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Namuwulya P, Ashraf S, Niebel M, Ssekagiri A, Tushabe P, Kakooza P, Tong L, Bukenya H, Jerome H, Davis C, Birungi M, Turyahabwe I, Mugaga A, Eliku JP, Francis A, Nakabazzi L, Nsubuga F, Katushabe E, Kisakye A, Ampeire I, Nanteza A, Kaleebu P, Bakamutumaho B, Nsamba P, Kazibwe A, da Silva Filipe A, Tweyongyere R, Bwogi J, Thomson EC. Viruses associated with measles-like illnesses in Uganda. J Infect 2024; 88:106148. [PMID: 38588959 PMCID: PMC11060986 DOI: 10.1016/j.jinf.2024.106148] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/10/2024]
Abstract
OBJECTIVES In this study, we investigated the causes of measles-like illnesses (MLI) in the Uganda national surveillance program in order to inform diagnostic assay selection and vaccination strategies. METHODS We used metagenomic next-generation sequencing (M-NGS) on the Illumina platform to identify viruses associated with MLI (defined as fever and rash in the presence of either cough, coryza or conjunctivitis) in patient samples that had tested IgM negative for measles between 2010 and 2019. RESULTS Viral genomes were identified in 87/271 (32%) of samples, of which 44/271 (16%) contained 12 known viral pathogens. Expected viruses included rubella, human parvovirus B19, Epstein Barr virus, human herpesvirus 6B, human cytomegalovirus, varicella zoster virus and measles virus (detected within the seronegative window-period of infection) and the blood-borne hepatitis B virus. We also detected Saffold virus, human parvovirus type 4, the human adenovirus C2 and vaccine-associated poliovirus type 1. CONCLUSIONS The study highlights the presence of undiagnosed viruses causing MLI in Uganda, including vaccine-preventable illnesses. NGS can be used to monitor common viral infections at a population level, especially in regions where such infections are prevalent, including low and middle income countries to guide vaccination policy and optimize diagnostic assays.
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Affiliation(s)
| | - Shirin Ashraf
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Marc Niebel
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | | | | | | | - Lily Tong
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Henry Bukenya
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - Hanna Jerome
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Chris Davis
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Molly Birungi
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | - Arnold Mugaga
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | - Aine Francis
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | | | | | | | | | - Ann Nanteza
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | | | - Peninah Nsamba
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Anne Kazibwe
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | - Robert Tweyongyere
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | - Emma C Thomson
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK; London School of Hygiene and Tropical Medicine (LSHTM), London, UK.
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Cummings MJ, Bakamutumaho B, Tomoiaga AS, Owor N, Jain K, Price A, Kayiwa J, Namulondo J, Byaruhanga T, Muwanga M, Nsereko C, Nayiga I, Kyebambe S, Sameroff S, Che X, Lutwama JJ, Lipkin WI, O’Donnell MR. A Transcriptomic Classifier Model Identifies High-Risk Endotypes in a Prospective Study of Sepsis in Uganda. Crit Care Med 2024; 52:475-482. [PMID: 37548511 PMCID: PMC10847381 DOI: 10.1097/ccm.0000000000006023] [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: 08/08/2023]
Abstract
OBJECTIVES In high-income countries (HICs), sepsis endotypes defined by distinct pathobiological mechanisms, mortality risks, and responses to corticosteroid treatment have been identified using blood transcriptomics. The generalizability of these endotypes to low-income and middle-income countries (LMICs), where the global sepsis burden is concentrated, is unknown. We sought to determine the prevalence, prognostic relevance, and immunopathological features of HIC-derived transcriptomic sepsis endotypes in sub-Saharan Africa. DESIGN Prospective cohort study. SETTING Public referral hospital in Uganda. PATIENTS Adults ( n = 128) hospitalized with suspected sepsis. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Using whole-blood RNA sequencing data, we applied 19-gene and 7-gene classifiers derived and validated in HICs (SepstratifieR) to assign patients to one of three sepsis response signatures (SRS). The 19-gene classifier assigned 30 (23.4%), 92 (71.9%), and 6 (4.7%) patients to SRS-1, SRS-2, and SRS-3, respectively, the latter of which is designed to capture individuals transcriptionally closest to health. SRS-1 was defined biologically by proinflammatory innate immune activation and suppressed natural killer-cell, T-cell, and B-cell immunity, whereas SRS-2 was characterized by dampened innate immune activation, preserved lymphocyte immunity, and suppressed transcriptional responses to corticosteroids. Patients assigned to SRS-1 were predominantly (80.0% [24/30]) persons living with HIV with advanced immunosuppression and frequent tuberculosis. Mortality at 30-days differed significantly by endotype and was highest (48.1%) in SRS-1. Agreement between 19-gene and 7-gene SRS assignments was poor (Cohen's kappa 0.11). Patient stratification was suboptimal using the 7-gene classifier with 15.1% (8/53) of individuals assigned to SRS-3 deceased at 30-days. CONCLUSIONS Sepsis endotypes derived in HICs share biological and clinical features with those identified in sub-Saharan Africa, with major differences in host-pathogen profiles. Our findings highlight the importance of context-specific sepsis endotyping, the generalizability of conserved biological signatures of critical illness across disparate settings, and opportunities to develop more pathobiologically informed sepsis treatment strategies in LMICs.
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Affiliation(s)
- Matthew J. Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Barnabas Bakamutumaho
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
- Immunizable Diseases Unit, Uganda Virus Research Institute, Entebbe, Uganda
| | - Alin S. Tomoiaga
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Accounting, Business Analytics, Computer Information Systems, and Law, Manhattan College, New York, USA
| | - Nicholas Owor
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Adam Price
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - John Kayiwa
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Joyce Namulondo
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Timothy Byaruhanga
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Moses Muwanga
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | | | - Irene Nayiga
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | - Stephen Kyebambe
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Max R. O’Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
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3
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Cummings MJ, Bakamutumaho B, Lutwama JJ, Owor N, Che X, Astorkia M, Postler TS, Kayiwa J, Kiconco J, Muwanga M, Nsereko C, Rwamutwe E, Nayiga I, Kyebambe S, Haumba M, Bosa HK, Ocom F, Watyaba B, Kikaire B, Tomoiaga AS, Kisaka S, Kiwanuka N, Lipkin WI, O'Donnell MR. COVID-19 immune signatures in Uganda persist in HIV co-infection and diverge by pandemic phase. Nat Commun 2024; 15:1475. [PMID: 38368384 PMCID: PMC10874401 DOI: 10.1038/s41467-024-45204-3] [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: 04/25/2023] [Accepted: 01/17/2024] [Indexed: 02/19/2024] Open
Abstract
Little is known about the pathobiology of SARS-CoV-2 infection in sub-Saharan Africa, where severe COVID-19 fatality rates are among the highest in the world and the immunological landscape is unique. In a prospective cohort study of 306 adults encompassing the entire clinical spectrum of SARS-CoV-2 infection in Uganda, we profile the peripheral blood proteome and transcriptome to characterize the immunopathology of COVID-19 across multiple phases of the pandemic. Beyond the prognostic importance of myeloid cell-driven immune activation and lymphopenia, we show that multifaceted impairment of host protein synthesis and redox imbalance define core biological signatures of severe COVID-19, with central roles for IL-7, IL-15, and lymphotoxin-α in COVID-19 respiratory failure. While prognostic signatures are generally consistent in SARS-CoV-2/HIV-coinfection, type I interferon responses uniquely scale with COVID-19 severity in persons living with HIV. Throughout the pandemic, COVID-19 severity peaked during phases dominated by A.23/A.23.1 and Delta B.1.617.2/AY variants. Independent of clinical severity, Delta phase COVID-19 is distinguished by exaggerated pro-inflammatory myeloid cell and inflammasome activation, NK and CD8+ T cell depletion, and impaired host protein synthesis. Combining these analyses with a contemporary Ugandan cohort of adults hospitalized with influenza and other severe acute respiratory infections, we show that activation of epidermal and platelet-derived growth factor pathways are distinct features of COVID-19, deepening translational understanding of mechanisms potentially underlying SARS-CoV-2-associated pulmonary fibrosis. Collectively, our findings provide biological rationale for use of broad and targeted immunotherapies for severe COVID-19 in sub-Saharan Africa, illustrate the relevance of local viral and host factors to SARS-CoV-2 immunopathology, and highlight underemphasized yet therapeutically exploitable immune pathways driving COVID-19 severity.
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Affiliation(s)
- Matthew J Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA.
| | - Barnabas Bakamutumaho
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Julius J Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Nicholas Owor
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Maider Astorkia
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Thomas S Postler
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - John Kayiwa
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Jocelyn Kiconco
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | | | | | | | - Irene Nayiga
- Entebbe Regional Referral Hospital, Entebbe, Uganda
| | | | - Mercy Haumba
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Henry Kyobe Bosa
- Uganda Peoples' Defence Forces, Kampala, Uganda
- Ministry of Health, Kampala, Uganda
| | | | - Benjamin Watyaba
- European and Developing Countries Clinical Trials Partnership-Eastern Africa Consortium for Clinical Research, Uganda Virus Research Institute, Entebbe, Uganda
| | - Bernard Kikaire
- European and Developing Countries Clinical Trials Partnership-Eastern Africa Consortium for Clinical Research, Uganda Virus Research Institute, Entebbe, Uganda
- Department of Pediatrics, Makerere University College of Health Sciences, Kampala, Uganda
| | - Alin S Tomoiaga
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Accounting, Business Analytics, Computer Information Systems, and Law, Manhattan College, New York, NY, USA
| | - Stevens Kisaka
- Department of Epidemiology and Biostatistics, Makerere University School of Public Health, Kampala, Uganda
- Institute of Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | - Noah Kiwanuka
- Department of Epidemiology and Biostatistics, Makerere University School of Public Health, Kampala, Uganda
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Max R O'Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
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4
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Kayiwa JT, Nassuna C, Mulei S, Kiggundu G, Nakaseegu J, Nabbuto M, Amwine E, Nakamoga B, Nankinga S, Atuhaire P, Nabiryo P, Alunzi P, Mbaziira T, Isabirye P, Ayuro N, Owor N, Kiconco J, Bakamutumaho B, Middlebrook EA, Kaleebu P, Lutwama JJ, Bartlow AW. Integration of SARS-CoV-2 testing and genomic sequencing into influenza sentinel surveillance in Uganda, January to December 2022. Microbiol Spectr 2023; 11:e0132823. [PMID: 37811997 PMCID: PMC10715035 DOI: 10.1128/spectrum.01328-23] [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: 03/27/2023] [Accepted: 08/19/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE Respiratory pathogens cause high rates of morbidity and mortality globally and have high pandemic potential. During the SARS-CoV-2 pandemic, influenza surveillance was significantly interrupted because of resources being diverted to SARS-CoV-2 testing and sequencing. Based on recommendations from the World Health Organization, the Uganda Virus Research Institute, National Influenza Center laboratory integrated SARS-CoV-2 testing and genomic sequencing into the influenza surveillance program. We describe the results of influenza and SARS-CoV-2 testing of samples collected from 16 sentinel surveillance sites located throughout Uganda as well as SARS-CoV-2 testing and sequencing in other health centers. The surveillance system showed that both SARS-CoV-2 and influenza can be monitored in communities at the national level. The integration of SARS-CoV-2 detection and genomic surveillance into the influenza surveillance program will help facilitate the timely release of SARS-CoV-2 information for COVID-19 pandemic mitigation and provide important information regarding the persistent threat of influenza.
