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Anywaine Z, Hansen C, Warimwe GM, Abu-Baker Mustapher G, Nyakarahuka L, Balinandi S, Ario AR, Lutwama JJ, Elliott A, Kaleebu P. Severe morbidity and hospital-based mortality from Rift Valley fever disease between November 2017 and March 2020 among humans in Uganda. Virol J 2024; 21:104. [PMID: 38702807 PMCID: PMC11069174 DOI: 10.1186/s12985-024-02377-z] [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: 01/19/2024] [Accepted: 04/26/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Rift Valley fever (RVF) is a zoonotic viral disease of increasing intensity among humans in Africa and the Arabian Peninsula. In Uganda, cases reported prior to 2016 were mild or not fully documented. We report in this paper on the severe morbidity and hospital-based mortality of human cases in Uganda. METHODS Between November 2017 and March 2020 human cases reported to the Uganda Virus Research Institute (UVRI) were confirmed by polymerase chain reaction (PCR). Ethical and regulatory approvals were obtained to enrol survivors into a one-year follow-up study. Data were collected on socio-demographics, medical history, laboratory tests, potential risk factors, and analysed using Stata software. RESULTS Overall, 40 cases were confirmed with acute RVF during this period. Cases were not geographically clustered and nearly all were male (39/40; 98%), median age 32 (range 11-63). The median definitive diagnosis time was 7 days and a delay of three days between presumptive and definitive diagnosis. Most patients (31/40; 78%) presented with fever and bleeding at case detection. Twenty-eight (70%) cases were hospitalised, out of whom 18 (64%) died. Mortality was highest among admissions in regional referral (11/16; 69%) and district (4/5; 80%) hospitals, hospitalized patients with bleeding at case detection (17/27; 63%), and patients older than 44 years (9/9; 100%). Survivors mostly manifested a mild gastro-intestinal syndrome with nausea (83%), anorexia (75%), vomiting (75%), abdominal pain (50%), and diarrhoea (42%), and prolonged symptoms of severe disease including jaundice (67%), visual difficulties (67%), epistaxis (50%), haemoptysis (42%), and dysentery (25%). Symptom duration varied between two to 120 days. CONCLUSION RVF is associated with high hospital-based mortality, severe and prolonged morbidity among humans that present to the health care system and are confirmed by PCR. One-health composite interventions should be developed to improve environmental and livestock surveillance, prevent infections, promptly detect outbreaks, and improve patient outcomes.
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Affiliation(s)
- Zacchaeus Anywaine
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK.
- Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Plot 51 - 59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda.
| | - Christian Hansen
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK
| | - George M Warimwe
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Luke Nyakarahuka
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
- Department of Biosecurity, Ecosystems and Veterinary Public Health, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Stephen Balinandi
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Alex Riolexus Ario
- National Institute of Public Health, Ministry of Health, Kampala, Uganda
| | - Julius J Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Alison Elliott
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
- Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Plot 51 - 59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Pontiano Kaleebu
- Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Plot 51 - 59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
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Shin OS, Monticelli SR, Hjorth CK, Hornet V, Doyle M, Abelson D, Kuehne AI, Wang A, Bakken RR, Mishra A, Middlecamp M, Champney E, Stuart L, Maurer DP, Li J, Berrigan J, Barajas J, Balinandi S, Lutwama JJ, Lobel L, Zeitlin L, Walker LM, Dye JM, Chandran K, Herbert AS, Pauli NT, McLellan JS. Crimean-Congo Hemorrhagic Fever Survivors Elicit Protective Non-Neutralizing Antibodies that Target 11 Overlapping Regions on Viral Glycoprotein GP38. bioRxiv 2024:2024.03.02.583110. [PMID: 38496658 PMCID: PMC10942344 DOI: 10.1101/2024.03.02.583110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Crimean-Congo hemorrhagic fever virus can cause lethal disease in humans yet there are no approved medical countermeasures. Viral glycoprotein GP38, unique to Nairoviridae, is a target of protective antibodies, but extensive mapping of the human antibody response to GP38 has not been previously performed. Here, we isolated 188 GP38-specific antibodies from human survivors of infection. Competition experiments showed that these antibodies bind across five distinct antigenic sites, encompassing eleven overlapping regions. Additionally, we reveal structures of GP38 bound with nine of these antibodies targeting different antigenic sites. Although GP38-specific antibodies were non-neutralizing, several antibodies were found to have protection equal to or better than murine antibody 13G8 in two highly stringent rodent models of infection. Together, these data expand our understanding regarding this important viral protein and inform the development of broadly effective CCHFV antibody therapeutics.
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Affiliation(s)
| | - Stephanie R. Monticelli
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
- Geneva Foundation, Tacoma, WA 98042, USA
| | - Christy K. Hjorth
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | | | - Dafna Abelson
- Mapp Biopharmaceutical, Inc., San Diego, CA 92121, USA
| | - Ana I. Kuehne
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Albert Wang
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Russell R. Bakken
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Akaash Mishra
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | | | - Lauran Stuart
- Mapp Biopharmaceutical, Inc., San Diego, CA 92121, USA
| | | | | | - Jacob Berrigan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | | | | | - Leslie Lobel
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Larry Zeitlin
- Mapp Biopharmaceutical, Inc., San Diego, CA 92121, USA
| | | | - John M. Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Andrew S. Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | | | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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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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4
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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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5
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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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6
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Nyakarahuka L, Kyondo J, Telford C, Whitesell A, Tumusiime A, Mulei S, Baluku J, Cossaboom CM, Cannon DL, Montgomery JM, Lutwama JJ, Nichol ST, Balinandi SK, Klena JD, Shoemaker TR. Seroepidemiological investigation of Crimean Congo hemorrhagic fever virus in livestock in Uganda, 2017. PLoS One 2023; 18:e0288587. [PMID: 37943886 PMCID: PMC10635543 DOI: 10.1371/journal.pone.0288587] [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: 08/09/2022] [Accepted: 07/01/2023] [Indexed: 11/12/2023] Open
Abstract
Crimean-Congo Hemorrhagic fever (CCHF) is an important zoonotic disease transmitted to humans both by tick vectors and contact with fluids from an infected animal or human. Although animals are not symptomatic when infected, they are the main source of human infection. Uganda has reported sporadic human outbreaks of CCHF in various parts of the country since 2013. We designed a nationwide epidemiological study to investigate the burden of CCHF in livestock. A total of 3181 animals were sampled; 1732 cattle (54.4%), 1091 goats (34.3%), and 358 sheep (11.3%) resulting in overall livestock seropositivity of IgG antibodies against CCHF virus (CCHFV) of 31.4% (999/3181). Seropositivity in cattle was 16.9% and in sheep and goats was 48.8%. Adult and juvenile animals had higher seropositivity compared to recently born animals, and seropositivity was higher in female animals (33.5%) compared to male animals (24.1%). Local breeds had higher (36.8%) compared to exotic (2.8%) and cross breeds (19.3%). Animals that had a history of abortion or stillbirth had higher seropositivity compared to those without a history of abortion or stillbirth. CCHFV seropositivity appeared to be generally higher in northern districts of the country, though spatial trends among sampled districts were not examined. A multivariate regression analysis using a generalized linear mixed model showed that animal species, age, sex, region, and elevation were all significantly associated with CCHFV seropositivity after adjusting for the effects of other model predictors. This study shows that CCHFV is actively circulating in Uganda, posing a serious risk for human infection. The results from this study can be used to help target surveillance efforts for early case detection in animals and limit subsequent spillover into humans.
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Affiliation(s)
- Luke Nyakarahuka
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
- Department of Biosecurity, Ecosystems and Veterinary Public Health, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Jackson Kyondo
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Carson Telford
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Amy Whitesell
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Alex Tumusiime
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Sophia Mulei
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Jimmy Baluku
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Caitlin M. Cossaboom
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Deborah L. Cannon
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Joel M. Montgomery
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Stuart T. Nichol
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Stephen K. Balinandi
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - John D. Klena
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Trevor R. Shoemaker
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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7
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Amman BR, Schuh AJ, Akurut G, Kamugisha K, Namanya D, Sealy TK, Graziano JC, Enyel E, Wright EA, Balinandi S, Lutwama JJ, Kading RC, Atimnedi P, Towner JS. Micro‒Global Positioning Systems for Identifying Nightly Opportunities for Marburg Virus Spillover to Humans by Egyptian Rousette Bats. Emerg Infect Dis 2023; 29:2238-2245. [PMID: 37877537 PMCID: PMC10617345 DOI: 10.3201/eid2911.230362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Abstract
Marburg virus disease, caused by Marburg and Ravn orthomarburgviruses, emerges sporadically in sub-Saharan Africa and is often fatal in humans. The natural reservoir is the Egyptian rousette bat (ERB), which sheds virus in saliva, urine, and feces. Frugivorous ERBs discard test-bitten and partially eaten fruit, potentially leaving infectious virus behind that could be consumed by other susceptible animals or humans. Historically, 8 of 17 known Marburg virus disease outbreaks have been linked to human encroachment on ERB habitats, but no linkage exists for the other 9 outbreaks, raising the question of how bats and humans might intersect, leading to virus spillover. We used micro‒global positioning systems to identify nightly ERB foraging locations. ERBs from a known Marburg virus‒infected population traveled long distances to feed in cultivated fruit trees near homes. Our results show that ERB foraging behavior represents a Marburg virus spillover risk to humans and plausibly explains the origins of some past outbreaks.
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Balinandi S, Whitmer S, Mulei S, Nassuna C, Pimundu G, Muyigi T, Kainulainen M, Shedroff E, Krapiunaya I, Scholte F, Nyakarahuka L, Tumusiime A, Kyondo J, Baluku J, Kiconco J, Harris JR, Ario AR, Kagirita A, Bosa HK, Ssewanyana I, Nabadda S, Mwebesa HG, Aceng JR, Atwine D, Lutwama JJ, Shoemaker TR, Montgomery JM, Kaleebu P, Klena JD. Molecular characterization of the 2022 Sudan virus disease outbreak in Uganda. J Virol 2023; 97:e0059023. [PMID: 37750724 PMCID: PMC10617429 DOI: 10.1128/jvi.00590-23] [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: 04/20/2023] [Accepted: 08/08/2023] [Indexed: 09/27/2023] Open
Abstract
IMPORTANCE Ebola disease (EBOD) is a public health threat with a high case fatality rate. Most EBOD outbreaks have occurred in remote locations, but the 2013-2016 Western Africa outbreak demonstrated how devastating EBOD can be when it reaches an urban population. Here, the 2022 Sudan virus disease (SVD) outbreak in Mubende District, Uganda, is summarized, and the genetic relatedness of the new variant is evaluated. The Mubende variant exhibited 96% amino acid similarity with historic SUDV sequences from the 1970s and a high degree of conservation throughout the outbreak, which was important for ongoing diagnostics and highly promising for future therapy development. Genetic differences between viruses identified during the Mubende SVD outbreak were linked with epidemiological data to better interpret viral spread and contact tracing chains. This methodology should be used to better integrate discrete epidemiological and sequence data for future viral outbreaks.
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Affiliation(s)
| | - Shannon Whitmer
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sophia Mulei
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Godfrey Pimundu
- Uganda National Health Laboratory Services, Ministry of Health, Kampala, Uganda
| | - Tonny Muyigi
- Uganda National Health Laboratory Services, Ministry of Health, Kampala, Uganda
| | - Markus Kainulainen
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Elizabeth Shedroff
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Inna Krapiunaya
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Florine Scholte
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Luke Nyakarahuka
- Uganda Virus Research Institute, Entebbe, Uganda
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | | | - Jimmy Baluku
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | | | - Alex R. Ario
- Uganda Public Health Fellowship Program, Kampala, Uganda
| | | | - Henry K. Bosa
- Ministry of Health, Kampala, Uganda
- Kellogg College, University of Oxford, Oxford, United Kingdom
| | - Isaac Ssewanyana
- Uganda National Health Laboratory Services, Ministry of Health, Kampala, Uganda
| | - Susan Nabadda
- Uganda National Health Laboratory Services, Ministry of Health, Kampala, Uganda
| | | | | | | | | | - Trevor R. Shoemaker
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Joel M. Montgomery
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Pontiano Kaleebu
- Uganda Virus Research Institute, Entebbe, Uganda
- MRC/UVRI & LSHTM Uganda Research Unit, Entebbe, Uganda
| | - John D. Klena
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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9
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Nyakarahuka L, Kyondo J, Telford C, Whitesell A, Tumusiime A, Mulei S, Baluku J, Cossaboom CM, Cannon DL, Montgomery JM, Lutwama JJ, Nichol ST, Balinandi S, Klena JD, Shoemaker TR. A Countrywide Seroepidemiological Survey of Rift Valley Fever in Livestock, Uganda, 2017. Am J Trop Med Hyg 2023; 109:548-553. [PMID: 37524326 PMCID: PMC10484263 DOI: 10.4269/ajtmh.22-0504] [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: 08/08/2022] [Accepted: 05/01/2023] [Indexed: 08/02/2023] Open
Abstract
In 2016, an outbreak of Rift Valley fever was reported in the Kabale District in Uganda for the first time in 48 years. Three human cases were confirmed by polymerase chain reaction, and subsequent serological investigations revealed an overall IgG seropositivity of 13% in humans and 13% in animals. In response to this reemergence, we designed a countrywide survey to determine the seropositivity of anti-Rift Valley fever virus (RVFV) IgG antibodies in livestock. Samples were collected from 27 districts and tested for RVFV anti-IgG antibodies. A total of 3,181 livestock samples were tested, of which 54.4% were cattle (1,732 of 3,181), 34.3% were goats (1,091 of 3,181), and 11.3% were sheep (358 of 3,181). Overall RVFV seropositivity was 6.9% (221 of 3,181). Seroprevalence was greater in cattle (10.7%) compared with goats (2.6%) and sheep (2.0%), among females (7.5%) compared with males (5.2%), and among adults (7.6%) compared with juveniles (4.9%) and nurslings (6.4%). Exotic breeds and animals with a history of abortion or stillbirth also had greater odds of RVFV seropositivity. Animals grazed under tethering and paddocking had greater RVFV seropositivity compared with animals that grazed communally, and livestock in the western and eastern regions had the greatest seroprevalence. In a multivariate regression model, animal species (odds ratio [OR], 6.4; 95% CI, 3.5-11.4) and age (OR, 2.3; 95% CI, 1.4-3.6) were associated significantly with RVFV seropositivity. This study could be important in developing risk-based surveillance for early outbreak detection to limit the spread of RVFV in both human and animal populations.
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Affiliation(s)
- Luke Nyakarahuka
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
- Department of Biosecurity, Ecosystems and Veterinary Public Health, Makerere University, Kampala, Uganda
| | - Jackson Kyondo
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Carson Telford
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Amy Whitesell
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Alex Tumusiime
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Sophia Mulei
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Jimmy Baluku
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Caitlin M. Cossaboom
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Deborah L. Cannon
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Joel M. Montgomery
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Stuart T. Nichol
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Stephen Balinandi
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - John D. Klena
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Trevor R. Shoemaker
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, US Centers for Disease Control and Prevention, Atlanta, Georgia
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10
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Kigozi BK, Kharod GA, Bukenya H, Shadomy SV, Haberling DL, Stoddard RA, Galloway RL, Tushabe P, Nankya A, Nsibambi T, Mbidde EK, Lutwama JJ, Perniciaro JL, Nicholson WL, Bower WA, Bwogi J, Blaney DD. Investigating the etiology of acute febrile illness: a prospective clinic-based study in Uganda. BMC Infect Dis 2023; 23:411. [PMID: 37328808 PMCID: PMC10276394 DOI: 10.1186/s12879-023-08335-4] [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: 12/25/2022] [Accepted: 05/17/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Historically, malaria has been the predominant cause of acute febrile illness (AFI) in sub-Saharan Africa. However, during the last two decades, malaria incidence has declined due to concerted public health control efforts, including the widespread use of rapid diagnostic tests leading to increased recognition of non-malarial AFI etiologies. Our understanding of non-malarial AFI is limited due to lack of laboratory diagnostic capacity. We aimed to determine the etiology of AFI in three distinct regions of Uganda. METHODS A prospective clinic-based study that enrolled participants from April 2011 to January 2013 using standard diagnostic tests. Participant recruitment was from St. Paul's Health Centre (HC) IV, Ndejje HC IV, and Adumi HC IV in the western, central and northern regions, which differ by climate, environment, and population density. A Pearson's chi-square test was used to evaluate categorical variables, while a two-sample t-test and Krukalis-Wallis test were used for continuous variables. RESULTS Of the 1281 participants, 450 (35.1%), 382 (29.8%), and 449 (35.1%) were recruited from the western, central, and northern regions, respectively. The median age (range) was 18 (2-93) years; 717 (56%) of the participants were female. At least one AFI pathogen was identified in 1054 (82.3%) participants; one or more non-malarial AFI pathogens were identified in 894 (69.8%) participants. The non-malarial AFI pathogens identified were chikungunya virus, 716 (55.9%); Spotted Fever Group rickettsia (SFGR), 336 (26.2%) and Typhus Group rickettsia (TGR), 97 (7.6%); typhoid fever (TF), 74 (5.8%); West Nile virus, 7 (0.5%); dengue virus, 10 (0.8%) and leptospirosis, 2 (0.2%) cases. No cases of brucellosis were identified. Malaria was diagnosed either concurrently or alone in 404 (31.5%) and 160 (12.5%) participants, respectively. In 227 (17.7%) participants, no cause of infection was identified. There were statistically significant differences in the occurrence and distribution of TF, TGR and SFGR, with TF and TGR observed more frequently in the western region (p = 0.001; p < 0.001) while SFGR in the northern region (p < 0.001). CONCLUSION Malaria, arboviral infections, and rickettsioses are major causes of AFI in Uganda. Development of a Multiplexed Point-of-Care test would help identify the etiology of non-malarial AFI in regions with high AFI rates.
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Affiliation(s)
- Brian K Kigozi
- Uganda Virus Research Institute, Entebbe, Uganda.
