1
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Oguzie JU, Petros BA, Oluniyi PE, Mehta SB, Eromon PE, Nair P, Adewale-Fasoro O, Ifoga PD, Odia I, Pastusiak A, Gbemisola OS, Aiyepada JO, Uyigue EA, Edamhande AP, Blessing O, Airende M, Tomkins-Tinch C, Qu J, Stenson L, Schaffner SF, Oyejide N, Ajayi NA, Ojide K, Ogah O, Abejegah C, Adedosu N, Ayodeji O, Liasu AA, Okogbenin S, Okokhere PO, Park DJ, Folarin OA, Komolafe I, Ihekweazu C, Frost SDW, Jackson EK, Siddle KJ, Sabeti PC, Happi CT. Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria. Nat Commun 2023; 14:4693. [PMID: 37542071 PMCID: PMC10403498 DOI: 10.1038/s41467-023-40247-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/10/2023] [Indexed: 08/06/2023] Open
Abstract
Effective infectious disease surveillance in high-risk regions is critical for clinical care and pandemic preemption; however, few clinical diagnostics are available for the wide range of potential human pathogens. Here, we conduct unbiased metagenomic sequencing of 593 samples from febrile Nigerian patients collected in three settings: i) population-level surveillance of individuals presenting with symptoms consistent with Lassa Fever (LF); ii) real-time investigations of outbreaks with suspected infectious etiologies; and iii) undiagnosed clinically challenging cases. We identify 13 distinct viruses, including the second and third documented cases of human blood-associated dicistrovirus, and a highly divergent, unclassified dicistrovirus that we name human blood-associated dicistrovirus 2. We show that pegivirus C is a common co-infection in individuals with LF and is associated with lower Lassa viral loads and favorable outcomes. We help uncover the causes of three outbreaks as yellow fever virus, monkeypox virus, and a noninfectious cause, the latter ultimately determined to be pesticide poisoning. We demonstrate that a local, Nigerian-driven metagenomics response to complex public health scenarios generates accurate, real-time differential diagnoses, yielding insights that inform policy.
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Affiliation(s)
- Judith U Oguzie
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Brittany A Petros
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, 02139, USA
- Harvard/MIT MD-PhD Program, Boston, MA, 02115, USA
- Systems, Synthetic, and Quantitative Biology PhD Program, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Paul E Oluniyi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Samar B Mehta
- Department of Medicine, University of Maryland Medical Center, Baltimore, MA, USA
| | - Philomena E Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Parvathy Nair
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Opeoluwa Adewale-Fasoro
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Peace Damilola Ifoga
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Ikponmwosa Odia
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - Otitoola Shobi Gbemisola
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | | | | | | | - Osiemi Blessing
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Michael Airende
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Christopher Tomkins-Tinch
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - James Qu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Liam Stenson
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Nicholas Oyejide
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Nnenna A Ajayi
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Kingsley Ojide
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Onwe Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | | | | | | | | | | | | | - Daniel J Park
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Onikepe A Folarin
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Isaac Komolafe
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | | | - Simon D W Frost
- Microsoft Premonition, Redmond, WA, USA
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Katherine J Siddle
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
| | - Christian T Happi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
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2
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Servellita V, Sotomayor Gonzalez A, Lamson DM, Foresythe A, Huh HJ, Bazinet AL, Bergman NH, Bull RL, Garcia KY, Goodrich JS, Lovett SP, Parker K, Radune D, Hatada A, Pan CY, Rizzo K, Bertumen JB, Morales C, Oluniyi PE, Nguyen J, Tan J, Stryke D, Jaber R, Leslie MT, Lyons Z, Hedman HD, Parashar U, Sullivan M, Wroblewski K, Oberste MS, Tate JE, Baker JM, Sugerman D, Potts C, Lu X, Chhabra P, Ingram LA, Shiau H, Britt W, Gutierrez Sanchez LH, Ciric C, Rostad CA, Vinjé J, Kirking HL, Wadford DA, Raborn RT, St George K, Chiu CY. Adeno-associated virus type 2 in US children with acute severe hepatitis. Nature 2023; 617:574-580. [PMID: 36996871 PMCID: PMC10170441 DOI: 10.1038/s41586-023-05949-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 03/10/2023] [Indexed: 04/01/2023]
Abstract
As of August 2022, clusters of acute severe hepatitis of unknown aetiology in children have been reported from 35 countries, including the USA1,2. Previous studies have found human adenoviruses (HAdVs) in the blood from patients in Europe and the USA3-7, although it is unclear whether this virus is causative. Here we used PCR testing, viral enrichment-based sequencing and agnostic metagenomic sequencing to analyse samples from 16 HAdV-positive cases from 1 October 2021 to 22 May 2022, in parallel with 113 controls. In blood from 14 cases, adeno-associated virus type 2 (AAV2) sequences were detected in 93% (13 of 14), compared to 4 (3.5%) of 113 controls (P < 0.001) and to 0 of 30 patients with hepatitis of defined aetiology (P < 0.001). In controls, HAdV type 41 was detected in blood from 9 (39.1%) of the 23 patients with acute gastroenteritis (without hepatitis), including 8 of 9 patients with positive stool HAdV testing, but co-infection with AAV2 was observed in only 3 (13.0%) of these 23 patients versus 93% of cases (P < 0.001). Co-infections by Epstein-Barr virus, human herpesvirus 6 and/or enterovirus A71 were also detected in 12 (85.7%) of 14 cases, with higher herpesvirus detection in cases versus controls (P < 0.001). Our findings suggest that the severity of the disease is related to co-infections involving AAV2 and one or more helper viruses.