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Affiliation(s)
- John T. Kayiwa
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Charity Nassuna
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Sophia Mulei
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Gladys Kiggundu
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Joweria Nakaseegu
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Maria Nabbuto
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Esther Amwine
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Bridget Nakamoga
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Sarah Nankinga
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Phiona Atuhaire
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Pheobe Nabiryo
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Pixy Alunzi
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Tony Mbaziira
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Paul Isabirye
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Noel Ayuro
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Nicholas Owor
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Jocelyn Kiconco
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Barnabas Bakamutumaho
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene & Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging and Re-emerging Viral Diseases, Uganda Virus Research Institute, Entebbe, Uganda
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Tushabe P, Bakamutumaho B, Eliku JP, Birungi M, Aine F, Namuwulya P, Bukenya H, Ampeire I, Kisakye A, Byabamazima CR, Bwogi J. Rubella virus genotype 2B endemicity and related utility of serum-based molecular characterization in Uganda. BMC Res Notes 2023; 16:218. [PMID: 37710238 PMCID: PMC10503080 DOI: 10.1186/s13104-023-06499-5] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/04/2023] [Indexed: 09/16/2023] Open
Abstract
There are 13 globally recognized rubella virus genotypes of which only 2 (1E and 2B) have been detected recently. The largest percentage of all reported rubella virus sequences come from China and Japan with Africa reporting limited data. In a bid to address the lack of rubella genotype data in Uganda and the World Health Organization Africa region, we sought to characterize rubella viruses retrospectively using sera collected from suspected measles patients that turned out rubella IgM positive.Seven sequences belonging to genotype 2B sub-lineage 2B-L2c were obtained. These sequences clustered with other genotype 2B sequences previously reported from Uganda. None of the other genotypes (1E and 1G) reported from Uganda in the earlier years were detected. In addition, none of the sequences were obtained after the introduction of the measles-rubella containing vaccine. The above highlight the need for continuous rubella virological surveillance to confirm interruption of endemic rubella genotype circulation.
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Affiliation(s)
- Phionah Tushabe
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda.
| | | | - James Peter Eliku
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
| | - Molly Birungi
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
| | - Francis Aine
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
| | - Prossy Namuwulya
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
| | - Henry Bukenya
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
| | - Immaculate Ampeire
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
- Ministry of Health Uganda, P.O. Box 7272, Kampala, Uganda
| | - Annet Kisakye
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
- World Health Organization, Uganda Country Office, P.O. Box 24578, Kampala, Uganda
| | - Charles R Byabamazima
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
- WHO Inter-Country Support Team Office for Eastern and Southern Africa (IST/ESA), Harare, Zimbabwe
| | - Josephine Bwogi
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
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Nanteza MB, Tushabe P, Bukenya H, Namuwulya P, Kabaliisa T, Birungi M, Tibanagwa M, Ampeire I, Kakooza P, Katushabe E, Bwogi J, Bakamutumaho B, Nanyunja M, Byabamazima CR. The road to a polio-free Uganda; contribution of the Expanded Program on Immunization Laboratory (EPI-LAB) at Uganda Virus Research Institute. Afr Health Sci 2023; 23:186-196. [PMID: 38357183 PMCID: PMC10862580 DOI: 10.4314/ahs.v23i3.23] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Background The control of poliomyelitis in Uganda dates back as far as 1950 and acute flaccid paralysis (AFP) surveillance has since been used as a criterion for identifying wild polioviruses. Poliovirus isolation was initially pursued through collaborative research however, in 1993, the Expanded Program on Immunization Laboratory (EPI-LAB) was established as a member of the Global Poliovirus Laboratory Network (GPLN) and spearheaded this activity at Uganda Virus Research Institute. Objectives The aim of this report is to document the progress and impact of the EPI-LAB on poliovirus eradication in Uganda. Methods Poliovirus detection and identification were achieved fundamentally through tissue culture and intra-typic differentiation of the poliovirus based on the real-time reverse transcriptase polymerase chain reaction (rRT PCR). The data obtained was entered into the national AFP database and analysed using EpiInfoTM statistical software. Results Quantitative and qualitative detection of wild and Sabin polioviruses corresponded with the polio campaigns. The WHO target indicators for AFP surveillance were achieved essentially throughout the study period. Conclusion Virological tracking coupled with attaining standard AFP surveillance indicators has been pivotal in achieving and maintaining the national wild polio-free status. Laboratory surveillance remains key in informing the certification process of polio eradication.
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Affiliation(s)
- Mary B Nanteza
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Phionah Tushabe
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Henry Bukenya
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Prossy Namuwulya
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Theopista Kabaliisa
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Molly Birungi
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Mayi Tibanagwa
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Immaculate Ampeire
- Ministry of Health, Government of Uganda, Plot 6, Lourdel Road, Nakasero P. O. Box 7272, Kampala, Uganda
| | - Proscovia Kakooza
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Edson Katushabe
- World Health Organization Office, Plot 60 Prince Charles Avenue, Kololo, Kampala
| | - Josephine Bwogi
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Barnabas Bakamutumaho
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Miriam Nanyunja
- World Health Organization AFRO, East and Southern Africa (ESA), Nairobi, 45335 Nairobi, Kenya
| | - Charles R Byabamazima
- World Health Organization AFRO, East and Southern Africa (ESA), Harare, 82-86 Enterprise Road, Highlands, P. O. Box BE 773, Belvedere, Harare, Zimbabwe
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7
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Nanteza MB, Bakamutumaho B, Tushabe P, Namuwulya P, Birungi M, Dhatemwa R, Eliku JP, Tibanagwa M, Kakooza P, Bukenya H, Bwogi J, Byabamazima CR. Sabin polio virus protein 1 (VP1) evolution in patients with acute flaccid paralysis from 2010 to 2016 in Uganda. Virol J 2023; 20:172. [PMID: 37533043 PMCID: PMC10399017 DOI: 10.1186/s12985-023-02143-7] [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: 10/12/2022] [Accepted: 07/26/2023] [Indexed: 08/04/2023] Open
Abstract
Acute flaccid paralysis (AFP) is a rare side effect of the oral polio vaccine but can be associated with outbreaks and permanent disability in patients harboring circulating vaccine-derived polioviruses (cVDPVs). With the advancement of polio abolition in a glimpse, cVDPVs are causing outbreaks and slowing the polio eradication process. The polio virus protein 1 (VP1) contains the binding site that is key for virus transmission. Understanding the evolution of VP1 among AFP patients could yield more insight into the early events of cVDPVs. Polioviruses were identified from stool specimens of AFP patients using cell culture; and confirmed by the real time RT PCR intra-typic differentiation and vaccine-derived poliovirus assays. Seventy-nine (79) Sabin-like poliovirus 1 (SL1) and 86 Sabin-like poliovirus 3 (SL3) were sequenced. The VP1 amino acid substitutions T106A in Sabin poliovirus 1 and A54V in Sabin poliovirus 3 were common among the AFP patients as has been found in previous studies. Other substitutions that were associated with AFP were: T290A and A54T in SL1 and SL3 respectively. Nucleotide mutations that were common among the AFP patients included T402C, C670A, and T816C in SL1, and G22A, C375Y, A472R, and A694T in SL3 polioviruses. Characterizing mutations that are associated with AFP could contribute to efforts pursued to mitigate the risk of vaccine-derived polioviruses and promote development of safer vaccines.
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Affiliation(s)
- Mary Bridget Nanteza
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda.
| | - Barnabas Bakamutumaho
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Phionah Tushabe
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Prossy Namuwulya
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Molly Birungi
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Rajab Dhatemwa
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - James Peter Eliku
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Mayi Tibanagwa
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | | | - Henry Bukenya
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Josephine Bwogi
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Charles Rutebarika Byabamazima
- World Health Organization AFRO, East and Southern Africa (ESA), 82-86 Enterprise Road, Highlands, Belvedere, P. O. Box BE 773, Harare, Zimbabwe
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Affiliation(s)
- Matthew J Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY; Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY.
| | - Barnabas Bakamutumaho
- National Influenza Centre, Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
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Cummings MJ, Bakamutumaho B, Jain K, Price A, Owor N, Kayiwa J, Namulondo J, Byaruhanga T, Muwanga M, Nsereko C, Nayiga I, Kyebambe S, Che X, Sameroff S, Tokarz R, Wong W, Postler TS, Larsen MH, Lipkin WI, Lutwama JJ, O’Donnell MR. Brief Report: Detection of Urine Lipoarabinomannan Is Associated With Proinflammatory Innate Immune Activation, Impaired Host Defense, and Organ Dysfunction in Adults With Severe HIV-Associated Tuberculosis in Uganda. J Acquir Immune Defic Syndr 2023; 93:79-85. [PMID: 36701194 PMCID: PMC10079575 DOI: 10.1097/qai.0000000000003159] [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: 01/27/2023]
Abstract
BACKGROUND The immunopathology of disseminated HIV-associated tuberculosis (HIV/TB), a leading cause of critical illness and death among persons living with HIV in sub-Saharan Africa, is incompletely understood. Reflective of hematogenously disseminated TB, detection of lipoarabinomannan (LAM) in urine is associated with greater bacillary burden and poor outcomes in adults with HIV/TB. METHODS We determined the relationship between detection of urine TB-LAM, organ dysfunction, and host immune responses in a prospective cohort of adults hospitalized with severe HIV/TB in Uganda. Generalized additive models were used to analyze the association between urine TB-LAM grade and concentrations of 14 soluble immune mediators. Whole-blood RNA-sequencing data were used to compare transcriptional profiles between patients with high- vs. low-grade TB-LAM results. RESULTS Among 157 hospitalized persons living with HIV, 40 (25.5%) had positive urine TB-LAM testing. Higher TB-LAM grade was associated with more severe physiologic derangement, organ dysfunction, and shock. Adjusted generalized additive models showed that higher TB-LAM grade was significantly associated with higher concentrations of mediators reflecting proinflammatory innate and T-cell activation and chemotaxis (IL-8, MIF, MIP-1β/CCL4, and sIL-2Ra/sCD25). Transcriptionally, patients with higher TB-LAM grades demonstrated multifaceted impairment of antibacterial defense including reduced expression of genes encoding cytotoxic and autophagy-related proteins and impaired cross-talk between innate and cell-mediated immune effectors. CONCLUSIONS Our findings add to emerging data suggesting pathobiological relationships between LAM, TB dissemination, innate cell activation, and evasion of host immunity in severe HIV/TB. Further translational studies are needed to elucidate the role for immunomodulatory therapies, in addition to optimized anti-TB treatment, in this often critically ill population.
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Affiliation(s)
- Matthew J. Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Barnabas Bakamutumaho
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
- Immunizable Diseases Unit, Uganda Virus Research Institute, Entebbe, Uganda
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Adam Price
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nicholas Owor
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - John Kayiwa
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Joyce Namulondo
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Timothy Byaruhanga
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Moses Muwanga
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | | | - Irene Nayiga
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | - Stephen Kyebambe
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Wai Wong
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Thomas S. Postler
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Michelle H. Larsen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Max R. O’Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
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Tushabe P, Bwogi J, Eliku JP, Aine F, Birungi M, Gaizi J, Nakabazzi L, Kabaliisa T, Turyahabwe I, Namuwulya P, Nanteza MB, Bukenya H, Kanyesigye C, Katushabe E, Ampeire I, Kisakye A, Bakamutumaho B, Byabamazima CR. Environmental surveillance detects circulating vaccine-derived poliovirus type 2 that was undetected by acute flaccid paralysis surveillance in 2021 in Uganda. Arch Virol 2023; 168:140. [PMID: 37059887 PMCID: PMC10104764 DOI: 10.1007/s00705-023-05759-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/14/2023] [Indexed: 04/16/2023]
Abstract
The success of the global polio eradication initiative is threatened by the genetic instability of the oral polio vaccine, which can result in the emergence of pathogenic vaccine-derived polioviruses following prolonged replication in the guts of individuals with primary immune deficiencies or in communities with low vaccination coverage. Through environmental surveillance, circulating vaccine-derived poliovirus type 2 was detected in Uganda in the absence of detection by acute flaccid paralysis (AFP) surveillance. This underscores the sensitivity of environmental surveillance and emphasizes its usefulness in supplementing AFP surveillance for poliovirus infections in the race towards global polio eradication.
