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Figueroa-Romero A, Atchadé A, Yadouleton A, Fiogbe M, Bonnet E, Yovo E, Accrombessi M, Hounsa S, Paper T, Dupont R, Gaudart J, Le Hesran JY, Massougbodji A, Cottrell G, González R. SARS-CoV-2 seroprevalence among Beninese pregnant women in the third year of the pandemic. BMC Public Health 2024; 24:1762. [PMID: 38956517 PMCID: PMC11221113 DOI: 10.1186/s12889-024-19087-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 06/10/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Pregnant women are a vulnerable population to COVID-19 given an increased susceptibility to severe SARS-CoV-2 infection and pregnancy complications. However, few SARS-CoV-2 serological surveys have been performed among this population to assess the extent of the infection in sub-Saharan countries. The objectives of this study were to determine SARS-CoV-2 seroprevalence among Beninese pregnant women, to identify spatial seropositivity clusters and to analyse factors associated with the infection. METHODS A cross-sectional study including women in their third trimester of pregnancy attending the antenatal care (ANC) clinics at Allada (south Benin) and Natitingou (north Benin) was conducted. Rapid diagnostic tests (RDT) for detection of IgG/IgM against the SARS-CoV-2 spike protein were performed using capillary blood. Seroprevalence of SARS-CoV-2 antibodies and associations between SARS-CoV-2 serostatus and maternal characteristics were analyzed by multivariate logistic regression. Spatial analyses were performed using the spatial scan statistics to identify spatial clusters of SARS-CoV-2 infection. RESULTS A total of 861 pregnant women were enrolled between May 4 and June 29, 2022. 58/861 (6.7%) participants reported having received COVID-19 vaccine. None of the participants had been diagnosed with COVID-19 during their pregnancy. SARS-CoV-2 antibodies were detected in 607/802 (75.7%; 95% CI 72.56%-78.62%) of unvaccinated participants. Several urban and rural spatial clusters of SARS-CoV-2 cases were identified in Allada and one urban spatial cluster was identified in Natitingou. Unvaccinated participants from Allada with at least one previous morbidity were at a three-times higher risk of presenting SARS-CoV-2 antibodies (OR = 2.89; 95%CI 1.19%-7.00%). CONCLUSION Three out of four pregnant women had SARS-CoV-2 antibodies, suggesting a high virus circulation among pregnant women in Benin, while COVID-19 vaccination coverage was low. Pregnant women with comorbidities may be at increased risk of SARS-CoV-2 infection. This population should be prioritized for COVID-19 diagnosis and vaccination in order to prevent its deleterious effects. TRIAL REGISTRATION NCT06170320 (retrospectively registered on December 21, 2023).
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Affiliation(s)
- Antía Figueroa-Romero
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic- Universitat de Barcelona, Barcelona, Spain.
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública, CIBERESP, Madrid, Spain.
