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Diarra M, Ndiaye R, Barry A, Talla C, Diagne MM, Dia N, Faye J, Sarr FD, Gaye A, Diallo A, Cisse M, Dieng I, Fall G, Tall A, Faye O, Faye O, Sall AA, Loucoubar C. Analysis of contact tracing data showed contribution of asymptomatic and non-severe infections to the maintenance of SARS-CoV-2 transmission in Senegal. Sci Rep 2023; 13:9121. [PMID: 37277417 DOI: 10.1038/s41598-023-35622-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/21/2023] [Indexed: 06/07/2023] Open
Abstract
During the COVID-19 pandemic in Senegal, contact tracing was done to identify transmission clusters, their analysis allowed to understand their dynamics and evolution. In this study, we used information from the surveillance data and phone interviews to construct, represent and analyze COVID-19 transmission clusters from March 2, 2020, to May 31, 2021. In total, 114,040 samples were tested and 2153 transmission clusters identified. A maximum of 7 generations of secondary infections were noted. Clusters had an average of 29.58 members and 7.63 infected among them; their average duration was 27.95 days. Most of the clusters (77.3%) are concentrated in Dakar, capital city of Senegal. The 29 cases identified as super-spreaders, i.e., the indexes that had the most positive contacts, showed few symptoms or were asymptomatic. Deepest transmission clusters are those with the highest percentage of asymptomatic members. The correlation between proportion of asymptomatic and degree of transmission clusters showed that asymptomatic strongly contributed to the continuity of transmission within clusters. During this pandemic, all the efforts towards epidemiological investigations, active case-contact detection, allowed to identify in a short delay growing clusters and help response teams to mitigate the spread of the disease.
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Affiliation(s)
- Maryam Diarra
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal
| | - Ramatoulaye Ndiaye
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal
| | - Aliou Barry
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal
| | - Cheikh Talla
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal
| | | | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Joseph Faye
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal
| | - Fatoumata Diene Sarr
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal
| | - Aboubacry Gaye
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal
| | - Amadou Diallo
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal
| | - Mamadou Cisse
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal
| | - Idrissa Dieng
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Gamou Fall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Adama Tall
- Scientific Direction, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oumar Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou A Sall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, BP 220, Dakar, Senegal.
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2
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Benabdessalem C, Hamouda WB, Marzouki S, Faye R, Mbow AA, Diouf B, Ndiaye O, Dia N, Faye O, Sall AA, Diagne CT, Amellal H, Ezzikouri S, Mioramalala DJN, Randrianarisaona F, Trabelsi K, Boumaiza M, Hamouda SB, Ouni R, Bchiri S, Chaaban A, Gdoura M, Gorgi Y, Sfar I, Yalaoui S, Khelil JB, Hamzaoui A, Abdallah M, Cherif Y, Petres S, Mok CKP, Escriou N, Quesney S, Dellagi K, Schoenhals M, Sarih M, Vigan-Womas I, Bettaieb J, Rourou S, Barbouche MR, Ahmed MB. Development and comparative evaluation of SARS-CoV-2 S-RBD and N based ELISA tests in various African endemic settings. Diagn Microbiol Infect Dis 2023; 105:115903. [PMID: 36805620 PMCID: PMC9867841 DOI: 10.1016/j.diagmicrobio.2023.115903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/08/2023] [Accepted: 01/18/2023] [Indexed: 01/23/2023]
Abstract
Management of the COVID-19 pandemic relies on molecular diagnostic methods supported by serological tools. Herein, we developed S-RBD- and N- based ELISA assays useful for infection rate surveillance as well as the follow-up of acquired protective immunity against SARS-CoV-2. ELISA assays were optimized using COVID-19 Tunisian patients' sera and prepandemic controls. Assays were further validated in 3 African countries with variable endemic settings. The receiver operating curve was used to evaluate the assay performances. The N- and S-RBD-based ELISA assays performances, in Tunisia, were very high (AUC: 0.966 and 0.98, respectively, p < 0.0001). Cross-validation analysis showed similar performances in different settings. Cross-reactivity, with malaria infection, against viral antigens, was noticed. In head-to-head comparisons with different commercial assays, the developed assays showed high agreement. This study demonstrates, the added value of the developed serological assays in low-income countries, particularly in ethnically diverse populations with variable exposure to local endemic infectious diseases.
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Affiliation(s)
- Chaouki Benabdessalem
- Laboratory of Transmission, Control and Immunobiology of Infection, Institut Pasteur de Tunis, Tunisia; University Tunis El Manar, Tunis, Tunisia.
| | - Wafa Ben Hamouda
- Laboratory of Transmission, Control and Immunobiology of Infection, Institut Pasteur de Tunis, Tunisia; University Tunis El Manar, Tunis, Tunisia
| | - Soumaya Marzouki
- Laboratory of Transmission, Control and Immunobiology of Infection, Institut Pasteur de Tunis, Tunisia; University Tunis El Manar, Tunis, Tunisia
| | | | | | | | | | - Ndongo Dia
- Institut Pasteur de Dakar, Dakar, Senegal
| | | | | | | | - Houda Amellal
- Department of Parasitology and Vectorial Diseases. Institut Pasteur du Maroc. Casablanca. Morocco
| | - Sayeh Ezzikouri
- Department of Parasitology and Vectorial Diseases. Institut Pasteur du Maroc. Casablanca. Morocco
| | | | | | - Khaled Trabelsi
- University Tunis El Manar, Tunis, Tunisia; Laboratory of Molecular Microbiology, Vaccinology, and Biotechnological Development, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Mohamed Boumaiza
- University Tunis El Manar, Tunis, Tunisia; Laboratory of Molecular Microbiology, Vaccinology, and Biotechnological Development, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Sonia Ben Hamouda
- Laboratory of Transmission, Control and Immunobiology of Infection, Institut Pasteur de Tunis, Tunisia; University Tunis El Manar, Tunis, Tunisia
| | - Rym Ouni
- Laboratory of Transmission, Control and Immunobiology of Infection, Institut Pasteur de Tunis, Tunisia; University Tunis El Manar, Tunis, Tunisia
| | - Soumaya Bchiri
- Laboratory of Transmission, Control and Immunobiology of Infection, Institut Pasteur de Tunis, Tunisia; University Tunis El Manar, Tunis, Tunisia
| | - Amani Chaaban
- University Tunis El Manar, Tunis, Tunisia; Laboratory of Molecular Microbiology, Vaccinology, and Biotechnological Development, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Mariem Gdoura
- Laboratory of Clinical Virology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Yousr Gorgi
- University Tunis El Manar, Tunis, Tunisia; Laboratory of Immunology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Imen Sfar
- University Tunis El Manar, Tunis, Tunisia; Laboratory of Immunology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Sadok Yalaoui
- University Tunis El Manar, Tunis, Tunisia; Laboratory of Immunology, Abderrahmen Mami University Hospital, Ariana, Tunisia
| | - Jalila Ben Khelil
- University Tunis El Manar, Tunis, Tunisia; Intensive care unit, Abderrahmen Mami University Hospital, Ariana, Tunisia
| | - Agnes Hamzaoui
- University Tunis El Manar, Tunis, Tunisia; Pneumology Department Abderrahmen Mami University Hospital, Ariana, Tunisia
| | - Meya Abdallah
- University Tunis El Manar, Tunis, Tunisia; Department of internal Medicine, Yasminette Hospital, Ben Arous, Tunisia
| | - Yosra Cherif
- University Tunis El Manar, Tunis, Tunisia; Department of internal Medicine, Yasminette Hospital, Ben Arous, Tunisia
| | | | - Chris Ka Pun Mok
- HKU-Pasteur Research Pole, School of Public Health, University of Hong Kong, Hong Kong; The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong
| | | | | | - Koussay Dellagi
- Institut Pasteur de Paris, Paris, France; Pasteur Network, Institut Pasteur, Paris, France
| | - Matthieu Schoenhals
- Immunology of Infectious Diseases, Institut Pasteur of Madagascar, Antananarivo, Madagascar
| | - M'hammed Sarih
- Department of Parasitology and Vectorial Diseases. Institut Pasteur du Maroc. Casablanca. Morocco
| | | | - Jihene Bettaieb
- Laboratory of Transmission, Control and Immunobiology of Infection, Institut Pasteur de Tunis, Tunisia; University Tunis El Manar, Tunis, Tunisia
| | - Samia Rourou
- University Tunis El Manar, Tunis, Tunisia; Laboratory of Molecular Microbiology, Vaccinology, and Biotechnological Development, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Mohamed Ridha Barbouche
- Laboratory of Transmission, Control and Immunobiology of Infection, Institut Pasteur de Tunis, Tunisia; University Tunis El Manar, Tunis, Tunisia; Department of Microbiology, Immunology, and infectious diseases. College of Medicine and Medical sciences, Arabian Gulf University, Manama, Bahrain
| | - Melika Ben Ahmed
- Laboratory of Transmission, Control and Immunobiology of Infection, Institut Pasteur de Tunis, Tunisia; University Tunis El Manar, Tunis, Tunisia
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3
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Grant R, Sacks JA, Abraham P, Chunsuttiwat S, Cohen C, Figueroa JP, Fleming T, Fine P, Goldblatt D, Hasegawa H, MacIntrye CR, Memish ZA, Miller E, Nishioka S, Sall AA, Sow S, Tomori O, Wang Y, Van Kerkhove MD, Wambo MA, Cohen HA, Mesfin S, Otieno JR, Subissi L, Briand S, Wentworth DE, Subbarao K. When to update COVID-19 vaccine composition. Nat Med 2023; 29:776-780. [PMID: 36807683 DOI: 10.1038/s41591-023-02220-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- Rebecca Grant
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Jilian A Sacks
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Priya Abraham
- Indian Council of Medical Research - National Institute of Virology, Pune, India
| | | | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Thomas Fleming
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Paul Fine
- London School of Hygiene and Tropical Medicine, London, UK
| | - David Goldblatt
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Hideki Hasegawa
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - C Raina MacIntrye
- Biosecurity Program, The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Ziad A Memish
- Research and Innovation Centre, King Saud Medical City, Ministry of Health and College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Elizabeth Miller
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | | | | | - Samba Sow
- Centre for Vaccine Development, Ministry of Health, Bamako, Mali
| | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria
| | - Youchun Wang
- Institute for Biological Product Control, National Institutes for Food and Drug Control, Beijing, China
| | - Maria D Van Kerkhove
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Marie-Ange Wambo
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Homa Attar Cohen
- Department of Acute Response Coordination, World Health Organization, Geneva, Switzerland
| | - Samuel Mesfin
- Department of Acute Response Coordination, World Health Organization, Geneva, Switzerland
| | - James R Otieno
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Lorenzo Subissi
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Sylvie Briand
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland.
| | - David E Wentworth
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kanta Subbarao
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
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4
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Grais RF, Sall AA, Cole ST. Science knows no country: fulfilling Louis Pasteur's legacy. Lancet 2022; 400:2163-2164. [PMID: 36528367 DOI: 10.1016/s0140-6736(22)02369-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022]
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5
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Rose NH, Dabo S, da Veiga Leal S, Sylla M, Diagne CT, Faye O, Faye O, Sall AA, McBride CS, Lambrechts L. Enhanced mosquito vectorial capacity underlies the Cape Verde Zika epidemic. PLoS Biol 2022; 20:e3001864. [PMID: 36288328 PMCID: PMC9604947 DOI: 10.1371/journal.pbio.3001864] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/03/2022] [Indexed: 11/07/2022] Open
Abstract
The explosive emergence of Zika virus (ZIKV) across the Pacific and Americas since 2007 was associated with hundreds of thousands of human cases and severe outcomes, including congenital microcephaly caused by ZIKV infection during pregnancy. Although ZIKV was first isolated in Uganda, Africa has so far been exempt from large-scale ZIKV epidemics, despite widespread susceptibility among African human populations. A possible explanation for this pattern is natural variation among populations of the primary vector of ZIKV, the mosquito Aedes aegypti. Globally invasive populations of Ae. aegypti outside of Africa are considered effective ZIKV vectors because they are human specialists with high intrinsic ZIKV susceptibility, whereas African populations of Ae. aegypti across the species’ native range are predominantly generalists with low intrinsic ZIKV susceptibility, making them less likely to spread viruses in the human population. We test this idea by studying a notable exception to the patterns observed across most of Africa: Cape Verde experienced a large ZIKV outbreak in 2015 to 2016. We find that local Ae. aegypti in Cape Verde have substantial human-specialist ancestry, show a robust behavioral preference for human hosts, and exhibit increased susceptibility to ZIKV infection, consistent with a key role for variation among mosquito populations in ZIKV epidemiology. These findings suggest that similar human-specialist populations of Ae. aegypti in the nearby Sahel region of West Africa, which may be expanding in response to rapid urbanization, could serve as effective vectors for ZIKV in the future. During 2015-2016, Cape Verde experienced the only documented large-scale Zika virus outbreak in Africa. This study provides an explanation for this puzzling exception by showing that Aedes aegypti mosquitoes in Cape Verde display atypical features, with substantial human-specialist ancestry, robust preference for humans, and enhanced Zika virus susceptibility.
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Affiliation(s)
- Noah H. Rose
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, United States of America
- * E-mail: (NHR); (LL)
| | - Stéphanie Dabo
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Insect-Virus Interactions Unit, Paris, France
| | - Silvânia da Veiga Leal
- Laboratório de Entomologia Médica, Instituto Nacional de Saúde Pública, Praia, Cabo Verde
| | - Massamba Sylla
- Department of Livestock Sciences and Techniques, University Sine Saloum El Hadji Ibrahima NIASS, Kaffrine, Senegal
| | - Cheikh T. Diagne
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, Dakar, Senegal
| | - Oumar Faye
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, Dakar, Senegal
| | - Ousmane Faye
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, Dakar, Senegal
| | - Amadou A. Sall
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, Dakar, Senegal
| | - Carolyn S. McBride
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, United States of America
| | - Louis Lambrechts
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Insect-Virus Interactions Unit, Paris, France
- * E-mail: (NHR); (LL)
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6
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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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7
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Diarra M, Barry A, Dia N, Diop M, Sonko I, Sagne S, Sarr FD, Talla C, Tall A, Faye J, Diop B, Diagne CT, Gaye A, Diallo A, Mbaye R, Cisse M, Taieb F, Faye O, Lakhe NA, Papa Samba B, Diallo K, Fall NM, Badiane AS, Fortes L, Diop M, Thioub D, Ly AB, Faye O, Seydi M, Bousso A, Sall AA, Loucoubar C. First wave COVID-19 pandemic in Senegal: Epidemiological and clinical characteristics. PLoS One 2022; 17:e0274783. [PMID: 36126041 PMCID: PMC9488827 DOI: 10.1371/journal.pone.0274783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
Background The novel coronavirus disease 2019 (COVID-19) pandemic has spread from China to the rest of the world. Africa seems less impacted with lower number of cases and deaths than other continents. Senegal recorded its first case on March 2, 2020. We present here data collected from March 2 to October 31, 2020 in Senegal. Methods Socio-demographic, epidemiological, clinical and virological information were collected on suspected cases. To determine factors associated with diagnosed infection, symptomatic disease and death, multivariable binary logistic regression and log binomial models were used. Epidemiological parameters such as the reproduction number and growth rate were estimated. Results 67,608 suspected cases were tested by the IPD laboratories (13,031 positive and 54,577 negative). All age categories were associated with SARS-CoV-2 infection, but also patients having diabetes or hypertension or other cardiovascular diseases. With diagnosed infection, patients over 65 years and those with hypertension and cardiovascular disease and diabetes were highly associated with death. Patients with co-morbidities were associated with symptomatic disease, but only the under 15 years were not associated with. Among infected, 27.67% were asymptomatic (40.9% when contacts were systematically tested; 12.11% when only symptomatic or high-risk contacts were tested). Less than 15 years-old were mostly asymptomatic (63.2%). Dakar accounted for 81.4% of confirmed cases. The estimated mean serial interval was 5.57 (± 5.14) days. The average reproduction number was estimated at 1.161 (95%CI: 1.159–1.162), the growth rate was 0.031 (95%CI: 0.028–0.034) per day. Conclusions Our findings indicated that factors associated with symptomatic COVID-19 and death are advanced age (over 65 years-old) and comorbidities such as diabetes and hypertension and cardiovascular disease.