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Affiliation(s)
- Phionah Tushabe
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda.
| | - Josephine Bwogi
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - James Peter Eliku
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Francis Aine
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Molly Birungi
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Joseph Gaizi
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Lucy Nakabazzi
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Theopista Kabaliisa
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Irene Turyahabwe
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Prossy Namuwulya
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Mary Bridget Nanteza
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Henry Bukenya
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Edson Katushabe
- World Health Organization, Uganda Country Office, Kampala, Uganda
| | | | - Annet Kisakye
- World Health Organization, Uganda Country Office, Kampala, Uganda
| | - Barnabas Bakamutumaho
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Charles R Byabamazima
- WHO Inter-Country Support Team Office for Eastern and Southern Africa (IST/ESA), Harare, Zimbabwe
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Cummings MJ, Bakamutumaho B, Jain K, Price A, Owor N, Kayiwa J, Namulondo J, Byaruhanga T, Muwanga M, Nsereko C, Sameroff S, Ian Lipkin W, Lutwama JJ, O’Donnell MR. Development of a Novel Clinicomolecular Risk Index to Enhance Mortality Prediction and Immunological Stratification of Adults Hospitalized with Sepsis in Sub-Saharan Africa: A Pilot Study from Uganda. Am J Trop Med Hyg 2023; 108:619-626. [PMID: 36646071 PMCID: PMC9978552 DOI: 10.4269/ajtmh.22-0483] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/16/2022] [Indexed: 01/18/2023] Open
Abstract
The global burden of sepsis is concentrated in sub-Saharan Africa (SSA), where epidemic HIV and unique pathogen diversity challenge the effective management of severe infections. In this context, patient stratification based on biomarkers of a dysregulated host response may identify subgroups more likely to respond to targeted immunomodulatory therapeutics. In a prospective cohort of adults hospitalized with suspected sepsis in Uganda, we applied machine learning methods to develop a prediction model for 30-day mortality that integrates physiology-based risk scores with soluble biomarkers reflective of key domains of sepsis immunopathology. After model evaluation and internal validation, whole-blood RNA sequencing data were analyzed to compare biological pathway enrichment and inferred immune cell profiles between patients assigned differential model-based risks of mortality. Of 260 eligible adults (median age, 32 years; interquartile range, 26-43 years; 59.2% female, 53.9% living with HIV), 62 (23.8%) died by 30 days after hospital discharge. Among 14 biomarkers, soluble tumor necrosis factor receptor 1 (sTNFR1) and angiopoietin 2 (Ang-2) demonstrated the greatest importance for mortality prediction in machine learning models. A clinicomolecular model integrating sTNFR1 and Ang-2 with the Universal Vital Assessment (UVA) risk score optimized 30-day mortality prediction across multiple performance metrics. Patients assigned to the high-risk, UVA-based clinicomolecular subgroup exhibited a transcriptional profile defined by proinflammatory innate immune and necroptotic pathway activation, T-cell exhaustion, and expansion of key immune cell subsets including regulatory and gamma-delta T cells. Clinicomolecular stratification of adults with suspected sepsis in Uganda enhanced 30-day mortality prediction and identified a high-risk subgroup with a therapeutically targetable immunological profile. Further studies are needed to advance pathobiologically informed sepsis management in SSA.
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Affiliation(s)
- Matthew J. Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York
| | - Barnabas Bakamutumaho
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
- Immunizable Diseases Unit, Uganda Virus Research Institute, Entebbe, Uganda
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York
| | - Adam Price
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York
| | - Nicholas Owor
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - John Kayiwa
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Joyce Namulondo
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Timothy Byaruhanga
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Moses Muwanga
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | | | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Max R. O’Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
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12
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Cummings MJ, Bakamutumaho B, Price A, Owor N, Kayiwa J, Namulondo J, Byaruhanga T, Jain K, Postler TS, Muwanga M, Nsereko C, Nayiga I, Kyebambe S, Che X, Sameroff S, Tokarz R, Shah SS, Larsen MH, Lipkin WI, Lutwama JJ, O’Donnell MR. HIV infection drives pro-inflammatory immunothrombotic pathway activation and organ dysfunction among adults with sepsis in Uganda. AIDS 2023; 37:233-245. [PMID: 36355913 PMCID: PMC9780191 DOI: 10.1097/qad.0000000000003410] [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: 11/12/2022]
Abstract
BACKGROUND The global burden of sepsis is concentrated in high HIV-burden settings in sub-Saharan Africa (SSA). Despite this, little is known about the immunopathology of sepsis in persons with HIV (PWH) in the region. We sought to determine the influence of HIV on host immune responses and organ dysfunction among adults hospitalized with suspected sepsis in Uganda. DESIGN Prospective cohort study. METHODS We compared organ dysfunction and 30-day outcome profiles of PWH and those without HIV. We quantified 14 soluble immune mediators, reflective of key domains of sepsis immunopathology, and performed whole-blood RNA-sequencing on samples from a subset of patients. We used propensity score methods to match PWH and those without HIV by demographics, illness duration, and clinical severity, and compared immune mediator concentrations and gene expression profiles across propensity score-matched groups. RESULTS Among 299 patients, 157 (52.5%) were PWH (clinical stage 3 or 4 in 80.3%, 67.7% with known HIV on antiretroviral therapy). PWH presented with more severe physiologic derangement and shock, and had higher 30-day mortality (34.5% vs. 10.2%; P < 0.001). Across propensity score-matched groups, PWH exhibited greater pro-inflammatory immune activation, including upregulation of interleukin (IL)-6, IL-8, IL-15, IL-17 and HMGB1 signaling, with concomitant T-cell exhaustion, prothrombotic pathway activation, and angiopoeitin-2-related endothelial dysfunction. CONCLUSIONS Sepsis-related organ dysfunction and mortality in Uganda disproportionately affect PWH, who demonstrate exaggerated activation of multiple immunothrombotic and metabolic pathways implicated in sepsis pathogenesis. Further investigations are needed to refine understanding of sepsis immunopathology in PWH, particularly mechanisms amenable to therapeutic manipulation.
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Affiliation(s)
- Matthew J. Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Barnabas Bakamutumaho
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
- Immunizable Diseases Unit, Uganda Virus Research Institute, Entebbe, Uganda
| | - Adam Price
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nicholas Owor
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - John Kayiwa
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Joyce Namulondo
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Timothy Byaruhanga
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Thomas S. Postler
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Moses Muwanga
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | | | - Irene Nayiga
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | - Stephen Kyebambe
- Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Shivang S. Shah
- Division of Infectious Diseases, Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Michelle H. Larsen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Max R. O’Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
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Bakamutumaho B, Lutwama JJ, Owor N, Kayiwa J, Kiconco J, Haumba M, Muwanga M, Nsereko C, Rwamutwe E, Nayiga I, Kyebambe S, Kyobe Bosa H, Ocom F, Watyaba B, Kikaire B, Kisaka S, Kiwanuka N, O’Donnell MR, Cummings MJ. Epidemiology, Clinical Characteristics, and Mortality of Hospitalized Patients with Severe COVID-19 in Uganda, 2020-2021. Ann Am Thorac Soc 2022; 19:2100-2103. [PMID: 35727227 PMCID: PMC9743472 DOI: 10.1513/annalsats.202203-244rl] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
| | | | | | - John Kayiwa
- Uganda Virus Research InstituteEntebbe, Uganda
| | | | | | | | | | | | - Irene Nayiga
- Entebbe Regional Referral Hospital,Entebbe, Uganda
| | | | | | | | | | - Bernard Kikaire
- Uganda Virus Research InstituteEntebbe, Uganda
- Makerere University College of Health SciencesKampala, Uganda
| | - Stevens Kisaka
- Makerere University College of Health SciencesKampala, Uganda
- Makerere University School of Public HealthKampala, Uganda
| | - Noah Kiwanuka
- Makerere University School of Public HealthKampala, Uganda
| | - Max R. O’Donnell
- Vagelos College of Physicians and Surgeons, Columbia UniversityNew York, New York
- Center for Infection and Immunity Columbia UniversityNew York, New York
- Mailman School of Public Health, Columbia UniversityNew York, New York
| | - Matthew J. Cummings
- Vagelos College of Physicians and Surgeons, Columbia UniversityNew York, New York
- Center for Infection and Immunity Columbia UniversityNew York, New York
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Cummings MJ, Bakamutumaho B, Price A, Owor N, Kayiwa J, Namulondo J, Byaruhanga T, Muwanga M, Nsereko C, Sameroff S, Tokarz R, Wong W, Shah SS, Larsen MH, Lipkin WI, Lutwama JJ, O’Donnell MR. Multidimensional analysis of the host response reveals prognostic and pathogen-driven immune subtypes among adults with sepsis in Uganda. Crit Care 2022; 26:36. [PMID: 35130948 PMCID: PMC8822787 DOI: 10.1186/s13054-022-03907-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/26/2022] [Indexed: 12/24/2022] Open
Abstract
Background The global burden of sepsis is concentrated in sub-Saharan Africa, where severe infections disproportionately affect young, HIV-infected adults and high-burden pathogens are unique. In this context, poor understanding of sepsis immunopathology represents a crucial barrier to development of locally-effective treatment strategies. We sought to determine inter-individual immunologic heterogeneity among adults hospitalized with sepsis in a sub-Saharan African setting, and characterize associations between immune subtypes, infecting pathogens, and clinical outcomes. Methods Among a prospective observational cohort of 288 adults hospitalized with suspected sepsis in Uganda, we applied machine learning methods to 14 soluble host immune mediators, reflective of key domains of sepsis immunopathology (innate and adaptive immune activation, endothelial dysfunction, fibrinolysis), to identify immune subtypes in randomly-split discovery (N = 201) and internal validation (N = 87) sub-cohorts. In parallel, we applied similar methods to whole-blood RNA-sequencing data from a consecutive subset of patients (N = 128) to identify transcriptional subtypes, which we characterized using biological pathway and immune cell-type deconvolution analyses. Results Unsupervised clustering consistently identified two immune subtypes defined by differential activation of pro-inflammatory innate and adaptive immune pathways, with transcriptional evidence of concomitant CD56(-)/CD16( +) NK-cell expansion, T-cell exhaustion, and oxidative-stress and hypoxia-induced metabolic and cell-cycle reprogramming in the hyperinflammatory subtype. Immune subtypes defined by greater pro-inflammatory immune activation, T-cell exhaustion, and metabolic reprogramming were consistently associated with a high-prevalence of severe and often disseminated HIV-associated tuberculosis, as well as more extensive organ dysfunction, worse functional outcomes, and higher 30-day mortality. Conclusions Our results highlight unique host- and pathogen-driven features of sepsis immunopathology in sub-Saharan Africa, including the importance of severe HIV-associated tuberculosis, and reinforce the need to develop more biologically-informed treatment strategies in the region, particularly those incorporating immunomodulation. Supplementary Information The online version contains supplementary material available at 10.1186/s13054-022-03907-3.
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Bakamutumaho B, Cummings MJ, Owor N, Kayiwa J, Namulondo J, Byaruhanga T, Muwanga M, Nsereko C, Rwamutwe E, Mutonyi R, Achan J, Wanyenze L, Ndazarwe A, Nakanjako R, Natuhwera R, Nsangi A, Bosa HK, Ocom F, O'Donnell MR, Kikaire B, Lutwama JJ. Severe COVID-19 in Uganda across Two Epidemic Phases: A Prospective Cohort Study. Am J Trop Med Hyg 2021; 105:740-744. [PMID: 34370701 PMCID: PMC8592357 DOI: 10.4269/ajtmh.21-0551] [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: 05/17/2021] [Accepted: 06/10/2021] [Indexed: 11/07/2022] Open
Abstract
Among a prospective cohort of children and adults admitted to a national COVID-19 treatment unit in Uganda from March to December 2020, we characterized the epidemiology of and risk factors for severe illness. Across two epidemic phases differentiated by varying levels of community transmission, the proportion of patients admitted with WHO-defined severe COVID-19 ranged from 5% (7/146; 95% CI: 2–10) to 33% (41/124; 95% CI: 25–42); 21% (26/124; 95% CI: 14–29%) of patients admitted during the peak phase received oxygen therapy. Severe COVID-19 was associated with older age, male sex, and longer duration of illness before admission. Coinfection with HIV was not associated with illness severity; malaria or tuberculosis coinfection was rare. No patients died during admission. Despite low mortality, hospital incidence of severe COVID-19 during the first epidemic peak in Uganda was substantial. Improvements in vaccine deployment and acute care capacity, including oxygen delivery, are urgently needed to prevent and manage severe COVID-19 in sub-Saharan Africa.