- College of Health Sciences, Clinical Epidemiology Unit, Makerere University, Kampala, Uganda.
| | - Grishma A Kharod
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
| | | | - Sean V Shadomy
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
| | - Dana L Haberling
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
| | - Robyn A Stoddard
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
| | - Renee L Galloway
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
| | | | - Annet Nankya
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Thomas Nsibambi
- Uganda Virus Research Institute, Entebbe, Uganda
- US Centers for Disease Control and Prevention, Kampala, Uganda
| | | | | | | | | | - William A Bower
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
| | | | - David D Blaney
- CDC Division of High-Consequence Pathogens and Pathology, Atlanta, USA
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11
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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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12
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Nabakooza G, Owuor DC, de Laurent ZR, Galiwango R, Owor N, Kayiwa JT, Jjingo D, Agoti CN, Nokes DJ, Kateete DP, Kitayimbwa JM, Frost SDW, Lutwama JJ. Phylogenomic analysis uncovers a 9-year variation of Uganda influenza type-A strains from the WHO-recommended vaccines and other Africa strains. Sci Rep 2023; 13:5516. [PMID: 37015946 PMCID: PMC10072032 DOI: 10.1038/s41598-023-30667-z] [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: 06/10/2022] [Accepted: 02/28/2023] [Indexed: 04/06/2023] Open
Abstract
Genetic characterisation of circulating influenza viruses directs annual vaccine strain selection and mitigation of infection spread. We used next-generation sequencing to locally generate whole genomes from 116 A(H1N1)pdm09 and 118 A(H3N2) positive patient swabs collected across Uganda between 2010 and 2018. We recovered sequences from 92% (215/234) of the swabs, 90% (193/215) of which were whole genomes. The newly-generated sequences were genetically and phylogenetically compared to the WHO-recommended vaccines and other Africa strains sampled since 1994. Uganda strain hemagglutinin (n = 206), neuraminidase (n = 207), and matrix protein (MP, n = 213) sequences had 95.23-99.65%, 95.31-99.79%, and 95.46-100% amino acid similarity to the 2010-2020 season vaccines, respectively, with several mutated hemagglutinin antigenic, receptor binding, and N-linked glycosylation sites. Uganda influenza type-A virus strains sequenced before 2016 clustered uniquely while later strains mixed with other Africa and global strains. We are the first to report novel A(H1N1)pdm09 subclades 6B.1A.3, 6B.1A.5(a,b), and 6B.1A.6 (± T120A) that circulated in Eastern, Western, and Southern Africa in 2017-2019. Africa forms part of the global influenza ecology with high viral genetic diversity, progressive antigenic drift, and local transmissions. For a continent with inadequate health resources and where social distancing is unsustainable, vaccination is the best option. Hence, African stakeholders should prioritise routine genome sequencing and analysis to direct vaccine selection and virus control.
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Affiliation(s)
- Grace Nabakooza
- Department of Immunology and Molecular Biology, Makerere University, Kampala, Uganda.
- Makerere University/UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Uganda Virus Research Institute (UVRI), Entebbe, Uganda.
- Centre for Computational Biology, Uganda Christian University, Mukono, Uganda.
- Oak Ridge Institute for Science and Education, Bioinformatics Research Fellow to the Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States.
| | - D Collins Owuor
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Zaydah R de Laurent
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Ronald Galiwango
- Makerere University/UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Uganda Virus Research Institute (UVRI), Entebbe, Uganda
- Centre for Computational Biology, Uganda Christian University, Mukono, Uganda
- The African Center of Excellence in Bioinformatics and Data Intensive Sciences (ACE), Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Nicholas Owor
- Department of Arbovirology Emerging and Re-Emerging Infectious Diseases, Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - John T Kayiwa
- Department of Arbovirology Emerging and Re-Emerging Infectious Diseases, Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - Daudi Jjingo
- The African Center of Excellence in Bioinformatics and Data Intensive Sciences (ACE), Infectious Diseases Institute, Makerere University, Kampala, Uganda
- Department of Computer Science, College of Computing, Makerere University, Kampala, Uganda
| | - Charles N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - D James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, United Kingdom
| | - David P Kateete
- Department of Immunology and Molecular Biology, Makerere University, Kampala, Uganda
- Makerere University/UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - John M Kitayimbwa
- Makerere University/UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Uganda Virus Research Institute (UVRI), Entebbe, Uganda
- Centre for Computational Biology, Uganda Christian University, Mukono, Uganda
| | - Simon D W Frost
- Microsoft Research, Redmond, Washington, 98052, United States
- London School of Hygiene and Tropical Medicine (LSHTM), Keppel St, Bloomsbury, London, United Kingdom
| | - Julius J Lutwama
- Department of Arbovirology Emerging and Re-Emerging Infectious Diseases, Uganda Virus Research Institute (UVRI), Entebbe, Uganda
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13
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Byaruhanga T, Kayiwa JT, Nankya AM, Ataliba IJ, McClure CP, Ball JK, Lutwama JJ. Arbovirus circulation, epidemiology and spatiotemporal distribution in Uganda. IJID Reg 2023; 6:171-176. [PMID: 36915800 PMCID: PMC10006739 DOI: 10.1016/j.ijregi.2023.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Background Arboviruses are endemic in Uganda; however, little is known about their epidemiology, seasonality and spatiotemporal distribution. Our study sought to provide information on arbovirus outbreaks from acute clinical presentations. Methods Immunoglobulin M (IgM) and confirmatory Plaque Reduction Neutralisation Test (PRNT) results for arbovirus diagnosis of samples collected from patients attending sentinel sites from 2016-19 were analysed retrospectively. Demographic data were analysed with SaTScan and SPSS software to determine the epidemiology and spatiotemporal distribution of arboviruses. Results Arbovirus activity peaked consistently during March-May rainy seasons. Overall, arbovirus seroprevalence was 9.5%. Of 137 IgM positives, 52.6% were confirmed by PRNT, of which 73.6% cases were observed in central Uganda with Yellow Fever Virus had the highest prevalence (27.8%). The 5-14 age group were four times more likely to be infected with an arbovirus p=0.003, 4.1 (95% CI 1.3-12.3). Significant arboviral activity was observed among outdoor workers(p=0.05) . Spatiotemporal analysis indicated arboviral activity in 23 of the 85 districts analysed.. Interpretation Our study shows that arbovirus activity peaks during the March-May rainy season and highlights the need for YFV mass vaccination to reduce the clinical burden of arboviruses transmitted within the region.
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Affiliation(s)
- Timothy Byaruhanga
- University of Nottingham School of Life Sciences, Wolfson Centre for Global Virus Research, Nottingham, UK
- Uganda Virus Research Institute, Department of Arbovirology, Emerging and Re-emerging infectious diseases
| | - John T. Kayiwa
- Uganda Virus Research Institute, Department of Arbovirology, Emerging and Re-emerging infectious diseases
| | - Annet M. Nankya
- Uganda Virus Research Institute, Department of Arbovirology, Emerging and Re-emerging infectious diseases
| | - Irene J. Ataliba
- Uganda Virus Research Institute, Department of Arbovirology, Emerging and Re-emerging infectious diseases
| | - C. Patrick McClure
- University of Nottingham School of Life Sciences, Wolfson Centre for Global Virus Research, Nottingham, UK
| | - Jonathan K. Ball
- University of Nottingham School of Life Sciences, Wolfson Centre for Global Virus Research, Nottingham, UK
| | - Julius J. Lutwama
- Uganda Virus Research Institute, Department of Arbovirology, Emerging and Re-emerging infectious diseases
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14
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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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15
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Ario AR, Aliddeki DM, Kadobera D, Bulage L, Kayiwa J, Wetaka MM, Kyazze S, Ocom F, Makumbi I, Mbaka P, Behumbiize P, Ayebazibwe I, Balinandi SK, Lutwama JJ, Crawley A, Divi N, Lule JR, Ojwang JC, Harris JR, Boore AL, Nelson LJ, Borchert J, Jarvis D. Uganda's experience in establishing an electronic compendium for public health emergencies. PLOS Glob Public Health 2023; 3:e0001402. [PMID: 36962840 PMCID: PMC10021891 DOI: 10.1371/journal.pgph.0001402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/28/2022] [Indexed: 02/12/2023]
Abstract
Uganda has implemented several interventions that have contributed to prevention, early detection, and effective response to Public Health Emergencies (PHEs). However, there are gaps in collecting and documenting data on the overall response to these PHEs. We set out to establish a comprehensive electronic database of PHEs that occurred in Uganda since 2000. We constituted a core development team, developed a data dictionary, and worked with Health Information Systems Program (HISP)-Uganda to develop and customize a compendium of PHEs using the electronic Integrated Disease Surveillance and Response (eIDSR) module on the District Health Information Software version 2 (DHIS2) platform. We reviewed literature for retrospective data on PHEs for the compendium. Working with the Uganda Public Health Emergency Operations Center (PHEOC), we prospectively updated the compendium with real-time data on reported PHEs. We developed a user's guide to support future data entry teams. An operational compendium was developed within the eIDSR module of the DHIS2 platform. The variables for PHEs data collection include those that identify the type, location, nature and time to response of each PHE. The compendium has been updated with retrospective PHE data and real-time prospective data collection is ongoing. Data within this compendium is being used to generate information that can guide future outbreak response and management. The compendium development highlights the importance of documenting outbreak detection and response data in a central location for future reference. This data provides an opportunity to evaluate and inform improvements in PHEs response.
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Affiliation(s)
- Alex Riolexus Ario
- Uganda Public Health Fellowship Program, Kampala, Uganda
- Uganda National Institute of Public Health, Kampala, Uganda
| | | | - Daniel Kadobera
- Uganda Public Health Fellowship Program, Kampala, Uganda
- Uganda National Institute of Public Health, Kampala, Uganda
| | - Lilian Bulage
- Uganda Public Health Fellowship Program, Kampala, Uganda
- Uganda National Institute of Public Health, Kampala, Uganda
| | - Joshua Kayiwa
- Uganda National Institute of Public Health, Kampala, Uganda
- Uganda Public Health Emergency Operations Center, Kampala, Uganda
| | - Milton M. Wetaka
- Uganda National Institute of Public Health, Kampala, Uganda
- Uganda Public Health Emergency Operations Center, Kampala, Uganda
| | - Simon Kyazze
- Uganda National Institute of Public Health, Kampala, Uganda
- Uganda Public Health Emergency Operations Center, Kampala, Uganda
| | - Felix Ocom
- Uganda National Institute of Public Health, Kampala, Uganda
- Uganda Public Health Emergency Operations Center, Kampala, Uganda
| | - Issa Makumbi
- Uganda National Institute of Public Health, Kampala, Uganda
- Uganda Public Health Emergency Operations Center, Kampala, Uganda
| | - Paul Mbaka
- Uganda National Institute of Public Health, Kampala, Uganda
- Division of Health Information, Ministry of Health, Kampala, Uganda
| | | | | | | | | | - Adam Crawley
- Ending Pandemics, San Francisco, California, United States of America
| | - Nomita Divi
- Ending Pandemics, San Francisco, California, United States of America
| | - John R. Lule
- US Centers for Disease Control and Prevention, Kampala, Uganda
| | | | - Julie R. Harris
- US Centers for Disease Control and Prevention, Kampala, Uganda
| | - Amy L. Boore
- US Centers for Disease Control and Prevention, Kampala, Uganda
| | - Lisa J. Nelson
- US Centers for Disease Control and Prevention, Kampala, Uganda
| | - Jeff Borchert
- Division of Vector-Borne Diseases, National Center for Emerging, Zoonotic, Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Dennis Jarvis
- Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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16
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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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17
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Perinet LC, Mutebi JP, Powers AM, Lutwama JJ, Mossel EC. Yata Virus (Family Rhabdoviridae, Genus Ephemerovirus) Isolation from Mosquitoes from Uganda, the First Reported Isolation since 1969. Diseases 2023; 11:diseases11010021. [PMID: 36810535 PMCID: PMC9944095 DOI: 10.3390/diseases11010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 01/31/2023] Open
Abstract
As a part of a systematic study of mosquitoes and associated viruses in Uganda, a virus was isolated from a pool of Mansonia uniformis collected in July 2017, in the Kitgum District of northern Uganda. Sequence analysis determined that the virus is Yata virus (YATAV; Ephemerovirus yata; family Rhabdoviridae). The only previous reported isolation of YATAV was in 1969 in Birao, Central African Republic, also from Ma. uniformis mosquitoes. The current sequence is over 99% identical at the nucleotide level to the original isolate, indicating a high level of YATAV genomic stability.
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Affiliation(s)
- Lara C. Perinet
- Division of Vector-Borne Diseases, US Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - John-Paul Mutebi
- Division of Vector-Borne Diseases, US Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Ann M. Powers
- Division of Vector-Borne Diseases, US Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging, and Re-emerging Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Eric C. Mossel
- Division of Vector-Borne Diseases, US Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
- Correspondence:
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18
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Kayiwa JT, Mayanja MN, Nakayiki TM, Senfuka F, Mugga J, Koehler JW, Mossel EC, Lutwama JJ. Phylogenetic Analysis of Wesselsbron Virus Isolated from Field-Captured Mosquitoes during a Rift Valley Fever Outbreak in Kabale District, Uganda-2016. Am J Trop Med Hyg 2023; 108:161-164. [PMID: 36410326 PMCID: PMC9833084 DOI: 10.4269/ajtmh.22-0481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/06/2022] [Indexed: 11/23/2022] Open
Abstract
After confirmation of two human cases of Rift Valley fever (RVF) in March 2016 in the Kabale district of Uganda, an entomological investigation was conducted with a focus on mosquito species composition and abundance of known and potential mosquito vector species, and virus testing to identify species most likely involved in Rift Valley fever virus transmission. This information could be used to forecast risk and facilitate improvement of prevention and response tools for use in preventing or controlling future outbreaks. From these collections, two virus isolates were obtained, one each from a pool of Aedes tricholabis and Ae. gibbinsi. Next-generation sequencing identified both isolates as Wesselsbron virus, family Flaviviridae, a neglected arbovirus of economic importance. These are the first reported Wesselsbron virus isolates from Uganda since 1966.
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Affiliation(s)
- John T. Kayiwa
- Department of Arbovirology, Emerging, and Re-emerging Diseases, Uganda Virus Research Institute, Entebbe, Uganda;,Address correspondence to John T. Kayiwa, Department of Arbovirology, Emerging, and Re-emerging Diseases, Uganda Virus Research Institute, P.O. Box 49, Plot 51-59 Nakiwogo Road, Entebbe, Uganda. E-mail:
| | - Martin N. Mayanja
- Department of Arbovirology, Emerging, and Re-emerging Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Teddy Muwawu Nakayiki
- Department of Arbovirology, Emerging, and Re-emerging Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Fred Senfuka
- Department of Arbovirology, Emerging, and Re-emerging Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Julius Mugga
- Department of Arbovirology, Emerging, and Re-emerging Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Jeffrey W. Koehler
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland
| | - Eric C. Mossel
- Division of Vector-Borne Diseases, U.S. Centers for Disease Control and Prevention, Fort Collins, Colorado
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging, and Re-emerging Diseases, Uganda Virus Research Institute, Entebbe, Uganda
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19
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Kading RC, Borland EM, Mossel EC, Nakayiki T, Nalikka B, Ledermann JP, Crabtree MB, Panella NA, Nyakarahuka L, Gilbert AT, Kerbis-Peterhans JC, Towner JS, Amman BR, Sealy TK, Miller BR, Lutwama JJ, Kityo RM, Powers AM. Exposure of Egyptian Rousette Bats ( Rousettus aegyptiacus) and a Little Free-Tailed Bat ( Chaerephon pumilus) to Alphaviruses in Uganda. Diseases 2022; 10:diseases10040121. [PMID: 36547207 PMCID: PMC9777265 DOI: 10.3390/diseases10040121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/18/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
The reservoir for zoonotic o'nyong-nyong virus (ONNV) has remained unknown since this virus was first recognized in Uganda in 1959. Building on existing evidence for mosquito blood-feeding on various frugivorous bat species in Uganda, and seroprevalence for arboviruses among bats in Uganda, we sought to assess if serum samples collected from bats in Uganda demonstrated evidence of exposure to ONNV or the closely related zoonotic chikungunya virus (CHIKV). In total, 652 serum samples collected from six bat species were tested by plaque reduction neutralization test (PRNT) for neutralizing antibodies against ONNV and CHIKV. Forty out of 303 (13.2%) Egyptian rousettes from Maramagambo Forest and 1/13 (8%) little free-tailed bats from Banga Nakiwogo, Entebbe contained neutralizing antibodies against ONNV. In addition, 2/303 (0.7%) of these Egyptian rousettes contained neutralizing antibodies to CHIKV, and 8/303 (2.6%) contained neutralizing antibodies that were nonspecifically reactive to alphaviruses. These data support the interepidemic circulation of ONNV and CHIKV in Uganda, although Egyptian rousette bats are unlikely to serve as reservoirs for these viruses given the inconsistent occurrence of antibody-positive bats.
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Affiliation(s)
- Rebekah C. Kading
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
- Arbovirus Diseases Branch, Division of Vector-Borne Diseases, U.S. Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
- Correspondence: ; Tel.: +1-970-491-7833
| | - Erin M. Borland
- Arbovirus Diseases Branch, Division of Vector-Borne Diseases, U.S. Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Eric C. Mossel
- Arbovirus Diseases Branch, Division of Vector-Borne Diseases, U.S. Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Teddy Nakayiki
- Department of Arbovirology, Emerging, and Re-Emerging Infections, Uganda Virus Research Institute, Entebbe, Uganda
| | - Betty Nalikka
- Department of Zoology, Entomology, and Fisheries Science, Makerere University, Kampala, Uganda
| | - Jeremy P. Ledermann
- Arbovirus Diseases Branch, Division of Vector-Borne Diseases, U.S. Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Mary B. Crabtree
- Arbovirus Diseases Branch, Division of Vector-Borne Diseases, U.S. Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Nicholas A. Panella
- Arbovirus Diseases Branch, Division of Vector-Borne Diseases, U.S. Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Luke Nyakarahuka
- Department of Arbovirology, Emerging, and Re-Emerging Infections, Uganda Virus Research Institute, Entebbe, Uganda
| | - Amy T. Gilbert
- Animal Plant Health Inspection Service, National Wildlife Research Center, United States Department of Agriculture, Fort Collins, CO 80521, USA
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens, United States Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Julian C. Kerbis-Peterhans
- Negaunee Integrative Research Center, Field Museum of Natural History, College of Arts & Sciences, Roosevelt University, Chicago, IL 60605, USA
| | - Jonathan S. Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens, United States Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Brian R. Amman
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens, United States Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Tara K. Sealy
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens, United States Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Barry R. Miller
- Arbovirus Diseases Branch, Division of Vector-Borne Diseases, U.S. Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging, and Re-Emerging Infections, Uganda Virus Research Institute, Entebbe, Uganda
| | - Robert M. Kityo
- Department of Zoology, Entomology, and Fisheries Science, Makerere University, Kampala, Uganda
| | - Ann M. Powers
- Arbovirus Diseases Branch, Division of Vector-Borne Diseases, U.S. Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
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20
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Atim SA, Ashraf S, Belij-Rammerstorfer S, Ademun AR, Vudriko P, Nakayiki T, Niebel M, Shepherd J, Balinandi S, Nakanjako G, Abaasa A, Johnson PC, Odongo S, Esau M, Bahati M, Kaleebu P, Lutwama JJ, Masembe C, Lambe T, Thomson EC, Tweyongyere R. Risk factors for Crimean-Congo Haemorrhagic Fever (CCHF) virus exposure in farming communities in Uganda. J Infect 2022; 85:693-701. [PMID: 36108783 PMCID: PMC9731351 DOI: 10.1016/j.jinf.2022.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 08/01/2022] [Accepted: 09/06/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Crimean-Congo Haemorrhagic Fever (CCHF) is an emerging human-health threat causing sporadic outbreaks in livestock farming communities. However, the full extent and the risks associated with exposure of such communities has not previously been well-described. METHODS We collected blood samples from 800 humans, 666 cattle, 549 goats and 32 dogs in districts within and outside Ugandan cattle corridor in a cross-sectional survey, and tested for CCHFV-specific IgG antibodies using Enzyme-Linked Immunosorbent Assays. Sociodemographic and epidemiological data were recorded using structured questionnaire. Ticks were collected to identify circulating nairoviruses by metagenomic sequencing. RESULTS CCHFV seropositivity was in 221/800 (27·6%) in humans, 612/666 (91·8%) in cattle, 413/549 (75·2%) in goats and 18/32 (56·2%) in dogs. Human seropositivity was associated with livestock farming (AOR=5·68, p<0·0001), age (AOR=2·99, p=0·002) and collecting/eating engorged ticks (AOR=2·13, p=0·004). In animals, seropositivity was higher in cattle versus goats (AOR=2·58, p<0·0001), female sex (AOR=2·13, p=0·002) and heavy tick infestation (>50 ticks: AOR=3·52, p=0·004). CCHFV was identified in multiple tick pools of Rhipicephalus appendiculatus. INTERPRETATION The very high CCHF seropositivity especially among livestock farmers and multiple regional risk factors associated exposures, including collecting/eating engorged ticks previously unrecognised, highlights need for further surveillance and sensitisation and control policies against the disease.