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Affiliation(s)
- Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Daryl M Lamson
- Wadsworth Center, New York State Department of Health, David Axelrod Institute, Albany, NY, USA
| | - Abiodun Foresythe
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Hee Jae Huh
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Adam L Bazinet
- National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, USA
| | - Nicholas H Bergman
- National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, USA
| | - Robert L Bull
- Federal Bureau of Investigation Laboratory Division/Scientific Response and Analysis Unit, Quantico, VA, USA
| | - Karla Y Garcia
- National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, USA
| | - Jennifer S Goodrich
- National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, USA
| | - Sean P Lovett
- National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, USA
| | - Kisha Parker
- National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, USA
| | - Diana Radune
- National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, USA
| | - April Hatada
- California Department of Public Health, Richmond, CA, USA
| | - Chao-Yang Pan
- California Department of Public Health, Richmond, CA, USA
| | - Kyle Rizzo
- California Department of Public Health, Richmond, CA, USA
| | - J Bradford Bertumen
- California Department of Public Health, Richmond, CA, USA
- Centers for Disease Control and Prevention, Atlanta, CA, USA
| | | | - Paul E Oluniyi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jenny Nguyen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jessica Tan
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Doug Stryke
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Rayah Jaber
- Florida Department of Health, Tallahassee, FL, USA
| | | | - Zin Lyons
- North Carolina Department of Health and Human Services, Raleigh, NC, USA
| | - Hayden D Hedman
- Centers for Disease Control and Prevention, Atlanta, CA, USA
- South Dakota Department of Health, Pierre, SD, USA
| | - Umesh Parashar
- Centers for Disease Control and Prevention, Atlanta, CA, USA
| | - Maureen Sullivan
- Association for Public Health Laboratories, Silver Spring, MD, USA
| | - Kelly Wroblewski
- Association for Public Health Laboratories, Silver Spring, MD, USA
| | | | | | - Julia M Baker
- Centers for Disease Control and Prevention, Atlanta, CA, USA
| | - David Sugerman
- Centers for Disease Control and Prevention, Atlanta, CA, USA
| | - Caelin Potts
- Centers for Disease Control and Prevention, Atlanta, CA, USA
| | - Xiaoyan Lu
- Centers for Disease Control and Prevention, Atlanta, CA, USA
| | - Preeti Chhabra
- Centers for Disease Control and Prevention, Atlanta, CA, USA
| | | | - Henry Shiau
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - William Britt
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Caroline Ciric
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Christina A Rostad
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Jan Vinjé
- Centers for Disease Control and Prevention, Atlanta, CA, USA
| | | | | | - R Taylor Raborn
- National Biodefense Analysis and Countermeasures Center (NBACC), Frederick, MD, USA
| | - Kirsten St George
- Wadsworth Center, New York State Department of Health, David Axelrod Institute, Albany, NY, USA
- Department of Biomedical Science, University at Albany, SUNY, Albany, NY, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
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3
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Uwanibe JN, Kayode TA, Oluniyi PE, Akano K, Olawoye IB, Ugwu CA, Happi CT, Folarin OA. The Prevalence of Undiagnosed Salmonella enterica Serovar Typhi in Healthy School-Aged Children in Osun State, Nigeria. Pathogens 2023; 12:pathogens12040594. [PMID: 37111480 PMCID: PMC10140884 DOI: 10.3390/pathogens12040594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/03/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Typhoid fever remains a significant public health concern due to cases of mis-/overdiagnosis. Asymptomatic carriers play a role in the transmission and persistence of typhoid fever, especially among children, where limited data exist in Nigeria and other endemic countries. We aim to elucidate the burden of typhoid fever among healthy school-aged children using the best surveillance tool(s). In a semi-urban/urban state (Osun), 120 healthy school-aged children under 15 years were enrolled. Whole blood and fecal samples were obtained from consenting children. ELISA targeting the antigen lipopolysaccharide (LPS) and anti-LPS antibodies of Salmonella Typhi, culture, polymerase chain reaction (PCR), and next-generation sequencing (NGS) were used to analyze the samples. At least one of the immunological markers was detected in 65.8% of children, with 40.8%, 37.5%, and 39% of children testing positive for IgM, IgG, and antigen, respectively. Culture, PCR, and NGS assays did not detect the presence of Salmonella Typhi in the isolates. This study demonstrates a high seroprevalence of Salmonella Typhi in these healthy children but no carriage, indicating the inability to sustain transmission. We also demonstrate that using a single technique is insufficient for typhoid fever surveillance in healthy children living in endemic areas.