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Affiliation(s)
| | - Matthew J Cummings
- Vagelos College of Physicians and Surgeons, Columbia University, New York, New York.,Mailman School of Public Health, Columbia University, New York, New York
| | | | - John Kayiwa
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | | | | | | | | | | | | | | | | | | | | | - Annet Nsangi
- Entebbe Regional Referral Hospital, Entebbe, Uganda
| | - Henry Kyobe Bosa
- Uganda Virus Research Institute, Entebbe, Uganda.,Uganda Peoples' Defence Force, Kampala, Uganda
| | | | - Max R O'Donnell
- Vagelos College of Physicians and Surgeons, Columbia University, New York, New York.,Mailman School of Public Health, Columbia University, New York, New York
| | - Bernard Kikaire
- Uganda Virus Research Institute, Entebbe, Uganda.,Makerere University College of Health Sciences, Kampala, Uganda
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Tushabe P, Howard W, Bwogi J, Birungi M, Eliku JP, Kakooza P, Bukenya H, Namuwulya P, Gaizi J, Tibanagwa M, Kabaliisa T, Mulindwa J, Muhanguzi D, Suchard M, Gumede N, Bakamutumaho B. Molecular characterization of non-polio enteroviruses isolated from acute flaccid paralysis patients in Uganda. J Med Virol 2021; 93:4720-4728. [PMID: 33458840 PMCID: PMC9787851 DOI: 10.1002/jmv.26804] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 12/18/2020] [Accepted: 01/14/2021] [Indexed: 12/31/2022]
Abstract
Enteroviruses (EVs) are RNA viruses that can cause many clinical syndromes including acute flaccid paralysis (AFP). Within the global polio laboratory network, EVs are categorized either as polioviruses or non-polio enteroviruses (NPEVs). Specific NPEVs have been described in polio-like residual paralytic events in AFP patients. Retrospective analysis of 112 NPEV isolates from AFP patients was performed and thirty one NPEV types were identified of which 91% were Enterovirus B and 9% were Enterovirus A species. The NPEVs were distributed across the country with most patients in the eastern region (41/89; 46.1%). The highest proportion of patients were children less than 5 years (77/89; 86.5%) and male patients were more common (54/89; 60.7%). Echovirus 11 (11/89; 12.4%) was frequently observed and phylogenetic analysis of these sequences revealed high diversity. Coxsackievirus B5 (CV-B5), CV-B6, E21, and EV-B69 were only seen in patients with residual paralysis. Analyses of the EV-A71 sequence indicated a unique genogroup.
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Affiliation(s)
| | - Wayne Howard
- National Institute for Communicable DiseasesJohannesburgSouth Africa
| | | | - Molly Birungi
- EPI LaboratoryUganda Virus Research InstituteEntebbeUganda
| | - James P. Eliku
- EPI LaboratoryUganda Virus Research InstituteEntebbeUganda
| | | | - Henry Bukenya
- EPI LaboratoryUganda Virus Research InstituteEntebbeUganda
| | | | - Joseph Gaizi
- EPI LaboratoryUganda Virus Research InstituteEntebbeUganda
| | - Mayi Tibanagwa
- EPI LaboratoryUganda Virus Research InstituteEntebbeUganda
| | | | - Julius Mulindwa
- Department of Biochemistry and Sports Sciences, College of Natural SciencesSchool of Biological Sciences, Makerere UniversityKampalaUganda
| | - Dennis Muhanguzi
- Department of Biomolecular Resources and Biolaboratory SciencesCollege of Veterinary Medicine, Animal Resources and Biosecurity, Makerere UniversityKampalaUganda
| | - Melinda Suchard
- National Institute for Communicable DiseasesJohannesburgSouth Africa,University of WitwatersrandJohannesburgSouth Africa
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17
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Cummings MJ, Bakamutumaho B, Owor N, Kayiwa J, Namulondo J, Byaruhanga T, Muwanga M, Nsereko C, Baldwin MR, Lutwama JJ, O'Donnell MR. Stratifying Sepsis in Uganda Using Rapid Pathogen Diagnostics and Clinical Data: A Prospective Cohort Study. Am J Trop Med Hyg 2021; 105:517-524. [PMID: 34125696 DOI: 10.4269/ajtmh.21-0138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/25/2021] [Indexed: 11/07/2022] Open
Abstract
The global burden of sepsis is concentrated in sub-Saharan Africa, where extensive pathogen diversity and limited laboratory capacity challenge targeted antimicrobial management of life-threatening infections. In this context, established and emerging rapid pathogen diagnostics may stratify sepsis patients into subgroups with prognostic and therapeutic relevance. In a prospective cohort of adults (age ≥18 years) hospitalized with suspected sepsis in Uganda, we stratified patients using rapid diagnostics for HIV, tuberculosis (TB), malaria, and influenza, and compared clinical characteristics and 30-day outcomes across these pathogen-driven subgroups. From April 2017 to August 2019, 301 adults were enrolled (median age, 32 years [interquartile range, 26-42 years]; female, n = 178 [59%]). A total of 157 patients (53%) were HIV infected. Sixty-one patients (20%) tested positive for malaria, 52 (17%), for TB (including 49 of 157 [31%] HIV-infected patients), and 17 (6%), for influenza. Co-infection was identified in 33 (11%) patients. The frequency of multi-organ failure, including shock and acute respiratory failure, was greatest among patients with HIV-associated TB. Mortality at 30 days was 19% among patients with malaria, 40% among patients with HIV-associated TB, 32% among HIV-infected patients without microbiological evidence of TB, 6% among patients with influenza, and 11% among patients without a pathogen identified. Despite improvements in anti-retroviral delivery, the burden of sepsis in Uganda remains concentrated among young, HIV-infected adults, with a high incidence of severe HIV-associated TB. In parallel with improvements in acute-care capacity, use of rapid pathogen diagnostics may enhance triage and antimicrobial management during emergency care for sepsis in sub-Saharan Africa, and could be used to enrich study populations when trialing pathogen-specific treatment strategies in the region.
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Affiliation(s)
- Matthew J Cummings
- 1Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Irving Medical Center, New York, New York.,2Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York
| | - Barnabas Bakamutumaho
- 3Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda.,4Immunizable Diseases Unit, Uganda Virus Research Institute, Entebbe, Uganda
| | - Nicholas Owor
- 3Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - John Kayiwa
- 3Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Joyce Namulondo
- 3Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Timothy Byaruhanga
- 3Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Moses Muwanga
- 5Entebbe General Referral Hospital, Ministry of Health, Entebbe, Uganda
| | | | - Matthew R Baldwin
- 1Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Irving Medical Center, New York, New York
| | - Julius J Lutwama
- 3Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Max R O'Donnell
- 1Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Irving Medical Center, New York, New York.,2Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York.,6Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
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18
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Bonaparte SC, Adams L, Bakamutumaho B, Barbosa Costa G, Cleaton JM, Gilbert AT, Osinubi M, Pieracci EG, Recuenco S, Tugumizemu V, Wamala J, Wallace RM. Rabies post-exposure healthcare-seeking behaviors and perceptions: Results from a knowledge, attitudes, and practices survey, Uganda, 2013. PLoS One 2021; 16:e0251702. [PMID: 34077427 PMCID: PMC8171952 DOI: 10.1371/journal.pone.0251702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/29/2020] [Accepted: 05/02/2021] [Indexed: 12/11/2022] Open
Abstract
Background Rabies is a viral disease of animals and people causing fatal encephalomyelitis if left untreated. Although effective pre- and post-exposure vaccines exist, they are not widely available in many endemic countries within Africa. Since many individuals in these countries remain at risk of infection, post-exposure healthcare-seeking behaviors are crucial in preventing infection and warrant examination. Methodology A rabies knowledge, attitudes, and practices survey was conducted at 24 geographically diverse sites in Uganda during 2013 to capture information on knowledge concerning the disease, response to potential exposure events, and vaccination practices. Characteristics of the surveyed population and of the canine-bite victim sub-population were described. Post-exposure healthcare-seeking behaviors of canine-bite victims were examined and compared to the related healthcare-seeking attitudes of non-bite victim respondents. Wealth scores were calculated for each household, rabies knowledge was scored for each non-bitten survey respondent, and rabies exposure risk was scored for each bite victim. Logistic regression was used to determine the independent associations between different variables and healthcare-seeking behaviors among canine-bite victims as well as attitudes of non-bitten study respondents. Results A total of 798 households were interviewed, capturing 100 canine-bite victims and a bite incidence of 2.3 per 100 person-years. Over half of bite victims actively sought medical treatment (56%), though very few received rabies post-exposure prophylaxis (3%). Bite victims who did not know or report the closest location where PEP could be received were less likely to seek medical care (p = 0.05). Respondents who did not report having been bitten by a dog with higher knowledge scores were more likely to respond that they would both seek medical care (p = 0.00) and receive PEP (p = 0.06) after a potential rabies exposure event. Conclusions There was varying discordance between what respondents who did not report having been bitten by a dog said they would do if bitten by a dog when compared to the behaviors exhibited by canine-bite victims captured in the KAP survey. Bite victims seldom elected to wash their wound or receive PEP. Having lower rabies knowledge was a barrier to theoretically seeking care and receiving PEP among not bitten respondents, indicating a need for effective and robust educational programs in the country.
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Affiliation(s)
- Sarah C. Bonaparte
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center of Emerging and Zoonotic Infectious Diseases, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- ORISE Fellow, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
| | - Laura Adams
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | | | - Galileu Barbosa Costa
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center of Emerging and Zoonotic Infectious Diseases, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- ORISE Fellow, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Julie M. Cleaton
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center of Emerging and Zoonotic Infectious Diseases, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- ORISE Fellow, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Amy T. Gilbert
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center of Emerging and Zoonotic Infectious Diseases, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Modupe Osinubi
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center of Emerging and Zoonotic Infectious Diseases, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Emily G. Pieracci
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center of Emerging and Zoonotic Infectious Diseases, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Sergio Recuenco
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center of Emerging and Zoonotic Infectious Diseases, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Victor Tugumizemu
- Veterinary Public Health Division, Ministry of Health, Kampala, Uganda
| | | | - Ryan M. Wallace
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center of Emerging and Zoonotic Infectious Diseases, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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19
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Ndumu DB, Bakamutumaho B, Miller E, Nakayima J, Downing R, Balinandi S, Monje F, Tumusiime D, Nanfuka M, Meunier N, Arinaitwe E, Rutebarika C, Kidega E, Kyondo J, Ademun R, Njenga KM, Veas F, Gonzalez JP. Serological evidence of Rift Valley fever virus infection among domestic ruminant herds in Uganda. BMC Vet Res 2021; 17:157. [PMID: 33849526 PMCID: PMC8045185 DOI: 10.1186/s12917-021-02867-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 04/03/2020] [Accepted: 03/31/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Prior to the first recorded outbreak of Rift Valley fever (RVF) in Uganda, in March 2016, earlier studies done until the 1970's indicated the presence of the RVF virus (RVFV) in the country, without any recorded outbreaks in either man or animals. While severe outbreaks of RVF occurred in the neighboring countries, none were reported in Uganda despite forecasts that placed some parts of Uganda at similar risk. The Ministry of Agriculture, Animal Industry and Fisheries (MAAIF) undertook studies to determine the RVF sero-prevalence in risk prone areas. Three datasets from cattle sheep and goats were obtained; one from retrospective samples collected in 2010-2011 from the northern region; the second from the western region in 2013 while the third was from a cross-sectional survey done in 2016 in the south-western region. Laboratory analysis involved the use of the Enzyme Linked Immunosorbent Assays (ELISA). Data were subjected to descriptive statistical analyses, including non-parametric chi-square tests for comparisons between districts and species in the regions. RESULTS During the Yellow Fever outbreak investigation of 2010-2011 in the northern region, a total sero-prevalence of 6.7% was obtained for anti RVFV reacting antibodies (IgG and IgM) among the domestic ruminant population. The 2013 sero-survey in the western region showed a prevalence of 18.6% in cattle and 2.3% in small ruminants. The 2016 sero-survey in the districts of Kabale, Kanungu, Kasese, Kisoro and Rubirizi, in the south-western region, had the respective district RVF sero-prevalence of 16.0, 2.1, 0.8, 15.1and 2.7% among the domestic ruminants combined for this region; bovines exhibited the highest cumulative sero-prevalence of 15.2%, compared to 5.3 and 4.0% respectively for sheep and goats per species for the region. CONCLUSIONS The absence of apparent outbreaks in Uganda, despite neighboring enzootic areas, having minimal restrictions to the exchange of livestock and their products across borders, suggest an unexpected RVF activity in the study areas that needs to be unraveled. Therefore, more in-depth studies are planned to mitigate the risk of an overt RVF outbreak in humans and animals as has occurred in neighboring countries.
