backbone of international research efforts and additional literature is needed on the topic for establishing benchmarks and driving goal-based approaches for its advancement in developing countries.
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Affiliation(s)
- Jeffrey G. Shaffer
- Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail:
| | - John S. Schieffelin
- Departments of Pediatrics and Internal Medicine, Sections of Pediatric & Adult Infectious Diseases, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Michael Gbakie
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Foday Alhasan
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Nicole B. Roberts
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, United States of America
| | - Augustine Goba
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Jessica Randazzo
- Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Mambu Momoh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Troy D. Moon
- Vanderbilt University Institute for Global Health, Nashville, Tennessee, United States of America
| | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Danielle C. Levy
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, United States of America
| | - Rachel M. Podgorski
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, United States of America
| | - Jessica N. Hartnett
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, United States of America
| | - Matt L. Boisen
- Zalgen Labs, LLC, Germantown, Maryland, United States of America
| | - Luis M. Branco
- Zalgen Labs, LLC, Germantown, Maryland, United States of America
| | - Robert Samuels
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Donald S. Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Robert F. Garry
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, United States of America
- Zalgen Labs, LLC, Germantown, Maryland, United States of America
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Carter R, Xiong X, Lusamba-Dikassa PS, Kuburhanwa EC, Kimanuka F, Salumu F, Clarysse G, Tutu BK, Yuma S, Iyeti AM, Hernandez JH, Shaffer JG, Bertrand JT, Villeneuve S, Prual A, Pyne-Mercier L, Nigussie A, Buekens P. Facility conditions, obstetric and neonatal care practices, and availability of emergency obstetric and neonatal care in 72 rural health facilities in the Democratic Republic of the Congo: A cross-sectional study. Gates Open Res 2019. [DOI: 10.12688/gatesopenres.12905.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Current facility conditions, obstetric and neonatal care practices, and availability of emergency obstetric and neonatal care (EmONC) were assessed in the Kwango and Kwilu provinces of the Democratic Republic of the Congo (DRC). Methods: This is an analysis of the baseline survey data from an ongoing clinical mentoring program among 72 rural health facilities in the DRC. Data collectors visited each of the facilities and collected data through a pre-programmed smartphone. Frequencies of selected indicators were calculated by province and facility type—general referral hospital (GRH) and primary health centers (HC). Results: Facility conditions varied across province and facility type. Maternity wards and delivery rooms were available in the highest frequency of rooms assessed (>95% of all facilities). Drinking water was available in 25.0% of all facilities; electricity was available in 49.2% of labor rooms and 67.6% of delivery rooms in all facilities. Antenatal, delivery, and postnatal care services were available but varied across facilities. While the proportion of blood pressure measured during antenatal care was high (94.9%), the antenatal screening rate for proteinuria was low (14.7%). The use of uterotonics immediately after birth was observed in high numbers across both provinces (94.4% in Kwango and 75.6% in Kwilu) and facility type (91.3% in GRH and 81.4% in HC). The provision of immediate postnatal care to mothers every 15 minutes was provided in less than 50% of all facilities. GRH facilities generally had higher frequencies of available equipment and more services available than HC. GRH facilities provided an average of 6 EmONC signal functions (range: 2-9). Conclusions: Despite poor facility conditions and a lack of supplies, GRH and HC facilities were able to provide EmONC care in rural DRC. These findings could guide the provision of essential needs to the health facilities for better delivery of maternal and neonatal care.
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Shaffer JG, Schieffelin JS, Grant DS, Goba A, Momoh M, Kanneh L, Levy DC, Hartnett JN, Boisen ML, Branco LM, Garry RF. Data set on Lassa fever in post-conflict Sierra Leone. Data Brief 2019; 23:103673. [PMID: 30788396 PMCID: PMC6369334 DOI: 10.1016/j.dib.2019.01.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 01/04/2019] [Accepted: 01/10/2019] [Indexed: 11/10/2022] Open
Abstract
Lassa fever is a rodent-borne illness that is endemic to parts of sub-Saharan Africa, including Sierra Leone, Nigeria, and Guinea. The disease is named after the town of Lassa, Nigeria where it was discovered in 1969. This data article focuses on the epidemiology of Lassa fever in Sierra Leone following a decade-long civil war that ended in 2002. The data were collected at Kenema Government Hospital (KGH) in Kenema, Sierra Leone, which maintains the country׳s only Lassa fever treatment facility and a biosafety level 3 (BSL-3) laboratory. The key data set variables include Lassa fever serostatus determined using antigen (Ag), immunoglobulin M (IgM), and immunoglobulin G (IgG) ELISA diagnostic techniques; and patient demographics, survival outcome, and treatment (ribavirin) status. The individual data used to generate the graphs and tables in the corresponding research manuscript published in PLOS Neglected Tropical Diseases in 2014 and its coding guide are provided as Supplementary material (Shaffer et al., 2014) [1].