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Affiliation(s)
- Jessica N Uwanibe
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede 232103, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Oshogbo 232102, Osun State, Nigeria
| | - Tolulope A Kayode
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede 232103, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Oshogbo 232102, Osun State, Nigeria
| | - Paul E Oluniyi
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede 232103, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Oshogbo 232102, Osun State, Nigeria
| | - Kazeem Akano
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede 232103, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Oshogbo 232102, Osun State, Nigeria
| | - Idowu B Olawoye
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede 232103, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Oshogbo 232102, Osun State, Nigeria
| | - Chinedu A Ugwu
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede 232103, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Oshogbo 232102, Osun State, Nigeria
| | - Christian T Happi
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede 232103, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Oshogbo 232102, Osun State, Nigeria
| | - Onikepe A Folarin
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede 232103, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Oshogbo 232102, Osun State, Nigeria
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4
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Olawoye IB, Oluniyi PE, Oguzie JU, Uwanibe JN, Kayode TA, Olumade TJ, Ajogbasile FV, Parker E, Eromon PE, Abechi P, Sobajo TA, Ugwu CA, George UE, Ayoade F, Akano K, Oyejide NE, Nosamiefan I, Fred-Akintunwa I, Adedotun-Sulaiman K, Brimmo FB, Adegboyega BB, Philip C, Adeleke RA, Chukwu GC, Ahmed MI, Ope-Ewe OO, Otitoola SG, Ogunsanya OA, Saibu MF, Sijuwola AE, Ezekiel GO, John OG, Akin-John JO, Akinlo OO, Fayemi OO, Ipaye TO, Nwodo DC, Omoniyi AE, Omwanghe IB, Terkuma CA, Okolie J, Ayo-Ale O, Ikponmwosa O, Benevolence E, Naregose GO, Patience AE, Blessing O, Micheal A, Jacqueline A, Aiyepada JO, Ebhodaghe P, Racheal O, Rita E, Rosemary GE, Solomon E, Anieno E, Edna Y, Chris AO, Donatus AI, Ogbaini-Emovon E, Tatfeng MY, Omunakwe HE, Bob-Manuel M, Ahmed RA, Onwuamah CK, Shaibu JO, Okwuraiwe A, Ataga AE, Bock-Oruma A, Daramola F, Yusuf IF, Fajola A, Ntia NA, Ekpo JJ, Moses AE, Moore-Igwe BW, Fakayode OE, Akinola M, Kida IM, Oderinde BS, Wudiri ZW, Adeyemi OO, Akanbi OA, Ahumibe A, Akinpelu A, Ayansola O, Babatunde O, Omoare AA, Chukwu C, Mba NG, Omoruyi EC, Olisa O, Akande OK, Nwafor IE, Ekeh MA, Ndoma E, Ewah RL, Duruihuoma RO, Abu A, Odeh E, Onyia V, Ojide CK, Okoro S, Igwe D, Ogah EO, Khan K, Ajayi NA, Ugwu CN, Ukwaja KN, Ugwu NI, Abejegah C, Adedosu N, Ayodeji O, Liasu AA, Isamotu RO, Gadzama G, Petros BA, Siddle KJ, Schaffner SF, Akpede G, Erameh CO, Baba MM, Oladiji F, Audu R, Ndodo N, Fowotade A, Okogbenin S, Okokhere PO, Park DJ, Mcannis BL, Adetifa IM, Ihekweazu C, Salako BL, Tomori O, Happi AN, Folarin OA, Andersen KG, Sabeti PC, Happi CT. Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria. Nat Commun 2023; 14:811. [PMID: 36781860 PMCID: PMC9924892 DOI: 10.1038/s41467-023-36449-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/26/2023] [Indexed: 02/15/2023] Open
Abstract
Identifying the dissemination patterns and impacts of a virus of economic or health importance during a pandemic is crucial, as it informs the public on policies for containment in order to reduce the spread of the virus. In this study, we integrated genomic and travel data to investigate the emergence and spread of the SARS-CoV-2 B.1.1.318 and B.1.525 (Eta) variants of interest in Nigeria and the wider Africa region. By integrating travel data and phylogeographic reconstructions, we find that these two variants that arose during the second wave in Nigeria emerged from within Africa, with the B.1.525 from Nigeria, and then spread to other parts of the world. Data from this study show how regional connectivity of Nigeria drove the spread of these variants of interest to surrounding countries and those connected by air-traffic. Our findings demonstrate the power of genomic analysis when combined with mobility and epidemiological data to identify the drivers of transmission, as bidirectional transmission within and between African nations are grossly underestimated as seen in our import risk index estimates.
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Affiliation(s)
- Idowu B Olawoye
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Paul E Oluniyi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Judith U Oguzie
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Jessica N Uwanibe
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Tolulope A Kayode
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Testimony J Olumade
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Fehintola V Ajogbasile
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Philomena E Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Priscilla Abechi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Tope A Sobajo
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Chinedu A Ugwu
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Uwem E George
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Femi Ayoade
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Kazeem Akano
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Nicholas E Oyejide
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Iguosadolo Nosamiefan
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Iyanuoluwa Fred-Akintunwa
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Kemi Adedotun-Sulaiman
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Farida B Brimmo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Babatunde B Adegboyega
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Courage Philip
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Richard A Adeleke
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Grace C Chukwu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Muhammad I Ahmed
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Oludayo O Ope-Ewe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Shobi G Otitoola
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), 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
| | - Mudasiru F Saibu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), 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
| | - Grace O Ezekiel
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Oluwagboadurami G John
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Julie O Akin-John
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Oluwasemilogo O Akinlo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Olanrewaju O Fayemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Testimony O Ipaye
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Deborah C Nwodo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Abolade E Omoniyi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Iyobosa B Omwanghe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Christabel A Terkuma
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Johnson Okolie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Olubukola Ayo-Ale
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Odia Ikponmwosa
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Ebo Benevolence
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | | | - Osiemi Blessing
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Airende Micheal
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - John O Aiyepada
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - Omiunu Racheal
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Esumeh Rita
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Giwa E Rosemary