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Affiliation(s)
- Maryam Diarra
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
- * E-mail:
| | - Aliou Barry
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mamadou Diop
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ibrahima Sonko
- Centre des Opérations d’Urgence Sanitaire (COUS), Ministry of Health, Dakar, Senegal
| | - Samba Sagne
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Fatoumata Diene Sarr
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cheikh Talla
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Adama Tall
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Joseph Faye
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Boly Diop
- Division Surveillance Epidémiologique, Direction de la Prévention, Ministry of Health, Dakar, Senegal
| | | | - Aboubacry Gaye
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou Diallo
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Rose Mbaye
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mamadou Cisse
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Fabien Taieb
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oumar Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | | | - Khardiata Diallo
- Service des Maladies Infectieuses, Fann Hospital, Dakar, Senegal
| | | | | | | | | | - Daouda Thioub
- Service des Maladies Infectieuses, Fann Hospital, Dakar, Senegal
| | - Alioune Badara Ly
- Centre des Opérations d’Urgence Sanitaire (COUS), Ministry of Health, Dakar, Senegal
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Moussa Seydi
- Service des Maladies Infectieuses, Fann Hospital, Dakar, Senegal
| | - Abdoulaye Bousso
- Centre des Opérations d’Urgence Sanitaire (COUS), Ministry of Health, Dakar, Senegal
| | - Amadou A. Sall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
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8
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Koundouno FR, Kafetzopoulou LE, Faye M, Renevey A, Soropogui B, Ifono K, Nelson EV, Kamano AA, Tolno C, Annibaldis G, Millimono SL, Camara J, Kourouma K, Doré A, Millimouno TE, Tolno FMB, Hinzmann J, Soubrier H, Hinrichs M, Thielebein A, Herzer G, Pahlmann M, Ki-Zerbo GA, Formenty P, Legand A, Wiley MR, Faye O, Diagne MM, Sall AA, Lemey P, Bah A, Günther S, Keita S, Duraffour S, Magassouba N. Detection of Marburg Virus Disease in Guinea. N Engl J Med 2022; 386:2528-2530. [PMID: 35767445 PMCID: PMC7613962 DOI: 10.1056/nejmc2120183] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Fara R Koundouno
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | - Annick Renevey
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Kékoura Ifono
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Emily V Nelson
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Aly A Kamano
- World Health Organization Guinea, Conakry, Guinea
| | | | | | - Saa L Millimono
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Karifa Kourouma
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | | | - Julia Hinzmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Hugo Soubrier
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Mette Hinrichs
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Anke Thielebein
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Glaucia Herzer
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Meike Pahlmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | | | | | | | | | | | | | | | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Sakoba Keita
- Agence Nationale de Sécurité Sanitaire, Conakry, Guinea
| | - Sophie Duraffour
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - N'Faly Magassouba
- Laboratoire des Fièvres Hémorragiques Virales de Guinée, Conakry, Guinea
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9
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Talla C, Loucoubar C, Roka JL, Barry MA, Ndiaye S, Diarra M, Thiam MS, Faye O, Dia M, Diop M, Ndiaye O, Tall A, Faye R, Mbow AA, Diouf B, Diallo JP, Keita IM, Ndiaye M, Woudenberg T, White M, Ting J, Diagne CT, Pasi O, Diop B, Sall AA, Vigan-Womas I, Faye O. Seroprevalence of anti-SARS-CoV-2 antibodies in Senegal: a national population-based cross-sectional survey, between October and November 2020. IJID Reg 2022; 3:117-125. [PMID: 35720135 PMCID: PMC8897837 DOI: 10.1016/j.ijregi.2022.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 11/17/2022]
Abstract
Objectives A nationwide cross-sectional epidemiological survey was conducted to capture the true extent of coronavirus disease 2019 (COVID-19) exposure in Senegal. Methods Multi-stage random cluster sampling of households was performed between October and November 2020, at the end of the first wave of COVID-19 transmission. Anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies were screened using three distinct ELISA assays. Adjusted prevalence rates for the survey design were calculated for each test separately, and thereafter combined. Crude and adjusted prevalence rates based on test performance were estimated to assess the seroprevalence. As some samples were collected in high malaria endemic areas, the relationship between SARS-CoV-2 seroreactivity and antimalarial humoral immunity was also investigated. Results Of the 1463 participants included in this study, 58.8% were female and 41.2% were male; their mean age was 29.2 years (range 0.20-84.8.0 years). The national seroprevalence was estimated at 28.4% (95% confidence interval 26.1-30.8%). There was substantial regional variability. All age groups were impacted, and the prevalence of SARS-CoV-2 was comparable in the symptomatic and asymptomatic groups. An estimated 4 744 392 (95% confidence interval 4 360 164-5 145 327) were potentially infected with SARS-CoV-2 in Senegal, while 16 089 COVID-19 RT-PCR laboratory-confirmed cases were reported by the national surveillance. No correlation was found between SARS-CoV-2 and Plasmodium seroreactivity. Conclusions These results provide a better estimate of SARS-CoV-2 dissemination in the Senegalese population. Preventive and control measures need to be reinforced in the country and especially in the south border regions.
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Affiliation(s)
- Cheikh Talla
- Epidemiology, Clinical Research and Data Sciences Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Sciences Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Jerlie Loko Roka
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Mamadou A. Barry
- Epidemiology, Clinical Research and Data Sciences Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Seynabou Ndiaye
- Epidemiology, Clinical Research and Data Sciences Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Maryam Diarra
- Epidemiology, Clinical Research and Data Sciences Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mareme Seye Thiam
- Epidemiology, Clinical Research and Data Sciences Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oumar Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Moussa Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mamadou Diop
- Epidemiology, Clinical Research and Data Sciences Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oumar Ndiaye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Adama Tall
- Epidemiology, Clinical Research and Data Sciences Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Rokhaya Faye
- Immunophysiopathology and Infectious Diseases Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Adji Astou Mbow
- Immunophysiopathology and Infectious Diseases Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Babacar Diouf
- Immunophysiopathology and Infectious Diseases Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Jean Pierre Diallo
- Prevention Department, Surveillance Division, Ministry of Health and Social Action, Dakar, Senegal
| | - Ibrahima Mamby Keita
- Prevention Department, Surveillance Division, Ministry of Health and Social Action, Dakar, Senegal
| | - Mamadou Ndiaye
- Prevention Department, Surveillance Division, Ministry of Health and Social Action, Dakar, Senegal
| | - Tom Woudenberg
- Malaria: Parasites and Hosts Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Michael White
- Malaria: Parasites and Hosts Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Jim Ting
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | | | - Omer Pasi
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Boly Diop
- Prevention Department, Surveillance Division, Ministry of Health and Social Action, Dakar, Senegal
| | - Amadou A. Sall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Inès Vigan-Womas
- Immunophysiopathology and Infectious Diseases Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
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10
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Mukadi-Bamuleka D, Bulabula-Penge J, De Weggheleire A, Jacobs BKM, Edidi-Atani F, Mambu-Mbika F, Mbala-Kingebeni P, Makiala-Mandanda S, Faye M, Diagne CT, Diagne MM, Faye O, Kajihara M, Faye O, Takada A, Sall AA, Muyembe-Tamfum JJ, van Griensven J, Ariën KK, Ahuka-Mundeke S. Field performance of three Ebola rapid diagnostic tests used during the 2018-20 outbreak in the eastern Democratic Republic of the Congo: a retrospective, multicentre observational study. Lancet Infect Dis 2022; 22:891-900. [PMID: 35298901 DOI: 10.1016/s1473-3099(21)00675-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/17/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND The Democratic Republic of the Congo has confronted 13 outbreaks of Ebola virus disease since 1976. Rapid diagnostic tests (RDTs) detecting viral antigens have been developed to circumvent difficulties encountered with RT-PCR for diagnosis in remote low-resource settings, but there is still uncertainty about their performance characteristics and usability during outbreaks. We aimed to assess the field performance of three antigen detection RDTs compared with the gold-standard Cepheid GeneXpert Ebola assay results. METHODS We conducted a retrospective, multicentre observational study using complete and de-identified databases of five mobile laboratories (managed by the Institut National de Recherche Biomédicale) to assess the performance of three Ebola virus disease RDTs (QuickNavi-Ebola, OraQuick Ebola Rapid Antigen Test, and Coris EBOLA Ag K-SeT rapid test) run on blood samples of patients with suspected Ebola virus disease in direct comparison with the Cepheid GeneXpert Ebola assay reference test during the 2018-20 outbreak in the eastern Democratic Republic of the Congo. We estimated the sensitivity and specificity of each test through generalised linear mixed models against the GeneXpert Ebola assay reference test and corrected for cycle threshold value and random site effects. FINDINGS 719 (7·9%) of 9157 samples had a positive GeneXpert Ebola assay result. The QuickNavi-Ebola RDT had a sensitivity of 87·4% (95% CI 63·6-96·8) around the mean cycle threshold value and a specificity of 99·6% (99·3-99·8). The OraQuick Ebola Rapid Antigen Test had a sensitivity of 57·4% (95% CI 38·8-75·8) and specificity of 98·3% (97·5-99·0), and the Coris EBOLA Ag K-SeT rapid test had a sensitivity of 38·9% (23·0-63·6) against the GeneXpert Ebola assay reference and specificity of 97·4% (85·3-99·6). The QuickNavi-Ebola RDT showed a robust performance with good sensitivity, particularly with increasing viral loads (ie, low cycle threshold values), and specificity. INTERPRETATION The three RDTs evaluated did not achieve the desired sensitivity and specificity of the WHO target product profile. Although the RDTs cannot triage and rule out Ebola virus infection among clinical suspects, they can still help to sort people with suspected Ebola virus disease into high-risk and low-risk groups while waiting for GeneXpert Ebola assay reference testing. FUNDING None. TRANSLATION For the French translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Daniel Mukadi-Bamuleka
- Department of Virology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Département de Biologie Médicale, Cliniques Universitaires de Kinshasa, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo.
| | - Junior Bulabula-Penge
- Department of Virology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Département de Biologie Médicale, Cliniques Universitaires de Kinshasa, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Anja De Weggheleire
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bart K M Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - François Edidi-Atani
- Department of Virology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Département de Biologie Médicale, Cliniques Universitaires de Kinshasa, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Fabrice Mambu-Mbika
- Department of Virology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Département de Biologie Médicale, Cliniques Universitaires de Kinshasa, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Placide Mbala-Kingebeni
- Department of Virology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Département de Biologie Médicale, Cliniques Universitaires de Kinshasa, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Sheila Makiala-Mandanda
- Department of Virology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Département de Biologie Médicale, Cliniques Universitaires de Kinshasa, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | | | | | | | - Oumar Faye
- Institut Pasteur de Dakar, Dakar, Senegal
| | - Masahiro Kajihara
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | | | - Ayato Takada
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | | | - Jean-Jacques Muyembe-Tamfum
- Department of Virology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Département de Biologie Médicale, Cliniques Universitaires de Kinshasa, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Johan van Griensven
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Kevin K Ariën
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Steve Ahuka-Mundeke
- Department of Virology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Département de Biologie Médicale, Cliniques Universitaires de Kinshasa, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
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11
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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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12
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Aubry F, Jacobs S, Darmuzey M, Lequime S, Delang L, Fontaine A, Jupatanakul N, Miot EF, Dabo S, Manet C, Montagutelli X, Baidaliuk A, Gámbaro F, Simon-Lorière E, Gilsoul M, Romero-Vivas CM, Cao-Lormeau VM, Jarman RG, Diagne CT, Faye O, Faye O, Sall AA, Neyts J, Nguyen L, Kaptein SJF, Lambrechts L. Recent African strains of Zika virus display higher transmissibility and fetal pathogenicity than Asian strains. Nat Commun 2021; 12:916. [PMID: 33568638 PMCID: PMC7876148 DOI: 10.1038/s41467-021-21199-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 01/16/2021] [Indexed: 11/09/2022] Open
Abstract
The global emergence of Zika virus (ZIKV) revealed the unprecedented ability for a mosquito-borne virus to cause congenital birth defects. A puzzling aspect of ZIKV emergence is that all human outbreaks and birth defects to date have been exclusively associated with the Asian ZIKV lineage, despite a growing body of laboratory evidence pointing towards higher transmissibility and pathogenicity of the African ZIKV lineage. Whether this apparent paradox reflects the use of relatively old African ZIKV strains in most laboratory studies is unclear. Here, we experimentally compare seven low-passage ZIKV strains representing the recently circulating viral genetic diversity. We find that recent African ZIKV strains display higher transmissibility in mosquitoes and higher lethality in both adult and fetal mice than their Asian counterparts. We emphasize the high epidemic potential of African ZIKV strains and suggest that they could more easily go unnoticed by public health surveillance systems than Asian strains due to their propensity to cause fetal loss rather than birth defects. Here, the authors compare seven low passage Zika virus (ZIKV) strains representing the recently circulating viral genetic diversity of African and Asian strains and find that African ZIKV strains have higher transmissibility in mosquitoes and higher lethality in both adult and fetal mice.
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Affiliation(s)
- Fabien Aubry
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Sofie Jacobs
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Maïlis Darmuzey
- GIGA-Stem Cells/GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), C.H.U. Sart Tilman, University of Liège, Liège, Belgium
| | - Sebastian Lequime
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium.,Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Leen Delang
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Albin Fontaine
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France.,IRD, SSA, AP-HM, UMR Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Aix Marseille University, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Natapong Jupatanakul
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani, Thailand
| | - Elliott F Miot
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Stéphanie Dabo
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Caroline Manet
- Mouse Genetics Laboratory, Institut Pasteur, Paris, France
| | | | - Artem Baidaliuk
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,Evolutionary Genomics of RNA Viruses Group, Institut Pasteur, Paris, France
| | - Fabiana Gámbaro
- Evolutionary Genomics of RNA Viruses Group, Institut Pasteur, Paris, France
| | | | - Maxime Gilsoul
- GIGA-Stem Cells/GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), C.H.U. Sart Tilman, University of Liège, Liège, Belgium
| | - Claudia M Romero-Vivas
- Laboratorio de Enfermedades Tropicales, Departamento de Medicina, Fundación Universidad del Norte, Barranquilla, Colombia
| | | | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Cheikh T Diagne
- Arbovirus and Viral Hemorrhagic Fevers Unit, Institut Pasteur Dakar, Dakar, Senegal
| | - Oumar Faye
- Arbovirus and Viral Hemorrhagic Fevers Unit, Institut Pasteur Dakar, Dakar, Senegal
| | - Ousmane Faye
- Arbovirus and Viral Hemorrhagic Fevers Unit, Institut Pasteur Dakar, Dakar, Senegal
| | - Amadou A Sall
- Arbovirus and Viral Hemorrhagic Fevers Unit, Institut Pasteur Dakar, Dakar, Senegal
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Laurent Nguyen
- GIGA-Stem Cells/GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), C.H.U. Sart Tilman, University of Liège, Liège, Belgium
| | - Suzanne J F Kaptein
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium.
| | - Louis Lambrechts
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.
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13
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El Wahed AA, Patel P, Maier M, Pietsch C, Rüster D, Böhlken-Fascher S, Kissenkötter J, Behrmann O, Frimpong M, Diagne MM, Faye M, Dia N, Shalaby MA, Amer H, Elgamal M, Zaki A, Ismail G, Kaiser M, Corman VM, Niedrig M, Landt O, Faye O, Sall AA, Hufert FT, Truyen U, Liebert UG, Weidmann M. Suitcase Lab for Rapid Detection of SARS-CoV-2 Based on Recombinase Polymerase Amplification Assay. Anal Chem 2021; 93:2627-2634. [PMID: 33471510 PMCID: PMC7839158 DOI: 10.1021/acs.analchem.0c04779] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [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: 11/12/2020] [Accepted: 01/11/2021] [Indexed: 12/30/2022]
Abstract
In March 2020, the SARS-CoV-2 virus outbreak was declared as a world pandemic by the World Health Organization (WHO). The only measures for controlling the outbreak are testing and isolation of infected cases. Molecular real-time polymerase chain reaction (PCR) assays are very sensitive but require highly equipped laboratories and well-trained personnel. In this study, a rapid point-of-need detection method was developed to detect the RNA-dependent RNA polymerase (RdRP), envelope protein (E), and nucleocapsid protein (N) genes of SARS-CoV-2 based on the reverse transcription recombinase polymerase amplification (RT-RPA) assay. RdRP, E, and N RT-RPA assays required approximately 15 min to amplify 2, 15, and 15 RNA molecules of molecular standard/reaction, respectively. RdRP and E RT-RPA assays detected SARS-CoV-1 and 2 genomic RNA, whereas the N RT-RPA assay identified only SARS-CoV-2 RNA. All established assays did not cross-react with nucleic acids of other respiratory pathogens. The RT-RPA assay's clinical sensitivity and specificity in comparison to real-time RT-PCR (n = 36) were 94 and 100% for RdRP; 65 and 77% for E; and 83 and 94% for the N RT-RPA assay. The assays were deployed to the field, where the RdRP RT-RPA assays confirmed to produce the most accurate results in three different laboratories in Africa (n = 89). The RPA assays were run in a mobile suitcase laboratory to facilitate the deployment at point of need. The assays can contribute to speed up the control measures as well as assist in the detection of COVID-19 cases in low-resource settings.