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Affiliation(s)
- Deo B. Ndumu
- Department of Animal Health, Ministry of Agriculture, Animal Industry and Fisheries (MAAIF), P. O. Box 513, Entebbe, Uganda
| | - Barnabas Bakamutumaho
- Uganda National Health Research Organization (UNHRO), Uganda Virus Research Institute (UVRI), P. O. Box 49, Entebbe, Uganda
| | | | - Jesca Nakayima
- National Livestock Resources Research Institute (NaLiRRI), Nakyesasa, Uganda
| | - Robert Downing
- Centers for Disease Control and Prevention (CDC) – UVRI, Entebbe, Uganda
| | - Stephen Balinandi
- Centers for Disease Control and Prevention (CDC) – UVRI, Entebbe, Uganda
| | - Fred Monje
- Department of Animal Health, Ministry of Agriculture, Animal Industry and Fisheries (MAAIF), P. O. Box 513, Entebbe, Uganda
| | - Dan Tumusiime
- Department of Animal Health, Ministry of Agriculture, Animal Industry and Fisheries (MAAIF), P. O. Box 513, Entebbe, Uganda
| | - Mary Nanfuka
- Department of Animal Health, Ministry of Agriculture, Animal Industry and Fisheries (MAAIF), P. O. Box 513, Entebbe, Uganda
| | - Natascha Meunier
- Royal Veterinary College, University of London, Royal College Street, London, NW1 0TU UK
| | - Eugene Arinaitwe
- Department of Animal Health, Ministry of Agriculture, Animal Industry and Fisheries (MAAIF), P. O. Box 513, Entebbe, Uganda
| | - Chris Rutebarika
- Department of Animal Health, Ministry of Agriculture, Animal Industry and Fisheries (MAAIF), P. O. Box 513, Entebbe, Uganda
| | - Eugene Kidega
- Department of Animal Health, Ministry of Agriculture, Animal Industry and Fisheries (MAAIF), P. O. Box 513, Entebbe, Uganda
| | - Jackson Kyondo
- Uganda National Health Research Organization (UNHRO), Uganda Virus Research Institute (UVRI), P. O. Box 49, Entebbe, Uganda
| | - Rose Ademun
- Department of Animal Health, Ministry of Agriculture, Animal Industry and Fisheries (MAAIF), P. O. Box 513, Entebbe, Uganda
| | | | - Francisco Veas
- Molecular Comparative Immuno-Physiopathology Lab (LIPMC), Joint Research Unit-Ministry of Defense (UMR-MD), Faculty of Pharmacy, French Research Institute for Development (IRD), Montpellier University, 34093 Montpellier, France
| | - Jean-Paul Gonzalez
- Metabiota Inc., San Francisco, USA
- Georgetown University, School of Medicine, 3900 Reservoir Rd. NW, Washington, DC, 20007 USA
- Centaurus Biotech LLC., Commonwealth Trading Partners, CTP Inc. Alexandria, Virginia, USA
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20
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Cummings MJ, Tokarz R, Bakamutumaho B, Kayiwa J, Byaruhanga T, Owor N, Namagambo B, Wolf A, Mathema B, Lutwama JJ, Schluger NW, Lipkin WI, O'Donnell MR. Precision Surveillance for Viral Respiratory Pathogens: Virome Capture Sequencing for the Detection and Genomic Characterization of Severe Acute Respiratory Infection in Uganda. Clin Infect Dis 2020; 68:1118-1125. [PMID: 30099510 PMCID: PMC6424078 DOI: 10.1093/cid/ciy656] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 01/04/2018] [Accepted: 08/06/2018] [Indexed: 12/16/2022] Open
Abstract
Background Precision public health is a novel set of methods to target disease prevention and mitigation interventions to high-risk subpopulations. We applied a precision public health strategy to syndromic surveillance for severe acute respiratory infection (SARI) in Uganda by combining spatiotemporal analytics with genomic sequencing to detect and characterize viral respiratory pathogens with epidemic potential. Methods Using a national surveillance network we identified patients with unexplained, influenza-negative SARI from 2010 to 2015. Spatiotemporal analyses were performed retrospectively to identify clusters of unexplained SARI. Within clusters, respiratory viruses were detected and characterized in naso- and oropharyngeal swab samples using a novel oligonucleotide probe capture (VirCapSeq-VERT) and high-throughput sequencing platform. Linkage to conventional epidemiologic strategies further characterized transmission dynamics of identified pathogens. Results Among 2901 unexplained SARI cases, 9 clusters were detected, accounting for 301 (10.4%) cases. Clusters were more likely to occur in urban areas and during biannual rainy seasons. Within detected clusters, we identified an unrecognized outbreak of measles-associated SARI; sequence analysis implicated cocirculation of endemic genotype B3 and genotype D4 likely imported from England. We also detected a likely nosocomial SARI cluster associated with a novel picobirnavirus most closely related to swine and dromedary viruses. Conclusions Using a precision approach to public health surveillance, we detected and characterized the genomics of vaccine-preventable and zoonotic respiratory viruses associated with clusters of severe respiratory infections in Uganda. Future studies are needed to assess the feasibility, scalability, and impact of applying similar approaches during real-time public health surveillance in low-income settings.
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Affiliation(s)
- Matthew J Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York
| | - Rafal Tokarz
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York
| | | | - John Kayiwa
- National Influenza Center, Uganda Virus Research Institute, Entebbe
| | | | - Nicholas Owor
- National Influenza Center, Uganda Virus Research Institute, Entebbe
| | | | - Allison Wolf
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York
| | - Barun Mathema
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York
| | - Julius J Lutwama
- National Influenza Center, Uganda Virus Research Institute, Entebbe
| | - Neil W Schluger
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York.,Department of Epidemiology, Columbia University Mailman School of Public Health, New York.,Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York
| | - W Ian Lipkin
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York
| | - Max R O'Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York.,Department of Epidemiology, Columbia University Mailman School of Public Health, New York
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21
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Tushabe P, Bwogi J, Abernathy E, Birungi M, Eliku JP, Seguya R, Bukenya H, Namuwulya P, Kakooza P, Suppiah S, Kabaliisa T, Tibanagwa M, Ampaire I, Kisakye A, Bakainaga A, Byabamazima CR, Icenogle JP, Bakamutumaho B. Descriptive epidemiology of rubella disease and associated virus strains in Uganda. J Med Virol 2020; 92:279-287. [PMID: 31598987 PMCID: PMC7004003 DOI: 10.1002/jmv.25604] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/02/2019] [Indexed: 11/08/2022]
Abstract
Rubella virus causes a mild disease; however, infection during the first trimester of pregnancy may lead to congenital rubella syndrome (CRS) in over 80% of affected pregnancies. Vaccination is recommended and has been shown to effectively reduce CRS incidence. Uganda plans to introduce routine rubella vaccination in 2019. The World Health Organization recommends assessing the disease burden and obtaining the baseline molecular virological data before vaccine introduction. Sera collected during case-based measles surveillance from January 2005 to July 2018 were tested for rubella immunoglobulin M (IgM) antibodies. Sera from confirmed rubella outbreaks from January 2012 to August 2017 were screened using real-time reverse-transcription polymerase chain reaction (RT-PCR); for positive samples, a region within the E1 glycoprotein coding region was amplified and sequenced. Of the 23 196 suspected measles cases serologically tested in parallel for measles and rubella, 5334 (23%) were rubella IgM-positive of which 2710 (50.8%) cases were females with 2609 (96.3%) below 15 years of age. Rubella IgM-positive cases were distributed throughout the country and the highest number was detected in April, August, and November. Eighteen (18%) of the 100 sera screened were real-time RT-PCR-positive of which eight (44.4%) were successfully sequenced and genotypes 1G and 2B were identified. This study reports on the seroprevalence and molecular epidemiology of rubella. Increased knowledge of former and current rubella viruses circulating in Uganda will enhance efforts to monitor the impact of vaccination as Uganda moves toward control and elimination of rubella and CRS.
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Affiliation(s)
| | | | - Emily Abernathy
- Division of Viral Diseases, National Center for Immunization and Respiratory DiseasesUnited States Centers for Disease Control and PreventionAtlantaGeorgia
| | - Molly Birungi
- EPI LaboratoryUganda Virus Research InstituteEntebbeUganda
| | - James P. Eliku
- EPI LaboratoryUganda Virus Research InstituteEntebbeUganda
| | | | - Henry Bukenya
- EPI LaboratoryUganda Virus Research InstituteEntebbeUganda
| | | | | | - Suganthi Suppiah
- Division of Viral Diseases, National Center for Immunization and Respiratory DiseasesUnited States Centers for Disease Control and PreventionAtlantaGeorgia
| | | | - Mayi Tibanagwa
- EPI LaboratoryUganda Virus Research InstituteEntebbeUganda
| | | | | | | | - Charles R. Byabamazima
- WHO Inter‐Country Support Team Office For Eastern and Southern Africa (IST/ESA)HarareZimbabwe
| | - Joseph P. Icenogle
- Division of Viral Diseases, National Center for Immunization and Respiratory DiseasesUnited States Centers for Disease Control and PreventionAtlantaGeorgia
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22
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Emukule GO, Namagambo B, Owor N, Bakamutumaho B, Kayiwa JT, Namulondo J, Byaruhanga T, Tempia S, Chaves SS, Lutwama JJ. Influenza-associated pneumonia hospitalizations in Uganda, 2013-2016. PLoS One 2019; 14:e0219012. [PMID: 31306466 PMCID: PMC6629074 DOI: 10.1371/journal.pone.0219012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 02/07/2019] [Accepted: 06/13/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Influenza is an important contributor to acute respiratory illness, including pneumonia, and results in substantial morbidity and mortality globally. Understanding the local burden of influenza-associated severe disease can inform decisions on allocation of resources toward influenza control programs. Currently, there is no national influenza vaccination program in Uganda. METHODS In this study, we used data on pneumonia hospitalizations that were collected and reported through the Health Management Information System (HMIS) of the Ministry of Health, Uganda, and the laboratory-confirmed influenza positivity data from severe acute respiratory illness (SARI) surveillance in three districts (Wakiso, Mbarara, and Tororo) to estimate the age-specific incidence of influenza-associated pneumonia hospitalizations from January 2013 through December 2016. RESULTS The overall estimated mean annual rate of pneumonia hospitalizations in the three districts was 371 (95% confidence interval [CI] 323-434) per 100,000 persons, and was highest among children aged <5 years (1,524 [95% CI 1,286-1,849]) compared to persons aged ≥5 years (123 [95% CI 105-144]) per 100,000 persons. The estimated mean annual rate of influenza-associated pneumonia hospitalization was 34 (95% CI 23-48) per 100,000 persons (116 [95% CI 78-165] and 16 [95% CI 6-28] per 100,000 persons among children aged <5 years and those ≥5 years, respectively). Among children aged <5 years, the rate of hospitalized influenza-associated pneumonia was highest among those who were <2 years old (178 [95% CI 109-265] per 100,000 persons). Over the period of analysis, the estimated mean annual number of hospitalized influenza-associated pneumonia cases in the three districts ranged between 672 and 1,436, of which over 70% represent children aged <5 years. CONCLUSIONS The burden of influenza-associated pneumonia hospitalizations was substantial in Uganda, and was highest among young children aged <5 years. Influenza vaccination may be considered, especially for very young children.