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - Ekanem Anieno
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Yerumoh Edna
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Aire O Chris
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | | | - Mirabeau Y Tatfeng
- Department of Medical Laboratory Science, Niger Delta University, Amassoma, Bayelsa State, Nigeria
| | - Hannah E Omunakwe
- Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Rivers State, Nigeria
| | - Mienye Bob-Manuel
- Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Rivers State, Nigeria
| | - Rahaman A Ahmed
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Chika K Onwuamah
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Joseph O Shaibu
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Azuka Okwuraiwe
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | - Anthony E Ataga
- Molecular Laboratory, Regional Centre for Biotechnology and Bioresources Research, University of Port Harcourt, Port Harcourt, Rivers State, Nigeria
| | | | - Funmi Daramola
- Clinical Health, SPDC, Port Harcourt, Rivers State, Nigeria
| | | | - Akinwumi Fajola
- Regional Community Health, SPDC, Port Harcourt, Rivers State, Nigeria
| | | | - Julie J Ekpo
- Department of Medical Microbiology and Parasitology, University of Uyo, Uyo, Akwa Ibom State, Nigeria
| | - Anietie E Moses
- Department of Medical Microbiology and Parasitology, University of Uyo, Uyo, Akwa Ibom State, Nigeria
| | | | | | - Monilade Akinola
- WHO Polio Laboratory, University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
| | - Ibrahim M Kida
- Department of Immunology, University of Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | - Bamidele S Oderinde
- Department of Immunology, University of Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | - Zara W Wudiri
- Department of Community Medicine, University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
| | - Oluwapelumi O Adeyemi
- Department of Medical Microbiology and Parasitology. Faculty of Basic Clinical Sciences. College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | | | | | | | | | | | | | | | - Nwando G Mba
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Ewean C Omoruyi
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olasunkanmi Olisa
- Biorepository Clinical Virology Laboratory, University of Ibadan, Ibadan, Nigeria
| | - Olatunji K Akande
- Biorepository Clinical Virology Laboratory, University of Ibadan, Ibadan, Nigeria
| | - Ifeanyi E Nwafor
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Matthew A Ekeh
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Erim Ndoma
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Richard L Ewah
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Rosemary O Duruihuoma
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Augustine Abu
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Elizabeth Odeh
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Venatius Onyia
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Chiedozie K Ojide
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | - Sylvanus Okoro
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Daniel Igwe
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Emeka O Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Kamran Khan
- Department of Medicine, University of Toronto, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Nnennaya A Ajayi
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Collins N Ugwu
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Kingsley N Ukwaja
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Ngozi I Ugwu
- Haematology Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | | | | | | | | | | | - Galadima Gadzama
- Department of Medical Microbiology, University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
| | | | | | | | - George Akpede
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | | | - Marycelin M Baba
- WHO Polio Laboratory, University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
- Department of Immunology, University of Maiduguri Teaching Hospital, Maiduguri, Nigeria
| | - Femi Oladiji
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
| | - Rosemary Audu
- The Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria
| | | | - Adeola Fowotade
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria
| | | | | | - Danny J Park
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | | | | | | | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Anise N Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Onikepe A Folarin
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Christian T Happi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA.
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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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6
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Griffiths EJ, Timme RE, Mendes CI, Page AJ, Alikhan NF, Fornika D, Maguire F, Campos J, Park D, Olawoye IB, Oluniyi PE, Anderson D, Christoffels A, da Silva AG, Cameron R, Dooley D, Katz LS, Black A, Karsch-Mizrachi I, Barrett T, Johnston A, Connor TR, Nicholls SM, Witney AA, Tyson GH, Tausch SH, Raphenya AR, Alcock B, Aanensen DM, Hodcroft E, Hsiao WWL, Vasconcelos ATR, MacCannell DR. Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package. Gigascience 2022; 11:6529104. [PMID: 35169842 PMCID: PMC8847733 DOI: 10.1093/gigascience/giac003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/15/2021] [Accepted: 01/07/2022] [Indexed: 12/23/2022] Open
Abstract
Background The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility, and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a need for a fit-for-purpose, open-source SARS-CoV-2 contextual data standard. Results As such, we have developed a SARS-CoV-2 contextual data specification package based on harmonizable, publicly available community standards. The specification can be implemented via a collection template, as well as an array of protocols and tools to support both the harmonization and submission of sequence data and contextual information to public biorepositories. Conclusions Well-structured, rich contextual data add value, promote reuse, and enable aggregation and integration of disparate datasets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19. The package is now supported by the NCBI’s BioSample database.
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Affiliation(s)
| | - Ruth E Timme
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA
| | - Catarina Inês Mendes
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Andrew J Page
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, Norfolk NR4 7UQ, UK
| | - Nabil-Fareed Alikhan
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, Norfolk NR4 7UQ, UK
| | - Dan Fornika
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC V5Z 4R4, Canada
| | - Finlay Maguire
- Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 1W5, Canada
| | - Josefina Campos
- INEI-ANLIS “Dr Carlos G. Malbrán,” Buenos Aires C1282AFF, Argentina
| | - Daniel Park
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Idowu B Olawoye
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State 232103, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State 232103, Nigeria
| | - Paul E Oluniyi
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State 232103, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State 232103, Nigeria
| | - Dominique Anderson
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7530, South Africa
| | - Alan Christoffels
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7530, South Africa
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Rhiannon Cameron
- Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada
| | - Damion Dooley
- Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada