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Affiliation(s)
- Jeffrey G Shaffer
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - John S Schieffelin
- Departments of Pediatrics and Internal Medicine, Sections of Pediatric and Adult Infectious Diseases, Tulane University School of Medicine, New Orleans, LA, United States
| | - Donald S Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone.,Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Augustine Goba
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone.,Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Mambu Momoh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone.,Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone.,Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Danielle C Levy
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA, United States
| | - Jessica N Hartnett
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA, United States
| | | | | | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA, United States.,Zalgen Labs, LLC, Germantown, MD, United States
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Shaffer JG, Doumbia SO, Ndiaye D, Diarra A, Gomis JF, Nwakanma D, Abubakar I, Ahmad A, Affara M, Lukowski M, Valim C, Welty JC, Mather FJ, Keating J, Krogstad DJ. Development of a data collection and management system in West Africa: challenges and sustainability. Infect Dis Poverty 2018; 7:125. [PMID: 30541626 PMCID: PMC6292095 DOI: 10.1186/s40249-018-0494-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/17/2018] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Developing and sustaining a data collection and management system (DCMS) is difficult in malaria-endemic countries because of limitations in internet bandwidth, computer resources and numbers of trained personnel. The premise of this paper is that development of a DCMS in West Africa was a critically important outcome of the West African International Centers of Excellence for Malaria Research. The purposes of this paper are to make that information available to other investigators and to encourage the linkage of DCMSs to international research and Ministry of Health data systems and repositories. METHODS We designed and implemented a DCMS to link study sites in Mali, Senegal and The Gambia. This system was based on case report forms for epidemiologic, entomologic, clinical and laboratory aspects of plasmodial infection and malarial disease for a longitudinal cohort study and included on-site training for Principal Investigators and Data Managers. Based on this experience, we propose guidelines for the design and sustainability of DCMSs in environments with limited resources and personnel. RESULTS From 2012 to 2017, we performed biannual thick smear surveys for plasmodial infection, mosquito collections for anopheline biting rates and sporozoite rates and year-round passive case detection for malarial disease in four longitudinal cohorts with 7708 individuals and 918 households in Senegal, The Gambia and Mali. Major challenges included the development of uniform definitions and reporting, assessment of data entry error rates, unstable and limited internet access and software and technology maintenance. Strengths included entomologic collections linked to longitudinal cohort studies, on-site data centres and a cloud-based data repository. CONCLUSIONS At a time when research on diseases of poverty in low and middle-income countries is a global priority, the resources available to ensure accurate data collection and the electronic availability of those data remain severely limited. Based on our experience, we suggest the development of a regional DCMS. This approach is more economical than separate data centres and has the potential to improve data quality by encouraging shared case definitions, data validation strategies and analytic approaches including the molecular analysis of treatment successes and failures.
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Affiliation(s)
- Jeffrey G. Shaffer
- Departments of Biostatistics (1440 Canal St., Suite 1610) and Tropical Medicine, (#8317 1430 Tulane Avenue, J.B. Johnston Building, Room 510), New Orleans, LA 70112-2699 USA
| | - Seydou O. Doumbia
- University of the Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Ayouba Diarra
- University of the Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | | | | | | | | | - Muna Affara
- Medical Research Council Unit, Fajara, The Gambia
| | | | - Clarissa Valim
- Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - James C. Welty
- Departments of Biostatistics (1440 Canal St., Suite 1610) and Tropical Medicine, (#8317 1430 Tulane Avenue, J.B. Johnston Building, Room 510), New Orleans, LA 70112-2699 USA
| | - Frances J. Mather
- Departments of Biostatistics (1440 Canal St., Suite 1610) and Tropical Medicine, (#8317 1430 Tulane Avenue, J.B. Johnston Building, Room 510), New Orleans, LA 70112-2699 USA
| | - Joseph Keating
- Departments of Biostatistics (1440 Canal St., Suite 1610) and Tropical Medicine, (#8317 1430 Tulane Avenue, J.B. Johnston Building, Room 510), New Orleans, LA 70112-2699 USA
| | - Donald J. Krogstad
- Departments of Biostatistics (1440 Canal St., Suite 1610) and Tropical Medicine, (#8317 1430 Tulane Avenue, J.B. Johnston Building, Room 510), New Orleans, LA 70112-2699 USA