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Affiliation(s)
- Stella A. Atim
- College of Veterinary Medicine, Animal Resources and Biosecurity (CoVAB), Makerere University, Kampala, Uganda,MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom,Ministry of Agriculture, Animal Industry and Fisheries, Entebbe, Uganda
| | - Shirin Ashraf
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | | | - Anna R Ademun
- Ministry of Agriculture, Animal Industry and Fisheries, Entebbe, Uganda
| | - Patrick Vudriko
- College of Veterinary Medicine, Animal Resources and Biosecurity (CoVAB), Makerere University, Kampala, Uganda
| | - Teddy Nakayiki
- Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute, Entebbe, Uganda
| | - Marc Niebel
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - James Shepherd
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Stephen Balinandi
- Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute, Entebbe, Uganda
| | - Gladys Nakanjako
- Ministry of Agriculture, Animal Industry and Fisheries, Entebbe, Uganda,Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute, Entebbe, Uganda
| | - Andrew Abaasa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe Uganda
| | - Paul C.D. Johnson
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Steven Odongo
- College of Veterinary Medicine, Animal Resources and Biosecurity (CoVAB), Makerere University, Kampala, Uganda
| | - Martin Esau
- Ministry of Agriculture, Animal Industry and Fisheries, Entebbe, Uganda
| | - Milton Bahati
- Ministry of Agriculture, Animal Industry and Fisheries, Entebbe, Uganda
| | - Pontiano Kaleebu
- Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute, Entebbe, Uganda,MRC/UVRI and LSHTM Uganda Research Unit, Entebbe Uganda
| | - Julius J Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute, Entebbe, Uganda
| | - Charles Masembe
- College of Natural Resources (CoNAS), Makerere University, Kampala, Uganda
| | - Teresa Lambe
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Emma C. Thomson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom,London School of Hygiene and Tropical Medicine, London, UK
| | - Robert Tweyongyere
- College of Veterinary Medicine, Animal Resources and Biosecurity (CoVAB), Makerere University, Kampala, Uganda,Corresponding Authors.
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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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22
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Tegally H, San JE, Cotten M, Moir M, Tegomoh B, Mboowa G, Martin DP, Baxter C, Lambisia AW, Diallo A, Amoako DG, Diagne MM, Sisay A, Zekri ARN, Gueye AS, Sangare AK, Ouedraogo AS, Sow A, Musa AO, Sesay AK, Abias AG, Elzagheid AI, Lagare A, Kemi AS, Abar AE, Johnson AA, Fowotade A, Oluwapelumi AO, Amuri AA, Juru A, Kandeil A, Mostafa A, Rebai A, Sayed A, Kazeem A, Balde A, Christoffels A, Trotter AJ, Campbell A, Keita AK, Kone A, Bouzid A, Souissi A, Agweyu A, Naguib A, Gutierrez AV, Nkeshimana A, Page AJ, Yadouleton A, Vinze A, Happi AN, Chouikha A, Iranzadeh A, Maharaj A, Batchi-Bouyou AL, Ismail A, Sylverken AA, Goba A, Femi A, Sijuwola AE, Marycelin B, Salako BL, Oderinde BS, Bolajoko B, Diarra B, Herring BL, Tsofa B, Lekana-Douki B, Mvula B, Njanpop-Lafourcade BM, Marondera BT, Khaireh BA, Kouriba B, Adu B, Pool B, McInnis B, Brook C, Williamson C, Nduwimana C, Anscombe C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Mapanguy CM, Loucoubar C, Onwuamah CK, Ihekweazu C, Malaka CN, Peyrefitte C, Grace C, Omoruyi CE, Rafaï CD, Morang’a CM, Erameh C, Lule DB, Bridges DJ, Mukadi-Bamuleka D, Park D, Rasmussen DA, Baker D, Nokes DJ, Ssemwanga D, Tshiabuila D, Amuzu DSY, Goedhals D, Grant DS, Omuoyo DO, Maruapula D, Wanjohi DW, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong’era EM, Ngabana EN, Abworo EO, Otieno E, Shumba E, Barasa E, Ahmed EB, Ahmed EA, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Manuel E, Leendertz F, Taweh FM, Wasfi F, Abdelmoula F, Takawira FT, Derrar F, Ajogbasile FV, Treurnicht F, Onikepe F, Ntoumi F, Muyembe FM, Ragomzingba FEZ, Dratibi FA, Iyanu FA, Mbunsu GK, Thilliez G, Kay GL, Akpede GO, van Zyl GU, Awandare GA, Kpeli GS, Schubert G, Maphalala GP, Ranaivoson HC, Omunakwe HE, Onywera H, Abe H, Karray H, Nansumba H, Triki H, Kadjo HAA, Elgahzaly H, Gumbo H, Mathieu H, Kavunga-Membo H, Smeti I, Olawoye IB, Adetifa IMO, Odia I, Ben Boubaker IB, Mohammad IA, Ssewanyana I, Wurie I, Konstantinus IS, Halatoko JWA, Ayei J, Sonoo J, Makangara JCC, Tamfum JJM, Heraud JM, Shaffer JG, Giandhari J, Musyoki J, Nkurunziza J, Uwanibe JN, Bhiman JN, Yasuda J, Morais J, Kiconco J, Sandi JD, Huddleston J, Odoom JK, Morobe JM, Gyapong JO, Kayiwa JT, Okolie JC, Xavier JS, Gyamfi J, Wamala JF, Bonney JHK, Nyandwi J, Everatt J, Nakaseegu J, Ngoi JM, Namulondo J, Oguzie JU, Andeko JC, Lutwama JJ, Mogga JJH, O’Grady J, Siddle KJ, Victoir K, Adeyemi KT, Tumedi KA, Carvalho KS, Mohammed KS, Dellagi K, Musonda KG, Duedu KO, Fki-Berrajah L, Singh L, Kepler LM, Biscornet L, de Oliveira Martins L, Chabuka L, Olubayo L, Ojok LD, Deng LL, Ochola-Oyier LI, Tyers L, Mine M, Ramuth M, Mastouri M, ElHefnawi M, Mbanne M, Matsheka MI, Kebabonye M, Diop M, Momoh M, Lima Mendonça MDL, Venter M, Paye MF, Faye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina MG, Owusu M, Wiley MR, Tatfeng MY, Ayekaba MO, Abouelhoda M, Beloufa MA, Seadawy MG, Khalifa MK, Matobo MM, Kane M, Salou M, Mbulawa MB, Mwenda M, Allam M, Phan MVT, Abid N, Rujeni N, Abuzaid N, Ismael N, Elguindy N, Top NM, Dia N, Mabunda N, Hsiao NY, Silochi NB, Francisco NM, Saasa N, Bbosa N, Murunga N, Gumede N, Wolter N, Sitharam N, Ndodo N, Ajayi NA, Tordo N, Mbhele N, Razanajatovo NH, Iguosadolo N, Mba N, Kingsley OC, Sylvanus O, Femi O, Adewumi OM, Testimony O, Ogunsanya OA, Fakayode O, Ogah OE, Oludayo OE, Faye O, Smith-Lawrence P, Ondoa P, Combe P, Nabisubi P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Okokhere PO, Bejon P, Dussart P, Bester PA, Mbala PK, Kaleebu P, Abechi P, El-Shesheny R, Joseph R, Aziz RK, Essomba RG, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Neto Rodrigues RMDESA, Audu RA, Carr RAA, Gargouri S, Masmoudi S, Bootsma S, Sankhe S, Mohamed SI, Femi S, Mhalla S, Hosch S, Kassim SK, Metha S, Trabelsi S, Agwa SH, Mwangi SW, Doumbia S, Makiala-Mandanda S, Aryeetey S, Ahmed SS, Ahmed SM, Elhamoumi S, Moyo S, Lutucuta S, Gaseitsiwe S, Jalloh S, Andriamandimby SF, Oguntope S, Grayo S, Lekana-Douki S, Prosolek S, Ouangraoua S, van Wyk S, Schaffner SF, Kanyerezi S, Ahuka-Mundeke S, Rudder S, Pillay S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Mohale T, Le-Viet T, Velavan TP, Schindler T, Maponga TG, Bedford T, Anyaneji UJ, Chinedu U, Ramphal U, George UE, Enouf V, Nene V, Gorova V, Roshdy WH, Karim WA, Ampofo WK, Preiser W, Choga WT, Ahmed YA, Ramphal Y, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR, Ouma AEO, von Gottberg A, Githinji G, Moeti M, Tomori O, Sabeti PC, Sall AA, Oyola SO, Tebeje YK, Tessema SK, de Oliveira T, Happi C, Lessells R, Nkengasong J, Wilkinson E. The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. Science 2022; 378:eabq5358. [PMID: 36108049 PMCID: PMC9529057 DOI: 10.1126/science.abq5358] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022]
Abstract
Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.
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Affiliation(s)
- Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James E. San
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Matthew Cotten
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Bryan Tegomoh
- The Biotechnology Centre of the University of Yaoundé I, Yaoundé, Cameroon
- CDC Foundation, Atlanta, Georgia, Nebraska Department of Health and Human Services, Lincoln, NE, USA
| | - Gerald Mboowa
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | | | - Amadou Diallo
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Daniel G. Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
| | | | - Abay Sisay
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abdel-Rahman N. Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Abdou Salam Gueye
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Abdoul K. Sangare
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
| | - Abdoul-Salam Ouedraogo
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | | | - Abdualmoniem O. Musa
- Faculty of Medicine and Health Sciences, Kassala University, Kassala City, Sudan
- Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Gezira, Gezira, Sudan
- General Administration of Laboratories and Blood Banks, Ministry of Health, Kassala State, Sudan
| | | | - Abe G. Abias
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | | | - Adamou Lagare
- Center for Medical and Sanitary Research (CERMES), Niamey, Niger
| | | | - Aden Elmi Abar
- Laboratoire de la Caisse Nationale de Sécurité Sociale, Djibouti, Republic of Djibouti
| | - Adeniji A. Johnson
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeola Fowotade
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeyemi O. Oluwapelumi
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
- The Pirbright Institute, Woking, UK
| | - Adrienne A. Amuri
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Agnes Juru
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Ahmed Kandeil
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ahmed Sayed
- Genomics and Epigenomics Program, Research Department CCHE57357, Cairo, Egypt
| | - Akano Kazeem
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Aladje Balde
- Laboratório de Biologia Molecular Jean Piaget, Bissau, Guinea-Bissau
- University Jean Piaget in Guinea-Bissau, Bissau, Guinea-Bissau
| | - Alan Christoffels
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
- SAMRC Bioinformatics Unit, SA Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | | | - Allan Campbell
- Central Public Health Reference Laboratories, Freetown, Sierra Leone
| | - Alpha K. Keita
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier University, 34090, Montpellier, France
| | - Amadou Kone
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Amal Bouzid
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Amel Naguib
- Central Public Health Laboratories (CPHL), Cairo, Egypt
| | | | | | | | - Anges Yadouleton
- Laboratoire des Fièvres Hémorragiques Virales du Benin, Cotonou, Benin
| | - Anika Vinze
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Anise N. Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Anissa Chouikha
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Apporach and Technological Innovation for a Better Health”, LR20IPT02, Pasteur Institute, Tunis 1002, Tunisia
| | - Arash Iranzadeh
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arisha Maharaj
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Armel L. Batchi-Bouyou
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Marien Ngouabi, Brazzaville, Republic of the Congo
| | - Arshad Ismail
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Augustina A. Sylverken
- Kwame Nkrumah University of Science and Technology, Department of Theoretical and Applied Biology, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Augustine Goba
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Ayoade Femi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Ayotunde E. Sijuwola
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Baba Marycelin
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
- Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Borno State, Nigeria
| | - Babatunde L. Salako
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Bamidele S. Oderinde
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bankole Bolajoko
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Bassirou Diarra
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Belinda L. Herring
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | | | - Bernard Lekana-Douki
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
- Département de Parasitologie-Mycologie Université des Sciences de la Santé (USS), Libreville, Gabon
| | - Bernard Mvula
- National HIV Reference Laboratory, Community Health Sciences Unit, Ministry of Health, Lilongwe, Malawi
| | | | | | - Bouh Abdi Khaireh
- National Medical and Molecular Biology Laboratory, Ministry of Health, Djibouti, Republic of Djibouti
- Africa CDC, Rapid Responder, Team Djibouti, Djibouti, Djibouti
| | - Bourema Kouriba
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
| | - Bright Adu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Brigitte Pool
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health Seychelles, Victoria, Seychelles
| | - Bronwyn McInnis
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Cara Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Carolyn Williamson
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | - Catherine Anscombe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- SAMRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Chantal G. Akoua-Koffi
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
- UFR Sciences Médicales, Universite Alassane Ouattara, Bouaké, Côte d’Ivoire
| | - Charles N. Agoti
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Public Health, Pwani University, Kilifi, Kenya
| | - Chastel M. Mapanguy
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Faculty of Science and Techniques, University Marien Ngouabi, Brazzaville, Republic of the Congo
| | | | - Chika K. Onwuamah
- Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Chikwe Ihekweazu
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Christian N. Malaka
- Laboratoire des Arbovirus, Fièvres Hémorragiques virales, Virus Emergents et Zoonoses, Institut Pasteur de Bangui, Bangui, Central African Republic
| | | | - Chukwa Grace
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Chukwuma E. Omoruyi
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Clotaire D. Rafaï
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
| | - Collins M. Morang’a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Cyril Erameh
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Daniel B. Lule
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | | | - Daniel Mukadi-Bamuleka
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
| | - Danny Park
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - David A. Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | | | - David J. Nokes
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Deogratius Ssemwanga
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Dominic S. Y. Amuzu
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Dominique Goedhals
- PathCare Vermaak, Pretoria, South Africa and Division of Virology, University of the Free State, Bloemfontein, South Africa
| | - Donald S. Grant
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | | | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Dorcas W. Wanjohi
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | | | - Eddy K. Lusamaki
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier University, 34090, Montpellier, France
| | | | | | - Edith N. Ngabana
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Edward O. Abworo
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Edward Otieno
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Edwin Shumba
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | - Edwine Barasa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - El Bara Ahmed
- INRSP, Nouakchott, Mauritania
- Faculté de Médecine de Nouakchott, Nouakchott, Mauritani
| | - Elhadi A. Ahmed
- Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Gezira, Gezira, Sudan
| | - Emmanuel Lokilo
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
| | | | - Eromon Philomena
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Etilé A. Anoh
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | - Eusebio Manuel
- Direcção Nacional da Saúde Pública, Ministério da Saúde, Luanda, Angola
| | | | - Fahn M. Taweh
- National Public Health Reference Laboratory–National Public Health Institute of Liberia, Monrovia, Liberia
| | - Fares Wasfi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
| | - Fatma Abdelmoula
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | | | - Fawzi Derrar
- National Influenza Centre, Institut Pasteur d’Algérie, Algiers, Algeria
| | - Fehintola V. Ajogbasile
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Florette Treurnicht
- Department of Virology, National Health Laboratory Service (NHLS), Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Folarin Onikepe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Francine Ntoumi
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Francisca M. Muyembe
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | | | - Fred A. Dratibi
- WHO Int Comoros, Moroni, Union of Comoros
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Fred-Akintunwa Iyanu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Gabriel K. Mbunsu
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | | | | | - George O. Akpede
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Gert U. van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Grace S. Kpeli
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | | | - Gugu P. Maphalala
- Ministry of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini
| | | | - Hannah E. Omunakwe
- Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Nigeria
| | - Harris Onywera
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Hela Karray
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Henda Triki
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
| | | | - Hesham Elgahzaly
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Hlanai Gumbo
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Hota Mathieu
- Doctoral School of Technical and Environmental Sciences, Department of Biology and Human Health, N’Djamena, Chad
| | - Hugo Kavunga-Membo
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
| | - Ibtihel Smeti
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Idowu B. Olawoye
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Ifedayo M. O. Adetifa
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Ikponmwosa Odia
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Ilhem Boutiba Ben Boubaker
- Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Research Laboratory LR99ES09, Tunis, Tunisia
| | - Iluoreh Ahmed Mohammad
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | - Isatta Wurie
- College of Medicine and Allied Health Science, University of Sierra Leone, Freetown, Sierra Leone
| | | | | | - James Ayei
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | - Janaki Sonoo
- Virology/Molecular Biology Department, Central Health Laboratory, Victoria Hospital, Ministry of Health and Wellness, Port Louis, Mauritius
| | - Jean-Claude C. Makangara
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Jean-Jacques M. Tamfum
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Jean-Michel Heraud
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | | | - Jessica N. Uwanibe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Jinal N. Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Joana Morais
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
- Departamento de Bioquímica, Faculdade de Medicina, Universidade Agostinho Neto, Luanda, Angola
| | | | - John D. Sandi
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - John K. Odoom
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - John O. Gyapong
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - John T. Kayiwa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Johnson C. Okolie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Joicymara S. Xavier
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
| | - Jones Gyamfi
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | - Joseph H. K. Bonney
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Joseph Nyandwi
- National Institute of Public Health, Bujumbura, Burundi
- Faculty of Medicine, University of Burundi, Bujumbura, Burundi
| | - Josie Everatt
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Joyce M. Ngoi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | | | - Judith U. Oguzie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Julia C. Andeko
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | | | | | - Katherine J. Siddle
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Kayode T. Adeyemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Kefentse A. Tumedi
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
| | | | | | | | | | - Kwabena O. Duedu
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | - Lamia Fki-Berrajah
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Lenora M. Kepler
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Leon Biscornet
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health Seychelles, Victoria, Seychelles
| | | | | | - Luicer Olubayo
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
| | - Lul Deng Ojok
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | - Lul Lojok Deng
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | | | - Lynn Tyers
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Magalutcheemee Ramuth
- Virology/Molecular Biology Department, Central Health Laboratory, Victoria Hospital, Ministry of Health and Wellness, Port Louis, Mauritius
| | - Maha Mastouri
- Laboratory of Transmissible Diseases and Biologically Active Substances (LR99ES27), Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Mahmoud ElHefnawi
- Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, Cairo, Egypt
| | - Maimouna Mbanne
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | | | - Mamadou Diop
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mambu Momoh
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- Eastern Technical University of Sierra Leone, Kenema, Sierra Leone
| | | | - Marietjie Venter
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Marietou F. Paye
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Martin Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | | | - Matoke-Muhia Damaris
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Maximillian G. Mpina
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- Ifakara Health Insitute, Ifakara, Tanzania
| | - Michael Owusu
- Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Michael R. Wiley
- University of Nebraska Medical Center (UNMC), Omaha, NE, USA
- PraesensBio, Lincoln, NE, USA
| | - Mirabeau Y. Tatfeng
- Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria
| | | | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo, Egypt
- King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | | | - Mohamed G. Seadawy
- Biological Prevention Department, Ministry of Defence, Cairo, Egypt