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Affiliation(s)
- Gideon O. Emukule
- Centers for Disease Control and Prevention, Kenya Country Office, Nairobi, Kenya
| | - Barbara Namagambo
- Uganda Virus Research Institute, National Influenza Centre (UVRI-NIC), Entebbe, Uganda
| | - Nicholas Owor
- Uganda Virus Research Institute, National Influenza Centre (UVRI-NIC), Entebbe, Uganda
| | - Barnabas Bakamutumaho
- Uganda Virus Research Institute, National Influenza Centre (UVRI-NIC), Entebbe, Uganda
| | - John T. Kayiwa
- Uganda Virus Research Institute, National Influenza Centre (UVRI-NIC), Entebbe, Uganda
| | - Joyce Namulondo
- Uganda Virus Research Institute, National Influenza Centre (UVRI-NIC), Entebbe, Uganda
| | - Timothy Byaruhanga
- Uganda Virus Research Institute, National Influenza Centre (UVRI-NIC), Entebbe, Uganda
| | - Stefano Tempia
- Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Sandra S. Chaves
- Centers for Disease Control and Prevention, Kenya Country Office, Nairobi, Kenya
- Influenza Division, National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Julius J. Lutwama
- Uganda Virus Research Institute, National Influenza Centre (UVRI-NIC), Entebbe, Uganda
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Yang W, Cummings MJ, Bakamutumaho B, Kayiwa J, Owor N, Namagambo B, Byaruhanga T, Lutwama JJ, O'Donnell MR, Shaman J. Dynamics of influenza in tropical Africa: Temperature, humidity, and co-circulating (sub)types. Influenza Other Respir Viruses 2018; 12:446-456. [PMID: 29573157 PMCID: PMC6005592 DOI: 10.1111/irv.12556] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The association of influenza with meteorological variables in tropical climates remains controversial. Here, we investigate the impact of weather conditions on influenza in the tropics and factors that may contribute to this uncertainty. METHODS We computed the monthly viral positive rate for each of the 3 circulating influenza (sub)types (ie, A/H1N1, A/H3N2, and B) among patients presenting with influenza-like illness (ILI) or severe acute respiratory infections (SARI) in 2 Ugandan cities (Entebbe and Kampala). Using this measure as a proxy for influenza activity, we applied regression models to examine the impact of temperature, relative humidity, absolute humidity, and precipitation, as well as interactions among the 3 influenza viruses on the epidemic dynamics of each influenza (sub)type. A full analysis including all 4 weather variables was done for Entebbe during 2007-2015, and a partial analysis including only temperature and precipitation was done for both cities during 2008-2014. RESULTS For Entebbe, the associations with weather variables differed by influenza (sub)type; with adjustment for viral interactions, the models showed that precipitation and temperature were negatively correlated with A/H1N1 activity, but not for A/H3N2 or B. A mutually negative association between A/H3N2 and B activity was identified in both Entebbe and Kampala. CONCLUSION Our findings suggest that key interactions exist among influenza (sub)types at the population level in the tropics and that such interactions can modify the association of influenza activity with weather variables. Studies of the relationship between influenza and weather conditions should therefore determine and account for co-circulating influenza (sub)types.
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Affiliation(s)
- Wan Yang
- Department of Environmental Health SciencesColumbia UniversityNew YorkNYUSA
| | - Matthew J. Cummings
- Division of Pulmonary, Allergy, and Critical Care MedicineColumbia UniversityNew YorkNYUSA
| | | | - John Kayiwa
- National Influenza CenterUganda Virus Research InstituteEntebbeUganda
| | - Nicholas Owor
- National Influenza CenterUganda Virus Research InstituteEntebbeUganda
| | - Barbara Namagambo
- National Influenza CenterUganda Virus Research InstituteEntebbeUganda
| | | | - Julius J. Lutwama
- National Influenza CenterUganda Virus Research InstituteEntebbeUganda
| | - Max R. O'Donnell
- Division of Pulmonary, Allergy, and Critical Care MedicineColumbia UniversityNew YorkNYUSA
- Department of EpidemiologyColumbia UniversityNew YorkNYUSA
| | - Jeffrey Shaman
- Department of Environmental Health SciencesColumbia UniversityNew YorkNYUSA
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24
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Nanteza MB, Bakamutumaho B, Kisakye A, Namuwulya P, Bukenya H, Katushabe E, Bwogi J, Byabamazima CR, Williams R, Gumede N. The detection of 3 ambiguous type 2 vaccine-derived polioviruses (VDPV2s) in Uganda. Virol J 2018; 15:77. [PMID: 29699577 PMCID: PMC5922010 DOI: 10.1186/s12985-018-0990-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 01/18/2018] [Accepted: 04/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Oral Polio Vaccine (OPV or Sabin) is genetically unstable and may mutate to form vaccine-derived polioviruses (VDPVs). METHODS In 2014, two VDPVs type 2 were identified during routine surveillance of acute flaccid paralysis (AFP) cases. Consequently, a retrospective VDPV survey was conducted to ensure that there was no circulating VDPV in the country. All Sabin poliovirus isolates identified in Uganda 6 months before and 6 months after were re-screened; Sabin 1 and 3 polioviruses were re-screened for Sabin 2 and Sabin 2 polioviruses were re-screened for VDPVs type 2. The Poliovirus rRT-PCR ITD/VDPV 4.0 assay and sequencing were used respectively. RESULTS The first two VDPVs type2 were identified in Eastern Uganda and the third was identified during the survey from South-western Uganda. These regions had low OPV coverage and poor AFP surveillance indicators. CONCLUSION The retrospective VDPV survey was a useful strategy to screen for VDPVs more exhaustively. Supplementary surveillance methods need to be encouraged.
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Affiliation(s)
- Mary Bridget Nanteza
- Uganda Virus Research Institute (UVRI), Plot 51 - 59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda.
| | - Barnabas Bakamutumaho
- Uganda Virus Research Institute (UVRI), Plot 51 - 59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Annet Kisakye
- World Health Organization (WHO), Plot 60 Prince Charles Avenue, Kololo, P.O. Box 24578, Kampala, Uganda
| | - Prossy Namuwulya
- Uganda Virus Research Institute (UVRI), Plot 51 - 59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Henry Bukenya
- Uganda Virus Research Institute (UVRI), Plot 51 - 59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Edson Katushabe
- World Health Organization (WHO), Plot 60 Prince Charles Avenue, Kololo, P.O. Box 24578, Kampala, Uganda
| | - Josephine Bwogi
- Uganda Virus Research Institute (UVRI), Plot 51 - 59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | | | - Raffaella Williams
- National Institute for Communicable Diseases (NICD), 1 Modderfontein Road Sandringham Johannesburg. Private Bag x4, Sandringham, 2131, South Africa.,NSW HIV State Reference Laboratory, St Vicent's Hospital, Darlinghurst, NSW, 2010, Australia
| | - Nicksy Gumede
- World Health Organization, Regional Office for Africa, P.O. Box 06, Brazzaville, Republic of Congo
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25
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Yang W, Cummings MJ, Bakamutumaho B, Kayiwa J, Owor N, Namagambo B, Byaruhanga T, Lutwama JJ, O'Donnell MR, Shaman J. Transmission dynamics of influenza in two major cities of Uganda. Epidemics 2018; 24:43-48. [PMID: 29576517 DOI: 10.1016/j.epidem.2018.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 09/18/2017] [Revised: 02/08/2018] [Accepted: 03/13/2018] [Indexed: 11/19/2022] Open
Abstract
In this paper, we report the epidemic characteristics of the three co-circulating influenza viruses (i.e., A/H1N1, A/H3N2, and B) in two tropical African cities-Kampala and Entebbe, Uganda-over an eight-year period (2008-2015). Using wavelet methods, we show that influenza epidemics recurred annually during the study period. In most months, two or more influenza viruses co-circulated at the same time. However, the epidemic timing differed by influenza (sub)type. Influenza A/H3N2 caused epidemics approximately every 2 years in both cities and tended to alternate with A/H1N1 or B. Influenza A/H1N1 and B produced smaller but more frequent epidemics and biennial epidemics of these two viruses tended to be synchronous. In addition, epidemics of A/H3N2 were more synchronized in the two cities (located ca.37 km apart) than that of A/H1N1 or influenza B.
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Affiliation(s)
- Wan Yang
- Department of Environmental Health Sciences, Columbia University, New York, New York, USA.
| | - Matthew J Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University, New York, New York, USA
| | | | - John Kayiwa
- National Influenza Center, Uganda Virus Research Institute, Entebbe, Uganda
| | - Nicholas Owor
- National Influenza Center, Uganda Virus Research Institute, Entebbe, Uganda
| | - Barbara Namagambo
- National Influenza Center, Uganda Virus Research Institute, Entebbe, Uganda
| | - Timothy Byaruhanga
- National Influenza Center, Uganda Virus Research Institute, Entebbe, Uganda
| | - Julius J Lutwama
- National Influenza Center, Uganda Virus Research Institute, Entebbe, Uganda
| | - Max R O'Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University, New York, New York, USA; Department of Epidemiology, Columbia University, New York, New York, USA
| | - Jeffrey Shaman
- Department of Environmental Health Sciences, Columbia University, New York, New York, USA
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26
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Cummings MJ, Bakamutumaho B, Yang W, Wamala JF, Kayiwa J, Owor N, Namagambo B, Byaruhanga T, Wolf A, Lutwama JJ, Shaman J, O'Donnell MR. Emergence, Epidemiology, and Transmission Dynamics of 2009 Pandemic A/H1N1 Influenza in Kampala, Uganda, 2009-2015. Am J Trop Med Hyg 2018; 98:203-206. [PMID: 29141723 DOI: 10.4269/ajtmh.17-0524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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
In sub-Saharan Africa, little is known about the epidemiology of pandemic-prone influenza viruses in urban settings. Using data from a prospective sentinel surveillance network, we characterized the emergence, epidemiology, and transmission dynamics of 2009 pandemic A/H1N1 influenza (H1N1pdm09) in Kampala, Uganda. After virus introduction via international air travel from England in June 2009, we estimated the basic reproductive number in Kampala to be 1.06-1.13, corresponding to attack rates of 12-22%. We subsequently identified 613 cases of influenza in Kampala from 2009 to 2015, of which 191 (31.2%) were infected with H1N1pdm09. Patients infected with H1N1pdm09 were more likely to be older adult (ages 35-64) males with illness onset during rainy season months. Urban settings in sub-Saharan Africa are vulnerable to importation and intense transmission of pandemic-prone influenza viruses. Enhanced surveillance and influenza pandemic preparedness in these settings is needed.
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Affiliation(s)
- Matthew J Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York
| | | | - Wan Yang
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Joseph F Wamala
- South Sudan Country Office, World Health Organization, Juba, South Sudan.,Epidemiology and Surveillance Division, Ministry of Health, Kampala, Uganda
| | - John Kayiwa
- National Influenza Center, Uganda Virus Research Institute, Entebbe, Uganda
| | - Nicholas Owor
- National Influenza Center, Uganda Virus Research Institute, Entebbe, Uganda
| | - Barbara Namagambo
- National Influenza Center, Uganda Virus Research Institute, Entebbe, Uganda
| | - Timothy Byaruhanga
- National Influenza Center, Uganda Virus Research Institute, Entebbe, Uganda
| | - Allison Wolf
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York
| | - Julius J Lutwama
- National Influenza Center, Uganda Virus Research Institute, Entebbe, Uganda
| | - Jeffrey Shaman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York
| | - Max R O'Donnell
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York.,Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York
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27
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Wallace RM, Mehal J, Nakazawa Y, Recuenco S, Bakamutumaho B, Osinubi M, Tugumizemu V, Blanton JD, Gilbert A, Wamala J. The impact of poverty on dog ownership and access to canine rabies vaccination: results from a knowledge, attitudes and practices survey, Uganda 2013. Infect Dis Poverty 2017; 6:97. [PMID: 28569185 PMCID: PMC5452361 DOI: 10.1186/s40249-017-0306-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 09/23/2016] [Accepted: 04/17/2017] [Indexed: 12/25/2022] Open
Abstract
Background Rabies is a neglected disease despite being responsible for more human deaths than any other zoonosis. A lack of adequate human and dog surveillance, resulting in low prioritization, is often blamed for this paradox. Estimation methods are often employed to describe the rabies burden when surveillance data are not available, however these figures are rarely based on country-specific data. Methods In 2013 a knowledge, attitudes, and practices survey was conducted in Uganda to understand dog population, rabies vaccination, and human rabies risk factors and improve in-country and regional rabies burden estimates. Poisson and multi-level logistic regression techniques were conducted to estimate the total dog population and vaccination coverage. Results Twenty-four villages were selected, of which 798 households completed the survey, representing 4 375 people. Dog owning households represented 12.9% of the population, for which 175 dogs were owned (25 people per dog). A history of vaccination was reported in 55.6% of owned dogs. Poverty and human population density highly correlated with dog ownership, and when accounted for in multi-level regression models, the human to dog ratio fell to 47:1 and the estimated national canine-rabies vaccination coverage fell to 36.1%. This study estimates there are 729 486 owned dogs in Uganda (95% CI: 719 919 – 739 053). Ten percent of survey respondents provided care to dogs they did not own, however unowned dog populations were not enumerated in this estimate. 89.8% of Uganda’s human population was estimated to reside in a community that can support enzootic canine rabies transmission. Conclusions This study is the first to comprehensively evaluate the effect of poverty on dog ownership in Africa. These results indicate that describing a dog population may not be as simple as applying a human: dog ratio, and factors such as poverty are likely to heavily influence dog ownership and vaccination coverage. These modelled estimates should be confirmed through further field studies, however, if validated, canine rabies elimination through mass vaccination may not be as difficult as previously considered in Uganda. Data derived from this study should be considered to improve models for estimating the in-country and regional rabies burden. Electronic supplementary material The online version of this article (doi:10.1186/s40249-017-0306-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Jason Mehal
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Yoshinori Nakazawa
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sergio Recuenco
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Modupe Osinubi
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Victor Tugumizemu
- Veterinary Public Health Division, Ministry of Health, Kampala, Uganda
| | - Jesse D Blanton
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Amy Gilbert
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
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28
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Cummings MJ, Wamala JF, Bakamutumaho B, Davis JL. Vital signs: the first step in prevention and management of critical illness in resource-limited settings. Intensive Care Med 2016; 42:1519-20. [PMID: 27207339 PMCID: PMC7094923 DOI: 10.1007/s00134-016-4381-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew J Cummings
- Department of Medicine, Columbia University Medical Center, 177 Fort Washington Avenue, Milstein Hospital Building, 6C-12, New York, NY, USA.