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Rudd KE, Seymour CW, Aluisio AR, Augustin ME, Bagenda DS, Beane A, Byiringiro JC, Chang CCH, Colas LN, Day NPJ, De Silva AP, Dondorp AM, Dünser MW, Faiz MA, Grant DS, Haniffa R, Van Hao N, Kennedy JN, Levine AC, Limmathurotsakul D, Mohanty S, Nosten F, Papali A, Patterson AJ, Schieffelin JS, Shaffer JG, Thuy DB, Thwaites CL, Urayeneza O, White NJ, West TE, Angus DC. Association of the Quick Sequential (Sepsis-Related) Organ Failure Assessment (qSOFA) Score With Excess Hospital Mortality in Adults With Suspected Infection in Low- and Middle-Income Countries. JAMA 2018; 319:2202-2211. [PMID: 29800114 PMCID: PMC6134436 DOI: 10.1001/jama.2018.6229] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 04/23/2018] [Indexed: 12/29/2022]
Abstract
Importance The quick Sequential (Sepsis-Related) Organ Failure Assessment (qSOFA) score has not been well-evaluated in low- and middle-income countries (LMICs). Objective To assess the association of qSOFA with excess hospital death among patients with suspected infection in LMICs and to compare qSOFA with the systemic inflammatory response syndrome (SIRS) criteria. Design, Settings, and Participants Retrospective secondary analysis of 8 cohort studies and 1 randomized clinical trial from 2003 to 2017. This study included 6569 hospitalized adults with suspected infection in emergency departments, inpatient wards, and intensive care units of 17 hospitals in 10 LMICs across sub-Saharan Africa, Asia, and the Americas. Exposures Low (0), moderate (1), or high (≥2) qSOFA score (range, 0 [best] to 3 [worst]) or SIRS criteria (range, 0 [best] to 4 [worst]) within 24 hours of presentation to study hospital. Main Outcomes and Measures Predictive validity (measured as incremental hospital mortality beyond that predicted by baseline risk factors, as a marker of sepsis or analogous severe infectious course) of the qSOFA score (primary) and SIRS criteria (secondary). Results The cohorts were diverse in enrollment criteria, demographics (median ages, 29-54 years; males range, 36%-76%), HIV prevalence (range, 2%-43%), cause of infection, and hospital mortality (range, 1%-39%). Among 6218 patients with nonmissing outcome status in the combined cohort, 643 (10%) died. Compared with a low or moderate score, a high qSOFA score was associated with increased risk of death overall (19% vs 6%; difference, 13% [95% CI, 11%-14%]; odds ratio, 3.6 [95% CI, 3.0-4.2]) and across cohorts (P < .05 for 8 of 9 cohorts). Compared with a low qSOFA score, a moderate qSOFA score was also associated with increased risk of death overall (8% vs 3%; difference, 5% [95% CI, 4%-6%]; odds ratio, 2.8 [95% CI, 2.0-3.9]), but not in every cohort (P < .05 in 2 of 7 cohorts). High, vs low or moderate, SIRS criteria were associated with a smaller increase in risk of death overall (13% vs 8%; difference, 5% [95% CI, 3%-6%]; odds ratio, 1.7 [95% CI, 1.4-2.0]) and across cohorts (P < .05 for 4 of 9 cohorts). qSOFA discrimination (area under the receiver operating characteristic curve [AUROC], 0.70 [95% CI, 0.68-0.72]) was superior to that of both the baseline model (AUROC, 0.56 [95% CI, 0.53-0.58; P < .001) and SIRS (AUROC, 0.59 [95% CI, 0.57-0.62]; P < .001). Conclusions and Relevance When assessed among hospitalized adults with suspected infection in 9 LMIC cohorts, the qSOFA score identified infected patients at risk of death beyond that explained by baseline factors. However, the predictive validity varied among cohorts and settings, and further research is needed to better understand potential generalizability.
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Affiliation(s)
- Kristina E. Rudd
- Department of Medicine and the International Respiratory and Severe Illness Center (INTERSECT), University of Washington, Seattle
| | - Christopher W. Seymour
- Clinical Research, Investigation, and Systems Modeling of Acute Illness (CRISMA) Center, Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Adam R. Aluisio
- Department of Emergency Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | | | - Danstan S. Bagenda
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha
| | - Abi Beane
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Jean Claude Byiringiro
- Division of Clinical Education and Research, University Teaching Hospital of Kigali, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Chung-Chou H. Chang
- Departments of Medicine and Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Nicholas P. J. Day
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Oxford Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford, United Kingdom
| | - A. Pubudu De Silva
- National Intensive Care Surveillance, Colombo, Sri Lanka
- Intensive Care National Audit & Research Centre, London, United Kingdom
| | - Arjen M. Dondorp
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Oxford Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford, United Kingdom
| | - Martin W. Dünser
- Department of Anesthesiology and Intensive Care Medicine, Kepler University Hospital, Johannes Kepler University Linz, Linz, Austria
| | - M. Abul Faiz
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Dev Care Foundation, Dhaka, Bangladesh
| | - Donald S. Grant
- Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Rashan Haniffa
- National Intensive Care Surveillance, Colombo, Sri Lanka
| | - Nguyen Van Hao
- Adult Intensive Care Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Department of Infectious Diseases, University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Jason N. Kennedy
- Clinical Research, Investigation, and Systems Modeling of Acute Illness (CRISMA) Center, Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Adam C. Levine
- Department of Emergency Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Direk Limmathurotsakul
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Oxford Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford, United Kingdom