- Faculty of Science, Fayoum University, Fayoum, Egypt
| | | | | | - Mouhamed Kane
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | | | | | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - My V. T. Phan
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biologically Active Substances (LR99ES27), Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- High Institute of Biotechnology of Monastir, University of Monastir, Rue Taher Haddad 5000, Monastir, Tunisia
| | - Nadine Rujeni
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Nadir Abuzaid
- Department of Microbiology, Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Sudan
| | - Nalia Ismael
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | | | | | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Nédio Mabunda
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Nei-yuan Hsiao
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | - Ngiambudulu M. Francisco
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
| | - Ngonda Saasa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Nicholas Bbosa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | | | - Nicksy Gumede
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Nicole Wolter
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Nikita Sitharam
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Nnaemeka Ndodo
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Nnennaya A. Ajayi
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Noël Tordo
- Institut Pasteur de Guinée, Conarky, Guinea
| | - Nokuzola Mbhele
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Nosamiefan Iguosadolo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Nwando Mba
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Ojide C. Kingsley
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Okogbenin Sylvanus
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Oladiji Femi
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences. College of Health Sciences. University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Olubusuyi M. Adewumi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olumade Testimony
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Olusola A. Ogunsanya
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Oluwatosin Fakayode
- Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria
| | - Onwe E. Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Ope-Ewe Oludayo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Pascale Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | | | - Patricia Nabisubi
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | | | - Paul E. Oluniyi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Paulo Arnaldo
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Peter Kojo Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Peter O. Okokhere
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- Department of Medicine, Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Edo State, Nigeria
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Phillip A. Bester
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | - Placide K. Mbala
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Pontiano Kaleebu
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Priscilla Abechi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Rabeh El-Shesheny
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
- Infectious Hazards Preparedness, World Health Organization, Eastern Mediterranean Regional Office, Cairo, Egypt
| | - Rageema Joseph
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Ramy Karam Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Microbiology and Immunology Research Program, Children’s Cancer Hospital Egypt, Cairo, Egypt
| | - René G. Essomba
- National Public Health Laboratory, Ministry of Public Health of Cameroon, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon
| | - Reuben Ayivor-Djanie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | - Richard Njouom
- Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon
| | - Richard O. Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richmond Gorman
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Rosa Maria D. E. S. A. Neto Rodrigues
- Coordenadora da rede do Diagnóstico Tuberculose/HIV/COVID-19 na Instituição - Laboratório Nacional de Referência da Tuberculose em São Tomé e Príncipe, São Tomé, São Tomé and Principe
- Ponto focal para Melhoria da qualidade dos Laboratórios (SLIPTA) ao nível de São Tomé e Príncipe, São Tomé, São Tomé and Principe
| | - Rosemary A. Audu
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Rosina A. A. Carr
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | - Saba Gargouri
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Safietou Sankhe
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Saibu Femi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Salma Mhalla
- University of Tunis El Manar, Faculty of Medicine of Tunis, Research Laboratory LR99ES09, Tunis, Tunisia
- Faculty of Medicine of Monastir, University of Monastir, Monastir, Tunisia
| | - Salome Hosch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Samar Kamal Kassim
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Samar Metha
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sameh Trabelsi
- Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia
| | - Sara Hassan Agwa
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Sarah Wambui Mwangi
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Seydou Doumbia
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Sheila Makiala-Mandanda
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Sherihane Aryeetey
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | | | - Siham Elhamoumi
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Silvia Lutucuta
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simbirie Jalloh
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | | | - Sobajo Oguntope
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | - Sonia Lekana-Douki
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Soumeya Ouangraoua
- Centre MURAZ, Ouagadougou, Burkina Faso
- National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso
| | - Stephanie van Wyk
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Stephen F. Schaffner
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Stephen Kanyerezi
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | - Steve Ahuka-Mundeke
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | | | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Susan Nabadda
- Central Public Health Laboratories (CPHL), Kampala, Uganda
| | - Sylvie Behillil
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
| | | | - Sylvie van der Werf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
| | - Tapfumanei Mashe
- National Microbiology Reference Laboratory, Harare, Zimbabwe
- World Health Organization, Harare, Zimbabwe
| | - Thabo Mohale
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Thirumalaisamy P. Velavan
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
| | - Tobias Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- University of Basel, Basel, Switzerland
| | - Tongai G. Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ugwu Chinedu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa
| | - Uwem E. George
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Vincent Enouf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
| | - Vishvanath Nene
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Vivianne Gorova
- World Health Organization, WHO Lesotho, Maseru, Lesotho
- Med24 Medical Centre, Ruwa, Zimbabwe
| | | | - Wasim Abdul Karim
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - William K. Ampofo
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Wonderful T. Choga
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Yahaya Ali Ahmed
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Yajna Ramphal
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Yemaachi Biotech, Accra, Ghana
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Yvan Butera
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
| | | | - Africa Pathogen Genomics Initiative (Africa PGI)
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- The Biotechnology Centre of the University of Yaoundé I, Yaoundé, Cameroon
- CDC Foundation, Atlanta, Georgia, Nebraska Department of Health and Human Services, Lincoln, NE, USA
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
- West African Health Organisation, Bobo-Dioulasso, Burkina Faso
- Faculty of Medicine and Health Sciences, Kassala University, Kassala City, Sudan
- Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Gezira, Gezira, Sudan
- General Administration of Laboratories and Blood Banks, Ministry of Health, Kassala State, Sudan
- MRC Unit The Gambia at LSHTM, Fajara, Gambia
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
- Libyan Biotechnology Research Center, Tripoli, Libya
- Center for Medical and Sanitary Research (CERMES), Niamey, Niger
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Laboratoire de la Caisse Nationale de Sécurité Sociale, Djibouti, Republic of Djibouti
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
- The Pirbright Institute, Woking, UK
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
- National Microbiology Reference Laboratory, Harare, Zimbabwe
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Genomics and Epigenomics Program, Research Department CCHE57357, Cairo, Egypt
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- Laboratório de Biologia Molecular Jean Piaget, Bissau, Guinea-Bissau
- University Jean Piaget in Guinea-Bissau, Bissau, Guinea-Bissau
- SAMRC Bioinformatics Unit, SA Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
- Quadram Institute Bioscience, Norwich, UK
- Central Public Health Reference Laboratories, Freetown, Sierra Leone
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier University, 34090, Montpellier, France
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Central Public Health Laboratories (CPHL), Cairo, Egypt
- National Institute of Public Health, Bujumbura, Burundi
- Laboratoire des Fièvres Hémorragiques Virales du Benin, Cotonou, Benin
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Apporach and Technological Innovation for a Better Health”, LR20IPT02, Pasteur Institute, Tunis 1002, Tunisia
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Marien Ngouabi, Brazzaville, Republic of the Congo
- Kwame Nkrumah University of Science and Technology, Department of Theoretical and Applied Biology, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
- Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Borno State, Nigeria
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
- Département de Parasitologie-Mycologie Université des Sciences de la Santé (USS), Libreville, Gabon
- National HIV Reference Laboratory, Community Health Sciences Unit, Ministry of Health, Lilongwe, Malawi
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
- National Medical and Molecular Biology Laboratory, Ministry of Health, Djibouti, Republic of Djibouti
- Africa CDC, Rapid Responder, Team Djibouti, Djibouti, Djibouti
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health Seychelles, Victoria, Seychelles
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- National Health Laboratory Service (NHLS), Cape Town, South Africa
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
- University of Nebraska Medical Center (UNMC), Omaha, NE, USA
- SAMRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
- UFR Sciences Médicales, Universite Alassane Ouattara, Bouaké, Côte d’Ivoire
- School of Public Health, Pwani University, Kilifi, Kenya
- Faculty of Science and Techniques, University Marien Ngouabi, Brazzaville, Republic of the Congo
- Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
- Laboratoire des Arbovirus, Fièvres Hémorragiques virales, Virus Emergents et Zoonoses, Institut Pasteur de Bangui, Bangui, Central African Republic
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- PATH, Lusaka, Zambia
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
- Uganda Virus Research Institute, Entebbe, Uganda
- PathCare Vermaak, Pretoria, South Africa and Division of Virology, University of the Free State, Bloemfontein, South Africa
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Macha Research Trust, Choma, Zambia
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- INRSP, Nouakchott, Mauritania
- Faculté de Médecine de Nouakchott, Nouakchott, Mauritani
- Rwanda National Reference Laboratory, Kigali, Rwanda
- Robert Koch-Institute, Berlin, Germany
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Paris, France
- Direcção Nacional da Saúde Pública, Ministério da Saúde, Luanda, Angola
- National Public Health Reference Laboratory–National Public Health Institute of Liberia, Monrovia, Liberia
- Faculty of Pharmacy of Monastir, Monastir, Tunisia
- National Influenza Centre, Institut Pasteur d’Algérie, Algiers, Algeria
- Department of Virology, National Health Laboratory Service (NHLS), Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
- Ministère de Santé Publique et de la Solidarité Nationale, Ndjamena, Chad
- WHO Int Comoros, Moroni, Union of Comoros
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
- Ministry of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini
- Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Nigeria
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
- Central Public Health Laboratories (CPHL), Kampala, Uganda
- Institut Pasteur de Côte d’Ivoire, Departement des Virus Epidemiques, Abidjan, Côte d’Ivoire
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
- Doctoral School of Technical and Environmental Sciences, Department of Biology and Human Health, N’Djamena, Chad
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
- Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Research Laboratory LR99ES09, Tunis, Tunisia
- College of Medicine and Allied Health Science, University of Sierra Leone, Freetown, Sierra Leone
- Namibia Institute of Pathology, Windhoek, Namibia
- National Institute of Hygiene, Lomé, Togo
- Virology/Molecular Biology Department, Central Health Laboratory, Victoria Hospital, Ministry of Health and Wellness, Port Louis, Mauritius
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
- WHO Burundi, Gitega, Burundi
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
- Departamento de Bioquímica, Faculdade de Medicina, Universidade Agostinho Neto, Luanda, Angola
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
- WHO South Sudan, Juba, South Sudan
- Faculty of Medicine, University of Burundi, Bujumbura, Burundi
- Pasteur Network, Institut Pasteur, Paris, France
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- Instituto Nacional de Saúde Pública, Praia, Cape Verde
- Zambia National Public Health Institute, Lusaka, Zambia
- Public Health Institute of Malawi, Lilongwe, Malawi
- National Health Laboratory, Gaborone, Botswana
- Laboratory of Transmissible Diseases and Biologically Active Substances (LR99ES27), Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
- Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, Cairo, Egypt
- Ministry of Health and Wellness, Gaborone, Botswana
- Eastern Technical University of Sierra Leone, Kenema, Sierra Leone
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
- National Reference Laboratory Lesotho, Maseru, Lesotho
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- Ifakara Health Insitute, Ifakara, Tanzania
- Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- PraesensBio, Lincoln, NE, USA
- Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo, Egypt
- King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
- Biological Prevention Department, Ministry of Defence, Cairo, Egypt
- Faculty of Science, Fayoum University, Fayoum, Egypt
- Molecular Pathology Lab, Children’s Cancer Hospital, Cairo, Egypt
- Laboratoire Biolim FSS/Université de Lomé, Lomé, Togo
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
- High Institute of Biotechnology of Monastir, University of Monastir, Rue Taher Haddad 5000, Monastir, Tunisia
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Department of Microbiology, Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Sudan
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
- Institut Pasteur de Guinée, Conarky, Guinea
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences. College of Health Sciences. University of Ilorin, Ilorin, Kwara State, Nigeria
- Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
- Mayotte Hospital Center, Mayotte, France
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
- Department of Medicine, Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Edo State, Nigeria
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
- Infectious Hazards Preparedness, World Health Organization, Eastern Mediterranean Regional Office, Cairo, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Microbiology and Immunology Research Program, Children’s Cancer Hospital Egypt, Cairo, Egypt
- National Public Health Laboratory, Ministry of Public Health of Cameroon, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon
- Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon
- Coordenadora da rede do Diagnóstico Tuberculose/HIV/COVID-19 na Instituição - Laboratório Nacional de Referência da Tuberculose em São Tomé e Príncipe, São Tomé, São Tomé and Principe
- Ponto focal para Melhoria da qualidade dos Laboratórios (SLIPTA) ao nível de São Tomé e Príncipe, São Tomé, São Tomé and Principe
- National Public Health Reference Laboratory (NPHRL), Mogadishu, Somalia
- Faculty of Medicine of Monastir, University of Monastir, Monastir, Tunisia
- University of Basel, Basel, Switzerland
- Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre MURAZ, Ouagadougou, Burkina Faso
- National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
- World Health Organization, Harare, Zimbabwe
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa
- World Health Organization, WHO Lesotho, Maseru, Lesotho
- Med24 Medical Centre, Ruwa, Zimbabwe
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Yemaachi Biotech, Accra, Ghana
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Ahmed E. O. Ouma
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Matshidiso Moeti
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Pardis C. Sabeti
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Amadou A. Sall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Samuel O. Oyola
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Yenew K. Tebeje
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Sofonias K. Tessema
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - John Nkengasong
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
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Lule SA, Gibb R, Kizito D, Nakanjako G, Mutyaba J, Balinandi S, Owen L, Jones KE, Abubakar I, Lutwama JJ, Field N. Widespread exposure to Crimean-Congo haemorrhagic fever in Uganda might be driven by transmission from Rhipicephalus ticks: Evidence from cross-sectional and modelling studies. J Infect 2022; 85:683-692. [PMID: 36152736 DOI: 10.1016/j.jinf.2022.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Crimean-Congo haemorrhagic fever (CCHF) is a widespread tick-borne viral infection, present across Africa and Eurasia, which might pose a cryptic public health problem in Uganda. We aimed to understand the magnitude and distribution of CCHF risk in humans, livestock and ticks across Uganda by synthesising epidemiological (cross-sectional) and ecological (modelling) studies. METHODS We conducted a cross-sectional study at three urban abattoirs receiving cattle from across Uganda. We sampled humans (n = 478), livestock (n = 419) and ticks (n = 1065) and used commercially-available kits to detect human and livestock CCHF virus (CCHFV) antibodies and antigen in tick pools. We developed boosted regression tree models to evaluate the correlates and geographical distribution of expected tick and wildlife hosts, and of human CCHF exposures, drawing on continent-wide data. FINDINGS The cross-sectional study found CCHFV IgG/IgM seroprevalence in humans of 10·3% (7·8-13·3), with antibody detection positively associated with reported history of tick bite (age-adjusted odds ratio = 2·09 (1·09-3·98)). Cattle had a seroprevalence of 69·7% (65·1-73·4). Only one Hyalomma tick (CCHFV-negative) was found. However, CCHFV antigen was detected in Rhipicephalus (5·9% of 304 pools) and Amblyomma (2·9% of 34 pools) species. Modelling predicted high human CCHF risk across much of Uganda, low environmental suitability for Hyalomma, and high suitability for Rhipicephalus and Amblyomma. INTERPRETATION Our epidemiological and ecological studies provide complementary evidence that CCHF exposure risk is widespread across Uganda. We challenge the idea that Hyalomma ticks are consistently the principal reservoir and vector for CCHFV, and postulate that Rhipicephalus might be important for CCHFV transmission in Uganda, due to high frequency of infected ticks and predicted environmental suitability. FUNDING UCL Global Challenges Research Fund (GCRF) and Pan-African Network on Emerging and Re-Emerging Infections (PANDORA-ID-NET) funded by the European and Developing Countries Clinical Trials Partnership (EDCTP) under the EU Horizon 2020 Framework Programme for Research and Innovation.
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Affiliation(s)
- Swaib A Lule
- Institute for Global Health (IGH), University College London, London, UK
| | - Rory Gibb
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Dennison Kizito
- Department of Arbovirology, Emerging and Re-Emerging Infectious Diseases (DAERID), Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - Gladys Nakanjako
- Department of Arbovirology, Emerging and Re-Emerging Infectious Diseases (DAERID), Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - Joseph Mutyaba
- Department of Arbovirology, Emerging and Re-Emerging Infectious Diseases (DAERID), Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - Stephen Balinandi
- Department of Arbovirology, Emerging and Re-Emerging Infectious Diseases (DAERID), Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - Leah Owen
- Institute for Global Health (IGH), University College London, London, UK
| | - Kate E Jones
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Ibrahim Abubakar
- Institute for Global Health (IGH), University College London, London, UK
| | - Julius J Lutwama
- Department of Arbovirology, Emerging and Re-Emerging Infectious Diseases (DAERID), Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - Nigel Field
- Institute for Global Health (IGH), University College London, London, UK.