| | - Joseph F Wamala
- Department of National Disease Control, Ministry of Health, Kampala, Uganda
| | | | - J Lucian Davis
- Laboratory of Epidemiology and Public Health, Yale University School of Public Health, New Haven, CT, USA.,Section of Pulmonary and Critical Care Medicine, Yale University School of Medicine, New Haven, CT, USA
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29
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Cummings MJ, Bakamutumaho B, O'Donnell MR. Unfinished business: severe acute respiratory infection in sub-Saharan Africa. Intensive Care Med 2016; 42:1515-6. [PMID: 27172822 DOI: 10.1007/s00134-016-4383-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2016] [Indexed: 01/11/2023]
Affiliation(s)
- Matthew J Cummings
- Department of Medicine, Columbia University Medical Center, 177 Fort Washington Avenue, Milstein Hospital Building, 6C-12, New York, NY, USA.
| | | | - Max R O'Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York, NY, USA.,Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
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30
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Gerbi GB, Williams R, Bakamutumaho B, Liu S, Downing R, Drobeniuc J, Kamili S, Xu F, Holmberg SD, Teshale EH. Hepatitis E as a cause of acute jaundice syndrome in northern Uganda, 2010-2012. Am J Trop Med Hyg 2014; 92:411-4. [PMID: 25448237 DOI: 10.4269/ajtmh.14-0196] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Hepatitis E virus (HEV) is a common cause of acute viral hepatitis in developing countries; however, its contribution to acute jaundice syndrome is not well-described. A large outbreak of hepatitis E occurred in northern Uganda from 2007 to 2009. In response to this outbreak, acute jaundice syndrome surveillance was established in 10 district healthcare facilities to determine the proportion of cases attributable to hepatitis E. Of 347 acute jaundice syndrome cases reported, the majority (42%) had hepatitis E followed by hepatitis B (14%), malaria (10%), hepatitis C (5%), and other/unknown (29%). Of hepatitis E cases, 72% occurred in Kaboong district, and 68% of these cases occurred between May and August of 2011. Residence in Kaabong district was independently associated with hepatitis E (adjusted odds ratio = 13; 95% confidence interval = 7-24). The findings from this surveillance show that an outbreak and sporadic transmission of hepatitis E occur in northern Uganda.
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Affiliation(s)
- Gemechu B Gerbi
- Centers for Disease Control and Prevention, Atlanta, Georgia; The Uganda Virus Research Institute, Centers for Disease Control and Prevention Influenza Surveillance Project, World Health Organization Influenza Collaborating Center, Entebbe, Uganda; Centers for Disease Control and Prevention-Uganda, Kampala, Uganda
| | - Roxanne Williams
- Centers for Disease Control and Prevention, Atlanta, Georgia; The Uganda Virus Research Institute, Centers for Disease Control and Prevention Influenza Surveillance Project, World Health Organization Influenza Collaborating Center, Entebbe, Uganda; Centers for Disease Control and Prevention-Uganda, Kampala, Uganda
| | - Barnabas Bakamutumaho
- Centers for Disease Control and Prevention, Atlanta, Georgia; The Uganda Virus Research Institute, Centers for Disease Control and Prevention Influenza Surveillance Project, World Health Organization Influenza Collaborating Center, Entebbe, Uganda; Centers for Disease Control and Prevention-Uganda, Kampala, Uganda
| | - Stephen Liu
- Centers for Disease Control and Prevention, Atlanta, Georgia; The Uganda Virus Research Institute, Centers for Disease Control and Prevention Influenza Surveillance Project, World Health Organization Influenza Collaborating Center, Entebbe, Uganda; Centers for Disease Control and Prevention-Uganda, Kampala, Uganda
| | - Robert Downing
- Centers for Disease Control and Prevention, Atlanta, Georgia; The Uganda Virus Research Institute, Centers for Disease Control and Prevention Influenza Surveillance Project, World Health Organization Influenza Collaborating Center, Entebbe, Uganda; Centers for Disease Control and Prevention-Uganda, Kampala, Uganda
| | - Jan Drobeniuc
- Centers for Disease Control and Prevention, Atlanta, Georgia; The Uganda Virus Research Institute, Centers for Disease Control and Prevention Influenza Surveillance Project, World Health Organization Influenza Collaborating Center, Entebbe, Uganda; Centers for Disease Control and Prevention-Uganda, Kampala, Uganda
| | - Saleem Kamili
- Centers for Disease Control and Prevention, Atlanta, Georgia; The Uganda Virus Research Institute, Centers for Disease Control and Prevention Influenza Surveillance Project, World Health Organization Influenza Collaborating Center, Entebbe, Uganda; Centers for Disease Control and Prevention-Uganda, Kampala, Uganda
| | - Fujie Xu
- Centers for Disease Control and Prevention, Atlanta, Georgia; The Uganda Virus Research Institute, Centers for Disease Control and Prevention Influenza Surveillance Project, World Health Organization Influenza Collaborating Center, Entebbe, Uganda; Centers for Disease Control and Prevention-Uganda, Kampala, Uganda
| | - Scott D Holmberg
- Centers for Disease Control and Prevention, Atlanta, Georgia; The Uganda Virus Research Institute, Centers for Disease Control and Prevention Influenza Surveillance Project, World Health Organization Influenza Collaborating Center, Entebbe, Uganda; Centers for Disease Control and Prevention-Uganda, Kampala, Uganda
| | - Eyasu H Teshale
- Centers for Disease Control and Prevention, Atlanta, Georgia; The Uganda Virus Research Institute, Centers for Disease Control and Prevention Influenza Surveillance Project, World Health Organization Influenza Collaborating Center, Entebbe, Uganda; Centers for Disease Control and Prevention-Uganda, Kampala, Uganda
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31
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Cummings MJ, Wamala JF, Komakech I, Lukwago L, Malimbo M, Omeke ME, Mayer D, Bakamutumaho B. Hepatitis E in Karamoja, Uganda, 2009–2012: epidemiology and challenges to control in a setting of semi-nomadic pastoralism. Trans R Soc Trop Med Hyg 2014; 108:648-55. [DOI: 10.1093/trstmh/tru123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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32
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Namuwulya P, Abernathy E, Bukenya H, Bwogi J, Tushabe P, Birungi M, Seguya R, Kabaliisa T, Alibu VP, Kayondo JK, Rivailler P, Icenogle J, Bakamutumaho B. Phylogenetic analysis of rubella viruses identified in Uganda, 2003-2012. J Med Virol 2014; 86:2107-13. [PMID: 24700073 DOI: 10.1002/jmv.23935] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [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] [Accepted: 02/27/2014] [Indexed: 11/07/2022]
Abstract
Molecular data on rubella viruses are limited in Uganda despite the importance of congenital rubella syndrome (CRS). Routine rubella vaccination, while not administered currently in Uganda, is expected to begin by 2015. The World Health Organization recommends that countries without rubella vaccination programs assess the burden of rubella and CRS before starting a routine vaccination program. Uganda is already involved in integrated case-based surveillance, including laboratory testing to confirm measles and rubella, but molecular epidemiologic aspects of rubella circulation have so far not been documented in Uganda. Twenty throat swab or oral fluid samples collected from 12 districts during routine rash and fever surveillance between 2003 and 2012 were identified as rubella virus RNA positive and PCR products encompassing the region used for genotyping were sequenced. Phylogenetic analysis of the 20 sequences identified 19 genotype 1G viruses and 1 genotype 1E virus. Genotype-specific trees showed that the Uganda viruses belonged to specific clusters for both genotypes 1G and 1E and grouped with similar sequences from neighboring countries. Genotype 1G was predominant in Uganda. More epidemiological and molecular epidemiological data are required to determine if genotype 1E is also endemic in Uganda. The information obtained in this study will assist the immunization program in monitoring changes in circulating genotypes.
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Byaruhanga T, Namagambo B, Kayiwa J, Lutwama J, Bakamutumaho B, Chiza R, Nabukenya I, Owor N. The dynamics of influenza isolates in Uganda: Their implications and way forward. Int J Infect Dis 2014. [DOI: 10.1016/j.ijid.2014.03.1102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Balinandi S, Bakamutumaho B, Kayiwa JT, Ongus J, Oundo J, Awor AC, Lutwama JJ. The viral aetiology of influenza-like illnesses in Kampala and Entebbe, Uganda, 2008. Afr J Lab Med 2013; 2:65. [PMID: 29043164 PMCID: PMC5637772 DOI: 10.4102/ajlm.v2i1.65] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 04/09/2013] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND As the threat of zoonoses and the emergence of pandemic-prone respiratory viruses increases, there is a need to establish baseline information on the incidence of endemic pathogens in countries worldwide. OBJECTIVES To investigate the presence of viruses associated with influenza-like illnesses (ILI) in Uganda. METHODS A cross-sectional study was conducted in which nasopharyngeal swab specimens were collected from patients diagnosed with ILI in Kampala and Entebbe between 14 August 2008 - 15 December 2008. A multiplex polymerase chain reaction assay for detecting 12 respiratory viruses was used. RESULTS A total of 369 patients (52.3% females) was enrolled; the median age was 6 years (range 1-70). One or more respiratory viruses were detected in 172 (46.6%) cases and their prevalence were influenza A virus (19.2%), adenovirus (8.7%), human rhinovirus A (7.9%), coronavirus OC43 (4.3%), parainfluenza virus 1 (2.7%), parainfluenza virus 3 (2.7%), influenza B virus (2.2%), respiratory syncytial virus B (2.2%), human metapneumovirus (1.4%), respiratory syncytial virus A (1.1%), parainfluenza virus 2 (0.5%) and coronavirus 229E (0.5%). There were 24 (14.0%) mixed infections. CONCLUSIONS This study identified some of the respiratory viruses associated with ILI in Uganda. The circulation of some of the viruses was previously unknown in the study population. These results are useful in order to guide future surveillance and case management strategies involving respiratory illnesses in Uganda.