| | - Sanjib Mohanty
- Ispat General Hospital, Rourkela, Odisha, India
- Center for Emerging Infectious Diseases, Asian Institute of Public Health, Bhubaneswar, Odisha, India
| | - François Nosten
- Oxford Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford, United Kingdom
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Alfred Papali
- Division of Pulmonary & Critical Care Medicine and Institute for Global Health, University of Maryland School of Medicine, Baltimore
- Division of Pulmonary & Critical Care Medicine, Atrium Health, Charlotte, North Carolina
| | | | - John S. Schieffelin
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, Louisiana
| | - Jeffrey G. Shaffer
- Department of Global Biostatistics and Data Science, Tulane University, New Orleans, Louisiana
| | - Duong Bich Thuy
- Adult Intensive Care Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Oxford University Clinical Research Unit (OUCRU), Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - C. Louise Thwaites
- Oxford Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford, United Kingdom
- Oxford University Clinical Research Unit (OUCRU), Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | - Nicholas J. White
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Oxford Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford, United Kingdom
| | - T. Eoin West
- Department of Medicine and the International Respiratory and Severe Illness Center (INTERSECT), University of Washington, Seattle
| | - Derek C. Angus
- Clinical Research, Investigation, and Systems Modeling of Acute Illness (CRISMA) Center, Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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Shantha JG, Mattia JG, Goba A, Barnes KG, Ebrahim FK, Kraft CS, Hayek BR, Hartnett JN, Shaffer JG, Schieffelin JS, Sandi JD, Momoh M, Jalloh S, Grant DS, Dierberg K, Chang J, Mishra S, Chan AK, Fowler R, O'Dempsey T, Kaluma E, Hendricks T, Reiners R, Reiners M, Gess LA, ONeill K, Kamara S, Wurie A, Mansaray M, Acharya NR, Liu WJ, Bavari S, Palacios G, Teshome M, Crozier I, Farmer PE, Uyeki TM, Bausch DG, Garry RF, Vandy MJ, Yeh S. Ebola Virus Persistence in Ocular Tissues and Fluids (EVICT) Study: Reverse Transcription-Polymerase Chain Reaction and Cataract Surgery Outcomes of Ebola Survivors in Sierra Leone. EBioMedicine 2018; 30:217-224. [PMID: 29622497 PMCID: PMC5952345 DOI: 10.1016/j.ebiom.2018.03.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 03/16/2018] [Accepted: 03/17/2018] [Indexed: 12/01/2022] Open
Abstract
Background Ebola virus disease (EVD) survivors are at risk for uveitis during convalescence. Vision loss has been observed following uveitis due to cataracts. Since Ebola virus (EBOV) may persist in the ocular fluid of EVD survivors for an unknown duration, there are questions about the safety and feasibility of vision restorative cataract surgery in EVD survivors. Methods We conducted a cross-sectional study of EVD survivors anticipating cataract surgery and patients with active uveitis to evaluate EBOV RNA persistence in ocular fluid, as well as vision outcomes post cataract surgery. Patients with aqueous humor that tested negative for EBOV RNA were eligible to proceed with manual small incision cataract surgery (MSICS). Findings We screened 137 EVD survivors from June 2016 – August 2017 for enrolment. We enrolled 50 EVD survivors; 46 with visually significant cataract, 1 with a subluxated lens, 2 with active uveitis and 1 with a blind painful eye due to uveitis. The median age was 24.0 years (IQR 17–35) and 35 patients (70%) were female. The median logMAR visual acuity (VA) was 3.0 (Snellen VA Hand motions; Interquartile Range, IQR: 1.2-3.0, Snellen VA 20/320 – Hand motions). All patients tested negative for EBOV RNA by RT-PCR in aqueous humor/vitreous fluid and conjunctiva at a median of 19 months (IQR 18-20) from EVD diagnosis in Phase 1 of ocular fluid sampling and 34 months (IQR 32-36) from EVD diagnosis in Phase 2 of ocular fluid sampling. Thirty-four patients underwent MSICS, with a preoperative median VA improvement from hand motions to 20/30 at three-month postoperative follow-up (P < 0.001). Interpretation EBOV persistence by RT-PCR was not identified in ocular fluid or conjunctivae of fifty EVD survivors with ocular disease. Cataract surgery can be performed safely with vision restorative outcomes in patients who test negative for EBOV RNA in ocular fluid specimens. These findings impact the thousands of West African EVD survivors at-risk for ocular complications who may also require eye surgery during EVD convalescence. Ebola virus disease (EVD) survivors are at-risk for severe vision impairment due to uveitis and subsequent cataract development. Fifty EVD survivors underwent ocular fluid sampling and tested negative for Ebola virus by RT-PCR. Thirty-four survivors underwent cataract surgery with excellent safety measures and vision restorative outcomes.
Ebola virus disease (EVD) survivors are at high risk for uveitis, an inflammatory condition affecting the eye that may lead to severe vision impairment, often from cataract. Because persistent Ebola virus (EBOV) has been identified within the immune privileged eye, understanding the prevalence of intraocular EBOV persistence is significant for patients, providers, and public health policy. In this study, 50 EVD survivors tested negative for EBOV by RT-PCR of their intraocular fluid. Thirty-four underwent cataract surgery with vision restorative outcomes. These findings improve our ability to impact vision care and quality-of-life for thousands of EVD survivors at-risk for eye disease.