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Balinandi S, Hayer J, Cholleti H, Wille M, Lutwama JJ, Malmberg M, Mugisha L. Identification and molecular characterization of highly divergent RNA viruses in cattle, Uganda. Virus Res 2022; 313:198739. [PMID: 35271887 DOI: 10.1016/j.virusres.2022.198739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 10/18/2022]
Abstract
The risk for the emergence of novel viral zoonotic diseases in animals and humans in Uganda is high given its geographical location with high biodiversity. We aimed to identify and characterize viruses in 175 blood samples from cattle selected in Uganda using molecular approaches. We identified 8 viral species belonging to 4 families (Flaviviridae, Peribunyaviridae, Reoviridae and Rhabdoviridae) and 6 genera (Hepacivirus, Pestivirus, Orthobunyavirus, Coltivirus, Dinovernavirus and Ephemerovirus). Four viruses were highly divergent and tetantively named Zikole virus (Family: Flaviviridae), Zeboroti virus (Family: Reoviridae), Zebtine virus (Family: Rhabdoviridae) and Kokolu virus (Family: Rhabdoviridae). In addition, Bovine hepacivirus, Obodhiang virus, Aedes pseudoscutellaris reovirus and Schmallenberg virus were identified for the first time in Ugandan cattle. We report 8 viral species belonging to 4 viral families including divergent ones in the blood of cattle in Uganda. Hence, cattle may be reservoir hosts for likely emergence of novel viruses with pathogenic potential to cause zoonotic diseases in different species with serious public health implications.
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Affiliation(s)
- Stephen Balinandi
- Uganda Virus Research Institute; Entebbe, Uganda; College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Juliette Hayer
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Harindranath Cholleti
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Michelle Wille
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Maja Malmberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Lawrence Mugisha
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda; Ecohealth Research Group, Conservation & Ecosystem Health Alliance (CEHA), Kampala, Uganda.
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25
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Nyakarahuka L, Mulei S, Whitmer S, Jackson K, Tumusiime A, Schuh A, Baluku J, Joyce A, Ocom F, Tusiime JB, Montgomery JM, Balinandi S, Lutwama JJ, Klena JD, Shoemaker TR. First laboratory confirmation and sequencing of Zaire ebolavirus in Uganda following two independent introductions of cases from the 10th Ebola Outbreak in the Democratic Republic of the Congo, June 2019. PLoS Negl Trop Dis 2022; 16:e0010205. [PMID: 35192613 PMCID: PMC8896669 DOI: 10.1371/journal.pntd.0010205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 03/04/2022] [Accepted: 01/26/2022] [Indexed: 11/18/2022] Open
Abstract
Uganda established a domestic Viral Hemorrhagic Fever (VHF) testing capacity in 2010 in response to the increasing occurrence of filovirus outbreaks. In July 2018, the neighboring Democratic Republic of Congo (DRC) experienced its 10th Ebola Virus Disease (EVD) outbreak and for the duration of the outbreak, the Ugandan Ministry of Health (MOH) initiated a national EVD preparedness stance. Almost one year later, on 10th June 2019, three family members who had contracted EVD in the DRC crossed into Uganda to seek medical treatment.
Samples were collected from all the suspected cases using internationally established biosafety protocols and submitted for VHF diagnostic testing at Uganda Virus Research Institute. All samples were initially tested by RT-PCR for ebolaviruses, marburgviruses, Rift Valley fever (RVF) virus and Crimean-Congo hemorrhagic fever (CCHF) virus. Four people were identified as being positive for Zaire ebolavirus, marking the first report of Zaire ebolavirus in Uganda. In-country Next Generation Sequencing (NGS) and phylogenetic analysis was performed for the first time in Uganda, confirming the outbreak as imported from DRC at two different time point from different clades. This rapid response by the MoH, UVRI and partners led to the control of the outbreak and prevention of secondary virus transmission.
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Affiliation(s)
- Luke Nyakarahuka
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
- Department of Biosecurity, Ecosystems and Veterinary Public Health, Makerere University, Kampala, Uganda
- * E-mail:
| | - Sophia Mulei
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Shannon Whitmer
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Kyondo Jackson
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Alex Tumusiime
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Amy Schuh
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jimmy Baluku
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Allison Joyce
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Felix Ocom
- Uganda Public Health Emergency Operations Center, Kampala, Uganda
| | | | - Joel M. Montgomery
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Stephen Balinandi
- 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
| | - John D. Klena
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Trevor R. Shoemaker
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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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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Schuh AJ, Kyondo J, Graziano J, Balinandi S, Kainulainen MH, Tumusiime A, Nyakarahuka L, Mulei S, Baluku J, Lonergan W, Mayer O, Masereka R, Masereka F, Businge E, Gatare A, Kabyanga L, Muhindo S, Mugabe R, Makumbi I, Kayiwa J, Wetaka MM, Brown V, Ojwang J, Nelson L, Millard M, Nichol ST, Montgomery JM, Taboy CH, Lutwama JJ, Klena JD. Rapid establishment of a frontline field laboratory in response to an imported outbreak of Ebola virus disease in western Uganda, June 2019. PLoS Negl Trop Dis 2021; 15:e0009967. [PMID: 34860831 PMCID: PMC8673597 DOI: 10.1371/journal.pntd.0009967] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 12/15/2021] [Accepted: 11/03/2021] [Indexed: 12/12/2022] Open
Abstract
The Democratic Republic of the Congo (DRC) declared an Ebola virus disease (EVD) outbreak in North Kivu in August 2018. By June 2019, the outbreak had spread to 26 health zones in northeastern DRC, causing >2,000 reported cases and >1,000 deaths. On June 10, 2019, three members of a Congolese family with EVD-like symptoms traveled to western Uganda’s Kasese District to seek medical care. Shortly thereafter, the Viral Hemorrhagic Fever Surveillance and Laboratory Program (VHF program) at the Uganda Virus Research Institute (UVRI) confirmed that all three patients had EVD. The Ugandan Ministry of Health declared an outbreak of EVD in Uganda’s Kasese District, notified the World Health Organization, and initiated a rapid response to contain the outbreak. As part of this response, UVRI and the United States Centers for Disease Control and Prevention, with the support of Uganda’s Public Health Emergency Operations Center, the Kasese District Health Team, the Superintendent of Bwera General Hospital, the United States Department of Defense’s Makerere University Walter Reed Project, and the United States Mission to Kampala’s Global Health Security Technical Working Group, jointly established an Ebola Field Laboratory in Kasese District at Bwera General Hospital, proximal to an Ebola Treatment Unit (ETU). The laboratory consisted of a rapid containment kit for viral inactivation of patient specimens and a GeneXpert Instrument for performing Xpert Ebola assays. Laboratory staff tested 76 specimens from alert and suspect cases of EVD; the majority were admitted to the ETU (89.3%) and reported recent travel to the DRC (58.9%). Although no EVD cases were detected by the field laboratory, it played an important role in patient management and epidemiological surveillance by providing diagnostic results in <3 hours. The integration of the field laboratory into Uganda’s National VHF Program also enabled patient specimens to be referred to Entebbe for confirmatory EBOV testing and testing for other hemorrhagic fever viruses that circulate in Uganda. Following an imported outbreak of Ebola virus disease in Uganda’s western Kasese District, the Uganda Virus Research Institute and the United States Centers for Disease Control and Prevention jointly established a frontline field laboratory to test specimens collected from alert and suspect cases for Ebola virus disease. Using a single room equipped with a rapid containment kit to safely inactivate patient specimens and a GeneXpert to perform the Xpert Ebola Assay, the field laboratory rapidly ruled-out Ebola virus disease as the cause of illness in 76 patients during its 46 operational days. All specimens were also referred to Uganda Virus Research Institute (Entebbe) for confirmatory Ebola virus testing and testing against a panel of viruses known to cause hemorrhagic fever in Uganda, in line with the National Viral Hemorrhagic Fever Program’s testing protocol and mandate. The Ebola field laboratory served as a valuable asset in the outbreak response by supporting patient management and epidemiological surveillance.
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Affiliation(s)
- Amy J. Schuh
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- United States Public Health Service Commissioned Corps, Rockville, Maryland, United States of America
- * E-mail: (AJS); (JDK)
| | - Jackson Kyondo
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - James Graziano
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Stephen Balinandi
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Markus H. Kainulainen
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Alex Tumusiime
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Luke Nyakarahuka
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Sophia Mulei
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Jimmy Baluku
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - William Lonergan
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Oren Mayer
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- United States Public Health Service Commissioned Corps, Rockville, Maryland, United States of America
| | | | | | | | | | | | | | - Raymond Mugabe
- Uganda Central Public Health Laboratories, Kampala, Uganda
| | - Issa Makumbi
- Uganda Public Health Emergency Operations Center, Kampala, Uganda
| | - Joshua Kayiwa
- Uganda Public Health Emergency Operations Center, Kampala, Uganda
| | | | - Vance Brown
- United States Centers for Disease Control and Prevention, Kampala, Uganda
| | - Joseph Ojwang
- United States Centers for Disease Control and Prevention, Kampala, Uganda
| | - Lisa Nelson
- United States Centers for Disease Control and Prevention, Kampala, Uganda
| | | | - Stuart T. Nichol
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Joel M. Montgomery
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- United States Public Health Service Commissioned Corps, Rockville, Maryland, United States of America
| | - Celine H. Taboy
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - John D. Klena
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail: (AJS); (JDK)
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Wilkinson E, Giovanetti M, Tegally H, San JE, Lessells R, Cuadros D, Martin DP, Rasmussen DA, Zekri ARN, Sangare AK, Ouedraogo AS, Sesay AK, Priscilla A, Kemi AS, Olubusuyi AM, Oluwapelumi AOO, Hammami A, Amuri AA, Sayed A, Ouma AEO, Elargoubi A, Ajayi NA, Victoria AF, Kazeem A, George A, Trotter AJ, Yahaya AA, Keita AK, Diallo A, Kone A, Souissi A, Chtourou A, Gutierrez AV, Page AJ, Vinze A, Iranzadeh A, Lambisia A, Ismail A, Rosemary A, Sylverken A, Femi A, Ibrahimi A, Marycelin B, Oderinde BS, Bolajoko B, Dhaala B, Herring BL, Njanpop-Lafourcade BM, Kleinhans B, McInnis B, Tegomoh B, Brook C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Peyrefitte C, Daubenberger C, Morang’a CM, Nokes DJ, Amoako DG, Bugembe DL, Park D, Baker D, Doolabh D, Ssemwanga D, Tshiabuila D, Bassirou D, Amuzu DSY, Goedhals D, Omuoyo DO, Maruapula D, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong’era EM, Ngabana EN, Shumba E, El Fahime E, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Leendertz F, Ajili F, Enoch FO, Wasfi F, Abdelmoula F, Mosha FS, Takawira FT, Derrar F, Bouzid F, Onikepe F, Adeola F, Muyembe FM, Tanser F, Dratibi FA, Mbunsu GK, Thilliez G, Kay GL, Githinji G, van Zyl G, Awandare GA, Schubert G, Maphalala GP, Ranaivoson HC, Lemriss H, Anise H, Abe H, Karray HH, Nansumba H, Elgahzaly HA, Gumbo H, Smeti I, Ayed IB, Odia I, Ben Boubaker IB, Gaaloul I, Gazy I, Mudau I, Ssewanyana I, Konstantinus I, Lekana-Douk JB, Makangara JCC, Tamfum JJM, Heraud JM, Shaffer JG, Giandhari J, Li J, Yasuda J, Mends JQ, Kiconco J, Morobe JM, Gyapong JO, Okolie JC, Kayiwa JT, Edwards JA, Gyamfi J, Farah J, Nakaseegu J, Ngoi JM, Namulondo J, Andeko JC, Lutwama JJ, O’Grady J, Siddle K, Adeyemi KT, Tumedi KA, Said KM, Hae-Young K, Duedu KO, Belyamani L, Fki-Berrajah L, Singh L, Martins LDO, Tyers L, Ramuth M, Mastouri M, Aouni M, el Hefnawi M, Matsheka MI, Kebabonye M, Diop M, Turki M, Paye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina M, Nwando M, Owusu M, Wiley MR, Youtchou MT, Ayekaba MO, Abouelhoda M, Seadawy MG, Khalifa MK, Sekhele M, Ouadghiri M, Diagne MM, Mwenda M, Allam M, Phan MVT, Abid N, Touil N, Rujeni N, Kharrat N, Ismael N, Dia N, Mabunda N, Hsiao NY, Silochi NB, Nsenga N, Gumede N, Mulder N, Ndodo N, Razanajatovo NH, Iguosadolo N, Judith O, Kingsley OC, Sylvanus O, Peter O, Femi O, Idowu O, Testimony O, Chukwuma OE, Ogah OE, Onwuamah CK, Cyril O, Faye O, Tomori O, Ondoa P, Combe P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Dussart P, Bester PA, Mbala PK, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Carr RAA, El Kabbaj S, Gargouri S, Masmoudi S, Sankhe S, Lawal SB, Kassim S, Trabelsi S, Metha S, Kammoun S, Lemriss S, Agwa SHA, Calvignac-Spencer S, Schaffner SF, Doumbia S, Mandanda SM, Aryeetey S, Ahmed SS, Elhamoumi S, Andriamandimby S, Tope S, Lekana-Douki S, Prosolek S, Ouangraoua S, Mundeke SA, Rudder S, Panji S, Pillay S, Engelbrecht S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Aanniz T, Mohale T, Le-Viet T, Schindler T, Anyaneji UJ, Chinedu U, Ramphal U, Jessica U, George U, Fonseca V, Enouf V, Gorova V, Roshdy WH, Ampofo WK, Preiser W, Choga WT, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR, Sall AA, Rebai A, von Gottberg A, Kouriba B, Williamson C, Bridges DJ, Chikwe I, Bhiman JN, Mine M, Cotten M, Moyo S, Gaseitsiwe S, Saasa N, Sabeti PC, Kaleebu P, Tebeje YK, Tessema SK, Happi C, Nkengasong J, de Oliveira T. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science 2021; 374:423-431. [PMID: 34672751 PMCID: PMC7613315 DOI: 10.1126/science.abj4336] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/03/2021] [Indexed: 01/05/2023]
Abstract
The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants.