| | - Aurore Atchadé
- Institut de Recherche Clinique du Bénin, Abomey-Calavi, Benin
| | - Anges Yadouleton
- Laboratoire des fièvres hémorragiques virales du Bénin, Ministère de la Santé du Bénin, Cotonou, 01BP918, Bénin
| | - Marc Fiogbe
- Institut de Recherche Clinique du Bénin, Abomey-Calavi, Benin
| | - Emmanuel Bonnet
- Institut de recherche pour le développement PRODIG UMR 215, CNRS Université Paris 1 Panthéon- Sorbonne, AgroParisTech 5, cours des Humanités, Aubervilliers, Île-de-France, F-93 322, France
| | - Emmanuel Yovo
- Institut de Recherche Clinique du Bénin, Abomey-Calavi, Benin
| | - Manfred Accrombessi
- Institut de Recherche Clinique du Bénin, Abomey-Calavi, Benin
- Faculty of Infectious and Tropical Diseases, Disease Control Department, London School of Hygiene & Tropical Medicine, London, UK
- Population Services International, Malaria Department, Country-Based Global Employee, Cotonou, Benin
| | - Sandrine Hounsa
- Institut de Recherche Clinique du Bénin, Abomey-Calavi, Benin
| | - Thierry Paper
- Biosynex S.A, 22 boulevard Sebastien Brant, Illkirch Graffenstaden, Strasbourg, F-67400, France
| | - Raphael Dupont
- Biosynex S.A, 22 boulevard Sebastien Brant, Illkirch Graffenstaden, Strasbourg, F-67400, France
| | - Jean Gaudart
- Aix Marseille Univ, IRD, INSERM, SESSTIM, ISSPAM, AP-HM, Hop La Timone, BioSTIC, Biostatistic and ICT, Marseille, France
| | - Jean-Yves Le Hesran
- Institut de Recherche pour le Développement, MERIT UMR216, Université Paris-Cité, Faculté de pharmacie, laboratoire de parasitologie, Paris, France
| | | | - Gilles Cottrell
- Institut de Recherche pour le Développement, MERIT UMR216, Université Paris-Cité, Faculté de pharmacie, laboratoire de parasitologie, Paris, France
| | - Raquel González
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic- Universitat de Barcelona, Barcelona, Spain
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública, CIBERESP, Madrid, Spain
- Department of Medicine, Faculty of Medicine, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
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2
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Traoré B, Guindo M, Konaté D, Kané F, Incandela N, Traore A, Kanté S, Sidibé M, Keita B, Kasse F, Tangara K, Diallo D, Maiga I, Thiam S, Cisse A, Siby K, Dicko A, Goita M, Kone D, Diallo M, Traore M, Coulibaly Y, Diakité M, Doumbia S, Dolo H, Balam S. Seroprevalence of SARS-CoV-2 Antibodies and Associated Factors in Bamako, Mali: A Population-Based Cross-Sectional Study in September 2022. Influenza Other Respir Viruses 2024; 18:e13343. [PMID: 39044355 PMCID: PMC11300109 DOI: 10.1111/irv.13343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/15/2024] [Accepted: 05/31/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND The sero-epidemiological characteristics of SARS-CoV-2 infections in Mali are not yet well understood. This study assessed SARS-CoV-2 antibody seroprevalence and factors associated with antibody responses in the general population of Bamako, the capital city and epicenter of COVID-19, to assess the magnitude of the pandemic and contribute to control strategy improvements in Mali. METHODS A cross-sectional survey was conducted in September 2022 to collect sociodemographic information, clinical characteristics, comorbid factors, and blood samples. ELISA was performed to determine anti-Spike (anti-S) and anti-RBD antibody levels. A total of 3601 participants were enrolled in REDCap. R-Studio was used for the statistical analysis. The chi-squared (χ2) test was used to compare the proportions across different groups. Logistic regression models were used to elucidate factors associated with antibody responses. RESULT The sex ratio for female-to-male was 3.6:1. The most representative groups were the 20-29-year-olds (28.9%, n = 1043) and the 30-39-year-olds (26.9%, n = 967). The COVID-19 vaccine coverage among the participants was 35.8%, with vaccines from Covishield AstraZeneca (13.4%), Johnson & Johnson (16.7%), Sinovac (3.9%), and BioNTech Pfizer (1.8%). Overall, S protein and RBD antibody seroprevalences were remarkably high in the study population (98% and 97%, respectively). Factors such as youth (1-9 years old) and male sex were associated with lower SARS-CoV-2 antibody responses, whereas COVID-19 vaccinations were associated with increased antibody responses. CONCLUSION This serosurvey demonstrated the high seroprevalence of SARS-CoV-2 antibodies and highlighted the factors influencing antibody responses, while clearly underlining an underestimation of the pandemic in Mali.