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Affiliation(s)
- Jessica G Shantha
- Emory Eye Center, Emory University School of Medicine, Atlanta, GA, United States; University of California San Francisco, Proctor Foundation, San Francisco, CA, United States
| | - John G Mattia
- Lunsar Baptist Eye Hospital, Port Loko, Sierra Leone
| | - Augustine Goba
- Kenema Government Hospital Lassa Hemorrhagic Fever Laboratory, Kenema, Sierra Leone
| | - Kayla G Barnes
- Department of Organismic and Evolutionary Biology, Harvard University, United States; Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | | | - Colleen S Kraft
- Department of Pathology and Laboratory Medicine, Department of Medicine, Division of Infectious Diseases, Atlanta, GA, United States
| | - Brent R Hayek
- Emory Eye Center, Emory University School of Medicine, Atlanta, GA, United States
| | | | - Jeffrey G Shaffer
- Department of Biostatistics and Bioinformatics, Tulane School of Public Health, New Orleans, LA, United States
| | | | - John D Sandi
- Kenema Government Hospital Lassa Hemorrhagic Fever Laboratory, Kenema, Sierra Leone
| | - Mambu Momoh
- Kenema Government Hospital Lassa Hemorrhagic Fever Laboratory, Kenema, Sierra Leone
| | - Simbirie Jalloh
- Kenema Government Hospital Lassa Hemorrhagic Fever Laboratory, Kenema, Sierra Leone
| | - Donald S Grant
- Kenema Government Hospital Lassa Hemorrhagic Fever Laboratory, Kenema, Sierra Leone; Department of Community Health, University of Sierra Leone, Freetown, Sierra Leone
| | | | - Joyce Chang
- Partners in Health, Boston, MA, United States
| | | | | | - Rob Fowler
- University of Toronto, Toronto, ON, Canada
| | | | - Erick Kaluma
- Comprehensive Program for Ebola Survivors, Freetown, Sierra Leone
| | - Taylor Hendricks
- Comprehensive Program for Ebola Survivors, Freetown, Sierra Leone
| | - Roger Reiners
- Lowell and Ruth Gess Eye Hospital, Freetown, Sierra Leone
| | | | - Lowell A Gess
- Lowell and Ruth Gess Eye Hospital, Freetown, Sierra Leone
| | | | | | - Alie Wurie
- Ministry of Health and Sanitation, Sierra Leone
| | - Mohamed Mansaray
- Sierra Leone Association of Ebola Survivors, Freetown, Sierra Leone
| | - Nisha R Acharya
- University of California San Francisco, Proctor Foundation, San Francisco, CA, United States
| | - William J Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Sina Bavari
- United Stated Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Gustavo Palacios
- United Stated Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Moges Teshome
- Lowell and Ruth Gess Eye Hospital, Freetown, Sierra Leone; Christian Blind Mission International, Washington, D.C., United States
| | - Ian Crozier
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | | | - Timothy M Uyeki
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Daniel G Bausch
- UK Public Health Rapid Support Team Public Health England/London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Robert F Garry
- Tulane University School of Medicine, New Orleans, LA, United States
| | | | - Steven Yeh
- Emory Eye Center, Emory University School of Medicine, Atlanta, GA, United States; Emory Global Health Institute, Emory University, Atlanta, GA, United States.
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Koita OA, Sangaré L, Miller HD, Sissako A, Coulibaly M, Thompson TA, Fongoro S, Diarra Y, Ba M, Maiga A, Diallo B, Mushatt DM, Mather FJ, Shaffer JG, Anwar AH, Krogstad DJ. AQ-13, an investigational antimalarial, versus artemether plus lumefantrine for the treatment of uncomplicated Plasmodium falciparum malaria: a randomised, phase 2, non-inferiority clinical trial. Lancet Infect Dis 2017; 17:1266-1275. [PMID: 28916443 PMCID: PMC5700806 DOI: 10.1016/s1473-3099(17)30365-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 05/16/2017] [Accepted: 06/08/2017] [Indexed: 12/02/2022]
Abstract
BACKGROUND Chloroquine was used for malaria treatment until resistant Plasmodium falciparum was identified. Because 4-aminoquinolines with modified side chains, such as AQ-13, are active against resistant parasites, we compared AQ-13 against artemether plus lumefantrine for treatment of uncomplicated P falciparum malaria. METHODS We did a randomised, non-inferiority trial. We screened men (≥18 years) with uncomplicated malaria in Missira (northeast Mali) and Bamako (capital of Mali) for eligibility (≥2000 asexual P falciparum parasites per μL of blood). Eligible participants were randomly assigned to either the artemether plus lumefantrine group or AQ-13 group by permuting blocks of four with a random number generator. Physicians and others caring for the participants were masked, except for participants who received treatment and the research pharmacist who implemented the randomisation and provided treatment. Participants received either 80 mg of oral artemether and 480 mg of oral lumefantrine twice daily for 3 days or 638·50 mg of AQ-13 base (two oral capsules) on days 1 and 2, and 319·25 mg base (one oral capsule) on day 3. Participants were monitored for parasite clearance (50 μL blood samples twice daily at 12 h intervals until two consecutive negative samples were obtained) and interviewed for adverse events (once every day) as inpatients during week 1. During the 5-week outpatient follow-up, participants were examined for adverse events and recurrent infection twice per week. All participants were included in the intention-to-treat analysis and per-protocol analysis, except for those who dropped out in the per-protocol analysis. The composite primary outcome was clearance of asexual parasites and fever by day 7, and absence of recrudescent infection by parasites with the same molecular markers from days 8 to 42 (defined as cure). Non-inferiority was considered established if the proportion of patients who were cured was higher for artemether plus lumefantrine than for AQ-13 and the upper limit of the 95% CI was less than the non-inferiority margin of 15%. This trial is registered at ClinicalTrials.gov, number NCT01614964. FINDINGS Between Aug 6 and Nov 18, 2013, and between Sept 18 and Nov 20, 2015, 66 Malian men with uncomplicated malaria were enrolled. 33 participants were randomly assigned to each group. There were no serious adverse events (grade 2-4) and asexual parasites were cleared by day 7 in both groups. 453 less-severe adverse events (≤grade 1) were reported: 214 in the combination group and 239 in the AQ-13 group. Two participants withdrew from the AQ-13 group after parasite clearance and three were lost to follow-up. In the artemether plus lumefantrine group, two participants had late treatment failures (same markers as original isolates). On the basis of the per-protocol analysis, the AQ-13 and artemether plus lumefantrine groups had similar proportions cured (28 [100%] of 28 vs 31 [93·9%] of 33; p=0·50) and AQ-13 was not inferior to artemether plus lumefantrine (difference -6·1%, 95% CI -14·7 to 2·4). Proportions cured were also similar between the groups in the intention-to-treat analysis (28 of 33, 84·8% for AQ-13 vs 31 of 33, 93·9% for artemether and lumefantrine; p=0·43) but the upper bound of the 95% CI exceeded the 15% non-inferiority margin (difference 9·1%, 95% CI -5·6 to 23·8). INTERPRETATION The per-protocol analysis suggested non-inferiority of AQ-13 to artemether plus lumefantrine. By contrast, the intention-to-treat analysis, which included two participants who withdrew and three who were lost to follow-up from the AQ-13 group, did not meet the criterion for non-inferiority of AQ-13, although there were no AQ-13 treatment failures. Studies with more participants (and non-immune participants) are needed to decide whether widespread use of modified 4-aminoquinolones should be recommended. FUNDING US Food and Drug Administration Orphan Product Development, National Institutes of Health, US Centers for Disease Control and Prevention, Burroughs-Wellcome Fund, US State Department, and WHO.