| | - Lee S Katz
- Center for Food Safety, University of Georgia, Atlanta, GA 30333, USA
- Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, GA 30333, USA
| | - Allison Black
- Department of Epidemiology, University of Washington, WA 98109, USA
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Tanya Barrett
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Anjanette Johnston
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Thomas R Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | | | - Adam A Witney
- Institute for Infection and Immunity, St George's, University of London, London SW17 0RE, UK
| | - Gregory H Tyson
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Simon H Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin 12277, Germany
| | - Amogelang R Raphenya
- Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Brian Alcock
- Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Cambridge CB10 1SA, UK
- The Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Emma Hodcroft
- Biozentrum, University of Basel, Basel 3012, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - William W L Hsiao
- Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC V5Z 4R4, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7 V6T 1Z7, Canada
| | - Ana Tereza R Vasconcelos
- Bioinformatics Laboratory National Laboratory of Scientific Computation LNCC/MCTI, Petrópolis 25651-075, Brazil
| | - Duncan R MacCannell
- Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, GA 30333, USA
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7
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Oluniyi PE, Ajogbasile FV, Zhou S, Fred-Akintunwa I, Polyak CS, Ake JA, Tovanabutra S, Iroezindu M, Rolland M, Happi CT. HIV-1 drug resistance and genetic diversity in a cohort of people with HIV-1 in Nigeria. AIDS 2022; 36:137-146. [PMID: 34628443 PMCID: PMC8654252 DOI: 10.1097/qad.0000000000003098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 09/13/2021] [Accepted: 09/20/2021] [Indexed: 12/25/2022]
Abstract
OBJECTIVE This study was designed to provide information on the genetic diversity of HIV-1 and drug resistance mutations in Nigeria, as there is limited understanding of variants circulating in the country. METHODS We used an advanced next-generation sequencing platform, Primer ID, to: investigate the presence of high and low abundance drug resistance mutations; characterize preexisting Integrase Strand Transfer Inhibitor (INSTI) mutations in antiretroviral therapy (ART)-experienced but dolutegravir-naive individuals; detect recent HIV-1 infections and characterize subtype diversity from a cohort of people with HIV-1 (PWH). RESULTS HIV-1 subtype analysis revealed the predominance of CRF02_AG and subtype G in our study population. At detection sensitivity of 30% abundance, drug resistance mutations (DRMs) were identified in 3% of samples. At a sensitivity level of 10%, DRMs were identified in 27.3% of samples. We did not detect any major INSTI mutation associated with dolutegravir-resistance. Only one recent infection was detected in our study population. CONCLUSION Our study suggests that dolutegravir-containing antiretroviral regimens will be effective in Nigeria. Our study also further emphasizes the high genetic diversity of HIV-1 in Nigeria and that CRF02_AG and subtype G are the dominant circulating forms of HIV-1 in Nigeria. These two circulating forms of the virus are largely driving the epidemic in the country.
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Affiliation(s)
- Paul E. Oluniyi
- Department of Biological Sciences, Faculty of Natural Sciences
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Fehintola V. Ajogbasile
- Department of Biological Sciences, Faculty of Natural Sciences
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Shuntai Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Iyanuoluwa Fred-Akintunwa
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Christina S. Polyak
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA
| | - Julie A. Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA
| | - Michael Iroezindu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
- HJF Medical Research International, Abuja, Nigeria
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA
| | - Christian T. Happi
- Department of Biological Sciences, Faculty of Natural Sciences
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
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8
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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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9
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Oluniyi PE, Ajogbasile F, Oguzie J, Uwanibe J, Kayode A, Happi A, Ugwu A, Olumade T, Ogunsanya O, Eromon PE, Folarin O, Frost SDW, Heeney J, Happi CT. VGEA: an RNA viral assembly toolkit. PeerJ 2021; 9:e12129. [PMID: 34567846 PMCID: PMC8428259 DOI: 10.7717/peerj.12129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 08/17/2021] [Indexed: 12/11/2022] Open
Abstract
Next generation sequencing (NGS)-based studies have vastly increased our understanding of viral diversity. Viral sequence data obtained from NGS experiments are a rich source of information, these data can be used to study their epidemiology, evolution, transmission patterns, and can also inform drug and vaccine design. Viral genomes, however, represent a great challenge to bioinformatics due to their high mutation rate and forming quasispecies in the same infected host, bringing about the need to implement advanced bioinformatics tools to assemble consensus genomes well-representative of the viral population circulating in individual patients. Many tools have been developed to preprocess sequencing reads, carry-out de novo or reference-assisted assembly of viral genomes and assess the quality of the genomes obtained. Most of these tools however exist as standalone workflows and usually require huge computational resources. Here we present (Viral Genomes Easily Analyzed), a Snakemake workflow for analyzing RNA viral genomes. VGEA enables users to map sequencing reads to the human genome to remove human contaminants, split bam files into forward and reverse reads, carry out de novo assembly of forward and reverse reads to generate contigs, pre-process reads for quality and contamination, map reads to a reference tailored to the sample using corrected contigs supplemented by the user's choice of reference sequences and evaluate/compare genome assemblies. We designed a project with the aim of creating a flexible, easy-to-use and all-in-one pipeline from existing/stand-alone bioinformatics tools for viral genome analysis that can be deployed on a personal computer. VGEA was built on the Snakemake workflow management system and utilizes existing tools for each step: fastp (Chen et al., 2018) for read trimming and read-level quality control, BWA (Li & Durbin, 2009) for mapping sequencing reads to the human reference genome, SAMtools (Li et al., 2009) for extracting unmapped reads and also for splitting bam files into fastq files, IVA (Hunt et al., 2015) for de novo assembly to generate contigs, shiver (Wymant et al., 2018) to pre-process reads for quality and contamination, then map to a reference tailored to the sample using corrected contigs supplemented with the user's choice of existing reference sequences, SeqKit (Shen et al., 2016) for cleaning shiver assembly for QUAST, QUAST (Gurevich et al., 2013) to evaluate/assess the quality of genome assemblies and MultiQC (Ewels et al., 2016) for aggregation of the results from fastp, BWA and QUAST. Our pipeline was successfully tested and validated with SARS-CoV-2 (n = 20), HIV-1 (n = 20) and Lassa Virus (n = 20) datasets all of which have been made publicly available. VGEA is freely available on GitHub at: https://github.com/pauloluniyi/VGEA under the GNU General Public License.