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Affiliation(s)
- Ahmed Abd El Wahed
- Institute
of Animal Hygiene and Veterinary Public Health, University of Leipzig, 04103 Leipzig, Germany
- Division
of Microbiology and Animal Hygiene, Georg-August-University, 37077 Goettingen, Germany
| | - Pranav Patel
- Expert
Molecular Diagnostics, 82256Fürstenfeldbruck, Germany
| | - Melanie Maier
- Institute
of Medical Microbiology and VirologyLeipzig
University Hospital, 04103 Leipzig, Germany
| | - Corinna Pietsch
- Institute
of Medical Microbiology and VirologyLeipzig
University Hospital, 04103 Leipzig, Germany
| | - Dana Rüster
- Institute
of Animal Hygiene and Veterinary Public Health, University of Leipzig, 04103 Leipzig, Germany
| | - Susanne Böhlken-Fascher
- Division
of Microbiology and Animal Hygiene, Georg-August-University, 37077 Goettingen, Germany
| | - Jonas Kissenkötter
- Division
of Microbiology and Animal Hygiene, Georg-August-University, 37077 Goettingen, Germany
| | - Ole Behrmann
- Institute
of Microbiology & Virology, Brandenburg Medical School, 01968 Senftenberg, Germany
| | - Michael Frimpong
- Kumasi Centre
for Collaborative Research in Tropical Medicine, Department of Molecular
Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Martin Faye
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Ndongo Dia
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Mohamed A. Shalaby
- Virology
Department, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
| | - Haitham Amer
- Virology
Department, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
| | - Mahmoud Elgamal
- Virology
Department, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
| | - Ali Zaki
- Department
of Medical Microbiology and Immunology, Faculty of Medicine, Ain Shams University, 11591 Cairo, Egypt
| | - Ghada Ismail
- Department
of Clinical Pathology, Faculty of Medicine, Ain Shams University, 11591 Cairo, Egypt
| | - Marco Kaiser
- GenExpress Gesellschaft für Proteindesign, 12103 Berlin, Germany
| | - Victor M. Corman
- Charité−Universitätsmedizin
Berlin, Institute
of Virology, Berlin, Germany
- German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | | | | | - Ousmane Faye
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Amadou A. Sall
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Frank T. Hufert
- Institute
of Microbiology & Virology, Brandenburg Medical School, 01968 Senftenberg, Germany
| | - Uwe Truyen
- Institute
of Animal Hygiene and Veterinary Public Health, University of Leipzig, 04103 Leipzig, Germany
| | - Uwe G. Liebert
- Institute
of Medical Microbiology and VirologyLeipzig
University Hospital, 04103 Leipzig, Germany
| | - Manfred Weidmann
- Institute
of Microbiology & Virology, Brandenburg Medical School, 01968 Senftenberg, Germany
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14
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Aubry F, Dabo S, Manet C, Filipović I, Rose NH, Miot EF, Martynow D, Baidaliuk A, Merkling SH, Dickson LB, Crist AB, Anyango VO, Romero-Vivas CM, Vega-Rúa A, Dusfour I, Jiolle D, Paupy C, Mayanja MN, Lutwama JJ, Kohl A, Duong V, Ponlawat A, Sylla M, Akorli J, Otoo S, Lutomiah J, Sang R, Mutebi JP, Cao-Lormeau VM, Jarman RG, Diagne CT, Faye O, Faye O, Sall AA, McBride CS, Montagutelli X, Rašić G, Lambrechts L. Enhanced Zika virus susceptibility of globally invasive Aedes aegypti populations. Science 2021; 370:991-996. [PMID: 33214283 DOI: 10.1126/science.abd3663] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/16/2020] [Indexed: 12/18/2022]
Abstract
The drivers and patterns of zoonotic virus emergence in the human population are poorly understood. The mosquito Aedes aegypti is a major arbovirus vector native to Africa that invaded most of the world's tropical belt over the past four centuries, after the evolution of a "domestic" form that specialized in biting humans and breeding in water storage containers. Here, we show that human specialization and subsequent spread of A. aegypti out of Africa were accompanied by an increase in its intrinsic ability to acquire and transmit the emerging human pathogen Zika virus. Thus, the recent evolution and global expansion of A. aegypti promoted arbovirus emergence not solely through increased vector-host contact but also as a result of enhanced vector susceptibility.
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Affiliation(s)
- Fabien Aubry
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Stéphanie Dabo
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Caroline Manet
- Mouse Genetics Laboratory, Institut Pasteur, Paris, France
| | - Igor Filipović
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Noah H Rose
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Elliott F Miot
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,Collège Doctoral, Sorbonne Université, Paris, France
| | - Daria Martynow
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Artem Baidaliuk
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,Collège Doctoral, Sorbonne Université, Paris, France
| | - Sarah H Merkling
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Laura B Dickson
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Anna B Crist
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Victor O Anyango
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Claudia M Romero-Vivas
- Laboratorio de Enfermedades Tropicales, Departamento de Medicina, Fundación Universidad del Norte, Barranquilla, Colombia
| | - Anubis Vega-Rúa
- Institut Pasteur of Guadeloupe, Laboratory of Vector Control Research, Transmission Reservoir and Pathogens Diversity Unit, Morne Jolivière, Guadeloupe, France
| | - Isabelle Dusfour
- Vector Control and Adaptation, Institut Pasteur de la Guyane, Vectopole Amazonien Emile Abonnenc, Cayenne, French Guiana, France
| | - Davy Jiolle
- MIVEGEC, Montpellier University, IRD, CNRS, Montpellier, France.,Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Christophe Paupy
- MIVEGEC, Montpellier University, IRD, CNRS, Montpellier, France.,Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Martin N Mayanja
- Department of Arbovirology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Julius J Lutwama
- Department of Arbovirology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Veasna Duong
- Virology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Alongkot Ponlawat
- Department of Entomology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Massamba Sylla
- Unité d'Entomologie, de Bactériologie, de Virologie, Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | - Jewelna Akorli
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Sampson Otoo
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Joel Lutomiah
- Arbovirus/Viral Hemorrhagic Fevers Laboratory, Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Rosemary Sang
- Arbovirus/Viral Hemorrhagic Fevers Laboratory, Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - John-Paul Mutebi
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | | | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Cheikh T Diagne
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, Dakar, Senegal
| | - Oumar Faye
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, Dakar, Senegal
| | - Ousmane Faye
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, Dakar, Senegal
| | - Amadou A Sall
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, Dakar, Senegal
| | - Carolyn S McBride
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | | | - Gordana Rašić
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Louis Lambrechts
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.
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15
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Staines HM, Kirwan DE, Clark DJ, Adams ER, Augustin Y, Byrne RL, Cocozza M, Cubas-Atienzar AI, Cuevas LE, Cusinato M, Davies BM, Davis M, Davis P, Duvoix A, Eckersley NM, Forton D, Fraser AJ, Garrod G, Hadcocks L, Hu Q, Johnson M, Kay GA, Klekotko K, Lewis Z, Macallan DC, Mensah-Kane J, Menzies S, Monahan I, Moore CM, Nebe-von-Caron G, Owen SI, Sainter C, Sall AA, Schouten J, Williams CT, Wilkins J, Woolston K, Fitchett JR, Krishna S, Planche T. IgG Seroconversion and Pathophysiology in Severe Acute Respiratory Syndrome Coronavirus 2 Infection. Emerg Infect Dis 2021; 27:85-91. [PMID: 33256890 PMCID: PMC7774532 DOI: 10.3201/eid2701.203074] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We investigated the dynamics of seroconversion in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. During March 29-May 22, 2020, we collected serum samples and associated clinical data from 177 persons in London, UK, who had SARS-CoV-2 infection. We measured IgG against SARS-CoV-2 and compared antibody levels with patient outcomes, demographic information, and laboratory characteristics. We found that 2.0%-8.5% of persons did not seroconvert 3-6 weeks after infection. Persons who seroconverted were older, were more likely to have concurrent conditions, and had higher levels of inflammatory markers. Non-White persons had higher antibody concentrations than those who identified as White; these concentrations did not decline during follow-up. Serologic assay results correlated with disease outcome, race, and other risk factors for severe SARS-CoV-2 infection. Serologic assays can be used in surveillance to clarify the duration and protective nature of humoral responses to SARS-CoV-2 infection.
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Affiliation(s)
| | | | | | - Emily R. Adams
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Yolanda Augustin
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Rachel L. Byrne
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Michael Cocozza
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Ana I. Cubas-Atienzar
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Luis E. Cuevas
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Martina Cusinato
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Benedict M.O. Davies
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Mark Davis
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Paul Davis
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Annelyse Duvoix
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Nicholas M. Eckersley
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Daniel Forton
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Alice J. Fraser
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Gala Garrod
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Linda Hadcocks
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Qinxue Hu
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Michael Johnson
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Grant A. Kay
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Kesja Klekotko
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Zawditu Lewis
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Derek C. Macallan
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Josephine Mensah-Kane
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Stefanie Menzies
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Irene Monahan
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Catherine M. Moore
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Gerhard Nebe-von-Caron
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Sophie I. Owen
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Chris Sainter
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Amadou A. Sall
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - James Schouten
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Christopher T. Williams
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - John Wilkins
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Kevin Woolston
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
| | - Joseph R.A. Fitchett
- St. George’s, University of London, London, UK (H.M. Staines, D.E. Kirwan, D.J. Clark, Y. Augustin, M. Cuisinato, B.M.O. Davies, N.M. Eckersley, D. Forton, L. Hadcocks, Q. Hu, D.C. Macallan, I. Monahan, C.M. Moore, S. Krishna, T. Planche)
- Liverpool School of Tropical Medicine, Liverpool, UK (E.R. Adams, R.L. Byrne, A.I. Cubas-Atienzar, L.E. Cuevas, A.J. Fraser, G. Garrod, G.A. Kay, S. Menzies, S.I. Owen, C.T. Williams)
- Mologic, Thurleigh, UK (M. Cocozza, M. Davis, P. Davis, A. Duvoix, M. Johnson, K. Klekotko, Z. Lewis, J. Mensah-Kane, G. Nebe-von-Caron, C. Sainter, J. Schouten, J. Wilkins, K. Woolston, J.R.A. Fitchett)
- St. George’s University Hospitals National Health Services Foundation Trust, London (D. Forton, S. Krishna, T. Planche)
- Institut Pasteur, Dakar, Senegal (A.A. Sall)
- Universitätsklinikum Tübingen, Tübingen, Germany (S. Krishna)
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon (S. Krishna)
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16
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Diagne MM, Dieng I, Granjon L, Lucaccioni H, Sow A, Ndiaye O, Faye M, Bâ K, Bâ Y, Diallo M, Faye O, Duplantier JM, Diallo M, Handschumacher P, Faye O, Sall AA. Seoul Orthohantavirus in Wild Black Rats, Senegal, 2012-2013. Emerg Infect Dis 2020; 26:2460-2464. [PMID: 32946728 PMCID: PMC7510722 DOI: 10.3201/eid2610.201306] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Hantaviruses cause hemorrhagic fever in humans worldwide. However, few hantavirus surveillance campaigns occur in Africa. We detected Seoul orthohantavirus in black rats in Senegal, although we did not find serologic evidence of this disease in humans. These findings highlight the need for increased surveillance of hantaviruses in this region.
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17
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Fall C, Cappuyns A, Faye O, Pauwels S, Fall G, Dia N, Diagne MM, Diagne CT, Niang M, Mbengue A, Faye M, Dieng I, Gningue B, Bousso A, Faye O, Pauwels R, Sall AA. Field evaluation of a mobile biosafety laboratory in Senegal to strengthen rapid disease outbreak response and monitoring. Afr J Lab Med 2020; 9:1041. [PMID: 32934915 PMCID: PMC7479379 DOI: 10.4102/ajlm.v9i2.1041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 05/29/2020] [Indexed: 11/12/2022] Open
Abstract
Background Past and recent outbreaks have highlighted the vulnerability of humans to infectious diseases, which represent serious economic and health security threats. A paradigm shift in the management of sanitary crises is urgently needed. Based on lessons from the 2014 Ebola outbreak, the Praesens Foundation has developed an all-terrain mobile biosafety laboratory (MBS-Lab) for effective field diagnostics capabilities. Objective The aim of the study was to train African teams and run a field evaluation of the MBS-Lab, including robustness, technical and operational sustainability, biosafety, connectivity, turn-around times for testing and result delivery. Methods The MBS-Lab was deployed in Senegal in October 2017 for a six-month field assessment under various ecological conditions and was mobilised during the dengue outbreaks in 2017 and 2018. Results The MBS-Lab can be considered an off-grid solution that addresses field challenges with regard to working conditions, mobility, deployment, environment and personnel safety. Blood (n = 398) and nasal swab (n = 113) samples were collected from 460 study participants for molecular screening for acute febrile illnesses and respiratory infections. The results showed that malaria (particularly in Kédougou) and upper respiratory tract infections remain problematic. Suspected dengue samples were tested on board during the dengue outbreaks in 2017 (882 tests; 128 confirmed cases) and 2018 (1736 tests; 202 confirmed cases). Conclusion The MBS-Lab is an innovative solution for outbreak response, even in remote areas. The study demonstrated successful local ownership and community engagement. The MBS-Lab can also be considered an open mobile healthcare platform that offers various opportunities for field-deployable, point-of-care technologies for surveillance programmes.
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Affiliation(s)
- Cheikh Fall
- Department of Virology, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Oumar Faye
- Department of Virology, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Gamou Fall
- Department of Virology, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ndongo Dia
- Department of Virology, Institut Pasteur de Dakar, Dakar, Senegal
| | - Moussa M Diagne
- Department of Virology, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cheikh T Diagne
- Department of Virology, Institut Pasteur de Dakar, Dakar, Senegal
| | - Makhtar Niang
- Department of Virology, Institut Pasteur de Dakar, Dakar, Senegal
| | - Alassane Mbengue
- Department of Virology, Institut Pasteur de Dakar, Dakar, Senegal
| | - Martin Faye
- Department of Virology, Institut Pasteur de Dakar, Dakar, Senegal
| | - Idrissa Dieng
- Department of Virology, Institut Pasteur de Dakar, Dakar, Senegal
| | - Babacar Gningue
- Quality Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Abdoulaye Bousso
- Senegalese Health Emergency Operation Center, Ministry of Health, Dakar, Senegal
| | - Ousmane Faye
- Department of Virology, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Amadou A Sall
- Department of Virology, Institut Pasteur de Dakar, Dakar, Senegal
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18
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Wang J, Xu C, Wong YK, He Y, Adegnika AA, Kremsner PG, Agnandji ST, Sall AA, Liang Z, Qiu C, Liao FL, Jiang T, Krishna S, Tu Y. Preparedness is essential for malaria-endemic regions during the COVID-19 pandemic. Lancet 2020; 395:1094-1096. [PMID: 32192582 PMCID: PMC7158917 DOI: 10.1016/s0140-6736(20)30561-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Jigang Wang
- ShenZhen People's Hospital, ShenZhen, China; Artemisinin Research Center and the Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China; Central People's Hospital of Zhanjiang, Zhanjiang, Guangdong, China
| | - Chengchao Xu
- ShenZhen People's Hospital, ShenZhen, China; Artemisinin Research Center and the Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yin Kwan Wong
- Artemisinin Research Center and the Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China; Department of Anaesthesiology, Singapore General Hospital, Singapore
| | - Yingke He
- Department of Anaesthesiology, Singapore General Hospital, Singapore
| | - Ayôla A Adegnika
- Institut für Tropenmedizin, Universitätsklinikum Tübingen, Tübingen, Germany; Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Peter G Kremsner
- Institut für Tropenmedizin, Universitätsklinikum Tübingen, Tübingen, Germany; Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Selidji T Agnandji
- Institut für Tropenmedizin, Universitätsklinikum Tübingen, Tübingen, Germany; Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | | | - Zhen Liang
- ShenZhen People's Hospital, ShenZhen, China
| | - Chen Qiu
- ShenZhen People's Hospital, ShenZhen, China
| | - Fu Long Liao
- Artemisinin Research Center and the Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Tingliang Jiang
- Artemisinin Research Center and the Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Sanjeev Krishna
- Institut für Tropenmedizin, Universitätsklinikum Tübingen, Tübingen, Germany; Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon; Centre for Diagnostics and Antimicrobial Resistance, Institute for Infection Immunity, St George's University of London, London, UK; St George's University Hospitals NHS Foundation Trust, London, UK
| | - Youyou Tu
- Artemisinin Research Center and the Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
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19
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Diagne MM, Gaye A, Ndione MHD, Faye M, Fall G, Dieng I, Widen SG, Wood TG, Popov V, Guzman H, Bâ Y, Weaver SC, Diallo M, Tesh R, Faye O, Vasilakis N, Sall AA. Dianke virus: A new mesonivirus species isolated from mosquitoes in Eastern Senegal. Virus Res 2020; 275:197802. [PMID: 31697989 PMCID: PMC7075714 DOI: 10.1016/j.virusres.2019.197802] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 06/02/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 12/23/2022]
Abstract
An increasing number of insect-specific viruses are found around the world. Very recently, a new group of insect-specific viruses, the Mesoniviridae family, was discovered in Africa, Asia, North America and Australia. Here we report the first detection and isolation of a new virus belonging to Mesonivirus genus in Senegal, West Africa. The so-called Dianke virus was detected in 21 species of arthropods trapped in the eastern part of the country. Male individuals were also infected, supporting vertical transmission assertion of insect specific viruses. As described for other mesoniviruses, no viral replication was observed after inoculation of mammalian cells. Viral replication in mosquito cells was blocked at a temperature of 37 °C, highlighting the importance of thermal conditions in Mesonivirus host restriction. Similar to our study, where a diverse range of arthropod vectors were found infected by the new virus, several studies have detected mesonivirus infection in mosquitoes with concerns for human health. It has been shown that dual infections in mosquito can alter viral infectivity. Due to their extensive geographic distribution and host range, as well as their use as potential disease control agents in vector populations, more studies should be done for a better knowledge of arthropod-restricted viruses prevalence and diversity.