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Affiliation(s)
- Ousmane A Koita
- University of the Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Lansana Sangaré
- University of the Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Haiyan D Miller
- Department of Tropical Medicine and the Center for Infectious Diseases, Tulane University Health Sciences Center, New Orleans, LA, USA
| | - Aliou Sissako
- University of the Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Moctar Coulibaly
- University of the Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Trevor A Thompson
- Department of Tropical Medicine and the Center for Infectious Diseases, Tulane University Health Sciences Center, New Orleans, LA, USA
| | - Saharé Fongoro
- University of the Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Youssouf Diarra
- University of the Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mamadou Ba
- University of the Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Ababacar Maiga
- University of the Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Boubakar Diallo
- University of the Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - David M Mushatt
- Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, USA
| | - Frances J Mather
- Department of Global Biostatistics and Data Science, Tulane University Health Sciences Center, New Orleans, LA, USA
| | - Jeffrey G Shaffer
- Department of Global Biostatistics and Data Science, Tulane University Health Sciences Center, New Orleans, LA, USA
| | - Asif H Anwar
- Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, USA
| | - Donald J Krogstad
- Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, USA; Department of Tropical Medicine and the Center for Infectious Diseases, Tulane University Health Sciences Center, New Orleans, LA, USA.
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Labuda SM, Schieffelin JS, Shaffer JG, Stryjewska BM. Hansen's Disease and Rheumatoid Arthritis Crossover of Clinical Symptoms: A Case Series of 18 Patients in the United States. Am J Trop Med Hyg 2017; 97:1726-1730. [PMID: 29141716 DOI: 10.4269/ajtmh.17-0197] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Hansen's Disease (HD) is a rare, chronic granulomatous infection of the skin and peripheral nerves caused by the noncultivable organism Mycobacterium leprae. Arthritis is the third most common symptom of HD. Subjects with both confirmed HD on skin biopsy and chronic arthritis were identified at the National Hansen's Disease Program (NHDP). We conducted a series of medical chart reviews and extracted and logged personally deidentified data into a database and carried out descriptive analyses. Eighteen of 261 subjects presented to the NDHP with both HD and chronic arthritis between 2001 and 2015. Among these, 16 were male, 16 were white, and 15 were residents of Louisiana. The median age at diagnosis of HD was 67 years. Ten of these subjects were diagnosed with borderline lepromatous leprosy, seven were diagnosed with lepromatous, and one was diagnosed with borderline tuberculoid leprosy. Patients were symptomatic with arthritis for a median of 5.3 years before HD diagnosis. Sixty-two percent of patients (11) were diagnosed with rheumatoid arthritis (RA) before HD diagnosis, and 10 of which were seronegative RA. Hands, feet, wrists, and elbows were most commonly reported as affected joints. Over half of the patients (61%) had completed HD multidrug therapy at the time of review, and 73% of these subjects had persistent joint pain requiring steroids or methotrexate for symptomatic control. Chronic arthritis in HD patients is present in a series of US-acquired cases of HD. Arthritis did not resolve with successful treatment of HD in most cases.