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Affiliation(s)
- Bourama Traoré
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Merepen A. Guindo
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Drissa Konaté
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Fousseyni Kané
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Nathan C. Incandela
- Center for Polymers and Organic Solids, Department of Chemistry and BiochemistryUniversity of California Santa BarbaraSanta BarbaraCaliforniaUSA
| | - Abdouramane Traore
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Salimata Kanté
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Mariam Sidibé
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Bourama Keita
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Fatoumata Kasse
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Karamoko Tangara
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Dramane Diallo
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Issoufi Y. Maiga
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Salif Thiam
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Abdourhamane Cisse
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Khatry M. Siby
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Abdoul R. Dicko
- District Health Center of Commune 4 of BamakoMinister of Health and Social Development of MaliBamakoMali
| | - Mariam Goita
- District Health Center of Commune 4 of BamakoMinister of Health and Social Development of MaliBamakoMali
| | - Diakaridia Kone
- Hospital District Health of Commune 1 of BamakoMinister of Health and Social Development of MaliBamakoMali
| | - Mamadou Diallo
- District Health Center of Commune 6 of BamakoMinister of Health and Social Development of MaliBamakoMali
| | - Modibo Traore
- District Health Center of Commune 5 of BamakoMinister of Health and Social Development of MaliBamakoMali
| | - Yaya I. Coulibaly
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Mahamadou Diakité
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Seydou Doumbia
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Housseini Dolo
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
| | - Saidou Balam
- International Center for Excellence in Research (ICER), Faculty of Medicine and Odontostomatology (FMOS), Faculty of Pharmacy (FAPHA)University Clinical Research Center (UCRC) at the University of Sciences, Techniques and Technologies of Bamako (USTTB)BamakoMali
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Boyd CM, Seed KD. A phage satellite manipulates the viral DNA packaging motor to inhibit phage and promote satellite spread. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590561. [PMID: 38712175 PMCID: PMC11071384 DOI: 10.1101/2024.04.22.590561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
ICP1, a lytic bacteriophage of Vibrio cholerae, is parasitized by phage satellites, PLEs, which hijack ICP1 proteins for their own horizontal spread. PLEs' dependence on ICP1's DNA replication machinery, and virion components results in inhibition of ICP1's lifecycle. PLEs' are expected to depend on ICP1 factors for genome packaging, but the mechanism(s) PLEs use to inhibit ICP1 genome packaging is currently unknown. Here, we identify and characterize Gpi, PLE's indiscriminate genome packaging inhibitor. Gpi binds to ICP1's large terminase (TerL), the packaging motor, and blocks genome packaging. To overcome Gpi's negative effect on TerL, a component PLE also requires, PLE uses two genome packaging specifiers, GpsA and GpsB, that specifically allow packaging of PLE genomes. Surprisingly, PLE also uses mimicry of ICP1's pac site as a backup strategy to ensure genome packaging. PLE's pac site mimicry, however, is only sufficient if PLE can inhibit ICP1 at other stages of its lifecycle, suggesting an advantage to maintaining Gpi, GpsA, and GpsB. Collectively, these results provide mechanistic insights into another stage of ICP1's lifecycle that is inhibited by PLE, which is currently the most inhibitory of the documented phage satellites. More broadly, Gpi represents the first satellite-encoded inhibitor of a phage TerL.