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Affiliation(s)
- Moussa M Diagne
- Virology Department, Arbovirus and Hemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal.
| | - Alioune Gaye
- Medical Entology Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Marie Henriette Dior Ndione
- Virology Department, Arbovirus and Hemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal; Cheikh Anta Diop de Dakar University, Dakar, Senegal
| | - Martin Faye
- Virology Department, Arbovirus and Hemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Gamou Fall
- Virology Department, Arbovirus and Hemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Idrissa Dieng
- Virology Department, Arbovirus and Hemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal; Cheikh Anta Diop de Dakar University, Dakar, Senegal
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-1079, USA
| | - Thomas G Wood
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-1079, USA
| | - Vsevolod Popov
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555-0610, USA
| | - Hilda Guzman
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555-0610, USA
| | - Yamar Bâ
- Medical Entology Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Scott C Weaver
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555-0610, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-0609, USA
| | - Mawlouth Diallo
- Medical Entology Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Robert Tesh
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555-0610, USA
| | - Ousmane Faye
- Virology Department, Arbovirus and Hemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Nikos Vasilakis
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555-0610, USA
| | - Amadou A Sall
- Virology Department, Arbovirus and Hemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal
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20
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Weidmann M, Faye O, Faye O, Abd El Wahed A, Patel P, Batejat C, Manugerra JC, Adjami A, Niedrig M, Hufert FT, Sall AA. Development of Mobile Laboratory for Viral Hemorrhagic Fever Detection in Africa. J Infect Dis 2019; 218:1622-1630. [PMID: 29917112 PMCID: PMC6173574 DOI: 10.1093/infdis/jiy362] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 05/03/2018] [Accepted: 06/12/2018] [Indexed: 11/22/2022] Open
Abstract
Background A mobile laboratory transportable on commercial flights was developed to enable local response to viral hemorrhagic fever outbreaks. Methods The development progressed from use of mobile real-time reverse-transcription polymerase chain reaction to mobile real-time recombinase polymerase amplification. In this study, we describe various stages of the mobile laboratory development. Results A brief overview of mobile laboratory deployments, which culminated in the first on-site detection of Ebola virus disease (EVD) in March 2014, and their successful use in a campaign to roll back EVD cases in Conakry in the West Africa Ebola virus outbreak are described. Conclusions The developed mobile laboratory successfully enabled local teams to perform rapid disgnostic testing for viral hemorrhagic fever.
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Affiliation(s)
- Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Scotland, United Kingdom
- Correspondence: M. Weidmann, Dr. rer. nat., University of Stirling, Institute of Aquaculture, Stirling FK9 4LA, Scotland, United Kingdom ()
| | - Ousmane Faye
- Arbovirus Unit, Pasteur Institute, Dakar, Senegal
| | - Oumar Faye
- Arbovirus Unit, Pasteur Institute, Dakar, Senegal
| | - Ahmed Abd El Wahed
- Unit of Infection Models, German Primate Center, Goettingen, Germany
- Division of Microbiology and Animal Hygiene, University of Goettingen, Germany
| | | | - Christophe Batejat
- Laboratory for Urgent Response to Biological Threats (CIBU), Environment and Infectious Risks Unit, Institut Pasteur, Paris, France
| | - Jean Claude Manugerra
- Laboratory for Urgent Response to Biological Threats (CIBU), Environment and Infectious Risks Unit, Institut Pasteur, Paris, France
| | - Aimee Adjami
- Multi Disease Surveillance Centre WHO, Ougadougou, Burkina Faso
| | | | - Frank T Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane (and Member of the Faculty of Environment and Natural Sciences of B-TU Senftenberg site), Senftenberg, Brandenburg, Germany
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21
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Davi SD, Kissenkötter J, Faye M, Böhlken-Fascher S, Stahl-Hennig C, Faye O, Faye O, Sall AA, Weidmann M, Ademowo OG, Hufert FT, Czerny CP, Abd El Wahed A. Recombinase polymerase amplification assay for rapid detection of Monkeypox virus. Diagn Microbiol Infect Dis 2019; 95:41-45. [PMID: 31126795 PMCID: PMC9629024 DOI: 10.1016/j.diagmicrobio.2019.03.015] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/04/2019] [Accepted: 03/28/2019] [Indexed: 12/17/2022]
Abstract
In this study, a rapid method for the detection of Central and West Africa clades of Monkeypox virus (MPXV) using recombinase polymerase amplification (RPA) assay targeting the G2R gene was developed. MPXV, an Orthopoxvirus, is a zoonotic dsDNA virus, which is listed as a biothreat agent. RPA was operated at a single constant temperature of 42°C and produced results within 3 to 10 minutes. The MPXV-RPA-assay was highly sensitive with a limit of detection of 16 DNA molecules/μl. The clinical performance of the MPXV-RPA-assay was tested using 47 sera and whole blood samples from humans collected during the recent MPXV outbreak in Nigeria as well as 48 plasma samples from monkeys some of which were experimentally infected with MPXV. The specificity of the MPXV-RPA-assay was 100% (50/50), while the sensitivity was 95% (43/45). This new MPXV-RPA-assay is fast and can be easily utilised at low resource settings using a solar powered mobile suitcase laboratory.
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Affiliation(s)
- Saskia Dede Davi
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Senftenberg, Germany
| | - Jonas Kissenkötter
- Department of Animal Sciences, Microbiology and Animal Hygiene, Georg-August-University of Goettingen, Goettingen, Germany
| | | | - Susanne Böhlken-Fascher
- Department of Animal Sciences, Microbiology and Animal Hygiene, Georg-August-University of Goettingen, Goettingen, Germany
| | | | - Oumar Faye
- Institute Pasteur de Dakar, Dakar, Senegal
| | | | | | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Olusegun George Ademowo
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Frank T Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Senftenberg, Germany
| | - Claus-Peter Czerny
- Department of Animal Sciences, Microbiology and Animal Hygiene, Georg-August-University of Goettingen, Goettingen, Germany
| | - Ahmed Abd El Wahed
- Department of Animal Sciences, Microbiology and Animal Hygiene, Georg-August-University of Goettingen, Goettingen, Germany.
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Mbala-Kingebeni P, Aziza A, Di Paola N, Wiley MR, Makiala-Mandanda S, Caviness K, Pratt CB, Ladner JT, Kugelman JR, Prieto K, Chitty JA, Larson PA, Beitzel B, Ayouba A, Vidal N, Karhemere S, Diop M, Diagne MM, Faye M, Faye O, Aruna A, Nsio J, Mulangu F, Mukadi D, Mukadi P, Kombe J, Mulumba A, Villabona-Arenas CJ, Pukuta E, Gonzalez J, Bartlett ML, Sozhamannan S, Gross SM, Schroth GP, Tim R, Zhao JJ, Kuhn JH, Diallo B, Yao M, Fall IS, Ndjoloko B, Mossoko M, Lacroix A, Delaporte E, Sanchez-Lockhart M, Sall AA, Muyembe-Tamfum JJ, Peeters M, Palacios G, Ahuka-Mundeke S. Medical countermeasures during the 2018 Ebola virus disease outbreak in the North Kivu and Ituri Provinces of the Democratic Republic of the Congo: a rapid genomic assessment. Lancet Infect Dis 2019; 19:648-657. [PMID: 31000464 DOI: 10.1016/s1473-3099(19)30118-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/21/2019] [Accepted: 03/06/2019] [Indexed: 11/30/2022]
Abstract
BACKGROUND The real-time generation of information about pathogen genomes has become a vital goal for transmission analysis and characterisation in rapid outbreak responses. In response to the recently established genomic capacity in the Democratic Republic of the Congo, we explored the real-time generation of genomic information at the start of the 2018 Ebola virus disease (EVD) outbreak in North Kivu Province. METHODS We used targeted-enrichment sequencing to produce two coding-complete Ebola virus genomes 5 days after declaration of the EVD outbreak in North Kivu. Subsequent sequencing efforts yielded an additional 46 genomes. Genomic information was used to assess early transmission, medical countermeasures, and evolution of Ebola virus. FINDINGS The genomic information demonstrated that the EVD outbreak in the North Kivu and Ituri Provinces was distinct from the 2018 EVD outbreak in Équateur Province of the Democratic Republic of the Congo. Primer and probe mismatches to Ebola virus were identified in silico for all deployed diagnostic PCR assays, with the exception of the Cepheid GeneXpert GP assay. INTERPRETATION The first two coding-complete genomes provided actionable information in real-time for the deployment of the rVSVΔG-ZEBOV-GP Ebola virus envelope glycoprotein vaccine, available therapeutics, and sequence-based diagnostic assays. Based on the mutations identified in the Ebola virus surface glycoprotein (GP12) observed in all 48 genomes, deployed monoclonal antibody therapeutics (mAb114 and ZMapp) should be efficacious against the circulating Ebola virus variant. Rapid Ebola virus genomic characterisation should be included in routine EVD outbreak response procedures to ascertain efficacy of medical countermeasures. FUNDING Defense Biological Product Assurance Office.
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Affiliation(s)
- Placide Mbala-Kingebeni
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Amuri Aziza
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Nicholas Di Paola
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Michael R Wiley
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; College of Public Health, Northern Arizona University, Flagstaff, AZ, USA
| | - Sheila Makiala-Mandanda
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Katie Caviness
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Catherine B Pratt
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; College of Public Health, Northern Arizona University, Flagstaff, AZ, USA
| | - Jason T Ladner
- University of Nebraska Medical Center, Omaha, NE, USA; The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Karla Prieto
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; College of Public Health, Northern Arizona University, Flagstaff, AZ, USA
| | - Joseph A Chitty
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Peter A Larson
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Brett Beitzel
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Ahidjo Ayouba
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Nicole Vidal
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Stomy Karhemere
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | | | | | | | | | - Aaron Aruna
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Justus Nsio
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Felix Mulangu
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Daniel Mukadi
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Patrick Mukadi
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - John Kombe
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Anastasie Mulumba
- l'Organisation Mondiale de la Santé, Kinshasa, Democratic Republic of the Congo
| | | | - Elisabeth Pukuta
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Jeanette Gonzalez
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Maggie L Bartlett
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; Department of Pathology and Microbiology, Northern Arizona University, Flagstaff, AZ, USA
| | - Shanmuga Sozhamannan
- Defense Biological Product Assurance Office, Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense-Joint Project Management Office for Guardian, Frederick, MA, USA; The Tauri Group, Alexandria, VA, USA
| | | | | | | | | | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | | | - Michel Yao
- World Health Organization, Geneva, Switzerland
| | | | - Bathe Ndjoloko
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Mathias Mossoko
- Direction Générale de Lutte contre la Maladie, Kinshasa, Democratic Republic of the Congo
| | - Audrey Lacroix
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Eric Delaporte
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; Department of Pathology and Microbiology, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Jean-Jacques Muyembe-Tamfum
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Martine Peeters
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Gustavo Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA.
| | - Steve Ahuka-Mundeke
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of the Congo
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23
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Hachid A, Beloufa MA, Seghier M, Bahoura N, Dia M, Fall G, Sall AA. Evidence of West Nile virus circulation among humans in central northern Algeria. New Microbes New Infect 2019; 29:100512. [PMID: 30984402 PMCID: PMC6444287 DOI: 10.1016/j.nmni.2019.01.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 05/30/2018] [Revised: 01/12/2019] [Accepted: 01/25/2019] [Indexed: 10/27/2022] Open
Abstract
West Nile Virus (WNV) is the most widely distributed flavivirus worldwide. It is a mosquito-borne virus, and birds constitute its natural reservoir. Humans and equines are considered accidental hosts. Human WNV infections are usually asymptomatic or express as a mild febrile syndrome; however, in around 1% of cases they are responsible for more serious neurological diseases with a potentially lethal outcome. In the Mediterranean basin the virus circulation is regarded as endemic. Outbreaks of WNV meningoencephalitis are regularly notified, especially during summer and autumn seasons. In Algeria, although some surveys have reported WNV activity in the Sahara, to date few data are available about virus circulation in the northern part of the country. We conducted this study to detect possible WNV activity in this part of Algeria. For this purpose, in 2010 a total of 164 human sera were collected from native patients of the Algiers district and surrounding areas, then tested retrospectively for IgG anti-WNV by ELISA. Plaque reduction neutralization technique (PRNT) was used for result confirmation. In this cohort, 9.8% of the 164 collected sera returned positive for anti-WNV IgG; after confirmation by PRNT; 6.7% had specific neutralizing antibodies. No statistically significant difference was observed according to the sex or transfusion status of the patients. In conclusion, these data show for the first time serological evidence of WNV circulation in Algiers and its surrounding areas. They also highlight the need for implementing an integrated surveillance programme covering all aspects of WNV disease in order to better understand the circulation dynamics of WNV in this region. Other flaviviruses antigenically related to WNV should be investigated, given the evidence of serological cross-reaction, as specific IgG antibodies decrease after PRNT confirmation.
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Affiliation(s)
- A Hachid
- Département de Virologie Humaine, Institut Pasteur d'Algérie, Algeria.,Faculté de medecine d'Alger, Algerie
| | - M A Beloufa
- Département de Virologie Humaine, Institut Pasteur d'Algérie, Algeria.,Faculté de medecine d'Alger, Algerie
| | - M Seghier
- Département de Virologie Humaine, Institut Pasteur d'Algérie, Algeria.,Faculté de medecine d'Alger, Algerie
| | - N Bahoura
- Département de Virologie Humaine, Institut Pasteur d'Algérie, Algeria.,Faculté de medecine d'Alger, Algerie
| | - M Dia
- Laboratoire des Arbovirus et Virus de Fièvres Hémorragiques, Institut Pasteur de Dakar, Senegal
| | - G Fall
- Laboratoire des Arbovirus et Virus de Fièvres Hémorragiques, Institut Pasteur de Dakar, Senegal
| | - A A Sall
- Laboratoire des Arbovirus et Virus de Fièvres Hémorragiques, Institut Pasteur de Dakar, Senegal
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24
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Diallo D, Diagne CT, Buenemann M, Ba Y, Dia I, Faye O, Sall AA, Faye O, Watts DM, Weaver SC, Hanley KA, Diallo M. Biodiversity Pattern of Mosquitoes in Southeastern Senegal, Epidemiological Implication in Arbovirus and Malaria Transmission. J Med Entomol 2019; 56:453-463. [PMID: 30428055 PMCID: PMC6941392 DOI: 10.1093/jme/tjy204] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Indexed: 06/01/2023]
Abstract
The composition, density, diversity, and temporal distribution of mosquito species and the influence of temperature, relative humidity, and rainfall on these data were investigated in 50 sites across five land cover classes (forest, savannah, barren, village, and agriculture) in southeastern Senegal. Mosquitoes were collected monthly in each site between June 2009 and March 2011, with three people collecting mosquitoes landing on their legs for one to four consecutive days. In total, 81,219 specimens, belonging to 60 species and 7 genera, were collected. The most abundant species were Aedes furcifer (Edwards) (Diptera: Culicidae) (20.7%), Ae. vittatus (Bigot) (19.5%), Ae. dalzieli (Theobald) (14.7%), and Ae. luteocephalus (Newstead) (13.7%). Ae. dalzieli, Ae. furcifer, Ae. vittatus, Ae. luteocephalus, Ae. taylori Edwards, Ae. africanus (Theobald), Ae. minutus (Theobald), Anopheles coustani Laveran, Culex quinquefasciatus Say, and Mansonia uniformis (Theobald) comprised ≥10% of the total collection, in at least one land cover. The lowest species richness and Brillouin diversity index (HB = 1.55) were observed in the forest-canopy. The urban-indoor fauna showed the highest dissimilarity with other land covers and was most similar to the urban-outdoor fauna following Jaccard and Morisita index. Mosquito abundance peaked in June and October 2009 and July and October 2010. The highest species density was recorded in October. The maximum temperature was correlated positively with mean temperature and negatively with rainfall and relative humidity. Rainfall showed a positive correlation with mosquito abundance and species density. These data will be useful for understanding the transmission of arboviruses and human malaria in the region.