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Affiliation(s)
- Paul E Oluniyi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Fehintola Ajogbasile
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Judith Oguzie
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Jessica Uwanibe
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Adeyemi Kayode
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Anise Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Alphonsus Ugwu
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Testimony Olumade
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Olusola Ogunsanya
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Philomena Ehiaghe Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Onikepe Folarin
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
| | - Simon D W Frost
- Microsoft Research, Redmond, WA, United States of America.,London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Jonathan Heeney
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Christian T Happi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun, Nigeria
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10
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Happi AN, Ogunsanya OA, Oguzie JU, Oluniyi PE, Olono AS, Heeney JL, Happi CT. Microbial metagenomic approach uncovers the first rabbit haemorrhagic disease virus genome in Sub-Saharan Africa. Sci Rep 2021; 11:13689. [PMID: 34210997 PMCID: PMC8249450 DOI: 10.1038/s41598-021-91961-2] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 05/07/2021] [Indexed: 01/22/2023] Open
Abstract
Rabbit Haemorrhagic Disease (RHD) causes high morbidity and mortality in rabbits and hares. Here, we report the first genomic characterization of lagovirus GI.2 virus in domestic rabbits from sub-Saharan Africa. We used an unbiased microbial metagenomic Next Generation Sequencing (mNGS) approach to diagnose the pathogen causing the suspected outbreak of RHD in Ibadan, Nigeria. The liver, spleen, and lung samples of five rabbits from an outbreak in 2 farms were analyzed. The mNGS revealed one full and two partial RHDV2 genomes on both farms. Phylogenetic analysis showed close clustering with RHDV2 lineages from Europe (98.6% similarity with RHDV2 in the Netherlands, and 99.1 to 100% identity with RHDV2 in Germany), suggesting potential importation. Subsequently, all the samples were confirmed by RHDV virus-specific RT-PCR targeting the VP60 gene with the expected band size of 398 bp for the five rabbits sampled. Our findings highlight the need for increased genomic surveillance of RHDV2 to track its origin, understand its diversity and to inform public health policy in Nigeria, and Sub-Saharan Africa.
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Affiliation(s)
- Anise N Happi
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria. .,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
| | - Olusola A Ogunsanya
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Judith U Oguzie
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Paul E Oluniyi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Alhaji S Olono
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Jonathan L Heeney
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Christian T Happi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria. .,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
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11
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Ajogbasile FV, Kayode AT, Oluniyi PE, Akano KO, Uwanibe JN, Adegboyega BB, Philip C, John OG, Eromon PJ, Emechebe G, Finimo F, Ogbulafor N, Jiya N, Okafor U, Ambe J, Wammanda RD, Oguche S, Mokuolu OA, Sowunmi A, Folarin OA, Happi CT. Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis. Malar J 2021; 20:236. [PMID: 34039364 PMCID: PMC8152046 DOI: 10.1186/s12936-021-03734-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/13/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malaria remains a public health burden especially in Nigeria. To develop new malaria control and elimination strategies or refine existing ones, understanding parasite population diversity and transmission patterns is crucial. METHODS In this study, characterization of the parasite diversity and structure of Plasmodium falciparum isolates from 633 dried blood spot samples in Nigeria was carried out using 12 microsatellite loci of P. falciparum. These microsatellite loci were amplified via semi-nested polymerase chain reaction (PCR) and fragments were analysed using population genetic tools. RESULTS Estimates of parasite genetic diversity, such as mean number of different alleles (13.52), effective alleles (7.13), allelic richness (11.15) and expected heterozygosity (0.804), were high. Overall linkage disequilibrium was weak (0.006, P < 0.001). Parasite population structure was low (Fst: 0.008-0.105, AMOVA: 0.039). CONCLUSION The high level of parasite genetic diversity and low population structuring in this study suggests that parasite populations circulating in Nigeria are homogenous. However, higher resolution methods, such as the 24 SNP barcode and whole genome sequencing, may capture more specific parasite genetic signatures circulating in the country. The results obtained can be used as a baseline for parasite genetic diversity and structure, aiding in the formulation of appropriate therapeutic and control strategies in Nigeria.
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Affiliation(s)
- Fehintola V Ajogbasile
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria.,Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Adeyemi T Kayode
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria.,Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Paul E Oluniyi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria.,Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Kazeem O Akano
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria.,Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Jessica N Uwanibe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria.,Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Benjamin B Adegboyega
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria
| | - Courage Philip
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria
| | | | - Philomena J Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria
| | - George Emechebe
- Department of Paediatrics, Imo State University Teaching Hospital, Orlu, Nigeria
| | - Finimo Finimo
- Department of Paediatrics, Federal Medical Centre, Yenagoa, Nigeria
| | - Nnenna Ogbulafor
- Case Management Unit, National Malaria Elimination Programme, Federal Ministry of Health, Abuja, Nigeria
| | - Nma Jiya
- Department of Paediatrics, Uthman Dan Fodio University, Sokoto, Nigeria
| | - Uche Okafor
- Department of Paediatrics, University of Nigeria Teaching Hospital, University of Nigeria, Nsukka, Nigeria
| | - Jose Ambe
- Department of Paediatrics, University of Maiduguri, Maiduguri, Nigeria
| | | | - Stephen Oguche
- Department of Paediatrics, University of Jos Teaching Hospital, University of Jos, Jos, Nigeria
| | - Olugbenga A Mokuolu
- Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria
| | - Akintunde Sowunmi
- Institute of Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria.,Department of Pharmacology and Therapeutics, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Onikepe A Folarin
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria.,Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Christian T Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria. .,Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria.