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Affiliation(s)
- Stephen Balinandi
- Field Epidemiology and Laboratory Training Program, Kenya.,Uganda Virus Research Institute, Uganda
| | | | | | - Juliette Ongus
- Department of Medical Laboratory Sciences, Jomo Kenyatta University of Agriculture and Technology, Kenya
| | - Joseph Oundo
- Field Epidemiology and Laboratory Training Program, Kenya
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Radin JM, Katz MA, Tempia S, Talla Nzussouo N, Davis R, Duque J, Adedeji A, Adjabeng MJ, Ampofo WK, Ayele W, Bakamutumaho B, Barakat A, Cohen AL, Cohen C, Dalhatu IT, Daouda C, Dueger E, Francisco M, Heraud JM, Jima D, Kabanda A, Kadjo H, Kandeel A, Bi Shamamba SK, Kasolo F, Kronmann KC, Mazaba Liwewe ML, Lutwama JJ, Matonya M, Mmbaga V, Mott JA, Muhimpundu MA, Muthoka P, Njuguna H, Randrianasolo L, Refaey S, Sanders C, Talaat M, Theo A, Valente F, Venter M, Woodfill C, Bresee J, Moen A, Widdowson MA. Influenza surveillance in 15 countries in Africa, 2006-2010. J Infect Dis 2013; 206 Suppl 1:S14-21. [PMID: 23169960 DOI: 10.1093/infdis/jis606] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND In response to the potential threat of an influenza pandemic, several international institutions and governments, in partnership with African countries, invested in the development of epidemiologic and laboratory influenza surveillance capacity in Africa and the African Network of Influenza Surveillance and Epidemiology (ANISE) was formed. METHODS We used a standardized form to collect information on influenza surveillance system characteristics, the number and percent of influenza-positive patients with influenza-like illness (ILI), or severe acute respiratory infection (SARI) and virologic data from countries participating in ANISE. RESULTS Between 2006 and 2010, the number of ILI and SARI sites in 15 African countries increased from 21 to 127 and from 2 to 98, respectively. Children 0-4 years accounted for 48% of all ILI and SARI cases of which 22% and 10%, respectively, were positive for influenza. Influenza peaks were generally discernible in North and South Africa. Substantial cocirculation of influenza A and B occurred most years. CONCLUSIONS Influenza is a major cause of respiratory illness in Africa, especially in children. Further strengthening influenza surveillance, along with conducting special studies on influenza burden, cost of illness, and role of other respiratory pathogens will help detect novel influenza viruses and inform and develop targeted influenza prevention policy decisions in the region.
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Lutwama JJ, Bakamutumaho B, Kayiwa JT, Chiiza R, Namagambo B, Katz MA, Geissler AL. Clinic- and hospital-based sentinel influenza surveillance, Uganda 2007-2010. J Infect Dis 2013; 206 Suppl 1:S87-93. [PMID: 23169978 DOI: 10.1093/infdis/jis578] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND To assess the epidemiology and seasonality of influenza in Uganda, we established a sentinel surveillance system for influenza in 5 hospitals and 5 outpatient clinics in 4 geographically distinct regions, using standard case definitions for influenzalike illness (ILI) and severe acute respiratory illness (SARI). METHODS Nasopharyngeal and oropharyngeal specimens were collected from April 2007 through September 2010 from patients with ILI and SARI aged ≥ 2 months, tested for influenza A and B with real-time reverse-transcription polymerase chain reaction, and subtyped for seasonal A/H1, A/H3, A/H5, and 2009 pandemic influenza A (pH1N1). RESULTS Among the 2758 patients sampled, 2656 (96%) enrolled with ILI and 101 (4%) with SARI. Specimens from 359 (13.0%) were positive for influenza; 267 (74.4%) were influenza A, and 92 (25.6%) were influenza B. The median age of both patients with ILI and patients with SARI was 4 years (range, 2 months to 67 years); patients aged 5-14 years had the highest influenza-positive percentage (19.6%), and patients aged 0-4 years had the lowest percentage (9.1%). Influenza circulated throughout the year, but the percentage of influenza-positive specimens peaked during June-November, coinciding with the second rainy season. CONCLUSIONS Continued and increased surveillance is needed to better understand the morbidity and mortality of influenza in Uganda.
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Affiliation(s)
- Julius J Lutwama
- National Influenza Center, Uganda Virus Research Institute, Entebbe, Uganda
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Wamala JF, Okot C, Makumbi I, Natseri N, Kisakye A, Nanyunja M, Bakamutumaho B, Lutwama JJ, Sreedharan R, Xing J, Gaturuku P, Aisu T, Da Silveira F, Chungong S. Assessment of core capacities for the International Health Regulations (IHR[2005])--Uganda, 2009. BMC Public Health 2010; 10 Suppl 1:S9. [PMID: 21143831 PMCID: PMC3005581 DOI: 10.1186/1471-2458-10-s1-s9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [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] [Indexed: 11/24/2022] Open
Abstract
Background Uganda is currently implementing the International Health Regulations (IHR[2005]) within the context of Integrated Disease Surveillance and Response (IDSR). The IHR(2005) require countries to assess the ability of their national structures, capacities, and resources to meet the minimum requirements for surveillance and response. This report describes the results of the assessment undertaken in Uganda. Methods We conducted a descriptive cross-sectional assessment using the protocol developed by the World Health Organisation (WHO). The data collection tools were adapted locally and administered to a convenience sample of HR(2005) stakeholders, and frequency analyses were performed. Results Ugandan national laws relevant to the IHR(2005) existed, but they did not adequately support the full implementation of the IHR(2005). Correspondingly, there was a designated IHR National Focal Point (NFP), but surveillance activities and operational communications were limited to the health sector. All the districts (13/13) had designated disease surveillance offices, most had IDSR technical guidelines (92%, or 12/13), and all (13/13) had case definitions for infectious and zoonotic diseases surveillance. Surveillance guidelines were available at 57% (35/61) of the health facilities, while case definitions were available at 66% (40/61) of the health facilities. The priority diseases list, surveillance guidelines, case definitions and reporting tools were based on the IDSR strategy and hence lacked information on the IHR(2005). The rapid response teams at national and district levels lacked food safety, chemical and radio-nuclear experts. Similarly, there were no guidelines on the outbreak response to food, chemical and radio-nuclear hazards. Comprehensive preparedness plans incorporating IHR(2005) were lacking at national and district levels. A national laboratory policy existed and the strategic plan was being drafted. However, there were critical gaps hampering the efficient functioning of the national laboratory network. Finally, the points of entry for IHR(2005) implementation had not been designated. Conclusions The assessment highlighted critical gaps to guide the IHR(2005) planning process. The IHR(2005) action plan should therefore be developed to foster national and international public health security.
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Lukwago L, Wamala J, Erima B, Okot C, Bakamutumaho B, Nabukenya I, Lutwama J. H1N1 Pandemic: From imported cases in July 2009 to sustained transmission in school clusters in September, Uganda, 2009. Int J Infect Dis 2010. [DOI: 10.1016/j.ijid.2010.02.1697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Teshale EH, Howard CM, Grytdal SP, Handzel TR, Barry V, Kamili S, Drobeniuc J, Okware S, Downing R, Tappero JW, Bakamutumaho B, Teo CG, Ward JW, Holmberg SD, Hu DJ. Hepatitis E epidemic, Uganda. Emerg Infect Dis 2010; 16:126-9. [PMID: 20031058 PMCID: PMC2874362 DOI: 10.3201/eid1601.090764] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [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] [Indexed: 12/15/2022] Open
Abstract
In October 2007, an epidemic of hepatitis E was suspected in Kitgum District of northern Uganda where no previous epidemics had been documented. This outbreak has progressed to become one of the largest hepatitis E outbreaks in the world. By June 2009, the epidemic had caused illness in >10,196 persons and 160 deaths.
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Affiliation(s)
- Eyasu H Teshale
- Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Mailstop G37, Atlanta, GA 30333, USA.
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Bwogi J, Braka F, Makumbi I, Mishra V, Bakamutumaho B, Nanyunja M, Opio A, Downing R, Biryahwaho B, Lewis RF. Hepatitis B infection is highly endemic in Uganda: findings from a national serosurvey. Afr Health Sci 2009; 9:98-108. [PMID: 19652743 PMCID: PMC2707048] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Infant immunization against hepatitis B began in Uganda in 2002. OBJECTIVE To determine the baseline prevalence of hepatitis B virus (HBV) infection and explore risk factors. METHODS A hepatitis B prevalence study was nested in the 2005 national HIV/AIDS serobehavioural survey. Demographic characteristics and risk factors were explored by questionnaire. One third of blood specimens (n=5875) from adults aged 15 to 59 years were tested for hepatitis B core antibodies (HBcAb); positive specimens were tested for hepatitis B surface antigen (HBsAg). RESULTS HBcAb was present in 52.3% (95% CI: 51.0-53.6) of adults, and HBsAg in 10.3% (9.5-11.1). By 15-19 years of age, 40.0% had been infected with HBV. Prevalence of both markers was significantly higher across northern Uganda, in rural areas, among the poor and least educated, and in uncircumcised men. Other independent predictors of infection were age, ethnic group, occupation, number of sex partners, and HIV and HSV-2 status. CONCLUSION Hepatitis B virus infection is highly endemic in Uganda, with transmission occurring in childhood and adulthood. More than 1.4 million adults are chronically infected and some communities disproportionately affected. The hepatitis B infant immunization programme should be sustained and catch-up vaccination considered for older children.
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Affiliation(s)
- Josephine Bwogi
- EPI Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
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Towner JS, Sealy TK, Khristova ML, Albariño CG, Conlan S, Reeder SA, Quan PL, Lipkin WI, Downing R, Tappero JW, Okware S, Lutwama J, Bakamutumaho B, Kayiwa J, Comer JA, Rollin PE, Ksiazek TG, Nichol ST. Newly discovered ebola virus associated with hemorrhagic fever outbreak in Uganda. PLoS Pathog 2008; 4:e1000212. [PMID: 19023410 PMCID: PMC2581435 DOI: 10.1371/journal.ppat.1000212] [Citation(s) in RCA: 357] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Accepted: 10/20/2008] [Indexed: 02/04/2023] Open
Abstract
Over the past 30 years, Zaire and Sudan ebolaviruses have been responsible for large hemorrhagic fever (HF) outbreaks with case fatalities ranging from 53% to 90%, while a third species, Côte d'Ivoire ebolavirus, caused a single non-fatal HF case. In November 2007, HF cases were reported in Bundibugyo District, Western Uganda. Laboratory investigation of the initial 29 suspect-case blood specimens by classic methods (antigen capture, IgM and IgG ELISA) and a recently developed random-primed pyrosequencing approach quickly identified this to be an Ebola HF outbreak associated with a newly discovered ebolavirus species (Bundibugyo ebolavirus) distantly related to the Côte d'Ivoire ebolavirus found in western Africa. Due to the sequence divergence of this new virus relative to all previously recognized ebolaviruses, these findings have important implications for design of future diagnostic assays to monitor Ebola HF disease in humans and animals, and ongoing efforts to develop effective antivirals and vaccines. In this report we describe a newly discovered ebolavirus species which caused a large hemorrhagic fever outbreak in western Uganda. The virus is genetically distinct, differing by more than 30% at the genome level from all other known ebolavirus species. The unique nature of this virus created challenges for traditional filovirus molecular based diagnostic assays and genome sequencing approaches. Instead, we quickly determined over 70% of the virus genome using a recently developed random-primed pyrosequencing approach that allowed the rapid development of a molecular detection assay that was deployed in the disease outbreak response. This draft sequence allowed easy completion of the whole genome sequence using a traditional primer walking approach and prompt confirmation that this virus represented a new ebolavirus species. Current efforts to design effective diagnostics, antivirals and vaccines will need to take into account the distinct nature of this important new member of the filovirus family.
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Affiliation(s)
- Jonathan S. Towner
- Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Tara K. Sealy
- Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Marina L. Khristova
- Scientific Resources Program, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - César G. Albariño
- Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Sean Conlan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Serena A. Reeder
- Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Phenix-Lan Quan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Robert Downing
- Global AIDS Program, Centers for Disease Control and Prevention, Entebbe, Uganda
| | - Jordan W. Tappero
- Global AIDS Program, Centers for Disease Control and Prevention, Entebbe, Uganda
| | - Samuel Okware
- Ministry of Health, Republic of Uganda, Kampala, Uganda
| | | | | | - John Kayiwa
- Uganda Virus Research Institute, Entebbe, Uganda
| | - James A. Comer
- Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Pierre E. Rollin
- Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Thomas G. Ksiazek
- Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Stuart T. Nichol
- Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
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