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Affiliation(s)
- Diawo Diallo
- Unité d’entomologie médicale, Institut Pasteur de Dakar, Dakar, Sénégal
| | - Cheikh T Diagne
- Unité d’entomologie médicale, Institut Pasteur de Dakar, Dakar, Sénégal
| | | | - Yamar Ba
- Unité d’entomologie médicale, Institut Pasteur de Dakar, Dakar, Sénégal
| | - Ibrahima Dia
- Unité d’entomologie médicale, Institut Pasteur de Dakar, Dakar, Sénégal
| | - Oumar Faye
- Pole virologie, Institut Pasteur de Dakar, Sénégal
| | | | - Ousmane Faye
- Pole virologie, Institut Pasteur de Dakar, Sénégal
| | - Douglas M Watts
- Office of Research and Sponsored Projects, University of Texas at El Paso, El Paso, TX
| | - Scott C Weaver
- Institute for Human Infections and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University, Las Cruces, NM
| | - Mawlouth Diallo
- Unité d’entomologie médicale, Institut Pasteur de Dakar, Dakar, Sénégal
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25
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Niang M, Sane R, Sow A, Sadio BD, Chy S, Legrand E, Faye O, Diallo M, Sall AA, Menard D, Toure-Balde A. Asymptomatic Plasmodium vivax infections among Duffy-negative population in Kedougou, Senegal. Trop Med Health 2018; 46:45. [PMID: 30618490 PMCID: PMC6311047 DOI: 10.1186/s41182-018-0128-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 12/11/2018] [Indexed: 02/08/2023] Open
Abstract
Background In the southeastern Senegal, the report of Plasmodium vivax infections among febrile patients in Kedougou constitutes a new emerging health problem. Methods Samples from 48 asymptomatic schoolchildren sampled twice a year over 2 years were used to explore the reservoir of P. vivax parasite infections in this region. Both Duffy genotyping and Plasmodium species diagnostic assays were performed. Results PCR assays detected Plasmodium genomic DNA in 38.5% (74/192) of samples. Pure P. falciparum and P. vivax infections were identified in 79.7% (59/74) and 20.3% (15/74) of samples, respectively. All schoolchildren were classified as Duffy-negative by genotyping. P. vivax infections were detected in five children: in two children during both years, in one child in 2010 and on May 2011, and only in 2010 for the remaining two children. Conclusions This unexpectedly high proportion of P. vivax infections in asymptomatic Duffy-negative children highlights to consider vivax malaria as an emerging problem in Senegal.
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Affiliation(s)
- Makhtar Niang
- 1Immunology Unit, Pasteur Institute of Dakar, BP 220 Dakar, Senegal
| | - Rokhaya Sane
- 1Immunology Unit, Pasteur Institute of Dakar, BP 220 Dakar, Senegal.,2Department of Animal Biology, Cheikh Anta Diop University of Dakar, Dakar, Senegal
| | - Abdourahmane Sow
- 3Arbovirus and Viral Hemorrhagic Fevers Unit, Pasteur Institute of Dakar, BP 220 Dakar, Senegal.,West African Health Organization, Ouagadougou, Burkina Faso
| | - Bacary D Sadio
- 3Arbovirus and Viral Hemorrhagic Fevers Unit, Pasteur Institute of Dakar, BP 220 Dakar, Senegal
| | - Sophy Chy
- Malaria Molecular Epidemiology Unit, Institute Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Eric Legrand
- 6Groupe Génétique du Paludisme et Résistance, Unité Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, France
| | - Ousmane Faye
- 3Arbovirus and Viral Hemorrhagic Fevers Unit, Pasteur Institute of Dakar, BP 220 Dakar, Senegal
| | - Mawlouth Diallo
- 7Medical Entomology Unit, Pasteur Institute of Dakar, BP 220 Dakar, Senegal
| | - Amadou A Sall
- 3Arbovirus and Viral Hemorrhagic Fevers Unit, Pasteur Institute of Dakar, BP 220 Dakar, Senegal
| | - Didier Menard
- 6Groupe Génétique du Paludisme et Résistance, Unité Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, France
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26
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Soghaier MA, Abdelgadir DM, Abdelkhalig SM, Kafi H, Zarroug IMA, Sall AA, Eldegai MH, Elageb RM, Osman MM, Khogali H. Evidence of pre-existing active Zika virus circulation in Sudan prior to 2012. BMC Res Notes 2018; 11:906. [PMID: 30567583 PMCID: PMC6299991 DOI: 10.1186/s13104-018-4027-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 12/17/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The purpose of this study is to provide the first evidence of Zika virus circulation (ZIK) in Sudan. Zika virus was first isolated in the Zika forest of Uganda in 1947, and in 2016, the World Health Assembly declared it a public health emergency of international concern. The discovery of Zika virus circulation in Sudan came as a secondary finding in a 2012 country-wide yellow fever prevalence study, when laboratory tests were done to exclude cross-reactions between flaviviruses. The study was cross-sectional community-based, with randomly selected participants through multi-stage cluster sampling. A sub-set of samples were tested for the Zika virus using ELISA, and the ones that demonstrated reactive results were subsequently tested by PRNT. RESULTS The prevalence of Zika IgG antibodies among ELISA-tested samples was 62.7% (59.4 to 66.1, 95% CI), and only one sample was found positive when tested by PRNT. This provided the first documented evidence for the pre-existing circulation of Zika virus circulation in Sudan. This evidence provides the foundation for future research in this field, and further structured studies should be conducted to determine the epidemiology and burden of the disease.
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Affiliation(s)
- Mohammed A. Soghaier
- Epidemiology and Zoonotic Diseases Department, Federal Ministry of Health, Osman Digna Street with Nile Avenue, PO Box 303, 1111 Khartoum, Sudan
| | - Deena M. Abdelgadir
- Epidemiology and Zoonotic Diseases Department, Federal Ministry of Health, Osman Digna Street with Nile Avenue, PO Box 303, 1111 Khartoum, Sudan
| | - Sozan M. Abdelkhalig
- The Department of Epidemiology, National Public Health Laboratory, Federal Ministry of Heath, Khartoum, Sudan
| | - Hamoda Kafi
- Department of Integrated Vector Management, Federal Ministry of Health, Khartoum, Sudan
| | - Isam M. A. Zarroug
- The Department of Medical Entomology, National Public Health Laboratory, Federal Ministry of Health, Khartoum, Sudan
| | | | - Mawahib H. Eldegai
- The Department of Epidemiology, National Public Health Laboratory, Federal Ministry of Heath, Khartoum, Sudan
| | - Rehab M. Elageb
- The Department of Epidemiology, National Public Health Laboratory, Federal Ministry of Heath, Khartoum, Sudan
| | - Muntasir M. Osman
- Epidemiology and Zoonotic Diseases Department, Federal Ministry of Health, Osman Digna Street with Nile Avenue, PO Box 303, 1111 Khartoum, Sudan
| | - Hayat Khogali
- Epidemiology and Zoonotic Diseases Department, Federal Ministry of Health, Osman Digna Street with Nile Avenue, PO Box 303, 1111 Khartoum, Sudan
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27
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Varma JK, Oppong-Otoo J, Ondoa P, Perovic O, Park BJ, Laxminarayan R, Peeling RW, Schultsz C, Li H, Ihekweazu C, Sall AA, Jaw B, Nkengasong JN. Africa Centres for Disease Control and Prevention's framework for antimicrobial resistance control in Africa. Afr J Lab Med 2018; 7:830. [PMID: 30568906 PMCID: PMC6295971 DOI: 10.4102/ajlm.v7i2.830] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/26/2018] [Indexed: 01/21/2023] Open
Affiliation(s)
- Jay K Varma
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia
| | - John Oppong-Otoo
- African Union, Inter-African Bureau for Animal Resources, Nairobi, Kenya
| | - Pascale Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | - Olga Perovic
- National Institute for Communicable Diseases, Johannesburg, South Africa
- University of Witwatersrand, Johannesburg, South Africa
| | - Benjamin J Park
- United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Ramanan Laxminarayan
- Center for Disease Dynamics, Economics and Policy, Washington, D.C., United States
- Princeton University, Princeton, New Jersey, United States
| | - Rosanna W Peeling
- London School of Tropical Medicine and Hygiene, London, England, United Kingdom
| | - Constance Schultsz
- Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands
| | - Han Li
- China Center for Disease Control and Prevention, Beijing, China
- China PLA Institute for Disease Control and Prevention, Beijing, China
| | | | | | - Baboucarr Jaw
- African Union, Inter-African Bureau for Animal Resources, Nairobi, Kenya
| | - John N Nkengasong
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia
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28
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Rojas A, Diagne CT, Stittleburg VD, Mohamed-Hadley A, de Guillén YA, Balmaseda A, Faye O, Faye O, Sall AA, Harris E, Pinsky BA, Waggoner JJ. Internally Controlled, Multiplex Real-Time Reverse Transcription PCR for Dengue Virus and Yellow Fever Virus Detection. Am J Trop Med Hyg 2018; 98:1833-1836. [PMID: 29611509 DOI: 10.4269/ajtmh.18-0024] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The differential diagnosis of dengue virus (DENV) and yellow fever virus (YFV) infections in endemic areas is complicated by nonspecific early clinical manifestations. In this study, we describe an internally controlled, multiplex real-time reverse transcription polymerase chain reaction (rRT-PCR) for the detection of DENV and YFV. The DENV-YFV assay demonstrated specific detection and had a dynamic range of 2.0-8.0 log10 copies/μL of eluate for each DENV serotype and YFV. Clinical performance was similar to a published pan-DENV assay: 48/48 acute-phase samples from dengue cases were detected in both assays. For YFV detection, mock samples were prepared with nine geographically diverse YFV isolates over a range of concentrations. The DENV-YFV assay detected 62/65 replicates, whereas 54/65 were detected using a reference YFV rRT-PCR. Given the reemergence of DENV and YFV in areas around the world, the DENV-YFV assay should be a useful tool to narrow the differential diagnosis and provide early case detection.
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Affiliation(s)
- Alejandra Rojas
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay
| | | | - Victoria D Stittleburg
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Alisha Mohamed-Hadley
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Yvalena Arévalo de Guillén
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay
| | - Angel Balmaseda
- Sustainable Sciences Institute, Managua, Nicaragua.,Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Oumar Faye
- Institut Pasteur de Dakar, Dakar, Sénégal
| | | | | | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California.,Sustainable Sciences Institute, Managua, Nicaragua
| | - Benjamin A Pinsky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California.,Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Jesse J Waggoner
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia.,Department of Global Health, Rollins School of Public Health, Atlanta, Georgia
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29
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Althouse BM, Guerbois M, Cummings DAT, Diop OM, Faye O, Faye A, Diallo D, Sadio BD, Sow A, Faye O, Sall AA, Diallo M, Benefit B, Simons E, Watts DM, Weaver SC, Hanley KA. Role of monkeys in the sylvatic cycle of chikungunya virus in Senegal. Nat Commun 2018. [PMID: 29535306 PMCID: PMC5849707 DOI: 10.1038/s41467-018-03332-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Arboviruses spillover into humans either as a one-step jump from a reservoir host species into humans or as a two-step jump from the reservoir to an amplification host species and thence to humans. Little is known about arbovirus transmission dynamics in reservoir and amplification hosts. Here we elucidate the role of monkeys in the sylvatic, enzootic cycle of chikungunya virus (CHIKV) in the region around Kédougou, Senegal. Over 3 years, 737 monkeys were captured, aged using anthropometry and dentition, and tested for exposure to CHIKV by detection of neutralizing antibodies. Infant monkeys were positive for CHIKV even when the virus was not detected in a concurrent survey of mosquitoes and when population immunity was too high for monkeys alone to support continuous transmission. We conclude that monkeys in this region serve as amplification hosts of CHIKV. Additional efforts are needed to identify other hosts capable of supporting continuous circulation.
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Affiliation(s)
- Benjamin M Althouse
- Institute for Disease Modeling, Bellevue, 98005, WA, USA. .,Information School, University of Washington, Seattle, 98105, WA, USA. .,Department of Biology, New Mexico State University, Las Cruces, 88003, NM, USA.
| | - Mathilde Guerbois
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, 77555, TX, USA
| | - Derek A T Cummings
- Emerging Pathogens Institute, University of Florida, Gainesville, 32608, FL, USA
| | | | | | | | | | | | | | - Oumar Faye
- Institut Pasteur de Dakar, Dakar, Senegal
| | | | | | - Brenda Benefit
- Department of Anthropology, New Mexico State University, Las Cruces, 88003, NM, USA
| | - Evan Simons
- Department of Anthropology, New Mexico State University, Las Cruces, 88003, NM, USA
| | - Douglas M Watts
- Office of Research and Sponsored Projects, University of Texas at El Paso, El Paso, 79968, TX, USA.,Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, 77555, TX, USA
| | - Scott C Weaver
- Institute for Human Infections and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, 77555, TX, USA
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University, Las Cruces, 88003, NM, USA
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30
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Faye O, Pratt CB, Faye M, Fall G, Chitty JA, Diagne MM, Wiley MR, Yinka-Ogunleye AF, Aruna S, Etebu EN, Aworabhi N, Ogoina D, Numbere W, Mba N, Palacios G, Sall AA, Ihekweazu C. Genomic characterisation of human monkeypox virus in Nigeria. Lancet Infect Dis 2018; 18:246. [PMID: 29361427 PMCID: PMC9628790 DOI: 10.1016/s1473-3099(18)30043-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 12/28/2017] [Indexed: 11/25/2022]
Affiliation(s)
| | - Catherine B Pratt
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Disease, Frederick, MD 21702, USA; College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | | | | | - Joseph A Chitty
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Disease, Frederick, MD 21702, USA
| | | | - Michael R Wiley
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Disease, Frederick, MD 21702, USA; College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Sola Aruna
- Nigeria Centre for Disease Control, Abuja, Nigeria; Measure Evaluation, Abuja, Nigeria
| | | | | | - Dimie Ogoina
- Niger Delta University Teaching Hospital/Niger Delta University, Yenagoa, Nigeria
| | - Wari Numbere
- Nigeria Field Epidemiology and Laboratory Training Program, Ibadan, Nigeria
| | - Nwando Mba
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Gustavo Palacios
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Disease, Frederick, MD 21702, USA.
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31
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Keita M, Duraffour S, Loman NJ, Rambaut A, Diallo B, Magassouba N, Carroll MW, Quick J, Sall AA, Glynn JR, Formenty P, Subissi L, Faye O. Unusual Ebola Virus Chain of Transmission, Conakry, Guinea, 2014-2015. Emerg Infect Dis 2018; 22:2149-2152. [PMID: 27869596 PMCID: PMC5189159 DOI: 10.3201/eid2212.160847] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In October 2015, a new case of Ebola virus disease in Guinea was detected. Case investigation, serology, and whole-genome sequencing indicated possible transmission of the virus from an Ebola virus disease survivor to another person and then to the case-patient reported here. This transmission chain over 11 months suggests slow Ebola virus evolution.
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32
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Niang M, Diop F, Niang O, Sadio BD, Sow A, Faye O, Diallo M, Sall AA, Perraut R, Toure-Balde A. Unexpected high circulation of Plasmodium vivax in asymptomatic children from Kédougou, southeastern Senegal. Malar J 2017; 16:497. [PMID: 29284488 PMCID: PMC5747145 DOI: 10.1186/s12936-017-2146-8] [Citation(s) in RCA: 19] [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: 08/14/2017] [Accepted: 12/18/2017] [Indexed: 01/06/2023] Open
Abstract
Background Malaria in Senegal is due essentially to infections by Plasmodium falciparum and, to a lesser extent to Plasmodium malariae and Plasmodium ovale. By the use of molecular methods, detection of Plasmodium vivax has been recently reported in the region of Kedougou, raising the question of appraisal of its potential prevalence in this setting. Methods A retrospective serological study was carried out using 188 samples taken from 2010 to 2011 in a longitudinal school survey during which 48 asymptomatic children (9–11 years) were recruited. Four collections of samples collected during two successive dry and rainy seasons were analysed for antibody responses to P. vivax and P. falciparum. Recombinant P. falciparum and P. vivax MSP1 antigens and total P. falciparum schizont lysate from African 07/03 strain (adapted to culture) were used for ELISA. Nested PCR amplification was used for molecular detection of P. vivax. Results A surprising high prevalence of IgG responses against P. vivax MSP1 was evidenced with 53% of positive samples and 58% of the individuals that were found positive to this antigen. There was 77% of responders to P. falciparum outlined by 63% of positive samples. Prevalence of responders did not differ as function of seasons. Levels of antibodies to P. falciparum fluctuated with significant increasing between dry and rainy season (P < 0.05), contrary to responses to P. vivax. There was a significant reciprocal relationship (P < 10−3) between antibody responses to the different antigens, but with weak coefficient of correlation (Rho around 0.3) underlining a variable profile at the individual level. Clear molecular signature was found in positive IgG to P. vivax msp1 samples by PCR. Conclusion This cross-sectional longitudinal study highlights the unexpected high circulation of P. vivax in this endemic area. Sero-immunology and molecular methods are powerful additive tools to identify endemic sites where relevant control measures have to be settled and monitored.