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Affiliation(s)
- Sarah M Labuda
- Tulane University School of Medicine, New Orleans, Louisiana
| | | | - Jeffrey G Shaffer
- Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
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Xiong X, Dickey RP, Buekens P, Shaffer JG, Pridjian G. Response to Letters to the Editor Birth Defects Outcomes in Pregnancies Conceived through In Vitro Fertilization. Paediatr Perinat Epidemiol 2017; 31:481-482. [PMID: 28815658 DOI: 10.1111/ppe.12395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xu Xiong
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Richard P Dickey
- Department of Obstetrics and Gynecology, Section of Reproductive Endocrinology and Infertility, Louisiana State University School of Medicine, Mandeville, LA.,The Fertility Institute of New Orleans, Mandeville, LA
| | - Pierre Buekens
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Jeffrey G Shaffer
- Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Gabriella Pridjian
- Department of Obstetrics and Gynecology, Tulane University School of Medicine, New Orleans, LA
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Xiong X, Dickey RP, Buekens P, Shaffer JG, Pridjian G. Use of Intracytoplasmic Sperm Injection and Birth Outcomes in Women Conceiving through In Vitro Fertilization. Paediatr Perinat Epidemiol 2017; 31:108-115. [PMID: 28140471 DOI: 10.1111/ppe.12339] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Despite questionable evidence of benefits over conventional in vitro fertilization (IVF), intracytoplasmic sperm injection (ICSI) use has markedly increased in recent decades among couples without male factor infertility. We assessed the frequency of ICSI use and its effect on birth outcomes. METHODS A retrospective cohort study was conducted in 141 030 women conceiving through IVF using 2006-2010 data from the Society for Assisted Reproductive Technology (SART). RESULTS Between 2006 and 2010, overall ICSI use in women conceiving through IVF increased from 68.9% to 73.1%. This increase was greater among women without male factor infertility (53.0-59.2%) than in women with male factor infertility (92.0-93.4%). Women conceiving through IVF with and without ICSI had similar rates of multiple pregnancy, preterm delivery, stillbirth, and neonatal death. However, ICSI pregnancies were associated with an increased risk of birth defects over conventional IVF (3.0% for ICSI vs. 2.5% for conventional IVF; adjusted odds ratio (OR) 1.2, 95% confidence interval (CI) 1.2, 1.3). These increases were observed in both women conceiving through ICSI with male factor infertility (3.2% vs. 2.5%; OR 1.4, 95% CI 1.3, 1.5) and without male factor infertility (2.7% vs. 2.5%; OR 1.1, 95% CI 1.1, 1.2). CONCLUSIONS Higher rates of birth defects were observed among women conceiving through ICSI. Since approximately half of all ICSI procedures are performed in couples without male factor infertility, ICSI may be overused in practice.
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Affiliation(s)
- Xu Xiong
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Richard P Dickey
- Section of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Louisiana State University School of Medicine, and The Fertility Institute of New Orleans, Mandeville, LA
| | - Pierre Buekens
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Jeffrey G Shaffer
- Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Gabriella Pridjian
- Department of Obstetrics and Gynecology, Tulane University School of Medicine, New Orleans, LA
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Lo Iacono G, Cunningham AA, Fichet-Calvet E, Garry RF, Grant DS, Leach M, Moses LM, Nichols G, Schieffelin JS, Shaffer JG, Webb CT, Wood JLN. A Unified Framework for the Infection Dynamics of Zoonotic Spillover and Spread. PLoS Negl Trop Dis 2016; 10:e0004957. [PMID: 27588425 PMCID: PMC5010258 DOI: 10.1371/journal.pntd.0004957] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/06/2016] [Indexed: 01/26/2023] Open
Abstract
A considerable amount of disease is transmitted from animals to humans and many of these zoonoses are neglected tropical diseases. As outbreaks of SARS, avian influenza and Ebola have demonstrated, however, zoonotic diseases are serious threats to global public health and are not just problems confined to remote regions. There are two fundamental, and poorly studied, stages of zoonotic disease emergence: ‘spillover’, i.e. transmission of pathogens from animals to humans, and ‘stuttering transmission’, i.e. when limited human-to-human infections occur, leading to self-limiting chains of transmission. We developed a transparent, theoretical framework, based on a generalization of Poisson processes with memory of past human infections, that unifies these stages. Once we have quantified pathogen dynamics in the reservoir, with some knowledge of the mechanism of contact, the approach provides a tool to estimate the likelihood of spillover events. Comparisons with independent agent-based models demonstrates the ability of the framework to correctly estimate the relative contributions of human-to-human vs animal transmission. As an illustrative example, we applied our model to Lassa fever, a rodent-borne, viral haemorrhagic disease common in West Africa, for which data on human outbreaks were available. The approach developed here is general and applicable to a range of zoonoses. This kind of methodology is of crucial importance for the scientific, medical and public health communities working at the interface between animal and human diseases to assess the risk associated with the disease and to plan intervention and appropriate control measures. The Lassa case study revealed important knowledge gaps, and opportunities, arising from limited knowledge of the temporal patterns in reporting, abundance of and infection prevalence in, the host reservoir. Many dangerous diseases emerge via spillover from animals, with limited human-to-human infection (stuttering-transmission) often being the first stage of human disease spread. Understanding the conditions (biological, environmental and socio-economic factors) that regulate spillover and disease spread is key to its mitigation. Here we are interested in questions such as: If we have quantified pathogen dynamics in the reservoir, with some knowledge of the mechanism of contact, can we estimate the likelihood of spillover events? Can we tease apart how much the disease is transmitted by animals and how much by humans? We developed a unified mathematical framework, based on Poisson processes with memory of past events, to understand the dynamics of spillover and stuttering-transmission. This framework, which can be applied across the disease transmission spectrum, allows the teasing apart of the disease burden attributed to animal-human and human-human transmission. Using this model, we can infer human disease risk based on knowledge of infection patterns in the animal reservoir host and the contact mechanisms required for transmission to humans.