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Affiliation(s)
- Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James E. San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Diego Cuadros
- Department of Geography and GIS, University of Cincinnati, Cincinnati, OH, USA
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - David A. Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Abdel-Rahman N. Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Abdoul K. Sangare
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
| | - Abdoul-Salam Ouedraogo
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | | | - Abechi Priscilla
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Adedotun-Sulaiman Kemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | - Adeyemi O. O. Oluwapelumi
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Adnène Hammami
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Adrienne A. Amuri
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Ahmad Sayed
- Genomics Research Program, Children’s Cancer Hospital, Cairo, Egypt
| | - Ahmed E. O. Ouma
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Aida Elargoubi
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Nnennaya A. Ajayi
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Ajogbasile F. Victoria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Akano Kazeem
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Ali A. Yahaya
- World Health Organization, Africa Region, Brazzaville Congo
| | - Alpha K. Keita
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea
- TransVIHMI, Montpellier University/IRD/INSERM, Montpellier, France
| | - Amadou Diallo
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou Kone
- Mali-University Clinical Research Center (UCRC), Bamako, Mali
| | - Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Amel Chtourou
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | | | | | - Anika Vinze
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Arash Iranzadeh
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arnold Lambisia
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Arshad Ismail
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Audu Rosemary
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | | | - Ayoade Femi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Baba Marycelin
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bamidele S. Oderinde
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bankole Bolajoko
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | | | - Bronwyn Kleinhans
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Bronwyn McInnis
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Bryan Tegomoh
- The Biotechnology Center of the University of Yaoundé I, Cameroon and CDC Foundation, Yaounde, Cameroon
| | - Cara Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | | | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Chantal G. Akoua-Koffi
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | - Charles N. Agoti
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- School of Public Health, Pwani University, Kilifi, Kenya
| | | | | | - Collins M. Morang’a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - D. James Nokes
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Daniel G. Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Danny Park
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | | | - Deelan Doolabh
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Deogratius Ssemwanga
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Diarra Bassirou
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Dominic S. Y. Amuzu
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Dominique Goedhals
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | | | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | | | - Eddy K. Lusamaki
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Edgar Simulundu
- University of Zambia, School of Veterinary Medicine, Department of Disease Control, Lusaka, Zambia
| | | | - Edith N. Ngabana
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Edwin Shumba
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | - Elmostafa El Fahime
- Functional Genomic Platform/National Centre for Scientific and Technical Research (CNRST), Rabat, Morocco
| | - Emmanuel Lokilo
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
| | | | - Eromon Philomena
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Etilé A. Anoh
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | | | - Faida Ajili
- Research Unit of Autoimmune Diseases UR17DN02, Military Hospital of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Fakayode O. Enoch
- Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria
| | - Fares Wasfi
- Laboratory of Clinical Virology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Fatma Abdelmoula
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | | | | | - Fawzi Derrar
- National Influenza Centre, Viral Respiratory Laboratory, Algiers, Algeria
| | - Feriel Bouzid
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Folarin Onikepe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Fowotade Adeola
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Francisca M. Muyembe
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Frank Tanser
- Lincoln International Institute for Rural Health, University of Lincoln, Lincoln, UK
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
| | | | - Gabriel K. Mbunsu
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | | | - George Githinji
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Gert van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | | | - Gugu P. Maphalala
- Institution and Department, Ministry Of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini
| | | | - Hajar Lemriss
- Laboratory of Health Sciences and Technologies, High Institute of Health Sciences, Hassan 1st University, Settat, Morocco
| | - Happi Anise
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Hela H. Karray
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | | | - Hesham A. Elgahzaly
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Hlanai Gumbo
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Ibtihel Smeti
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ikhlas B. Ayed
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Ilhem Boutiba Ben Boubaker
- Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, 1006 Tunis, Tunisia
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Imed Gaaloul
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | - Inbal Gazy
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Innocent Mudau
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Jean B. Lekana-Douk
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | - Jean-Claude C. Makangara
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Jean-Jacques M. Tamfum
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Jean-Michel Heraud
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jingjing Li
- Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, PA, USA
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Joana Q. Mends
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | - John M. Morobe
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - John O. Gyapong
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Johnson C. Okolie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - John T. Kayiwa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Johnathan A. Edwards
- Lincoln International Institute for Rural Health, University of Lincoln, Lincoln, UK
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jones Gyamfi
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | | | - Joyce M. Ngoi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | | | - Julia C. Andeko
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | | | | | - Kayode T. Adeyemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Kefentse A. Tumedi
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
| | - Khadija M. Said
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Kim Hae-Young
- New York University Grossman School of Medicine, New York City, NY, USA
| | - Kwabena O. Duedu
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Lahcen Belyamani
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Lamia Fki-Berrajah
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Lynn Tyers
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Magalutcheemee Ramuth
- Virology/Molecular Biology Department, Central Health Laboratory, Ministry of Health and Wellness, Mauritius
| | - Maha Mastouri
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Mahjoub Aouni
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | - Mahmoud el Hefnawi
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo Egypt
| | | | | | - Mamadou Diop
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Manel Turki
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Marietou Paye
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | | | - Matoke-Muhia Damaris
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | - Maureen W. Mburu
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Maximillian Mpina
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- Ifakara Health Institute, Dar-es-Salaam, Tanzania
| | - Mba Nwando
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Michael Owusu
- Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Mirabeau T. Youtchou
- Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria
| | | | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo 12613, Egypt
- King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Mohamed G. Seadawy
- Biological Prevention Department, Main Chemical Laboratories, Egypt Army, Cairo, Egypt
| | | | - Mooko Sekhele
- National Reference Laboratory Lesotho, Maseru, Lesotho
| | - Mouna Ouadghiri
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | | | | | - Mushal Allam
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - My V. T. Phan
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
- Department of Biotechnology, High Institute of Biotechnology of Sidi Thabet, University of Manouba, BP-66, 2020 Ariana-Tunis, Tunisia
| | - Nadia Touil
- Genomic Center for Human Pathologies (GENOPATH), Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Nadine Rujeni
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Najla Kharrat
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Nalia Ismael
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Nedio Mabunda
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Nei-yuan Hsiao
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | - Ngoy Nsenga
- World Health Organization, Africa Region, Brazzaville Congo
| | - Nicksy Gumede
- World Health Organization, Africa Region, Brazzaville Congo
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa
| | | | | | - Nosamiefan Iguosadolo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Oguzie Judith
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Ojide C. Kingsley
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | | | | | - Oladiji Femi
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Olawoye Idowu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Olumade Testimony
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Omoruyi E. Chukwuma
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Onwe E. Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Chika K. Onwuamah
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | | | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Pascale Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | | | | | - Paul E. Oluniyi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Paulo Arnaldo
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Peter K. Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Phillip A. Bester
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | - Placide K. Mbala
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Reuben Ayivor-Djanie
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Richard Njouom
- Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon
| | - Richard O. Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richmond Gorman
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Rosina A. A. Carr
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Saâd El Kabbaj
- Laboratoire de Recherche et d’Analyses Médicales de la Gendarmerie Royale, Rabat, Morocco
| | - Saba Gargouri
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Safietou Sankhe
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Salako B. Lawal
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Samar Kassim
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Sameh Trabelsi
- Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia
| | - Samar Metha
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Sami Kammoun
- CHU Hedi Chaker Sfax, Service de Pneumologie, Tunis, Tunisia
| | - Sanaâ Lemriss
- Laboratoire de Recherche et d’Analyses Médicales de la Gendarmerie Royale, Rabat, Morocco
| | - Sara H. A. Agwa
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | | | | | - Seydou Doumbia
- Mali-University Clinical Research Center (UCRC), Bamako, Mali
| | - Sheila M. Mandanda
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | | | | | | | - Sobajo Tope
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Sonia Lekana-Douki
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Soumeya Ouangraoua
- Centre MURAZ, Ouagadougou, Burkina Faso
- National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso
| | - Steve A. Mundeke
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | - Sumir Panji
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Susan Nabadda
- Central Public Health Laboratories (CPHL), Kampala, Uganda
| | - Sylvie Behillil
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | | | - Sylvie van der Werf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | | | - Tarik Aanniz
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Thabo Mohale
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Tobias Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ugwu Chinedu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa
| | - Uwanibe Jessica
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Uwem George
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Coordenação Geral de Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - Vincent Enouf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | - Vivianne Gorova
- World Health Organization, WHO Lesotho, Maseru, Lesotho
- Med24 Medical Centre, Ruwa, Zimbabwe
| | | | - William K. Ampofo
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Wonderful T. Choga
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Yvan Butera
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
| | | | - Amadou A. Sall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Bourema Kouriba
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | - Carolyn Williamson
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | | | - Jinal N. Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Matthew Cotten
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ngonda Saasa
- University of Zambia, School of Veterinary Medicine, Department of Disease Control, Lusaka, Zambia
| | | | | | - Yenew K. Tebeje
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Sofonias K. Tessema
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - John Nkengasong
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
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29
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Mayanja MN, Mwiine FN, Lutwama JJ, Ssekagiri A, Egesa M, Thomson EC, Kohl A. Mosquito-borne arboviruses in Uganda: history, transmission and burden. J Gen Virol 2021; 102. [PMID: 34609940 DOI: 10.1099/jgv.0.001680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mosquito-transmitted arboviruses constitute a large proportion of emerging infectious diseases that are both a public health problem and a threat to animal populations. Many such viruses were identified in East Africa, a region where they remain important and from where new arboviruses may emerge. We set out to describe and review the relevant mosquito-borne viruses that have been identified specifically in Uganda. We focused on the discovery, burden, mode of transmission, animal hosts and clinical manifestation of those previously involved in disease outbreaks. A search for mosquito-borne arboviruses detected in Uganda was conducted using search terms 'Arboviruses in Uganda' and 'Mosquitoes and Viruses in Uganda' in PubMed and Google Scholar in 2020. Twenty-four mosquito-borne viruses from different animal hosts, humans and mosquitoes were documented. The majority of these were from family Peribunyaviridae, followed by Flaviviridae, Togaviridae, Phenuiviridae and only one each from family Rhabdoviridae and Reoviridae. Sixteen (66.7%) of the viruses were associated with febrile illnesses. Ten (41.7%) of them were first described locally in Uganda. Six of these are a public threat as they have been previously associated with disease outbreaks either within or outside Uganda. Historically, there is a high burden and endemicity of arboviruses in Uganda. Given the many diverse mosquito species known in the country, there is also a likelihood of many undescribed mosquito-borne viruses. Next generation diagnostic platforms have great potential to identify new viruses. Indeed, four novel viruses, two of which were from humans (Ntwetwe and Nyangole viruses) and two from mosquitoes (Kibale and Mburo viruses) were identified in the last decade using next generation sequencing. Given the unbiased approach of detection of viruses by this technology, its use will undoubtedly be critically important in the characterization of mosquito viromes which in turn will inform other diagnostic efforts.
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Affiliation(s)
- Martin N Mayanja
- School of Biosecurity, Biotechnical and Laboratory Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda.,MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Frank N Mwiine
- School of Biosecurity, Biotechnical and Laboratory Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Julius J Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Alfred Ssekagiri
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Moses Egesa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda.,Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
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30
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Mayanja MN, Mwiine FN, Lutwama JJ, Ssekagiri A, Egesa M, Thomson EC, Kohl A. Mosquito-borne arboviruses in Uganda: history, transmission and burden. J Gen Virol 2021; 102. [PMID: 34166178 DOI: 10.1099/jgv.0.001615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mosquito-transmitted arboviruses constitute a large proportion of emerging infectious diseases that are both a public health problem and a threat to animal populations. Many such viruses were identified in East Africa, a region where they remain important and from where new arboviruses may emerge. We set out to describe and review the relevant mosquito-borne viruses that have been identified specifically in Uganda. We focused on the discovery, burden, mode of transmission, animal hosts and clinical manifestation of those previously involved in disease outbreaks. A search for mosquito-borne arboviruses detected in Uganda was conducted using search terms 'Arboviruses in Uganda' and 'Mosquitoes and Viruses in Uganda' in PubMed and Google Scholar in 2020. Twenty-four mosquito-borne viruses from different animal hosts, humans and mosquitoes were documented. The majority of these were from family Peribunyaviridae, followed by Flaviviridae, Togaviridae, Phenuiviridae and only one each from family Rhabdoviridae and Reoviridae. Sixteen (66.7 %) of the viruses were associated with febrile illnesses. Ten (41.7 %) of them were first described locally in Uganda. Six of these are a public threat as they have been previously associated with disease outbreaks either within or outside Uganda. Historically, there is a high burden and endemicity of arboviruses in Uganda. Given the many diverse mosquito species known in the country, there is also a likelihood of many undescribed mosquito-borne viruses. New generation diagnostic platforms have great potential to identify new viruses. Indeed, four novel viruses, two of which were from humans (Ntwetwe and Nyangole viruses) and two from mosquitoes (Kibale and Mburo viruses) including the 2010 yellow fever virus (YFV) outbreak were identified in the last decade using next generation sequencing. Given the unbiased approach of detection of viruses by this technology, its use will undoubtedly be critically important in the characterization of mosquito viromes which in turn will inform other diagnostic efforts.
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Affiliation(s)
- Martin N Mayanja
- School of Biosecurity, Biotechnical and Laboratory Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda.,MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Frank N Mwiine
- School of Biosecurity, Biotechnical and Laboratory Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Julius J Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Alfred Ssekagiri
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Moses Egesa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda.,Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
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31
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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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32
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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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33
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Fels JM, Maurer DP, Herbert AS, Wirchnianski AS, Vergnolle O, Cross RW, Abelson DM, Moyer CL, Mishra AK, Aguilan JT, Kuehne AI, Pauli NT, Bakken RR, Nyakatura EK, Hellert J, Quevedo G, Lobel L, Balinandi S, Lutwama JJ, Zeitlin L, Geisbert TW, Rey FA, Sidoli S, McLellan JS, Lai JR, Bornholdt ZA, Dye JM, Walker LM, Chandran K. Protective neutralizing antibodies from human survivors of Crimean-Congo hemorrhagic fever. Cell 2021; 184:3486-3501.e21. [PMID: 34077751 DOI: 10.1016/j.cell.2021.05.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/19/2021] [Accepted: 04/29/2021] [Indexed: 12/31/2022]
Abstract
Crimean-Congo hemorrhagic fever virus (CCHFV) is a World Health Organization priority pathogen. CCHFV infections cause a highly lethal hemorrhagic fever for which specific treatments and vaccines are urgently needed. Here, we characterize the human immune response to natural CCHFV infection to identify potent neutralizing monoclonal antibodies (nAbs) targeting the viral glycoprotein. Competition experiments showed that these nAbs bind six distinct antigenic sites in the Gc subunit. These sites were further delineated through mutagenesis and mapped onto a prefusion model of Gc. Pairwise screening identified combinations of non-competing nAbs that afford synergistic neutralization. Further enhancements in neutralization breadth and potency were attained by physically linking variable domains of synergistic nAb pairs through bispecific antibody (bsAb) engineering. Although multiple nAbs protected mice from lethal CCHFV challenge in pre- or post-exposure prophylactic settings, only a single bsAb, DVD-121-801, afforded therapeutic protection. DVD-121-801 is a promising candidate suitable for clinical development as a CCHFV therapeutic.
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Affiliation(s)
- J Maximilian Fels
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - Andrew S Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA; The Geneva Foundation, Tacoma, WA 98402, USA
| | - Ariel S Wirchnianski
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Deparment of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Olivia Vergnolle
- Deparment of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Robert W Cross
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | | | | | - Akaash K Mishra
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jennifer T Aguilan
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ana I Kuehne
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | | | - Russell R Bakken
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Elisabeth K Nyakatura
- Deparment of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jan Hellert
- Structural Virology Unit, Department of Virology, CNRS UMR 3569, Institut Pasteur, Paris 75724, France
| | - Gregory Quevedo
- Deparment of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Leslie Lobel
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | | | | | - Larry Zeitlin
- Mapp Biopharmaceutical, Inc., San Diego, CA 92121, USA
| | - Thomas W Geisbert
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Felix A Rey
- Structural Virology Unit, Department of Virology, CNRS UMR 3569, Institut Pasteur, Paris 75724, France
| | - Simone Sidoli
- Deparment of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jonathan R Lai
- Deparment of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - John M Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Laura M Walker
- Adimab, LLC, Lebanon, NH 03766, USA; Adagio Therapeutics, Inc., Waltham, MA 02451, USA.
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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34
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Fagre AC, Lewis J, Miller MR, Mossel EC, Lutwama JJ, Nyakarahuka L, Nakayiki T, Kityo R, Nalikka B, Towner JS, Amman BR, Sealy TK, Foy B, Schountz T, Anderson J, Kading RC. Subgenomic flavivirus RNA (sfRNA) associated with Asian lineage Zika virus identified in three species of Ugandan bats (family Pteropodidae). Sci Rep 2021; 11:8370. [PMID: 33863991 PMCID: PMC8052318 DOI: 10.1038/s41598-021-87816-5] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/05/2021] [Indexed: 11/09/2022] Open
Abstract
Serological cross-reactivity among flaviviruses makes determining the prior arbovirus exposure of animals challenging in areas where multiple flavivirus strains are circulating. We hypothesized that prior infection with ZIKV could be confirmed through the presence of subgenomic flavivirus RNA (sfRNA) of the 3' untranslated region (UTR), which persists in tissues due to XRN-1 stalling during RNA decay. We amplified ZIKV sfRNA but not NS5 from three experimentally-infected Jamaican fruit bats, supporting the hypothesis of sfRNA tissue persistence. Applying this approach to 198 field samples from Uganda, we confirmed presence of ZIKV sfRNA, but not NS5, in four bats representing three species: Eidolon helvum (n = 2), Epomophorus labiatus (n = 1), and Rousettus aegyptiacus (n = 1). Amplified sequence was most closely related to Asian lineage ZIKV. Our results support the use of sfRNA as a means of identifying previous flavivirus infection and describe the first detection of ZIKV RNA in East African bats.
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Affiliation(s)
- Anna C Fagre
- Colorado State University, Fort Collins, CO, USA
| | | | | | - Eric C Mossel
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | | | | | | | | | | | | | - Brian R Amman
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tara K Sealy
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Brian Foy
- Colorado State University, Fort Collins, CO, USA
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35
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Mwanyika GO, Mboera LEG, Rugarabamu S, Makange M, Sindato C, Lutwama JJ, Paweska JT, Misinzo G. Circulation of dengue serotype 1 viruses during the 2019 outbreak in Dar es Salaam, Tanzania. Pathog Glob Health 2021; 115:467-475. [PMID: 33797341 DOI: 10.1080/20477724.2021.1905302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Dengue is an important mosquito-borne viral disease in humans in tropical and subtropical countries. In 2019, a total of 6917 dengue cases were reported in Tanzania based on serological analysis. The aim of this study was to confirm the presence of dengue virus (DENV) and conduct its genetic characterization. A total of 191 serum samples were collected from the outpatients seeking care from health facilities in Kinondoni and Ilala districts between March and May 2019. All the samples were initially tested for the presence of non-structural protein 1 and anti-DENV immunoglobulin G (IgG) and IgM using a commercial OnSite Duo Dengue Ag-IgG/IgM rapid test. Of the 191 sera, 110 (57.6%) were DENV seropositive. The presence of DENV ribonucleic acid was confirmed in 18.2% of the seropositive sera by reverse transcription polymerase chain reaction (RT-PCR). The RT-PCR products were cleaned and partial sequences of DENV polyprotein gene determined using dideoxynucleotide cycle sequencing followed by phylogenetic analysis. We present the occurrence of DENV serotype 1 (DENV-1) during the 2019 outbreak in Tanzania. The DENV-1 strains reported in the present study are highly identical and cluster with Asian DENV-1 strains indicating the possibility of intercontinental spread of DENV through globalization. We advocate for the need for molecular surveillance of dengue viruses during outbreaks to provide rapid evidence of the disease to guide public health interventions.
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Affiliation(s)
- Gaspary O Mwanyika
- SACIDS Africa Centre of Excellence for Infectious Diseases, Sokoine University of Agriculture, Morogoro, Tanzania.,Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro, Tanzania.,Department of Health Science and Technology, Mbeya University of Science and Technology, Mbeya, Tanzania
| | - Leonard E G Mboera
- SACIDS Africa Centre of Excellence for Infectious Diseases, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Sima Rugarabamu
- SACIDS Africa Centre of Excellence for Infectious Diseases, Sokoine University of Agriculture, Morogoro, Tanzania.,Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro, Tanzania.,Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar Es Salaam, Tanzania
| | - Mariam Makange
- SACIDS Africa Centre of Excellence for Infectious Diseases, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Calvin Sindato
- SACIDS Africa Centre of Excellence for Infectious Diseases, Sokoine University of Agriculture, Morogoro, Tanzania.,National Institute for Medical Research, Tabora Research Centre, Tabora, Tanzania
| | - Julius J Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Janusz T Paweska
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Gerald Misinzo
- SACIDS Africa Centre of Excellence for Infectious Diseases, Sokoine University of Agriculture, Morogoro, Tanzania.,Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro, Tanzania
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Mwanyika GO, Mboera LEG, Rugarabamu S, Ngingo B, Sindato C, Lutwama JJ, Paweska JT, Misinzo G. Dengue Virus Infection and Associated Risk Factors in Africa: A Systematic Review and Meta-Analysis. Viruses 2021; 13:v13040536. [PMID: 33804839 PMCID: PMC8063827 DOI: 10.3390/v13040536] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 01/09/2023] Open
Abstract
Dengue contributes a significant burden on global public health and economies. In Africa, the burden of dengue virus (DENV) infection is not well described. This review was undertaken to determine the prevalence of dengue and associated risk factors. A literature search was done on PubMed/MEDLINE, Scopus, Embase, and Google Scholar databases to identify articles published between 1960 and 2020. Meta-analysis was performed using a random-effect model at a 95% confidence interval, followed by subgroup meta-analysis to determine the overall prevalence. Between 1960 and 2020, 45 outbreaks were identified, of which 17 and 16 occurred in East and West Africa, respectively. Dengue virus serotype 1 (DENV-1) and DENV-2 were the dominant serotypes contributing to 60% of the epidemics. Of 2211 cases reported between 2009 and 2020; 1954 (88.4%) were reported during outbreaks. Overall, the prevalence of dengue was 29% (95% CI: 20–39%) and 3% (95% CI: 1–5%) during the outbreak and non-outbreak periods, respectively. Old age (6/21 studies), lack of mosquito control (6/21), urban residence (4/21), climate change (3/21), and recent history of travel (3/21) were the leading risk factors. This review reports a high burden of dengue and increased risk of severe disease in Africa. Our findings provide useful information for clinical practice and health policy decisions to implement effective interventions.
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Affiliation(s)
- Gaspary O. Mwanyika
- SACIDS Africa Centre of Excellence for Infectious Diseases, Sokoine University of Agriculture, P.O. Box 3297 Morogoro, Tanzania; (G.O.M.); (L.E.G.M.); (S.R.); (B.N.); (C.S.)
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, P.O. Box 3015 Morogoro, Tanzania
- Department of Health Science and Technology, Mbeya University of Science and Technology, P.O. Box 131 Mbeya, Tanzania
| | - Leonard E. G. Mboera
- SACIDS Africa Centre of Excellence for Infectious Diseases, Sokoine University of Agriculture, P.O. Box 3297 Morogoro, Tanzania; (G.O.M.); (L.E.G.M.); (S.R.); (B.N.); (C.S.)
| | - Sima Rugarabamu
- SACIDS Africa Centre of Excellence for Infectious Diseases, Sokoine University of Agriculture, P.O. Box 3297 Morogoro, Tanzania; (G.O.M.); (L.E.G.M.); (S.R.); (B.N.); (C.S.)
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, P.O. Box 3015 Morogoro, Tanzania
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65595 Dar es Salaam, Tanzania
| | - Baraka Ngingo
- SACIDS Africa Centre of Excellence for Infectious Diseases, Sokoine University of Agriculture, P.O. Box 3297 Morogoro, Tanzania; (G.O.M.); (L.E.G.M.); (S.R.); (B.N.); (C.S.)