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Affiliation(s)
- Caroline M. Boyd
- Plant and Microbial Biology, University of California - Berkeley, Berkeley, CA, 94720, USA
| | - Kimberley D. Seed
- Plant and Microbial Biology, University of California - Berkeley, Berkeley, CA, 94720, USA
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Johnson NV, Wall SC, Kramer KJ, Holt CM, Periasamy S, Richardson S, Suryadevara N, Andreano E, Paciello I, Pierleoni G, Piccini G, Huang Y, Ge P, Allen JD, Uno N, Shiakolas AR, Pilewski KA, Nargi RS, Sutton RE, Abu-Shmais AA, Parks R, Haynes BF, Carnahan RH, Crowe JE, Montomoli E, Rappuoli R, Bukreyev A, Ross TM, Sautto GA, McLellan JS, Georgiev IS. Discovery and Characterization of a Pan-betacoronavirus S2-binding antibody. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575741. [PMID: 38293237 PMCID: PMC10827111 DOI: 10.1101/2024.01.15.575741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Three coronaviruses have spilled over from animal reservoirs into the human population and caused deadly epidemics or pandemics. The continued emergence of coronaviruses highlights the need for pan-coronavirus interventions for effective pandemic preparedness. Here, using LIBRA-seq, we report a panel of 50 coronavirus antibodies isolated from human B cells. Of these antibodies, 54043-5 was shown to bind the S2 subunit of spike proteins from alpha-, beta-, and deltacoronaviruses. A cryo-EM structure of 54043-5 bound to the pre-fusion S2 subunit of the SARS-CoV-2 spike defined an epitope at the apex of S2 that is highly conserved among betacoronaviruses. Although non-neutralizing, 54043-5 induced Fc-dependent antiviral responses, including ADCC and ADCP. In murine SARS-CoV-2 challenge studies, protection against disease was observed after introduction of Leu234Ala, Leu235Ala, and Pro329Gly (LALA-PG) substitutions in the Fc region of 54043-5. Together, these data provide new insights into the protective mechanisms of non-neutralizing antibodies and define a broadly conserved epitope within the S2 subunit.
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Affiliation(s)
- Nicole V. Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Steven C. Wall
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Kevin J. Kramer
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Clinton M. Holt
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Program in Chemical and Physical Biology, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - Sivakumar Periasamy
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Simone Richardson
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | | | - Emanuele Andreano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena 53100, Italy
| | - Ida Paciello
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena 53100, Italy
| | - Giulio Pierleoni
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena 53100, Italy
| | | | - Ying Huang
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Pan Ge
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
| | - James D. Allen
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
| | - Naoko Uno
- Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44196, USA
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
| | - Andrea R. Shiakolas
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Kelsey A. Pilewski
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Rachel S. Nargi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - Rachel E. Sutton
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - Alexandria A. Abu-Shmais
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA
- Departments of Medicine and Immunology, Duke University, Durham, NC 27710, USA
| | - Robert H. Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
- Department of Pediatrics, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - Emanuele Montomoli
- VisMederi Research S.r.l., Siena 53100, Italy
- VisMederi S.r.l, Siena 53100, Italy
- Department of Molecular and Developmental Medicine, University of Siena, Siena 53100, Italy
| | - Rino Rappuoli
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena 53100, Italy
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena 53100, Italy
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Ted M. Ross
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
- Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44196, USA
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
| | - Giuseppe A. Sautto
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ivelin S. Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; Nashville, TN 73232, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center; Nashville, TN 37232, USA
- Department of Computer Science, Vanderbilt University; Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University; Nashville, TN 37232, USA
- Program in Computational Microbiology and Immunology, Vanderbilt University Medical Center; Nashville, TN 37232, USA