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Affiliation(s)
- Makhtar Niang
- Immunology Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Fode Diop
- Immunology Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oulimata Niang
- Immunology Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Bacary D Sadio
- Arbovirus and Viral Hemorrhagic Fevers Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Abdourahmane Sow
- Arbovirus and Viral Hemorrhagic Fevers Unit, Institut Pasteur de Dakar, Dakar, Senegal.,West African Health Organization, Ouagadougou, Burkina Faso
| | - Ousmane Faye
- Arbovirus and Viral Hemorrhagic Fevers Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mawlouth Diallo
- Medical Entomology Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou A Sall
- Arbovirus and Viral Hemorrhagic Fevers Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ronald Perraut
- Immunology Unit, Institut Pasteur de Dakar, Dakar, Senegal
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Diagne MM, Faye M, Faye O, Sow A, Balique F, Sembène M, Granjon L, Handschumacher P, Faye O, Diallo M, Sall AA. Emergence of Wesselsbron virus among black rat and humans in Eastern Senegal in 2013. One Health 2017; 3:23-28. [PMID: 28616499 PMCID: PMC5454166 DOI: 10.1016/j.onehlt.2017.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/23/2017] [Accepted: 02/07/2017] [Indexed: 10/25/2022] Open
Abstract
Wesselsbron disease is a neglected mosquito transmitted Flavivirus infection that causes abortions and has teratogenic effects on sheep and cattle in Africa. Human can also be infected. The detection of human or animal cases is complicated by the non-specific symptoms close to Rift Valley Fever (RVF) in domestic livestock species or Dengue like syndrome in humans. Then, these detections are usually made during RVF investigations in sheep. These domestic animals should take a role in the life cycle of the virus but some evidences of Wesselsbron virus (WSLV) presence in wild animals suggest that the latter may be involved in the virus maintenance in nature. However, the reservoir status of wild vertebrate in general and rodents particularly for WSLV is only based on an isolation from a Cape short-eared gerbil in southern Africa. Most of WSLV isolations are from southern parts of Africa even if it has been found in western and central Africa or Madagascar. In Senegal, there are serological evidences of WSLV circulation in human since the 1970s and some isolations, the last one of which dates back in 1992. Despite the detection of the virus on mosquitoes until the 2000s in different parts of the country, no new human case has been noted. In this paper, we report the WSLV re-emergence in eastern Senegal in 2013 with 2 human cases and its first isolation from a black rat Rattus rattus. Sequencing analyses show the circulation of the same strain between these humans and the commensal rodent. The putative impact on WSLV transmission to human populations could be more important if the reservoir status of the black rat is confirmed. Focused survey in human populations, specific entomological and mammalogical investigations would permit a better understanding of the life cycle of the virus and its impact on public health.
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Affiliation(s)
- Moussa M. Diagne
- Institut Pasteur de Dakar, Dakar, Sénégal
- Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | - Martin Faye
- Institut Pasteur de Dakar, Dakar, Sénégal
- Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | - Oumar Faye
- Institut Pasteur de Dakar, Dakar, Sénégal
| | | | | | - Mbacké Sembène
- Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
- IRD CBGP, CS 30016, 34988 Montferrier-sur-Lez cedex, France
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34
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Simon-Loriere E, Faye O, Prot M, Casademont I, Fall G, Fernandez-Garcia MD, Diagne MM, Kipela JM, Fall IS, Holmes EC, Sakuntabhai A, Sall AA. Autochthonous Japanese Encephalitis with Yellow Fever Coinfection in Africa. N Engl J Med 2017; 376:1483-1485. [PMID: 28402771 DOI: 10.1056/nejmc1701600] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
| | | | | | | | - Gamou Fall
- Institut Pasteur de Dakar, Dakar, Senegal
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35
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Urbanowicz RA, McClure CP, Sakuntabhai A, Sall AA, Kobinger G, Müller MA, Holmes EC, Rey FA, Simon-Loriere E, Ball JK. Human Adaptation of Ebola Virus during the West African Outbreak. Cell 2017; 167:1079-1087.e5. [PMID: 27814505 PMCID: PMC5101188 DOI: 10.1016/j.cell.2016.10.013] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/23/2016] [Accepted: 10/06/2016] [Indexed: 12/02/2022]
Abstract
The 2013–2016 outbreak of Ebola virus (EBOV) in West Africa was the largest recorded. It began following the cross-species transmission of EBOV from an animal reservoir, most likely bats, into humans, with phylogenetic analysis revealing the co-circulation of several viral lineages. We hypothesized that this prolonged human circulation led to genomic changes that increased viral transmissibility in humans. We generated a synthetic glycoprotein (GP) construct based on the earliest reported isolate and introduced amino acid substitutions that defined viral lineages. Mutant GPs were used to generate a panel of pseudoviruses, which were used to infect different human and bat cell lines. These data revealed that specific amino acid substitutions in the EBOV GP have increased tropism for human cells, while reducing tropism for bat cells. Such increased infectivity may have enhanced the ability of EBOV to transmit among humans and contributed to the wide geographic distribution of some viral lineages. EBOV adapted to humans during the West African outbreak Amino acid substitutions in the EBOV glycoprotein increase human cell tropism The same glycoprotein amino acid substitutions decrease tropism for bat cells
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Affiliation(s)
- Richard A Urbanowicz
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2RD, UK; NIHR Nottingham Digestive Diseases Biomedical Research Unit, The University of Nottingham, Nottingham University Hospitals NHS Trust, Nottingham NG7 2UH, UK
| | - C Patrick McClure
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2RD, UK; NIHR Nottingham Digestive Diseases Biomedical Research Unit, The University of Nottingham, Nottingham University Hospitals NHS Trust, Nottingham NG7 2UH, UK
| | - Anavaj Sakuntabhai
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, 75724 Paris Cedex 15, France; Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, 75015 Paris, France
| | - Amadou A Sall
- Arbovirus and Viral Hemorrhagic Fever Unit, Institut Pasteur de Dakar, BP 220 Dakar, Senegal
| | - Gary Kobinger
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, ON K1A 0K9, Canada; Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, MB R32T 2N2, Canada
| | - Marcel A Müller
- Institute of Virology, University of Bonn Medical Center, 53127 Bonn, Germany
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2050, Australia
| | - Félix A Rey
- Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France; Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3569, 75724 Paris Cedex 15, France
| | - Etienne Simon-Loriere
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, 75724 Paris Cedex 15, France; Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, 75015 Paris, France.
| | - Jonathan K Ball
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2RD, UK; NIHR Nottingham Digestive Diseases Biomedical Research Unit, The University of Nottingham, Nottingham University Hospitals NHS Trust, Nottingham NG7 2UH, UK.
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36
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Hamel R, Ferraris P, Wichit S, Diop F, Talignani L, Pompon J, Garcia D, Liégeois F, Sall AA, Yssel H, Missé D. African and Asian Zika virus strains differentially induce early antiviral responses in primary human astrocytes. Infect Genet Evol 2017; 49:134-137. [PMID: 28095299 DOI: 10.1016/j.meegid.2017.01.015] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 01/11/2017] [Accepted: 01/14/2017] [Indexed: 11/15/2022]
Abstract
ZIKA virus (ZIKV) is a newly emerging arbovirus. Since its discovery 60years ago in Uganda, it has spread throughout the Pacific, Latin America and the Caribbean, emphasizing the capacity of ZIKV to spread to non-endemic regions worldwide. Although infection with ZIKV often leads to mild disease, its recent emergence in the Americas has coincided with an increase in adults developing Guillain-Barré syndrome and neurological complications in new-borns, such as congenital microcephaly. Many questions remain unanswered regarding the complications caused by different primary isolates of ZIKV. Here, we report the permissiveness of primary human astrocytes for two clinically relevant, Asian and African ZIKV strains and show that both isolates strongly induce antiviral immune responses in these cells albeit with markedly different kinetics. This study describes for the first time the specific antiviral gene expression in infected primary human astrocytes, the major glial cells within the central nervous system.
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Affiliation(s)
- Rodolphe Hamel
- Laboratoire MIVEGEC, UMR 224 IRD/CNRS/UM, Montpellier, France
| | | | | | - Fodé Diop
- Laboratoire MIVEGEC, UMR 224 IRD/CNRS/UM, Montpellier, France
| | - Loïc Talignani
- Laboratoire MIVEGEC, UMR 224 IRD/CNRS/UM, Montpellier, France
| | - Julien Pompon
- Laboratoire MIVEGEC, UMR 224 IRD/CNRS/UM, Montpellier, France
| | - Déborah Garcia
- Laboratoire MIVEGEC, UMR 224 IRD/CNRS/UM, Montpellier, France
| | | | | | - Hans Yssel
- Centre d'Immunologie et des Maladies Infectieuses, INSERM, U1135, Sorbonne Universités, UPMC, APHP Hôpital Pitié-Salpêtrière, Paris, France
| | - Dorothée Missé
- Laboratoire MIVEGEC, UMR 224 IRD/CNRS/UM, Montpellier, France.
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37
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Niang M, Thiam LG, Loucoubar C, Sow A, Sadio BD, Diallo M, Sall AA, Toure-Balde A. Spatio-temporal analysis of the genetic diversity and complexity of Plasmodium falciparum infections in Kedougou, southeastern Senegal. Parasit Vectors 2017; 10:33. [PMID: 28103905 PMCID: PMC5244544 DOI: 10.1186/s13071-017-1976-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 01/10/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic analyses of the malaria parasite population and its temporal and spatial dynamics could provide an assessment of the effectiveness of disease control strategies. The genetic diversity of Plasmodium falciparum has been poorly documented in Senegal, and limited data are available from the Kedougou Region. This study examines the spatial and temporal variation of the genetic diversity and complexity of P. falciparum infections in acute febrile patients in Kedougou, southeastern Senegal. A total of 263 sera from patients presenting with acute febrile illness and attending Kedougou health facilities between July 2009 and July 2013 were obtained from a collection established as part of arbovirus surveillance in Kedougou. Samples identified as P. falciparum by nested PCR were characterized for their genetic diversity and complexity using msp-1 and msp-2 polymorphic markers. RESULTS Samples containing only P. falciparum accounted for 60.83% (160/263) of the examined samples. All three msp-1 allelic families (K1, MAD20 and RO33) and two msp-2 allelic families (FC27 and 3D7) were detected in all villages investigated over the 5-year collection period. The average genotype per allelic family was comparable between villages. Frequencies of msp-1 and msp-2 allelic types showed no correlation with age (Fisher's exact test, P = 0.59) or gender (Fisher's exact test, P = 0.973), and were similarly distributed throughout the 5-year sampling period (Fisher's exact test, P = 0.412) and across villages (Fisher's exact test, P = 0.866). Mean multiplicity of infection (MOI) for both msp-1 and msp-2 was highest in Kedougou village (2.25 and 2.21, respectively) and among younger patients aged ≤ 15 years (2.12 and 2.00, respectively). The mean MOI was highest in 2009 and decreased progressively onward. CONCLUSION Characterization of the genetic diversity and complexity of P. falciparum infections in Kedougou revealed no spatio-temporal variation in the genetic diversity of P. falciparum isolates. However, mean MOI varied with time of sera collection and decreased over the course of the study (July 2009 to July 2013). This suggests a slow progressive decrease of malaria transmission intensity in Kedougou Region despite the limited impact of preventive and control measures implemented by the National Malaria Control Programme on malaria morbidity and mortality.
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Affiliation(s)
- Makhtar Niang
- Institut Pasteur Dakar, Immunology Unit, 36 Avenue Pasteur, BP 220, Dakar, Senegal.
| | - Laty G Thiam
- Institut Pasteur Dakar, Immunology Unit, 36 Avenue Pasteur, BP 220, Dakar, Senegal.,Department of Animal Biology, Cheikh Anta Diop University of Dakar, Dakar, Senegal
| | - Cheikh Loucoubar
- Institut Pasteur Dakar, Biostatistics, Bioinformatics and Modeling Group, 36 Avenue Pasteur, BP 220, Dakar, Senegal
| | - Abdourahmane Sow
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, 36 Avenue Pasteur, BP 220, Dakar, Senegal
| | - Bacary D Sadio
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, 36 Avenue Pasteur, BP 220, Dakar, Senegal
| | - Mawlouth Diallo
- Institut Pasteur Dakar, Medical Entomology Unit, 36 Avenue Pasteur, BP 220, Dakar, Senegal
| | - Amadou A Sall
- Institut Pasteur Dakar, Arbovirus and Viral Hemorrhagic Fevers Unit, 36 Avenue Pasteur, BP 220, Dakar, Senegal
| | - Aissatou Toure-Balde
- Institut Pasteur Dakar, Immunology Unit, 36 Avenue Pasteur, BP 220, Dakar, Senegal
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38
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Kraemer MUG, Faria NR, Reiner RC, Golding N, Nikolay B, Stasse S, Johansson MA, Salje H, Faye O, Wint GRW, Niedrig M, Shearer FM, Hill SC, Thompson RN, Bisanzio D, Taveira N, Nax HH, Pradelski BSR, Nsoesie EO, Murphy NR, Bogoch II, Khan K, Brownstein JS, Tatem AJ, de Oliveira T, Smith DL, Sall AA, Pybus OG, Hay SI, Cauchemez S. Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015-16: a modelling study. Lancet Infect Dis 2016; 17:330-338. [PMID: 28017559 PMCID: PMC5332542 DOI: 10.1016/s1473-3099(16)30513-8] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/28/2016] [Accepted: 11/09/2016] [Indexed: 11/25/2022]
Abstract
BACKGROUND Since late 2015, an epidemic of yellow fever has caused more than 7334 suspected cases in Angola and the Democratic Republic of the Congo, including 393 deaths. We sought to understand the spatial spread of this outbreak to optimise the use of the limited available vaccine stock. METHODS We jointly analysed datasets describing the epidemic of yellow fever, vector suitability, human demography, and mobility in central Africa to understand and predict the spread of yellow fever virus. We used a standard logistic model to infer the district-specific yellow fever virus infection risk during the course of the epidemic in the region. FINDINGS The early spread of yellow fever virus was characterised by fast exponential growth (doubling time of 5-7 days) and fast spatial expansion (49 districts reported cases after only 3 months) from Luanda, the capital of Angola. Early invasion was positively correlated with high population density (Pearson's r 0·52, 95% CI 0·34-0·66). The further away locations were from Luanda, the later the date of invasion (Pearson's r 0·60, 95% CI 0·52-0·66). In a Cox model, we noted that districts with higher population densities also had higher risks of sustained transmission (the hazard ratio for cases ceasing was 0·74, 95% CI 0·13-0·92 per log-unit increase in the population size of a district). A model that captured human mobility and vector suitability successfully discriminated districts with high risk of invasion from others with a lower risk (area under the curve 0·94, 95% CI 0·92-0·97). If at the start of the epidemic, sufficient vaccines had been available to target 50 out of 313 districts in the area, our model would have correctly identified 27 (84%) of the 32 districts that were eventually affected. INTERPRETATION Our findings show the contributions of ecological and demographic factors to the ongoing spread of the yellow fever outbreak and provide estimates of the areas that could be prioritised for vaccination, although other constraints such as vaccine supply and delivery need to be accounted for before such insights can be translated into policy. FUNDING Wellcome Trust.