- Biology Department, St. John’s University of Tanzania, P.O. Box 47 Dodoma, Tanzania
| | - Calvin Sindato
- SACIDS Africa Centre of Excellence for Infectious Diseases, Sokoine University of Agriculture, P.O. Box 3297 Morogoro, Tanzania; (G.O.M.); (L.E.G.M.); (S.R.); (B.N.); (C.S.)
- Tabora Research Centre, National Institute for Medical Research, P.O. Box 482 Tabora, Tanzania
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, P.O. Box 49 Entebbe, Uganda;
| | - Janusz T. Paweska
- National Health Laboratory Service, National Institute for Communicable Diseases, Sandringham, 2192 Johannesburg, South Africa;
| | - Gerald Misinzo
- SACIDS Africa Centre of Excellence for Infectious Diseases, Sokoine University of Agriculture, P.O. Box 3297 Morogoro, Tanzania; (G.O.M.); (L.E.G.M.); (S.R.); (B.N.); (C.S.)
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, P.O. Box 3015 Morogoro, Tanzania
- Correspondence:
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Aubry F, Dabo S, Manet C, Filipović I, Rose NH, Miot EF, Martynow D, Baidaliuk A, Merkling SH, Dickson LB, Crist AB, Anyango VO, Romero-Vivas CM, Vega-Rúa A, Dusfour I, Jiolle D, Paupy C, Mayanja MN, Lutwama JJ, Kohl A, Duong V, Ponlawat A, Sylla M, Akorli J, Otoo S, Lutomiah J, Sang R, Mutebi JP, Cao-Lormeau VM, Jarman RG, Diagne CT, Faye O, Faye O, Sall AA, McBride CS, Montagutelli X, Rašić G, Lambrechts L. Enhanced Zika virus susceptibility of globally invasive Aedes aegypti populations. Science 2021; 370:991-996. [PMID: 33214283 DOI: 10.1126/science.abd3663] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/16/2020] [Indexed: 12/18/2022]
Abstract
The drivers and patterns of zoonotic virus emergence in the human population are poorly understood. The mosquito Aedes aegypti is a major arbovirus vector native to Africa that invaded most of the world's tropical belt over the past four centuries, after the evolution of a "domestic" form that specialized in biting humans and breeding in water storage containers. Here, we show that human specialization and subsequent spread of A. aegypti out of Africa were accompanied by an increase in its intrinsic ability to acquire and transmit the emerging human pathogen Zika virus. Thus, the recent evolution and global expansion of A. aegypti promoted arbovirus emergence not solely through increased vector-host contact but also as a result of enhanced vector susceptibility.
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Affiliation(s)
- Fabien Aubry
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Stéphanie Dabo
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Caroline Manet
- Mouse Genetics Laboratory, Institut Pasteur, Paris, France
| | - Igor Filipović
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Noah H Rose
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Elliott F Miot
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,Collège Doctoral, Sorbonne Université, Paris, France
| | - Daria Martynow
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Artem Baidaliuk
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,Collège Doctoral, Sorbonne Université, Paris, France
| | - Sarah H Merkling
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Laura B Dickson
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Anna B Crist
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Victor O Anyango
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Claudia M Romero-Vivas
- Laboratorio de Enfermedades Tropicales, Departamento de Medicina, Fundación Universidad del Norte, Barranquilla, Colombia
| | - Anubis Vega-Rúa
- Institut Pasteur of Guadeloupe, Laboratory of Vector Control Research, Transmission Reservoir and Pathogens Diversity Unit, Morne Jolivière, Guadeloupe, France
| | - Isabelle Dusfour
- Vector Control and Adaptation, Institut Pasteur de la Guyane, Vectopole Amazonien Emile Abonnenc, Cayenne, French Guiana, France
| | - Davy Jiolle
- MIVEGEC, Montpellier University, IRD, CNRS, Montpellier, France.,Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Christophe Paupy
- MIVEGEC, Montpellier University, IRD, CNRS, Montpellier, France.,Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Martin N Mayanja
- Department of Arbovirology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Julius J Lutwama
- Department of Arbovirology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Veasna Duong
- Virology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Alongkot Ponlawat
- Department of Entomology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Massamba Sylla
- Unité d'Entomologie, de Bactériologie, de Virologie, Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | - Jewelna Akorli
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Sampson Otoo
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Joel Lutomiah
- Arbovirus/Viral Hemorrhagic Fevers Laboratory, Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Rosemary Sang
- Arbovirus/Viral Hemorrhagic Fevers Laboratory, Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - John-Paul Mutebi
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | | | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Cheikh T Diagne
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, Dakar, Senegal
| | - Oumar Faye
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, Dakar, Senegal
| | - Ousmane Faye
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, Dakar, Senegal
| | - Amadou A Sall
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, Dakar, Senegal
| | - Carolyn S McBride
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | | | - Gordana Rašić
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Louis Lambrechts
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.
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Migisha R, Kwesiga B, Mirembe BB, Amanya G, Kabwama SN, Kadobera D, Bulage L, Nsereko G, Wadunde I, Tindyebwa T, Lubwama B, Kagirita AA, Kayiwa JT, Lutwama JJ, Boore AL, Harris JR, Bosa HK, Ario AR. Early cases of SARS-CoV-2 infection in Uganda: epidemiology and lessons learned from risk-based testing approaches - March-April 2020. Global Health 2020; 16:114. [PMID: 33239041 PMCID: PMC7686950 DOI: 10.1186/s12992-020-00643-7] [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: 07/20/2020] [Accepted: 11/13/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND On March 13, 2020, Uganda instituted COVID-19 symptom screening at its international airport, isolation and SARS-CoV-2 testing for symptomatic persons, and mandatory 14-day quarantine and testing of persons traveling through or from high-risk countries. On March 21, 2020, Uganda reported its first SARS-CoV-2 infection in a symptomatic traveler from Dubai. By April 12, 2020, 54 cases and 1257 contacts were identified. We describe the epidemiological, clinical, and transmission characteristics of these cases. METHODS A confirmed case was laboratory-confirmed SARS-CoV-2 infection during March 21-April 12, 2020 in a resident of or traveler to Uganda. We reviewed case-person files and interviewed case-persons at isolation centers. We identified infected contacts from contact tracing records. RESULTS Mean case-person age was 35 (±16) years; 34 (63%) were male. Forty-five (83%) had recently traveled internationally ('imported cases'), five (9.3%) were known contacts of travelers, and four (7.4%) were community cases. Of the 45 imported cases, only one (2.2%) was symptomatic at entry. Among all case-persons, 29 (54%) were symptomatic at testing and five (9.3%) were pre-symptomatic. Among the 34 (63%) case-persons who were ever symptomatic, all had mild disease: 16 (47%) had fever, 13 (38%) reported headache, and 10 (29%) reported cough. Fifteen (28%) case-persons had underlying conditions, including three persons with HIV. An average of 31 contacts (range, 4-130) were identified per case-person. Five (10%) case-persons, all symptomatic, infected one contact each. CONCLUSION The first 54 case-persons with SARS-CoV-2 infection in Uganda primarily comprised incoming air travelers with asymptomatic or mild disease. Disease would likely not have been detected in these persons without the targeted testing interventions implemented in Uganda. Transmission was low among symptomatic persons and nonexistent from asymptomatic persons. Routine, systematic screening of travelers and at-risk persons, and thorough contact tracing will be needed for Uganda to maintain epidemic control.
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Affiliation(s)
- Richard Migisha
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda.
| | - Benon Kwesiga
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | | | - Geofrey Amanya
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Steven N Kabwama
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Daniel Kadobera
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Lilian Bulage
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | | | - Ignatius Wadunde
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Tonny Tindyebwa
- Makerere University School of Public Health, Kampala, Uganda
| | | | | | | | | | - Amy L Boore
- US Centers for Disease Control and Prevention, Kampala, Uganda
| | - Julie R Harris
- US Centers for Disease Control and Prevention, Kampala, Uganda
| | - Henry Kyobe Bosa
- Uganda Virus Research Institute, Entebbe, Uganda.,Uganda People's Defence Forces, Kampala, Uganda
| | - Alex Riolexus Ario
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda.,Ministry of Health, Kampala, Uganda
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Mutebi JP, Lutwama JJ. Vector Competence of Aedes aegypti Populations from Entebbe, Uganda, for Zika Virus. Am J Trop Med Hyg 2020; 104:564-566. [PMID: 33241781 DOI: 10.4269/ajtmh.20-0220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 10/15/2020] [Indexed: 11/07/2022] Open
Abstract
We evaluated the vector competence of three strains of Aedes aegypti formosus from Entebbe, Uganda, for Zika virus (ZIKV). The aim was to find out if these strains were competent or incompetent vectors for ZIKV, to explain the lack of ZIKV outbreaks in the city of Entebbe. We observed transmission rates ranging from 33% to 78%; however, these rates were not statistically significantly different, suggesting that there were no real differences among the strains. Nonetheless, this showed that populations of Ae. aegypti formosus in Entebbe are competent vectors for ZIKV. The reason why there is no detectable transmission of ZIKV to humans in Entebbe is currently unknown. The lack of detectable transmission despite Ae. aegypti formosus competence for ZIKV suggests that other parameters, such as preference for nonhuman blood, may be limiting its ability to serve as a vector.
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Affiliation(s)
- John-Paul Mutebi
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention (CDC), Fort Collins, Colorado
| | - Julius J Lutwama
- Department of Arbovirology, Uganda Virus Research Institute, Entebbe, Uganda
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40
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Balinandi S, Chitimia-Dobler L, Grandi G, Nakayiki T, Kabasa W, Bbira J, Lutwama JJ, Bakkes DK, Malmberg M, Mugisha L. Morphological and molecular identification of ixodid tick species (Acari: Ixodidae) infesting cattle in Uganda. Parasitol Res 2020; 119:2411-2420. [PMID: 32533261 PMCID: PMC7366568 DOI: 10.1007/s00436-020-06742-z] [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: 02/13/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022]
Abstract
In Uganda, the role of ticks in zoonotic disease transmission is not well described, partly, due to limited available information on tick diversity. This study aimed to identify the tick species that infest cattle. Between September and November 2017, ticks (n = 4362) were collected from 5 districts across Uganda (Kasese, Hoima, Gulu, Soroti, and Moroto) and identified morphologically at Uganda Virus Research Institute. Morphological and genetic validation was performed in Germany on representative identified specimens and on all unidentified ticks. Ticks were belonging to 15 species: 8 Rhipicephalus species (Rhipicephalus appendiculatus, Rhipicephalus evertsi evertsi, Rhipicephalus microplus, Rhipicephalus decoloratus, Rhipicephalus afranicus, Rhipicephalus pulchellus, Rhipicephalus simus, and Rhipicephalus sanguineus tropical lineage); 5 Amblyomma species (Amblyomma lepidum, Amblyomma variegatum, Amblyomma cohaerens, Amblyomma gemma, and Amblyomma paulopunctatum); and 2 Hyalomma species (Hyalomma rufipes and Hyalomma truncatum). The most common species were R. appendiculatus (51.8%), A. lepidum (21.0%), A. variegatum (14.3%), R. evertsi evertsi (8.2%), and R. decoloratus (2.4%). R. afranicus is a new species recently described in South Africa and we report its presence in Uganda for the first time. The sequences of R. afranicus were 2.4% divergent from those obtained in Southern Africa. We confirm the presence of the invasive R. microplus in two districts (Soroti and Gulu). Species diversity was highest in Moroto district (p = 0.004) and geographical predominance by specific ticks was observed (p = 0.001). The study expands the knowledge on tick fauna in Uganda and demonstrates that multiple tick species with potential to transmit several tick-borne diseases including zoonotic pathogens are infesting cattle.
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Affiliation(s)
- Stephen Balinandi
- Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda.,College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O. Box 7062, Kampala, Uganda
| | | | - Giulio Grandi
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07, Uppsala, Sweden
| | - Teddy Nakayiki
- Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
| | - William Kabasa
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Johnson Bbira
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O. Box 7062, Kampala, Uganda
| | | | - Deon K Bakkes
- Gertrud Theiler Tick Museum, Epidemiology, Parasites and Vectors, Agricultural Research Council - Onderstepoort Veterinary Research, Pretoria, 0110, South Africa.,Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Merriman Street, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Maja Malmberg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07, Uppsala, Sweden. .,SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden.
| | - Lawrence Mugisha
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O. Box 7062, Kampala, Uganda.,Ecohealth Research Group, Conservation & Ecosystem Health Alliance, P.O. Box 34153, Kampala, Uganda
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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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Velazquez-Salinas L, Mwiine FN, Ahmed Z, Ochwo S, Munsey A, Lutwama JJ, Perez AM, VanderWaal K, Rieder E. Genetic Diversity of Circulating Foot and Mouth Disease Virus in Uganda Cross-Sectional Study During 2014-2017. Front Vet Sci 2020; 7:162. [PMID: 32270002 PMCID: PMC7109301 DOI: 10.3389/fvets.2020.00162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/05/2020] [Indexed: 01/23/2023] Open
Affiliation(s)
- Lauro Velazquez-Salinas
- Foreign Animal Disease Research Unit, USDA/ARS Plum Island Animal Disease Center, Greenport, NY, United States
- College of Veterinary Medicine, University of Minnesota, Minnesota, MN, United States
| | - Frank Norbert Mwiine
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, Kampala, Uganda
| | - Zaheer Ahmed
- Foreign Animal Disease Research Unit, USDA/ARS Plum Island Animal Disease Center, Greenport, NY, United States
| | - Sylvester Ochwo
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, Kampala, Uganda
| | - Anna Munsey
- College of Veterinary Medicine, University of Minnesota, Minnesota, MN, United States
| | - Julius J. Lutwama
- Department of Emerging and Re-emerging Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Andres M. Perez
- College of Veterinary Medicine, University of Minnesota, Minnesota, MN, United States
| | - Kimberly VanderWaal
- College of Veterinary Medicine, University of Minnesota, Minnesota, MN, United States
| | - Elizabeth Rieder
- Foreign Animal Disease Research Unit, USDA/ARS Plum Island Animal Disease Center, Greenport, NY, United States
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Apangu T, Acayo S, Atiku LA, Apio H, Candini G, Okoth F, Basabose JK, Ojosia L, Ajoga S, Mongiba G, Wetaka MM, Kayiwa J, Balinandi S, Schwartz A, Yockey B, Sexton C, Dietrich EA, Pappert R, Petersen JM, Mead PS, Lutwama JJ, Kugeler KJ. Intervention To Stop Transmission of Imported Pneumonic Plague - Uganda, 2019. MMWR Morb Mortal Wkly Rep 2020; 69:241-244. [PMID: 32134908 PMCID: PMC7367092 DOI: 10.15585/mmwr.mm6909a5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Kayiwa JT, Nankya AM, Ataliba I, Nassuna CA, Omara IE, Koehler JW, Dye JM, Mossel EC, Lutwama JJ. Dengue fever and chikungunya virus infections: identification in travelers in Uganda - 2017. Trop Dis Travel Med Vaccines 2019; 5:21. [PMID: 31798935 PMCID: PMC6884810 DOI: 10.1186/s40794-019-0099-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 11/21/2019] [Indexed: 02/07/2023]
Abstract
Arboviruses are (re-) emerging viruses that cause significant morbidity globally. Clinical manifestations usually consist of a non-specific febrile illness that may be accompanied by rash, arthralgia and arthritis and/or with neurological or hemorrhagic syndromes. The broad range of differential diagnoses of other infectious and non-infectious etiologies presents a challenge for clinicians. While knowledge of the geographic distribution of pathogens and the current epidemiological situation, incubation periods, exposure risk factors and vaccination history can help guide the diagnostic approach, the non-specific and variable clinical presentation can delay final diagnosis. This case report summarizes the laboratory-based findings of three travel-related cases of arbovirus infections in Uganda. These include a patient from Bangladesh with chikungunya virus infection and two cases of dengue fever from Ethiopia. Early detection of travel-imported cases by public health laboratories is important to reduce the risk of localized outbreaks of arboviruses such as dengue virus and chikungunya virus. Because of the global public health importance and the continued risk of (re-) emerging arbovirus infections, specific recommendations following diagnosis by clinicians should include obtaining travel histories from persons with arbovirus-compatible illness and include differential diagnoses when appropriate.
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Affiliation(s)
- John T Kayiwa
- 1Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Annet M Nankya
- 1Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Irene Ataliba
- 1Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Charity A Nassuna
- 1Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Isaac E Omara
- 1Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Jeffrey W Koehler
- 2US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD USA
| | - John M Dye
- 2US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD USA
| | - Eric C Mossel
- 3Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO USA
| | - Julius J Lutwama
- 1Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
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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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Mwiine FN, Velazquez-Salinas L, Ahmed Z, Ochwo S, Munsey A, Kenney M, Lutwama JJ, Maree FF, Lobel L, Perez AM, Rodriguez LL, VanderWaal K, Rieder E. Serological and phylogenetic characterization of foot and mouth disease viruses from Uganda during cross-sectional surveillance study in cattle between 2014 and 2017. Transbound Emerg Dis 2019; 66:2011-2024. [PMID: 31127983 DOI: 10.1111/tbed.13249] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 04/20/2019] [Accepted: 04/30/2019] [Indexed: 01/08/2023]
Abstract
Here, we report the results of a cross-sectional study designed to monitor the circulation and genetic diversity of foot and mouth disease virus (FMDV) in Uganda between 2014 and 2017. In this study, 13,614 sera and 2,068 oral-pharyngeal fluid samples were collected from cattle and analysed to determine FMDV seroprevalence, circulating serotypes and their phylogenetic relationships. Circulation of FMDV was evidenced by the detection of antibodies against non-structural proteins of FMDV or viral isolations in all districts sampled in Uganda. Sequence analysis revealed the presence of FMDV serotypes A, O, SAT 1 and SAT 2. FMDVs belonging to serotype O, isolated from 21 districts, were the most prevalent and were classified into six lineages within two East African topotypes, namely EA-1 and EA-2. Serotype A viruses belonging to the Africa G-I topotype were isolated from two districts. SAT 1 viruses grouped within topotypes I and IV and SAT 2 viruses within topotypes VII, IV and X were isolated from six and four districts respectively. Phylogenetic analysis of SAT 1 and SAT 2 sequences from cattle clustered with historical sequences from African buffalo, indicating possible interspecies transmission at the wildlife-livestock interface. In some cases, Uganda viruses also shared similarities to viral strains recovered from other regions in East Africa. This 3-year study period provides knowledge about the geographical distribution of FMDV serotypes isolated in Uganda and insights into the genetic diversity of the multiple serotypes circulating in the country. Knowledge of circulating FMDV viruses will assist in antigenic matching studies to devise improved FMDV control strategies with vaccination and vaccine strain selection for Uganda.