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Garchitorena A, Rasoloharimanana LT, Rakotonanahary RJ, Evans MV, Miller AC, Finnegan KE, Cordier LF, Cowley G, Razafinjato B, Randriamanambintsoa M, Andrianambinina S, Popper SJ, Hotahiene R, Bonds MH, Schoenhals M. Morbidity and mortality burden of COVID-19 in rural Madagascar: results from a longitudinal cohort and nested seroprevalence study. Int J Epidemiol 2023; 52:1745-1755. [PMID: 37793001 DOI: 10.1093/ije/dyad135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
INTRODUCTION Three years into the pandemic, there remains significant uncertainty about the true infection and mortality burden of COVID-19 in the World Health Organization Africa region. High quality, population-representative studies in Africa are rare and tend to be conducted in national capitals or large cities, leaving a substantial gap in our understanding of the impact of COVID-19 in rural, low-resource settings. Here, we estimated the spatio-temporal morbidity and mortality burden associated with COVID-19 in a rural health district of Madagascar until the first half of 2021. METHODS We integrated a nested seroprevalence study within a pre-existing longitudinal cohort conducted in a representative sample of 1600 households in Ifanadiana District, Madagascar. Socio-demographic and health information was collected in combination with dried blood spots for about 6500 individuals of all ages, which were analysed to detect IgG and IgM antibodies against four specific proteins of SARS-CoV-2 in a bead-based multiplex immunoassay. We evaluated spatio-temporal patterns in COVID-19 infection history and its associations with several geographic, socio-economic and demographic factors via logistic regressions. RESULTS Eighteen percent of people had been infected by April-June 2021, with seroprevalence increasing with individuals' age. COVID-19 primarily spread along the only paved road and in major towns during the first epidemic wave, subsequently spreading along secondary roads during the second wave to more remote areas. Wealthier individuals and those with occupations such as commerce and formal employment were at higher risk of being infected in the first wave. Adult mortality increased in 2020, particularly for older men for whom it nearly doubled up to nearly 40 deaths per 1000. Less than 10% of mortality in this period would be directly attributed to COVID-19 deaths if known infection fatality ratios are applied to observed seroprevalence in the district. CONCLUSION Our study provides a very granular understanding on COVID-19 transmission and mortality in a rural population of sub-Saharan Africa and suggests that the disease burden in these areas may have been substantially underestimated.
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Affiliation(s)
- Andres Garchitorena
- MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
- NGO Pivot, Ifanadiana, Madagascar
| | | | - Rado Jl Rakotonanahary
- NGO Pivot, Ifanadiana, Madagascar
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Michelle V Evans
- MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Ann C Miller
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Karen E Finnegan
- NGO Pivot, Ifanadiana, Madagascar
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Marius Randriamanambintsoa
- Direction de la Démographie et des Statistiques Sociales, Institut National de la Statistique, Antananarivo, Madagascar
| | - Samuel Andrianambinina
- Direction de la Démographie et des Statistiques Sociales, Institut National de la Statistique, Antananarivo, Madagascar
| | - Stephen J Popper
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | - Raphaël Hotahiene
- Direction de lutte contre les maladies transmissibles, Ministère de la Santé Publique, Antananarivo, Madagascar
| | - Matthew H Bonds
- NGO Pivot, Ifanadiana, Madagascar
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
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6
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Mendes FK, Landis MJ. PhyloJunction: a computational framework for simulating, developing, and teaching evolutionary models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571907. [PMID: 38168278 PMCID: PMC10760140 DOI: 10.1101/2023.12.15.571907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
We introduce PhyloJunction, a computational framework designed to facilitate the prototyping, testing, and characterization of evolutionary models. PhyloJunction is distributed as an open-source Python library that can be used to implement a variety of models, through its flexible graphical modeling architecture and dedicated model specification language. Model design and use are exposed to users via command-line and graphical interfaces, which integrate the steps of simulating, summarizing, and visualizing data. This paper describes the features of PhyloJunction - which include, but are not limited to, a general implementation of a popular family of phylogenetic diversification models - and, moving forward, how it may be expanded to not only include new models, but to also become a platform for conducting and teaching statistical learning.