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Affiliation(s)
- Giovanni Lo Iacono
- Department of Veterinary Medicine, Disease Dynamics Unit, University of Cambridge, Cambridge, United Kingdom
- Environmental Change Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, London, United Kingdom
- * E-mail:
| | | | | | - Robert F. Garry
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, United States of America
| | - Donald S. Grant
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
| | - Melissa Leach
- Institute of Development Studies, University of Sussex, Brighton, United Kingdom
| | - Lina M. Moses
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, United States of America
| | - Gordon Nichols
- Gastrointestinal, Emerging and Zoonotic Infections, Public Health England, London, United Kingdom
| | - John S. Schieffelin
- Sections of Infectious Disease, Departments of Pediatrics and Internal Medicine, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Bioinformatics, Tulane School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
| | - Colleen T. Webb
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - James L. N. Wood
- Department of Veterinary Medicine, Disease Dynamics Unit, University of Cambridge, Cambridge, United Kingdom
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50
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Cross RW, Boisen ML, Millett MM, Nelson DS, Oottamasathien D, Hartnett JN, Jones AB, Goba A, Momoh M, Fullah M, Bornholdt ZA, Fusco ML, Abelson DM, Oda S, Brown BL, Pham H, Rowland MM, Agans KN, Geisbert JB, Heinrich ML, Kulakosky PC, Shaffer JG, Schieffelin JS, Kargbo B, Gbetuwa M, Gevao SM, Wilson RB, Saphire EO, Pitts KR, Khan SH, Grant DS, Geisbert TW, Branco LM, Garry RF. Analytical Validation of the ReEBOV Antigen Rapid Test for Point-of-Care Diagnosis of Ebola Virus Infection. J Infect Dis 2016; 214:S210-S217. [PMID: 27587634 DOI: 10.1093/infdis/jiw293] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Ebola virus disease (EVD) is a severe viral illness caused by Ebola virus (EBOV). The 2013-2016 EVD outbreak in West Africa is the largest recorded, with >11 000 deaths. Development of the ReEBOV Antigen Rapid Test (ReEBOV RDT) was expedited to provide a point-of-care test for suspected EVD cases. METHODS Recombinant EBOV viral protein 40 antigen was used to derive polyclonal antibodies for RDT and enzyme-linked immunosorbent assay development. ReEBOV RDT limits of detection (LOD), specificity, and interference were analytically validated on the basis of Food and Drug Administration (FDA) guidance. RESULTS The ReEBOV RDT specificity estimate was 95% for donor serum panels and 97% for donor whole-blood specimens. The RDT demonstrated sensitivity to 3 species of Ebolavirus (Zaire ebolavirus, Sudan ebolavirus, and Bundibugyo ebolavirus) associated with human disease, with no cross-reactivity by pathogens associated with non-EBOV febrile illness, including malaria parasites. Interference testing exhibited no reactivity by medications in common use. The LOD for antigen was 4.7 ng/test in serum and 9.4 ng/test in whole blood. Quantitative reverse transcription-polymerase chain reaction testing of nonhuman primate samples determined the range to be equivalent to 3.0 × 105-9.0 × 108 genomes/mL. CONCLUSIONS The analytical validation presented here contributed to the ReEBOV RDT being the first antigen-based assay to receive FDA and World Health Organization emergency use authorization for this EVD outbreak, in February 2015.
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Affiliation(s)
- Robert W Cross
- Galveston National Laboratory, University of Texas Medical Branch
| | - Matthew L Boisen
- Corgenix, Broomfield, Colorado Department of Microbiology and Immunology Zalgen Labs, Germantown, Maryland
| | | | - Diana S Nelson
- Corgenix, Broomfield, Colorado Zalgen Labs, Germantown, Maryland
| | | | | | | | - Augustine Goba
- Lassa Fever Program, Kenema Government Hospital Ministry of Health and Sanitation
| | - Mambu Momoh
- Lassa Fever Program, Kenema Government Hospital Ministry of Health and Sanitation Eastern Polytechnic Institute, Kenema, Sierra Leone
| | - Mohamed Fullah
- Lassa Fever Program, Kenema Government Hospital Ministry of Health and Sanitation Eastern Polytechnic Institute, Kenema, Sierra Leone
| | | | | | | | | | | | - Ha Pham
- Corgenix, Broomfield, Colorado
| | | | - Krystle N Agans
- Galveston National Laboratory, University of Texas Medical Branch
| | - Joan B Geisbert
- Galveston National Laboratory, University of Texas Medical Branch
| | | | | | | | - John S Schieffelin
- Section of Infectious Diseases, Department of Pediatrics, School of Medicine
| | | | - Momoh Gbetuwa
- Lassa Fever Program, Kenema Government Hospital Ministry of Health and Sanitation
| | - Sahr M Gevao
- Lassa Fever Program, Kenema Government Hospital University of Sierra Leone, Freetown
| | | | | | | | - Sheik Humarr Khan
- Lassa Fever Program, Kenema Government Hospital Ministry of Health and Sanitation
| | - Donald S Grant
- Lassa Fever Program, Kenema Government Hospital Ministry of Health and Sanitation
| | | | | | - Robert F Garry
- Department of Microbiology and Immunology Zalgen Labs, Germantown, Maryland
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