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Affiliation(s)
- Frank Norbert Mwiine
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, Kampala, Uganda
| | - Lauro Velazquez-Salinas
- College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota.,Foreign Animal Disease Research Unit, Department of Agriculture Plum Island Animal Disease Center, ARS, USDA, Greenport, New York
| | - Zaheer Ahmed
- Foreign Animal Disease Research Unit, Department of Agriculture Plum Island Animal Disease Center, ARS, USDA, Greenport, New York
| | - Sylvester Ochwo
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, Kampala, Uganda
| | - Anna Munsey
- College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
| | - Mary Kenney
- Foreign Animal Disease Research Unit, Department of Agriculture Plum Island Animal Disease Center, ARS, USDA, Greenport, New York
| | - Julius J Lutwama
- Department of Emerging and Re-emerging Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Francois F Maree
- Onderstepoort Veterinary Institute, Agricultural Research Council, Onderstepoort, South Africa
| | - Leslie Lobel
- Department of Virology and Developmental Genetics, Ben Gurion University, Beer Sheva, Israel
| | - Andres M Perez
- College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
| | - Luis L Rodriguez
- Foreign Animal Disease Research Unit, Department of Agriculture Plum Island Animal Disease Center, ARS, USDA, Greenport, New York
| | - Kimberly VanderWaal
- College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
| | - Elizabeth Rieder
- Foreign Animal Disease Research Unit, Department of Agriculture Plum Island Animal Disease Center, ARS, USDA, Greenport, New York
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Balinandi S, Mugisha L, Bbira J, Kabasa W, Nakayiki T, Bakkes DK, Lutwama JJ, Chitimia-Dobler L, Malmberg M. General and Local Morphological Anomalies in Amblyomma lepidum (Acari: Ixodidae) and Rhipicephalus decoloratus Infesting Cattle in Uganda. J Med Entomol 2019; 56:873-877. [PMID: 30576463 PMCID: PMC6467642 DOI: 10.1093/jme/tjy221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Indexed: 06/09/2023]
Abstract
Morphological abnormalities in ticks seem to be rare phenomena in nature, and are underreported in Africa. In this article, we describe general and local anomalies in two Amblyomma lepidum females and one Rhipicephalus decoloratus female collected from cattle in Moroto and Kasese districts, Uganda. One A. lepidum specimen displayed metagynander gynandromorphism with the presence of both male and female features in the same organism. The second A. lepidum female showed slight asymmetry and lacked a genital aperture. The R. decoloratus displayed multiple anomalies that included asymmetry on the right side in association with ectromely, chitinous formations and constrictions on the left side. This article presents the first report of metagynander gynandromorphism, as well as genital aperture absence which is not linked to gynandromorphism, in A. lepidum collected from cattle.
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Affiliation(s)
- Stephen Balinandi
- Department of Arbovirology, Emerging and Reemrging Infections, Uganda Virus Research Institute, Entebbe, Uganda
- College of Veterinary Medicine, Animal Resources & Biosecurity (COVAB), Makerere University, Kampala, Uganda
| | - Lawrence Mugisha
- College of Veterinary Medicine, Animal Resources & Biosecurity (COVAB), Makerere University, Kampala, Uganda
- Ecohealth Research Group, Conservation & Ecosystem Health Alliance (CEHA), Kampala, Uganda
| | - Johnson Bbira
- College of Veterinary Medicine, Animal Resources & Biosecurity (COVAB), Makerere University, Kampala, Uganda
| | - William Kabasa
- College of Veterinary Medicine, Animal Resources & Biosecurity (COVAB), Makerere University, Kampala, Uganda
| | - Teddy Nakayiki
- Department of Arbovirology, Emerging and Reemrging Infections, Uganda Virus Research Institute, Entebbe, Uganda
| | - Deon K Bakkes
- Gertrud Theiler Tick Museum, Epidemiology, Parasites and Vectors, Agricultural Research Council – Onderstepoort Veterinary Research, Pretoria, South Africa
| | - Julius J Lutwama
- Department of Arbovirology, Emerging and Reemrging Infections, Uganda Virus Research Institute, Entebbe, Uganda
| | - Lidia Chitimia-Dobler
- Department of Virology-Rickettsiology, Bundeswehr Institute of Microbiology, Munich, Germany
- Parasitology Unit, University of Hohenheim, Stuttgart, Germany
| | - Maja Malmberg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Fagre AC, Lee JS, Kityo RM, Bergren NA, Mossel EC, Nakayiki T, Nalikka B, Nyakarahuka L, Gilbert AT, Peterhans JK, Crabtree MB, Towner JS, Amman BR, Sealy TK, Schuh AJ, Nichol ST, Lutwama JJ, Miller BR, Kading RC. Discovery and Characterization of Bukakata orbivirus ( Reoviridae:Orbivirus), a Novel Virus from a Ugandan Bat. Viruses 2019; 11:E209. [PMID: 30832334 PMCID: PMC6466370 DOI: 10.3390/v11030209] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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] [Received: 02/14/2019] [Revised: 02/26/2019] [Accepted: 02/26/2019] [Indexed: 12/19/2022] Open
Abstract
While serological and virological evidence documents the exposure of bats to medically-important arboviruses, their role as reservoirs or amplifying hosts is less well-characterized. We describe a novel orbivirus (Reoviridae:Orbivirus) isolated from an Egyptian fruit bat (Rousettus aegyptiacus leachii) trapped in 2013 in Uganda and named Bukakata orbivirus. This is the fifth orbivirus isolated from a bat, however genetic information had previously only been available for one bat-associated orbivirus. We performed whole-genome sequencing on Bukakata orbivirus and three other bat-associated orbiviruses (Fomede, Ife, and Japanaut) to assess their phylogenetic relationship within the genus Orbivirus and develop hypotheses regarding potential arthropod vectors. Replication kinetics were assessed for Bukakata orbivirus in three different vertebrate cell lines. Lastly, qRT-PCR and nested PCR were used to determine the prevalence of Bukakata orbivirus RNA in archived samples from three populations of Egyptian fruit bats and one population of cave-associated soft ticks in Uganda. Complete coding sequences were obtained for all ten segments of Fomede, Ife, and Japanaut orbiviruses and for nine of the ten segments for Bukakata orbivirus. Phylogenetic analysis placed Bukakata and Fomede in the tick-borne orbivirus clade and Ife and Japanaut within the Culicoides/phlebotomine sandfly orbivirus clade. Further, Bukakata and Fomede appear to be serotypes of the Chobar Gorge virus species. Bukakata orbivirus replicated to high titers (10⁶⁻10⁷ PFU/mL) in Vero, BHK-21 [C-13], and R06E (Egyptian fruit bat) cells. Preliminary screening of archived bat and tick samples do not support Bukakata orbivirus presence in these collections, however additional testing is warranted given the phylogenetic associations observed. This study provided complete coding sequence for several bat-associated orbiviruses and in vitro characterization of a bat-associated orbivirus. Our results indicate that bats may play an important role in the epidemiology of viruses in the genus Orbivirus and further investigation is warranted into vector-host associations and ongoing surveillance efforts.
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Affiliation(s)
- Anna C Fagre
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
| | - Justin S Lee
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
| | - Robert M Kityo
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, Kampala, Uganda.
| | - Nicholas A Bergren
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
| | - Eric C Mossel
- Arboviral Diseases Branch, Division of Vector-borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80523, USA.
| | - Teddy Nakayiki
- Department of Arbovirology, Emerging, and Re-emerging Viral Infections, Uganda Virus Research Institute, Entebbe, Uganda.
| | - Betty Nalikka
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, Kampala, Uganda.
| | - Luke Nyakarahuka
- Department of Arbovirology, Emerging, and Re-emerging Viral Infections, Uganda Virus Research Institute, Entebbe, Uganda.
- Department of Biosecurity, Ecosystems and Veterinary Public Health, Makerere University, Kampala, Uganda.
| | - Amy T Gilbert
- National Wildlife Research Center, US Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Fort Collins, CO 80521, USA.
| | - Julian Kerbis Peterhans
- College of Arts and Sciences, Roosevelt University, Collections & Research, The Field Museum of Natural History, Chicago, IL 60605, USA.
| | - Mary B Crabtree
- Arboviral Diseases Branch, Division of Vector-borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80523, USA.
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | - Brian R Amman
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | - Tara K Sealy
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | - Amy J Schuh
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
- United States Public Health Service, Commissioned Corps, Rockville, MD 20852, USA.
| | - Stuart T Nichol
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | - Julius J Lutwama
- Department of Arbovirology, Emerging, and Re-emerging Viral Infections, Uganda Virus Research Institute, Entebbe, Uganda.
| | - Barry R Miller
- Arboviral Diseases Branch, Division of Vector-borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80523, USA.
| | - Rebekah C Kading
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
- Arboviral Diseases Branch, Division of Vector-borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80523, USA.
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Nyakarahuka L, Shoemaker TR, Balinandi S, Chemos G, Kwesiga B, Mulei S, Kyondo J, Tumusiime A, Kofman A, Masiira B, Whitmer S, Brown S, Cannon D, Chiang CF, Graziano J, Morales-Betoulle M, Patel K, Zufan S, Komakech I, Natseri N, Chepkwurui PM, Lubwama B, Okiria J, Kayiwa J, Nkonwa IH, Eyu P, Nakiire L, Okarikod EC, Cheptoyek L, Wangila BE, Wanje M, Tusiime P, Bulage L, Mwebesa HG, Ario AR, Makumbi I, Nakinsige A, Muruta A, Nanyunja M, Homsy J, Zhu BP, Nelson L, Kaleebu P, Rollin PE, Nichol ST, Klena JD, Lutwama JJ. Marburg virus disease outbreak in Kween District Uganda, 2017: Epidemiological and laboratory findings. PLoS Negl Trop Dis 2019; 13:e0007257. [PMID: 30883555 PMCID: PMC6438581 DOI: 10.1371/journal.pntd.0007257] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 03/28/2019] [Accepted: 02/22/2019] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION In October 2017, a blood sample from a resident of Kween District, Eastern Uganda, tested positive for Marburg virus. Within 24 hour of confirmation, a rapid outbreak response was initiated. Here, we present results of epidemiological and laboratory investigations. METHODS A district task force was activated consisting of specialised teams to conduct case finding, case management and isolation, contact listing and follow up, sample collection and testing, and community engagement. An ecological investigation was also carried out to identify the potential source of infection. Virus isolation and Next Generation sequencing were performed to identify the strain of Marburg virus. RESULTS Seventy individuals (34 MVD suspected cases and 36 close contacts of confirmed cases) were epidemiologically investigated, with blood samples tested for MVD. Only four cases met the MVD case definition; one was categorized as a probable case while the other three were confirmed cases. A total of 299 contacts were identified; during follow- up, two were confirmed as MVD. Of the four confirmed and probable MVD cases, three died, yielding a case fatality rate of 75%. All four cases belonged to a single family and 50% (2/4) of the MVD cases were female. All confirmed cases had clinical symptoms of fever, vomiting, abdominal pain and bleeding from body orifices. Viral sequences indicated that the Marburg virus strain responsible for this outbreak was closely related to virus strains previously shown to be circulating in Uganda. CONCLUSION This outbreak of MVD occurred as a family cluster with no additional transmission outside of the four related cases. Rapid case detection, prompt laboratory testing at the Uganda National VHF Reference Laboratory and presence of pre-trained, well-prepared national and district rapid response teams facilitated the containment and control of this outbreak within one month, preventing nationwide and global transmission of the disease.
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Affiliation(s)
- Luke Nyakarahuka
- Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute (UVRI), Entebbe Uganda
- Department of Biosecurity, Ecosystems, and Veterinary Public Health, Collage of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala Uganda
| | - Trevor R. Shoemaker
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention (CDC), Atlanta, GA United States of America
| | - Stephen Balinandi
- Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute (UVRI), Entebbe Uganda
| | - Godfrey Chemos
- Kween District Health Team, Kween District Local Government, Kween, Uganda
| | - Benon Kwesiga
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Sophia Mulei
- Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute (UVRI), Entebbe Uganda
| | - Jackson Kyondo
- Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute (UVRI), Entebbe Uganda
| | - Alex Tumusiime
- Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute (UVRI), Entebbe Uganda
| | - Aaron Kofman
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention (CDC), Atlanta, GA United States of America
| | - Ben Masiira
- African Field Epidemiology Network, Kampala, Uganda
| | - Shannon Whitmer
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention (CDC), Atlanta, GA United States of America
| | - Shelley Brown
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention (CDC), Atlanta, GA United States of America
| | - Debi Cannon
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention (CDC), Atlanta, GA United States of America
| | - Cheng-Feng Chiang
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention (CDC), Atlanta, GA United States of America
| | - James Graziano
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention (CDC), Atlanta, GA United States of America
| | - Maria Morales-Betoulle
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention (CDC), Atlanta, GA United States of America
| | - Ketan Patel
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention (CDC), Atlanta, GA United States of America
| | - Sara Zufan
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention (CDC), Atlanta, GA United States of America
| | | | - Nasan Natseri
- World Health Organization – Country Office, Kampala, Uganda
| | | | | | | | - Joshua Kayiwa
- Public Health Emergency Operations Center, Ministry of Health, Kampala, Uganda
| | - Innocent H. Nkonwa
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Patricia Eyu
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Lydia Nakiire
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | | | - Leonard Cheptoyek
- Kween District Health Team, Kween District Local Government, Kween, Uganda
| | | | - Michael Wanje
- Kween District Health Team, Kween District Local Government, Kween, Uganda
| | | | - Lilian Bulage
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | | | - Alex R. Ario
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Issa Makumbi
- Public Health Emergency Operations Center, Ministry of Health, Kampala, Uganda
| | | | | | | | - Jaco Homsy
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention (CDC), Atlanta, GA United States of America
| | - Bao-Ping Zhu
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Lisa Nelson
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention (CDC), Atlanta, GA United States of America
| | - Pontiano Kaleebu
- Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute (UVRI), Entebbe Uganda
| | - Pierre E. Rollin
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention (CDC), Atlanta, GA United States of America
| | - Stuart T. Nichol
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention (CDC), Atlanta, GA United States of America
| | - John D. Klena
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention (CDC), Atlanta, GA United States of America
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute (UVRI), Entebbe Uganda
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Kwagonza L, Masiira B, Kyobe-Bosa H, Kadobera D, Atuheire EB, Lubwama B, Kagirita A, Katushabe E, Kayiwa JT, Lutwama JJ, Ojwang JC, Makumbi I, Ario AR, Borchert J, Zhu BP. Outbreak of yellow fever in central and southwestern Uganda, February-may 2016. BMC Infect Dis 2018; 18:548. [PMID: 30390621 PMCID: PMC6215607 DOI: 10.1186/s12879-018-3440-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [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: 01/03/2018] [Accepted: 10/12/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND On 28 March, 2016, the Ministry of Health received a report on three deaths from an unknown disease characterized by fever, jaundice, and hemorrhage which occurred within a one-month period in the same family in central Uganda. We started an investigation to determine its nature and scope, identify risk factors, and to recommend eventually control measures for future prevention. METHODS We defined a probable case as onset of unexplained fever plus ≥1 of the following unexplained symptoms: jaundice, unexplained bleeding, or liver function abnormalities. A confirmed case was a probable case with IgM or PCR positivity for yellow fever. We reviewed medical records and conducted active community case-finding. In a case-control study, we compared risk factors between case-patients and asymptomatic control-persons, frequency-matched by age, sex, and village. We used multivariate conditional logistic regression to evaluate risk factors. We also conducted entomological studies and environmental assessments. RESULTS From February to May, we identified 42 case-persons (35 probable and seven confirmed), of whom 14 (33%) died. The attack rate (AR) was 2.6/100,000 for all affected districts, and highest in Masaka District (AR = 6.0/100,000). Men (AR = 4.0/100,000) were more affected than women (AR = 1.1/100,000) (p = 0.00016). Persons aged 30-39 years (AR = 14/100,000) were the most affected. Only 32 case-patients and 128 controls were used in the case control study. Twenty three case-persons (72%) and 32 control-persons (25%) farmed in swampy areas (ORadj = 7.5; 95%CI = 2.3-24); 20 case-patients (63%) and 32 control-persons (25%) who farmed reported presence of monkeys in agriculture fields (ORadj = 3.1, 95%CI = 1.1-8.6); and 20 case-patients (63%) and 35 control-persons (27%) farmed in forest areas (ORadj = 3.2; 95%CI = 0.93-11). No study participants reported yellow fever vaccination. Sylvatic monkeys and Aedes mosquitoes were identified in the nearby forest areas. CONCLUSION This yellow fever outbreak was likely sylvatic and transmitted to a susceptible population probably by mosquito bites during farming in forest and swampy areas. A reactive vaccination campaign was conducted in the affected districts after the outbreak. We recommended introduction of yellow fever vaccine into the routine Uganda National Expanded Program on Immunization and enhanced yellow fever surveillance.
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Affiliation(s)
- Leocadia Kwagonza
- Uganda Public Health Fellowship Program, P.O. Box 7272, Kampala, Uganda. .,Ministry of Health of Uganda, Kampala, Uganda. .,Makerere University school of Public Health, Kampala, Uganda.
| | - Ben Masiira
- Uganda Public Health Fellowship Program, P.O. Box 7272, Kampala, Uganda.,Ministry of Health of Uganda, Kampala, Uganda.,Makerere University school of Public Health, Kampala, Uganda
| | - Henry Kyobe-Bosa
- Uganda Public Health Fellowship Program, P.O. Box 7272, Kampala, Uganda
| | - Daniel Kadobera
- Uganda Public Health Fellowship Program, P.O. Box 7272, Kampala, Uganda.,Ministry of Health of Uganda, Kampala, Uganda
| | - Emily B Atuheire
- Uganda Public Health Fellowship Program, P.O. Box 7272, Kampala, Uganda.,Ministry of Health of Uganda, Kampala, Uganda.,Makerere University school of Public Health, Kampala, Uganda
| | | | | | - Edson Katushabe
- World Health Organization, Uganda Country Office, Kampala, Uganda
| | | | | | - Joseph C Ojwang
- United States Centers for Disease Control and Prevention, Kampala, Uganda
| | | | - Alex Riolexus Ario
- Uganda Public Health Fellowship Program, P.O. Box 7272, Kampala, Uganda.,Ministry of Health of Uganda, Kampala, Uganda
| | - Jeff Borchert
- United States Centers for Disease Control and Prevention, Kampala, Uganda
| | - Bao-Ping Zhu
- United States Centers for Disease Control and Prevention, Kampala, Uganda.,Division of Global Health Protection, Center for Global Health, United States Centers for Disease Control and Prevention, Atlanta, GA, USA
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