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Affiliation(s)
- Fábio K. Mendes
- Department of Biology, Washington University in St. Louis, St. Louis, MO
| | - Michael J. Landis
- Department of Biology, Washington University in St. Louis, St. Louis, MO
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Ige FA, Ohihoin GA, Osuolale K, Dada A, Onyia N, Johnson A, Okwuraiwe AP, Odediran O, Liboro G, Aniedobe M, Mogaji S, Nwaiwu SO, Akande IR, Audu RA, Salako BL. Seroprevalence of SARS-CoV-2 IgG among healthcare workers in Lagos, Nigeria. PLoS One 2023; 18:e0292440. [PMID: 37796780 PMCID: PMC10553227 DOI: 10.1371/journal.pone.0292440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023] Open
Abstract
Healthcare workers (HCWs) are disproportionately infected with SARS-CoV-2 when compared to members of the general public; estimating the seroprevalence of SARS-CoV-2 antibody and SARS-CoV-2 infection rate among HCWs is therefore crucial. This study was carried out in four health facilities in Lagos Nigeria to determine the prevalence of IgG antibodies (seroprevalence) and SARS-CoV-2 active infection rate via a positive rtPCR result, the cross-sectional study was conducted between December 2020 and July 2021. Nasopharyngeal and blood samples were collected from HCWs and screened for SARS-CoV-2 infection using the rtPCR technique and antibody using the Abbott anti-SARS-CoV-2 IgG CMIA assay, respectively. Demographic and occupational exposures data were obtained and analysed using descriptive and inferential statistics, variables significant via inferential statistics were subjected to a multivariate analysis. A total of 413 participants were enrolled, with a mean age in years of 38.4±11.0. The seroprevalence was 30.9% (115/372) while 63/395 (15.9%) were actively infected with the virus. HCWs whose job role had direct contact with patients had a higher percentage of SARS-CoV-2 infection when compared with those not in direct contact, also being a health care worker was significantly associated with getting a positive COVID-19 PCR result. In conclusion the SARS-CoV-2 seroprevalence seen in this study was higher than national serosurvey estimates indicating HCWs are at higher risk of COVID-19 infection when compared to the general public. Vaccination and effective implementation of infection control measures are important to protect HCWs.
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Affiliation(s)
- Fehintola Anthonia Ige
- Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Gregory Aigbe Ohihoin
- Clinical Science Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Kazeem Osuolale
- Monitoring and Evaluation Unit, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | | | - Ngozi Onyia
- Paelon Memorial Medical Center, Victoria Island, Lagos, Nigeria
| | | | - Azuka Patrick Okwuraiwe
- Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Omoladun Odediran
- Body Soul and Spirit Project, Department of Community Health and Primary Care College of Medicine, University of Lagos, Lagos, Nigeria
| | - Gideon Liboro
- Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Maureen Aniedobe
- Clinical Diagnostic Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | | | - Stephanie Ogechi Nwaiwu
- Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Ibukun Ruth Akande
- Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Rosemary Ajuma Audu
- Center for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Babatunde Lawal Salako
- Clinical Science Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
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Mansuy JM, Kenfack MT, Burel S, Pollani C, Bidzogo Lebobo M, Ekaé CO, Berry A, Izopet J. High SARS-CoV-2 IgG seroprevalence among pregnant Cameroun women 14 months after the beginning of the pandemic. Public Health 2023; 222:e12-e13. [PMID: 36270828 PMCID: PMC9485418 DOI: 10.1016/j.puhe.2022.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022]
Affiliation(s)
- J-M Mansuy
- Virology Department, Centre Hospitalier Universitaire (CHU) de Toulouse, 31059 Toulouse, France.