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12
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Kayode AT, Akano K, Ajogbasile FV, Uwanibe JN, Oluniyi PE, Bankole BE, Eromon PJ, Sowunmi A, Folarin OA, Volkman SK, McInnis B, Sabeti P, Wirth DF, Happi CT. Polymorphisms in Plasmodium falciparum chloroquine resistance transporter (Pfcrt) and multidrug-resistant gene 1 (Pfmdr-1) in Nigerian children 10 years post-adoption of artemisinin-based combination treatments. Int J Parasitol 2021; 51:301-310. [PMID: 33359205 PMCID: PMC7940560 DOI: 10.1016/j.ijpara.2020.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 01/29/2020] [Revised: 09/08/2020] [Accepted: 10/03/2020] [Indexed: 12/13/2022]
Abstract
The emergence and spread of Plasmodium falciparum parasites resistant to artemisinin derivatives and their partners in southeastern Asia threatens malaria control and elimination efforts, and heightens the need for an alternative therapy. We have explored the distribution of P. falciparum chloroquine resistance transporter (Pfcrt) and multidrug-resistant gene 1 (Pfmdr-1) haplotypes 10 years following adoption of artemisinin-based combination therapies in a bid to investigate the possible re-emergence of Chloroquine-sensitive parasites in Nigeria, and investigated the effect of these P. falciparum haplotypes on treatment outcomes of patients treated with artemisinin-based combination therapies. A total of 271 children aged <5 years with uncomplicated falciparum malaria were included in this study. Polymorphisms on codons 72-76 of the Pfcrt gene and codon 86 and 184 of Pfmdr-1 were determined using the high resolution melting assay. Of 240 (88.6%) samples successfully genotyped with HRM for Pfcrt, wildtype C72M74N75K76 (42.9%) and mutant C72I74E75T76 (53.8%) were observed. Also, wildtype N86Y184 (62.9%) and mutant N86F184 (21.1%), Y86Y184 (6.4%), and Y86F184 (0.4%) haplotypes of Pfmdr-1 were observed. Measures of responsiveness to ACTs were similar in children infected with P. falciparum crt haplotypes (C72I74E75T76 and C72M74N75K76) and major mdr-1 haplotypes (N86Y184, N86F184 and Y86Y184). Despite a 10 year gap since the malaria treatment policy changed to ACTs, over 50% of the P. falciparum parasites investigated in this study harboured the Chloroquine-resistant C72I74E75T76 haplotype, however this did not compromise the efficacy of artemisinin-based combination therapies. Should complete artemisinin resistance emerge from or spread to Nigeria, chloroquine might not be a good alternative therapy.
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Affiliation(s)
- Adeyemi T Kayode
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria; Department of Biological Sciences, Redeemer's University, Ede, Nigeria
| | - Kazeem Akano
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria; Department of Biological Sciences, Redeemer's University, Ede, Nigeria
| | - Fehintola V Ajogbasile
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria; Department of Biological Sciences, Redeemer's University, Ede, Nigeria
| | - Jessica N Uwanibe
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria; Department of Biological Sciences, Redeemer's University, Ede, Nigeria
| | - Paul E Oluniyi
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria; Department of Biological Sciences, Redeemer's University, Ede, Nigeria
| | - Bolajoko E Bankole
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria; Department of Biological Sciences, Redeemer's University, Ede, Nigeria
| | - Philomena J Eromon
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria
| | - Akintunde Sowunmi
- Institute of Medical Research and Training, College of Medicine, University of Ibadan; Department of Pharmacology and Therapeutics, University of Ibadan, Ibadan, Nigeria
| | - Onikepe A Folarin
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria; Department of Biological Sciences, Redeemer's University, Ede, Nigeria
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Pardis Sabeti
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Christian T Happi
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria; Department of Biological Sciences, Redeemer's University, Ede, Nigeria; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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13
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Kayode AT, Ajogbasile FV, Akano K, Uwanibe JN, Oluniyi PE, Eromon PJ, Folarin OA, Sowunmi A, Wirth DF, Happi CT. Polymorphisms in Plasmodium falciparum dihydropteroate synthetase and dihydrofolate reductase genes in Nigerian children with uncomplicated malaria using high-resolution melting technique. Sci Rep 2021; 11:471. [PMID: 33436791 PMCID: PMC7803958 DOI: 10.1038/s41598-020-80017-6] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 12/01/2020] [Indexed: 11/28/2022] Open
Abstract
In 2005, the Nigerian Federal Ministry of Health revised the treatment policy for uncomplicated malaria with the introduction of artemisinin-based combination therapies (ACTs). This policy change discouraged the use of Sulphadoxine-pyrimethamine (SP) as the second-line treatment of uncomplicated falciparum malaria. However, SP is used as an intermittent preventive treatment of malaria in pregnancy (IPTp) and seasonal malaria chemoprevention (SMC) in children aged 3–59 months. There have been increasing reports of SP resistance especially in the non-pregnant population in Nigeria, thus, the need to continually monitor the efficacy of SP as IPTp and SMC by estimating polymorphisms in dihydropteroate synthetase (dhps) and dihydrofolate reductase (dhfr) genes associated with SP resistance. The high resolution-melting (HRM) assay was used to investigate polymorphisms in codons 51, 59, 108 and 164 of the dhfr gene and codons 437, 540, 581 and 613 of the dhps gene. DNA was extracted from 271 dried bloodspot filter paper samples obtained from children (< 5 years old) with uncomplicated malaria. The dhfr triple mutant I51R59N108, dhps double mutant G437G581 and quadruple dhfr I51R59N108 + dhps G437 mutant haplotypes were observed in 80.8%, 13.7% and 52.8% parasites, respectively. Although the quintuple dhfr I51R59N108 + dhps G437E540 and sextuple dhfr I51R59N108 + dhps G437E540G581 mutant haplotypes linked with in-vivo and in-vitro SP resistance were not detected, constant surveillance of these haplotypes should be done in the country to detect any change in prevalence.