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Affiliation(s)
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
| | - Robert C Reiner
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA
| | - Nick Golding
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, UK; School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Birgit Nikolay
- Mathematical Modelling of Infectious Diseases and Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France; Centre National de la Recherche Scientifique, URA 3012, Paris, France
| | - Stephanie Stasse
- Health Programme, European Commission, International Cooperation and Development, Delegation en RDC, Kinshasa, Democratic Republic of the Congo
| | - Michael A Johansson
- Centers for Disease Control and Prevention, San Juan, PR, USA; Center for Communicable Disease Dynamics, Harvard T H Chan School of Public Health, MA, USA
| | - Henrik Salje
- Mathematical Modelling of Infectious Diseases and Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France; Centre National de la Recherche Scientifique, URA 3012, Paris, France; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ousmane Faye
- Arbovirus and Viral Hemorrhagic Fever Unit, Institut Pasteur da Dakar, Dakar, Senegal
| | - G R William Wint
- Environmental Research Group Oxford, Department of Zoology, Oxford, UK
| | | | - Freya M Shearer
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, UK
| | - Sarah C Hill
- Department of Zoology, University of Oxford, Oxford, UK
| | | | | | - Nuno Taveira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Portugal; Centro de Investigacao Interdisciplinar Egas Moniz, Instituto Superior de Ciencias da Saude Egas Moniz, Caparica, Portugal
| | - Heinrich H Nax
- Computational Social Science, ETH Zurich, Zurich, Switzerland
| | | | - Elaine O Nsoesie
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA
| | - Nicholas R Murphy
- School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Isaac I Bogoch
- Divisions of General Internal Medicine and Infectious Diseases, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada
| | | | - Andrew J Tatem
- WorldPop, Department of Geography and Environment, University of Southampton, Southampton, UK; Flowminder Foundation, Stockholm, Sweden
| | - Tulio de Oliveira
- School of Laboratory Medicine and Medical Sciences, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - David L Smith
- Department of Zoology, University of Oxford, Oxford, UK; Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA; Sanaria Institute for Global Health and Tropical Medicine, Rockville, MD, USA
| | - Amadou A Sall
- Arbovirus and Viral Hemorrhagic Fever Unit, Institut Pasteur da Dakar, Dakar, Senegal
| | | | - Simon I Hay
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA; Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, UK
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases and Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France; Centre National de la Recherche Scientifique, URA 3012, Paris, France
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Donald CL, Brennan B, Cumberworth SL, Rezelj VV, Clark JJ, Cordeiro MT, Freitas de Oliveira França R, Pena LJ, Wilkie GS, Da Silva Filipe A, Davis C, Hughes J, Varjak M, Selinger M, Zuvanov L, Owsianka AM, Patel AH, McLauchlan J, Lindenbach BD, Fall G, Sall AA, Biek R, Rehwinkel J, Schnettler E, Kohl A. Full Genome Sequence and sfRNA Interferon Antagonist Activity of Zika Virus from Recife, Brazil. PLoS Negl Trop Dis 2016; 10:e0005048. [PMID: 27706161 PMCID: PMC5051680 DOI: 10.1371/journal.pntd.0005048] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/19/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The outbreak of Zika virus (ZIKV) in the Americas has transformed a previously obscure mosquito-transmitted arbovirus of the Flaviviridae family into a major public health concern. Little is currently known about the evolution and biology of ZIKV and the factors that contribute to the associated pathogenesis. Determining genomic sequences of clinical viral isolates and characterization of elements within these are an important prerequisite to advance our understanding of viral replicative processes and virus-host interactions. METHODOLOGY/PRINCIPAL FINDINGS We obtained a ZIKV isolate from a patient who presented with classical ZIKV-associated symptoms, and used high throughput sequencing and other molecular biology approaches to determine its full genome sequence, including non-coding regions. Genome regions were characterized and compared to the sequences of other isolates where available. Furthermore, we identified a subgenomic flavivirus RNA (sfRNA) in ZIKV-infected cells that has antagonist activity against RIG-I induced type I interferon induction, with a lesser effect on MDA-5 mediated action. CONCLUSIONS/SIGNIFICANCE The full-length genome sequence including non-coding regions of a South American ZIKV isolate from a patient with classical symptoms will support efforts to develop genetic tools for this virus. Detection of sfRNA that counteracts interferon responses is likely to be important for further understanding of pathogenesis and virus-host interactions.
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Affiliation(s)
- Claire L. Donald
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Benjamin Brennan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | | | - Veronica V. Rezelj
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Jordan J. Clark
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Marli T. Cordeiro
- Fundação Oswaldo Cruz-PE/Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Campus da UFPE-Cidade Universitária, Recife/PE, Brasil
| | - Rafael Freitas de Oliveira França
- Fundação Oswaldo Cruz-PE/Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Campus da UFPE-Cidade Universitária, Recife/PE, Brasil
| | - Lindomar J. Pena
- Fundação Oswaldo Cruz-PE/Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Campus da UFPE-Cidade Universitária, Recife/PE, Brasil
| | - Gavin S. Wilkie
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Ana Da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Christopher Davis
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Margus Varjak
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Martin Selinger
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Luíza Zuvanov
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Ania M. Owsianka
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Brett D. Lindenbach
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, United States of America
| | - Gamou Fall
- Pole de Virologie, Unité des arbovirus et virus des fièvres hémorragiques, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou A. Sall
- Pole de Virologie, Unité des arbovirus et virus des fièvres hémorragiques, Institut Pasteur de Dakar, Dakar, Senegal
| | - Roman Biek
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine and Radcliffe Department of Medicine, University of Oxford, Oxford, England, United Kingdom
| | - Esther Schnettler
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
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Patel P, Abd El Wahed A, Faye O, Prüger P, Kaiser M, Thaloengsok S, Ubol S, Sakuntabhai A, Leparc-Goffart I, Hufert FT, Sall AA, Weidmann M, Niedrig M. A Field-Deployable Reverse Transcription Recombinase Polymerase Amplification Assay for Rapid Detection of the Chikungunya Virus. PLoS Negl Trop Dis 2016; 10:e0004953. [PMID: 27685649 PMCID: PMC5042537 DOI: 10.1371/journal.pntd.0004953] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/03/2016] [Indexed: 01/02/2023] Open
Abstract
Background Chikungunya virus (CHIKV) is a mosquito-borne virus currently transmitted in about 60 countries. CHIKV causes acute flu-like symptoms and in many cases prolonged musculoskeletal and joint pain. Detection of the infection is mostly done using RT-RCR or ELISA, which are not suitable for point-of-care diagnosis. Methodology/Principal Findings In this study, a reverse transcription recombinase polymerase amplification (RT-RPA) assay for the detection of the CHIKV was developed. The assay sensitivity, specificity, and cross-reactivity were tested. CHIKV RT-RPA assay detected down to 80 genome copies/reaction in a maximum of 15 minutes. It successfully identified 18 isolates representing the three CHIKV genotypes. No cross-reactivity was detected to other alphaviruses and arboviruses except O'nyong'nyong virus, which could be differentiated by a modified RPA primer pair. Seventy-eight samples were screened both by RT-RPA and real-time RT-PCR. The diagnostic sensitivity and specificity of the CHIKV RT-RPA assay were determined at 100%. Conclusions/Significance The developed RT-RPA assay represents a promising method for the molecular detection of CHIKV at point of need. CHIKV is transmitted to humans via mosquitos. CHIKV induces clinical signs similar to Influenza, Dengue, and Zika viruses. We have developed a molecular assay for the detection of CHIKV genome based on isothermal„recombinase polymerase amplification (RPA) assay”performed at 42°C. The result was obtained in maximum of 15 minutes, which is 4–6 times faster than the current molecular diagnostic techniques. Our CHIKV RPA assay is rapid and sensitive, as well as easy to use at the point of need.
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Affiliation(s)
- Pranav Patel
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Ahmed Abd El Wahed
- Division of Microbiology and Animal Hygiene, Georg-August-University, Goettingen, Germany
| | - Oumar Faye
- Arbovirus Unit, Pasteur Institute, Dakar, Senegal
| | - Pauline Prüger
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Marco Kaiser
- GenExpress Gesellschaft für Proteindesign, Berlin, Germany
| | - Sasikanya Thaloengsok
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sukathida Ubol
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Anavaj Sakuntabhai
- Functional Genetics of Infectious Diseases Unit, Institute Pasteur, Paris, France
| | | | - Frank T. Hufert
- Institute of Microbiology & Virology, Brandenburg Medical School Fontane, Senftenberg, Germany
| | | | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Matthias Niedrig
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
- * E-mail:
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Weidmann M, Avsic-Zupanc T, Bino S, Bouloy M, Burt F, Chinikar S, Christova I, Dedushaj I, El-Sanousi A, Elaldi N, Hewson R, Hufert FT, Humolli I, Jansen van Vuren P, Koçak Tufan Z, Korukluoglu G, Lyssen P, Mirazimi A, Neyts J, Niedrig M, Ozkul A, Papa A, Paweska J, Sall AA, Schmaljohn CS, Swanepoel R, Uyar Y, Weber F, Zeller H. Biosafety standards for working with Crimean-Congo hemorrhagic fever virus. J Gen Virol 2016; 97:2799-2808. [PMID: 27667586 DOI: 10.1099/jgv.0.000610] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In countries from which Crimean-Congo haemorrhagic fever (CCHF) is absent, the causative virus, CCHF virus (CCHFV), is classified as a hazard group 4 agent and handled in containment level (CL)-4. In contrast, most endemic countries out of necessity have had to perform diagnostic tests under biosafety level (BSL)-2 or -3 conditions. In particular, Turkey and several of the Balkan countries have safely processed more than 100 000 samples over many years in BSL-2 laboratories. It is therefore advocated that biosafety requirements for CCHF diagnostic procedures should be revised, to allow the tests required to be performed under enhanced BSL-2 conditions with appropriate biosafety laboratory equipment and personal protective equipment used according to standardized protocols in the countries affected. Downgrading of CCHFV research work from CL-4, BSL-4 to CL-3, BSL-3 should also be considered.
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Affiliation(s)
- Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, UK
| | - Tatjana Avsic-Zupanc
- Institute of Microbiology and Immunology, Medical Faculty of Ljubljana, Ljubljana, Slovenia
| | - Silvia Bino
- Institute of Public Health, Control of Infectious Diseases Department, Tirana, Albania
| | - Michelle Bouloy
- Institut Pasteur, Bunyaviruses Molecular Genetics, Paris, France
| | - Felicity Burt
- Department of Medical Microbiology and Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Sadegh Chinikar
- Laboratory of Arboviruses and Viral Hemorrhagic Fevers (National Ref Lab), Pasteur Institute of Iran, Tehran, Iran
| | - Iva Christova
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Isuf Dedushaj
- National Institute of Public Health in Kosovo, Pristina, Kosovo
| | - Ahmed El-Sanousi
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Nazif Elaldi
- Department of Infectious Diseases and Clinical Microbiology, Cumhuriyet University, Faculty of Medicine, Sivas, Turkey
| | - Roger Hewson
- Public Health England, Porton Down, Wiltshire, Salisbury, UK
| | - Frank T Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School, Senftenberg, Germany
| | - Isme Humolli
- National Institute of Public Health in Kosovo, Pristina, Kosovo
| | | | - Zeliha Koçak Tufan
- Infectious Diseases and Clinical Microbiology Department, Yildirim Beyazit University, Ankara Ataturk Training and Research Hospital, Ankara, Turkey
| | - Gülay Korukluoglu
- Public Health Institution of Turkey, Virology Reference and Research Laboratory, Ankara, Turkey
| | - Pieter Lyssen
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Ali Mirazimi
- Institute for Laboratory Medicine, Department for Clinical Microbiology, Karolinska Institute, and Karolinska Hospital University, Stockholm, Sweden
| | - Johan Neyts
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Matthias Niedrig
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses, Robert Koch Institute, Berlin, Germany
| | - Aykut Ozkul
- Department of Virology, Ankara University, Faculty of Veterinary Medicine, Ankara, Turkey
| | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Janusz Paweska
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | | | - Connie S Schmaljohn
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
| | - Robert Swanepoel
- Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, South Africa
| | - Yavuz Uyar
- Department of Medical Microbiology, Cerrahpasa Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Friedemann Weber
- Institute for Virology, Justus Liebig-University Giessen, Giessen, Germany
| | - Herve Zeller
- European Centre for Disease Prevention and Control, Stockholm, Sweden
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Niang M, Loucoubar C, Sow A, Diagne MM, Faye O, Faye O, Diallo M, Toure-Balde A, Sall AA. Genetic diversity of Plasmodium falciparum isolates from concurrent malaria and arbovirus co-infections in Kedougou, southeastern Senegal. Malar J 2016; 15:155. [PMID: 26969623 PMCID: PMC4788873 DOI: 10.1186/s12936-016-1208-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 03/02/2016] [Indexed: 11/24/2022] Open
Abstract
Background Concurrent malaria and arbovirus infections are common and represent an important public health concern in regions where both diseases are endemic. The present study investigates the genetic diversity and complexity of Plasmodium falciparum infection in concurrent malaria-arbovirus infections in Kedougou region, southeastern Senegal. Methods Parasite DNA was extracted from 60 to 27 sera samples collected from P. falciparum isolates of malaria and concurrent malaria-arbovirus infected patients, respectively, and followed by PCR-genotyping targeting the msp-1 (block2) and msp-2 (block3) allelic families. Results The mean number of genotype per allelic family was comparable between the two groups. K1 was the predominant msp-1 allelic type both in malaria (94.91 %) and arbovirus-malaria (92.59 %) groups, whereas IC/3D7 was the most prevalent msp-2 allelic type in malaria (94.91 %) and arbovirus-malaria (96.29 %) groups. Frequencies of msp-1 and msp-2 allelic types were statistically comparable between the two groups (Fisher exact test, P > 0.05) and were not associated with age. FC27 was strikingly the least prevalent in both groups and was absent in children under 5 years of age. The proportions of P. falciparum isolates from malaria-infected patients carrying the three msp-1 allelic types (67.44 %) or the two msp-2 allelic types (76.47 %) were significantly higher than those from arbovirus-malaria co-infected patients (Exact binomial test, P < 0.05). The multiplicities of infection (MOI) were low and comparable for msp-1 (1.19 vs 1.22) and msp-2 (1.11 vs 1.10), respectively between malaria and arbovirus-malaria groups. Conclusion The study showed no difference in the genetic diversity between P. falciparum isolates from malaria and concurrent malaria-arbovirus infected patients in Kedougou. The MOI was low despite intense malaria transmission in Kedougou. The overall results suggest a limited or no influence of arbovirus infections on P. falciparum diversity and complexity of malaria infection.
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Affiliation(s)
- Makhtar Niang
- Immunology Unit, Institut Pasteur Dakar, 36 Avenue Pasteur, 220, Dakar, Senegal.
| | - Cheikh Loucoubar
- Arbovirus and Viral Hemorrhagic Fevers Unit, Institut Pasteur Dakar, 36 Avenue Pasteur, 220, Dakar, Senegal
| | - Abdourahmane Sow
- Arbovirus and Viral Hemorrhagic Fevers Unit, Institut Pasteur Dakar, 36 Avenue Pasteur, 220, Dakar, Senegal
| | - Moussa Moise Diagne
- Arbovirus and Viral Hemorrhagic Fevers Unit, Institut Pasteur Dakar, 36 Avenue Pasteur, 220, Dakar, Senegal
| | - Oumar Faye
- Arbovirus and Viral Hemorrhagic Fevers Unit, Institut Pasteur Dakar, 36 Avenue Pasteur, 220, Dakar, Senegal
| | - Ousmane Faye
- Arbovirus and Viral Hemorrhagic Fevers Unit, Institut Pasteur Dakar, 36 Avenue Pasteur, 220, Dakar, Senegal
| | - Mawlouth Diallo
- Medical Entomology Unit, Institut Pasteur Dakar, 36 Avenue Pasteur, 220, Dakar, Senegal
| | | | - Amadou A Sall
- Arbovirus and Viral Hemorrhagic Fevers Unit, Institut Pasteur Dakar, 36 Avenue Pasteur, 220, Dakar, Senegal
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van Griensven J, Edwards T, de Lamballerie X, Semple MG, Gallian P, Baize S, Horby PW, Raoul H, Magassouba N, Antierens A, Lomas C, Faye O, Sall AA, Fransen K, Buyze J, Ravinetto R, Tiberghien P, Claeys Y, De Crop M, Lynen L, Bah EI, Smith PG, Delamou A, De Weggheleire A, Haba N. Evaluation of Convalescent Plasma for Ebola Virus Disease in Guinea. N Engl J Med 2016; 374:33-42. [PMID: 26735992 PMCID: PMC5856332 DOI: 10.1056/nejmoa1511812] [Citation(s) in RCA: 377] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND In the wake of the recent outbreak of Ebola virus disease (EVD) in several African countries, the World Health Organization prioritized the evaluation of treatment with convalescent plasma derived from patients who have recovered from the disease. We evaluated the safety and efficacy of convalescent plasma for the treatment of EVD in Guinea. METHODS In this nonrandomized, comparative study, 99 patients of various ages (including pregnant women) with confirmed EVD received two consecutive transfusions of 200 to 250 ml of ABO-compatible convalescent plasma, with each unit of plasma obtained from a separate convalescent donor. The transfusions were initiated on the day of diagnosis or up to 2 days later. The level of neutralizing antibodies against Ebola virus in the plasma was unknown at the time of administration. The control group was 418 patients who had been treated at the same center during the previous 5 months. The primary outcome was the risk of death during the period from 3 to 16 days after diagnosis with adjustments for age and the baseline cycle-threshold value on polymerase-chain-reaction assay; patients who had died before day 3 were excluded. The clinically important difference was defined as an absolute reduction in mortality of 20 percentage points in the convalescent-plasma group as compared with the control group. RESULTS A total of 84 patients who were treated with plasma were included in the primary analysis. At baseline, the convalescent-plasma group had slightly higher cycle-threshold values and a shorter duration of symptoms than did the control group, along with a higher frequency of eye redness and difficulty in swallowing. From day 3 to day 16 after diagnosis, the risk of death was 31% in the convalescent-plasma group and 38% in the control group (risk difference, -7 percentage points; 95% confidence interval [CI], -18 to 4). The difference was reduced after adjustment for age and cycle-threshold value (adjusted risk difference, -3 percentage points; 95% CI, -13 to 8). No serious adverse reactions associated with the use of convalescent plasma were observed. CONCLUSIONS The transfusion of up to 500 ml of convalescent plasma with unknown levels of neutralizing antibodies in 84 patients with confirmed EVD was not associated with a significant improvement in survival. (Funded by the European Union's Horizon 2020 Research and Innovation Program and others; ClinicalTrials.gov number, NCT02342171.).