| | - M T Kenfack
- Health Care Center of the CASS, Yaoundé, Cameroon
| | - S Burel
- Virology Department, Centre Hospitalier Universitaire (CHU) de Toulouse, 31059 Toulouse, France
| | - C Pollani
- Virology Department, Centre Hospitalier Universitaire (CHU) de Toulouse, 31059 Toulouse, France
| | | | - C O Ekaé
- Health Care Center of the CASS, Yaoundé, Cameroon
| | - A Berry
- Parasitology - Mycology Department Centre Hospitalier Universitaire (CHU) de Toulouse, 31059 Toulouse, France; INSERM UMR1291 - CNRS UMR5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), 31300 Toulouse, France
| | - J Izopet
- Virology Department, Centre Hospitalier Universitaire (CHU) de Toulouse, 31059 Toulouse, France; INSERM UMR1291 - CNRS UMR5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), 31300 Toulouse, France
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Krebs AS, Liu HF, Zhou Y, Rey JS, Levintov L, Shen J, Howe A, Perilla JR, Bartesaghi A, Zhang P. Molecular architecture and conservation of an immature human endogenous retrovirus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544027. [PMID: 37333227 PMCID: PMC10274761 DOI: 10.1101/2023.06.07.544027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
A significant part of the human genome consists of endogenous retroviruses sequences. Human endogenous retrovirus K (HERV-K) is the most recently acquired endogenous retrovirus, is activated and expressed in many cancers and amyotrophic lateral sclerosis and possibly contributes to the aging process. To understand the molecular architecture of endogenous retroviruses, we determined the structure of immature HERV-K from native virus-like particles (VLPs) using cryo-electron tomography and subtomogram averaging (cryoET STA). The HERV-K VLPs show a greater distance between the viral membrane and immature capsid lattice, correlating with the presence of additional peptides, SP1 and p15, between the capsid (CA) and matrix (MA) proteins compared to the other retroviruses. The resulting cryoET STA map of the immature HERV-K capsid at 3.2 Å resolution shows a hexamer unit oligomerized through a 6-helix bundle which is further stabilized by a small molecule in the same way as the IP6 in immature HIV-1 capsid. The HERV-K immature CA hexamer assembles into the immature lattice via highly conserved dimmer and trimer interfaces, whose interactions were further detailed through all-atom molecular dynamics simulations and supported by mutational studies. A large conformational change mediated by the flexible linker between the N-terminal and the C-terminal domains of CA occurs between the immature and the mature HERV-K capsid protein, analogous to HIV-1. Comparison between HERV-K and other retroviral immature capsid structures reveals a highly conserved mechanism for the assembly and maturation of retroviruses across genera and evolutionary time.
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Affiliation(s)
- Anna-Sophia Krebs
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Hsuan-Fu Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ye Zhou
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Juan S. Rey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Lev Levintov
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Juan Shen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Andrew Howe
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Juan R. Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Alberto Bartesaghi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Computer Science, Duke University, Durham, NC 27708, USA
- Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK
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Chechet GD, Kwaga JKP, Yahaya J, Noyes H, MacLeod A, Adamson WE. SARS-CoV-2 seroprevalence at urban and rural sites in Kaduna State, Nigeria, during October/November 2021, immediately prior to detection of the Omicron variant. Int J Epidemiol 2022; 51:1361-1370. [PMID: 35771662 PMCID: PMC9278217 DOI: 10.1093/ije/dyac141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/16/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Nigeria is Africa's most populated country. By November 2021 it had experienced three waves of SARS-CoV-2 infection. Peer-reviewed seroprevalence data assessing the proportion of the Nigerian population that have been infected were extremely limited. METHODS We conducted a serosurvey in one urban site (n = 400) and one rural site (n = 402) in Kaduna State, Nigeria between 11 October 2021 and 8 November 2021. Z-tests were used to compare seroprevalence across age groups, locations and sexes. T tests were used to determine whether age or household size are associated with seropositivity. Associations between seropositivity and recent history of common Covid-19 symptoms were tested using logistic regression. RESULTS SARS-CoV-2 antibodies were detected in 42.5% an 53.5% of participants at the urban and rural sites, respectively The overall age- and sex- stratified seroprevalence was 43.7% (42.2% for unvaccinated individuals). The data indicate an infection rate in Kaduna State ≥359-fold the rate derived from polymerase chain reaction-confirmed cases. In the urban site, seroprevalence among females and participants aged <20 was lower than other groups. Reporting loss of sense of taste and/or smell was strongly associated with seropositive status. Associations with seropositivity were also found for the reporting of dry cough, fever, headache, nausea and sore throat. CONCLUSIONS This study provides baseline SARS-CoV-2 seroprevalence in Kaduna State, Nigeria, immediately prior to the spread of the Omicron variant. It indicates that in October/November 2021, approximately 56% of the population did not have detectable antibodies, and population subgroups with particularly low seroprevalence remain. It highlights limitations in using PCR-confirmed cases to estimate infection rates. The data will inform public health strategies in Nigeria and other sub-Saharan African countries with limited SARS-CoV-2 seroprevalence data.