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Affiliation(s)
- Adeyemi T Kayode
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria.,Department of Biological Sciences, Redeemer's University, Ede, Nigeria
| | - Fehintola V Ajogbasile
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria.,Department of Biological Sciences, Redeemer's University, Ede, Nigeria
| | - Kazeem Akano
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria.,Department of Biological Sciences, Redeemer's University, Ede, Nigeria
| | - Jessica N Uwanibe
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria.,Department of Biological Sciences, Redeemer's University, Ede, Nigeria
| | - Paul E Oluniyi
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria.,Department of Biological Sciences, Redeemer's University, Ede, Nigeria
| | - Philomena J Eromon
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria
| | - Onikepe A Folarin
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria
| | - Akintunde Sowunmi
- Institute of Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria.,Department of Pharmacology and Therapeutics, University of Ibadan, Ibadan, Nigeria
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christian T Happi
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria. .,Department of Biological Sciences, Redeemer's University, Ede, Nigeria. .,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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14
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Abstract
In a pattern repeated across a range of ecological niches, arenaviruses have evolved a compact four-gene genome to orchestrate a complex life cycle in a narrow range of susceptible hosts. A number of mammalian arenaviruses cross-infect humans, often causing a life-threatening viral hemorrhagic fever. Among this group of geographically bound zoonoses, Lassa virus has evolved a unique niche that leads to significant and sustained human morbidity and mortality. As a biosafety level 4 pathogen, direct study of the pathogenesis of Lassa virus is limited by the sparse availability, high operating costs, and technical restrictions of the high-level biocontainment laboratories required for safe experimentation. In this chapter, we introduce the relationship between genome structure and the life cycle of Lassa virus and outline reverse genetic approaches used to probe and describe functional elements of the Lassa virus genome. We then review the tools used to obtain viral genomic sequences used for phylogeny and molecular diagnostics, before shifting to a population perspective to assess the contributions of phylogenetic analysis in understanding the evolution and ecology of Lassa virus in West Africa. We finally consider the future outlook and clinical applications for genetic study of Lassa virus.
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Affiliation(s)
- Raphaëlle Klitting
- Department of Immunology and Microbiology, The Scripps Research Institute , La Jolla, CA, USA
| | - Samar B Mehta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Judith U Oguzie
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemers University, Ede, Osun State, Nigeria
| | - Paul E Oluniyi
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemers University, Ede, Osun State, Nigeria
| | - Matthias G Pauthner
- Department of Immunology and Microbiology, The Scripps Research Institute , La Jolla, CA, USA
| | | | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute , La Jolla, CA, USA.
| | - Christian T Happi
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemers University, Ede, Osun State, Nigeria
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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15
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Ajogbasile FV, Oguzie JU, Oluniyi PE, Eromon PE, Uwanibe JN, Mehta SB, Siddle KJ, Odia I, Winnicki SM, Akpede N, Akpede G, Okogbenin S, Ogbaini-Emovon E, MacInnis BL, Folarin OA, Modjarrad K, Schaffner SF, Tomori O, Ihekweazu C, Sabeti PC, Happi CT. Real-time Metagenomic Analysis of Undiagnosed Fever Cases Unveils a Yellow Fever Outbreak in Edo State, Nigeria. Sci Rep 2020; 10:3180. [PMID: 32081931 PMCID: PMC7035389 DOI: 10.1038/s41598-020-59880-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 11/15/2019] [Accepted: 02/03/2020] [Indexed: 01/21/2023] Open
Abstract
Fifty patients with unexplained fever and poor outcomes presented at Irrua Specialist Teaching Hospital (ISTH) in Edo State, Nigeria, an area endemic for Lassa fever, between September 2018 - January 2019. After ruling out Lassa fever, plasma samples from these epidemiologically-linked cases were sent to the African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria, where we carried out metagenomic sequencing which implicated yellow fever virus (YFV) as the etiology of this outbreak. Twenty-nine of the 50 samples were confirmed positive for YFV by reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR), 14 of which resulted in genome assembly. Maximum likelihood phylogenetic analysis revealed that these YFV sequences formed a tightly clustered clade more closely related to sequences from Senegal than sequences from earlier Nigerian isolates, suggesting that the YFV clade responsible for this outbreak in Edo State does not descend directly from the Nigerian YFV outbreaks of the last century, but instead reflects a broader diversity and dynamics of YFV in West Africa. Here we demonstrate the power of metagenomic sequencing for identifying ongoing outbreaks and their etiologies and informing real-time public health responses, resulting in accurate and prompt disease management and control.
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Affiliation(s)
- Fehintola V Ajogbasile
- 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
| | - 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
| | - Paul E Oluniyi
- 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
| | - Philomena E Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Jessica N Uwanibe
- 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
| | - Samar B Mehta
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Beth Israel Deaconess Medical Center, Division of Infectious Diseases, Boston, Massachusetts, USA
| | - Katherine J Siddle
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Ikponmwosa Odia
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Sarah M Winnicki
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Nosa Akpede
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - George Akpede
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Sylvanus Okogbenin
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Ephraim Ogbaini-Emovon
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Bronwyn L MacInnis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Onikepe A Folarin
- 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
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Stephen F Schaffner
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | | | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Christian T 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.
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA.
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