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Affiliation(s)
- Gloria D Chechet
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
- Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria
| | - Jacob K P Kwaga
- Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, Ahmadu Bello University, Zaria, Nigeria
| | - Joseph Yahaya
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
- Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria
| | - Harry Noyes
- Centre for Genomic Research, University of Liverpool, Liverpool, UK
| | - Annette MacLeod
- Institute of Biodiversity, Life Sciences, and Animal Health, University of Glasgow, Glasgow, UK
| | - Walt E Adamson
- Institute of Biodiversity, Life Sciences, and Animal Health, University of Glasgow, Glasgow, UK
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Alber D, Haidara FC, Luoma J, Adubra L, Ashorn P, Ashorn U, Badji H, Cloutman-Green E, Diallo F, Ihamuotila R, Klein N, Martell O, Onwuchekwa UU, Samaké O, Sow SO, Traore A, Wilson K, Ducker C, Fan YM. SARS-CoV-2 infection and antibody seroprevalence in routine surveillance patients, healthcare workers and general population in Kita region, Mali: an observational study 2020-2021. BMJ Open 2022; 12:e060367. [PMID: 35710236 PMCID: PMC9207578 DOI: 10.1136/bmjopen-2021-060367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVE To estimate the degree of SARS-CoV-2 transmission among healthcare workers (HCWs) and general population in Kita region of Mali. DESIGN Routine surveillance in 12 health facilities, HCWs serosurvey in five health facilities and community serosurvey in 16 villages in or near Kita town, Mali. SETTING Kita region, western Mali; local health centres around the central (regional) referral health centre. PARTICIPANTS Patients in routine surveillance, HCWs in local health centres and community members of all ages in populations associated with study health centres. MAIN OUTCOME MEASURES Seropositivity of ELISA test detecting SARS-CoV-2-specific total antibodies and real-time RT-PCR confirmed SARS-CoV-2 infection. RESULTS From 2392 routine surveillance samples, 68 (2.8%, 95% CI: 2.2% to 3.6%) tested positive for SARS-CoV-2 by RT-PCR. The monthly positivity rate was 0% in June-August 2020 and gradually increased to 6% by December 2020 and 6.2% by January 2021, then declined to 5.5%, 3.3%, 3.6% and 0.8% in February, March, April and May 2021, respectively. From 397 serum samples collected from 113 HCWs, 175 (44.1%, 95% CI: 39.1% to 49.1%) were positive for SARS-CoV-2 antibodies. The monthly seroprevalence was around 10% from September to November 2020 and increased to over 40% from December 2020 to May 2021. For community serosurvey in December 2020, overall seroprevalence of SARS-CoV-2 antibodies was 27.7%. The highest age-stratified seroprevalence was observed in participants aged 60-69 years (45.5%, 95% CI: 32.3% to 58.6%). The lowest was in children aged 0-9 years (14.0%, 95% CI: 7.4% to 20.6%). CONCLUSIONS SARS-CoV-2 in rural Mali is much more widespread than assumed by national testing data and particularly in the older population and frontline HCWs. The observation is contrary to the widely expressed view, based on limited data, that COVID-19 infection rates were lower in 2020-2021 in West Africa than in other settings.
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Affiliation(s)
- Dagmar Alber
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | - Juho Luoma
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Laura Adubra
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Per Ashorn
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland
| | - Ulla Ashorn
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Henry Badji
- Center for Vaccine Development-Mali, Bamako, Mali
| | - Elaine Cloutman-Green
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | - Rikhard Ihamuotila
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Nigel Klein
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | | | - Oumar Samaké
- Center for Vaccine Development-Mali, Bamako, Mali
| | - Samba O Sow
- Center for Vaccine Development-Mali, Bamako, Mali
| | - Awa Traore
- Center for Vaccine Development-Mali, Bamako, Mali
| | - Kevin Wilson
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Yue-Mei Fan
- Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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