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Affiliation(s)
- Johan van Griensven
- From the Institute of Tropical Medicine, Antwerp (J.G., K.F., J.B., R.R., Y.C., M.D.C., L.L., A.D.W.), Médecins sans Frontières, Brussels (A.A., C.L.), and the Clinical Pharmacology and Pharmacotherapy Department, Katholieke Universiteit Leuven, Leuven (R.R.) - all in Belgium; Medical Research Council Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London (T.E., P.G.S.), Institute of Translational Medicine and National Institute for Health Research (NIHR) Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool (M.G.S.), and Centre for Tropical Medicine and Global Health, University of Oxford, Oxford (P.W.H.) - all in the United Kingdom; Aix Marseille University (X.L., P.G.), French Institute of Research for Development (X.L.), École des Hautes Études en Santé Publique (X.L.), and Institut Hospitalo-Universitaire Méditerranée Infection (X.L., P.G.), Marseille, Etablissement Français du Sang, La Plaine Saint Denis (P.G., P.T.), Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Centre International de Recherche en Infectiologie (S.B.), Laboratoire P4 INSERM-Jean Mérieux (H.R.), Lyon, and Université de Franche Comté, Etablissement Français du Sang, INSERM UMR 1098, Besançon (P.T.) - all in France; Laboratory of Viral Hemorrhagic Fever, Gamal Abdel Nasser University of Conakry (N.M.), Service des Maladies Infectieuses et Tropicales de l'Hôpital National Donka, Conakry (E.I.B.), National Blood Transfusion Center (N.H.), Conakry, and National Center for Training and Research in Rural Health of Maferinyah, Forecariah (A.D.) - all in Guinea; and Institut Pasteur de Dakar, Dakar, Senegal (O.F., A.A.S.)
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Simon-Loriere E, Faye O, Faye O, Koivogui L, Magassouba N, Keita S, Thiberge JM, Diancourt L, Bouchier C, Vandenbogaert M, Caro V, Fall G, Buchmann JP, Matranga CB, Sabeti PC, Manuguerra JC, Holmes EC, Sall AA. Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic. Nature 2015; 524:102-4. [PMID: 26106863 PMCID: PMC10601606 DOI: 10.1038/nature14612] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 06/05/2015] [Indexed: 11/09/2022]
Abstract
An epidemic of Ebola virus disease of unprecedented scale has been ongoing for more than a year in West Africa. As of 29 April 2015, there have been 26,277 reported total cases (of which 14,895 have been laboratory confirmed) resulting in 10,899 deaths. The source of the outbreak was traced to the prefecture of Guéckédou in the forested region of southeastern Guinea. The virus later spread to the capital, Conakry, and to the neighbouring countries of Sierra Leone, Liberia, Nigeria, Senegal and Mali. In March 2014, when the first cases were detected in Conakry, the Institut Pasteur of Dakar, Senegal, deployed a mobile laboratory in Donka hospital to provide diagnostic services to the greater Conakry urban area and other regions of Guinea. Through this process we sampled 85 Ebola viruses (EBOV) from patients infected from July to November 2014, and report their full genome sequences here. Phylogenetic analysis reveals the sustained transmission of three distinct viral lineages co-circulating in Guinea, including the urban setting of Conakry and its surroundings. One lineage is unique to Guinea and closely related to the earliest sampled viruses of the epidemic. A second lineage contains viruses probably reintroduced from neighbouring Sierra Leone on multiple occasions, while a third lineage later spread from Guinea to Mali. Each lineage is defined by multiple mutations, including non-synonymous changes in the virion protein 35 (VP35), glycoprotein (GP) and RNA-dependent RNA polymerase (L) proteins. The viral GP is characterized by a glycosylation site modification and mutations in the mucin-like domain that could modify the outer shape of the virion. These data illustrate the ongoing ability of EBOV to develop lineage-specific and potentially phenotypically important variation.
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Affiliation(s)
- Etienne Simon-Loriere
- Institut Pasteur, Functional Genetics of Infectious Diseases Unit, Paris Cedex 15, 75724 France
- CNRS URA3012, Paris, 75015 France
| | - Ousmane Faye
- Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, Dakar, BP 220 Senegal
| | - Oumar Faye
- Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, Dakar, BP 220 Senegal
| | - Lamine Koivogui
- Institut National de Santé Publique de Guinée, Conakry, Guinea
| | - Nfaly Magassouba
- Projet de fièvres hémorragiques de Guinée, Université Gamal Abdel Nasser, Conakry, BP 1147 Guinea
| | | | - Jean-Michel Thiberge
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d’Intervention Biologique d’Urgence, Paris Cedex 15, 75724 France
| | - Laure Diancourt
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d’Intervention Biologique d’Urgence, Paris Cedex 15, 75724 France
| | | | - Matthias Vandenbogaert
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d’Intervention Biologique d’Urgence, Paris Cedex 15, 75724 France
| | - Valérie Caro
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d’Intervention Biologique d’Urgence, Paris Cedex 15, 75724 France
| | - Gamou Fall
- Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, Dakar, BP 220 Senegal
| | - Jan P. Buchmann
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, 2006 New South Wales Australia
| | | | - Pardis C. Sabeti
- Broad Institute, 75 Ames Street, Cambridge, 02142 Massachusetts USA
- Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, 02138 Massachusetts USA
| | - Jean-Claude Manuguerra
- Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d’Intervention Biologique d’Urgence, Paris Cedex 15, 75724 France
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, 2006 New South Wales Australia
| | - Amadou A. Sall
- Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, Dakar, BP 220 Senegal
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Niang M, Thiam LG, Sow A, Loucoubar C, Bob NS, Diop F, Diouf B, Niass O, Mansourou A, Varela ML, Perraut R, Sall AA, Toure-Balde A. A molecular survey of acute febrile illnesses reveals Plasmodium vivax infections in Kedougou, southeastern Senegal. Malar J 2015; 14:281. [PMID: 26186936 PMCID: PMC4506577 DOI: 10.1186/s12936-015-0808-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/10/2015] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Control efforts towards malaria due to Plasmodium falciparum significantly decreased the incidence of the disease in many endemic countries including Senegal. Surprisingly, in Kedougou (southeastern Senegal) P. falciparum malaria remains highly prevalent and the relative contribution of other Plasmodium species to the global malaria burden is very poorly documented, partly due to the low sensitivity of routine diagnostic tools. Molecular methods offer better estimate of circulating Plasmodium species in a given area. A molecular survey was carried out to document circulating malaria parasites in Kedougou region. METHODS A total of 263 long-term stored sera obtained from patients presenting with acute febrile illness in Kedougou between July 2009 and July 2013 were used for malaria parasite determination. Sera were withdrawn from a collection established as part of a surveillance programme of arboviruses infections in the region. Plasmodium species were characterized by a nested PCR-based approach targeting the 18S small sub-unit ribosomal RNA genes of Plasmodium spp. RESULTS Of the 263 sera screened in this study, Plasmodium genomic DNA was amplifiable by nested PCR from 62.35% (164/263) of samples. P. falciparum accounted for the majority of infections either as single in 85.97% (141/164) of Plasmodium-positive samples or mixed with Plasmodium ovale (11.58%, 19/164) or Plasmodium vivax (1.21%, 2/164). All 19 (11.58%) P. ovale-infected patients were mixed with P. falciparum, while no Plasmodium malariae was detected in this survey. Four patients (2.43%) were found to be infected by P. vivax, two of whom were mixed with P. falciparum. P. vivax infections originated from Bandafassi and Ninefesha villages and concerned patients aged 4, 9, 10, and 15 years old, respectively. DNA sequences alignment and phylogenetic analysis demonstrated that sequences from Kedougou corresponded to P. vivax, therefore confirming the presence of P. vivax infections in Senegal. CONCLUSION The results confirm the high prevalence of P. falciparum in Kedougou and provide the first molecular evidence of P. vivax infections in Senegal. These findings pave the ways for further investigations of P. vivax infections in Senegal and its contribution to the global burden of malaria disease before targeted strategies can be deployed.
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Affiliation(s)
- Makhtar Niang
- Immunology Unit, Pasteur Institute of Dakar, Dakar, Senegal.
| | - Laty Gaye Thiam
- Immunology Unit, Pasteur Institute of Dakar, Dakar, Senegal.
- Department of Animal Biology, Cheikh Anta Diop University of de Dakar, Dakar, Senegal.
| | - Abdourahmane Sow
- Arbovirus and Viral Haemorrhagic Fevers Unit, Pasteur Institute of Dakar, Dakar, Senegal.
| | - Cheikh Loucoubar
- Arbovirus and Viral Haemorrhagic Fevers Unit, Pasteur Institute of Dakar, Dakar, Senegal.
| | - Ndeye Sakha Bob
- Arbovirus and Viral Haemorrhagic Fevers Unit, Pasteur Institute of Dakar, Dakar, Senegal.
| | - Fode Diop
- Immunology Unit, Pasteur Institute of Dakar, Dakar, Senegal.
| | - Babacar Diouf
- Immunology Unit, Pasteur Institute of Dakar, Dakar, Senegal.
| | - Oumy Niass
- Immunology Unit, Pasteur Institute of Dakar, Dakar, Senegal.
| | | | | | - Ronald Perraut
- Immunology Unit, Pasteur Institute of Dakar, Dakar, Senegal.
| | - Amadou A Sall
- Arbovirus and Viral Haemorrhagic Fevers Unit, Pasteur Institute of Dakar, Dakar, Senegal.
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Jaenisch T, Junghanss T, Wills B, Brady OJ, Eckerle I, Farlow A, Hay SI, McCall PJ, Messina JP, Ofula V, Sall AA, Sakuntabhai A, Velayudhan R, Wint GRW, Zeller H, Margolis HS, Sankoh O. Dengue expansion in Africa-not recognized or not happening? Emerg Infect Dis 2015; 20. [PMID: 25271370 PMCID: PMC4193177 DOI: 10.3201/eid2010.140487] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Addressing this expansion is essential before control and prevention of dengue are implemented. An expert conference on Dengue in Africa was held in Accra, Ghana, in February 2013 to consider key questions regarding the possible expansion of dengue in Africa. Four key action points were highlighted to advance our understanding of the epidemiology of dengue in Africa. First, dengue diagnostic tools must be made more widely available in the healthcare setting in Africa. Second, representative data need to be collected across Africa to uncover the true burden of dengue. Third, established networks should collaborate to produce these types of data. Fourth, policy needs to be informed so the necessary steps can be taken to provide dengue vector control and health services.
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Freire CCM, Iamarino A, Soumaré POL, Faye O, Sall AA, Zanotto PMA. Reassortment and distinct evolutionary dynamics of Rift Valley Fever virus genomic segments. Sci Rep 2015; 5:11353. [PMID: 26100494 PMCID: PMC4477411 DOI: 10.1038/srep11353] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 05/21/2015] [Indexed: 11/09/2022] Open
Abstract
Rift Valley Fever virus (RVFV) is a member of Bunyaviridae family that causes a febrile disease affecting mainly ruminants and occasionally humans in Africa, with symptoms that range from mid to severe. RVFV has a tri-segmented ssRNA genome that permits reassortment and could generate more virulent strains. In this study, we reveal the importance of reassortment for RVFV evolution using viral gene genealogy inference and phylodynamics. We uncovered seven events of reassortment that originated RVFV lineages with discordant origins among segments. Moreover, we also found that despite similar selection regimens, the three segments have distinct evolutionary dynamics; the longer segment L evolves at a significant lower rate. Episodes of discordance between population size estimates per segment also coincided with reassortment dating. Our results show that RVFV segments are decoupled enough to have distinct demographic histories and to evolve under different molecular rates.
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Affiliation(s)
- Caio C M Freire
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of Sao Paulo, Sao Paulo, Brazil
| | - Atila Iamarino
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of Sao Paulo, Sao Paulo, Brazil
| | | | | | | | - Paolo M A Zanotto
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of Sao Paulo, Sao Paulo, Brazil
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Abd El Wahed A, Patel P, Faye O, Thaloengsok S, Heidenreich D, Matangkasombut P, Manopwisedjaroen K, Sakuntabhai A, Sall AA, Hufert FT, Weidmann M. Recombinase Polymerase Amplification Assay for Rapid Diagnostics of Dengue Infection. PLoS One 2015; 10:e0129682. [PMID: 26075598 PMCID: PMC4468249 DOI: 10.1371/journal.pone.0129682] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 05/12/2015] [Indexed: 12/28/2022] Open
Abstract
Background Over 2.5 billion people are exposed to the risk of contracting dengue fever (DF). Early diagnosis of DF helps to diminish its burden on public health. Real-time reverse transcription polymerase amplification assays (RT-PCR) are the standard method for molecular detection of the dengue virus (DENV). Real-time RT-PCR analysis is not suitable for on-site screening since mobile devices are large, expensive, and complex. In this study, two RT-recombinase polymerase amplification (RT-RPA) assays were developed to detect DENV1-4. Methodology/Principal Findings Using two quantitative RNA molecular standards, the analytical sensitivity of a RT-RPA targeting the 3´non-translated region of DENV1-4 was found to range from 14 (DENV4) to 241 (DENV1-3) RNA molecules detected. The assay was specific and did not cross detect other Flaviviruses. The RT-RPA assay was tested in a mobile laboratory combining magnetic-bead based total nucleic acid extraction and a portable detection device in Kedougou (Senegal) and in Bangkok (Thailand). In Kedougou, the RT-RPA was operated at an ambient temperature of 38°C with auxiliary electricity tapped from a motor vehicle and yielded a clinical sensitivity and specificity of 98% (n=31) and 100% (n=23), respectively. While in the field trial in Bangkok, the clinical sensitivity and specificity were 72% (n=90) and 100%(n=41), respectively. Conclusions/Significance During the first 5 days of infection, the developed DENV1-4 RT-RPA assays constitute a suitable accurate and rapid assay for DENV diagnosis. Moreover, the use of a portable fluorescence-reading device broadens its application potential to the point-of-care for outbreak investigations.
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Affiliation(s)
- Ahmed Abd El Wahed
- Unit of Infection Models, German Primate Center, Goettingen, Germany
- Department of Virology, Mansoura University, Dakahlia, Egypt
| | - Pranav Patel
- CBS1-Highly Pathogenic Viruses, Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Oumar Faye
- Arbovirus Unit, Pasteur Institute, Dakar, Senegal
| | - Sasikanya Thaloengsok
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Doris Heidenreich
- Department of Virology, University Medical Center, Goettingen, Germany
| | - Ponpan Matangkasombut
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Systems Biology of Diseases Research Unit at Faculty of Science and Center of Emerging and Neglected Infectious Diseases, Mahidol University, Bangkok, Thailand
| | | | - Anavaj Sakuntabhai
- Functional Genetics of Infectious Diseases Unit, Institute Pasteur, Paris, France
| | | | - Frank T. Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor-Fontane, Senftenberg, Brandenburg, Germany
| | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
- * E-mail:
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50
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Althouse BM, Hanley KA, Diallo M, Sall AA, Ba Y, Faye O, Diallo D, Watts DM, Weaver SC, Cummings DAT. Impact of climate and mosquito vector abundance on sylvatic arbovirus circulation dynamics in Senegal. Am J Trop Med Hyg 2014; 92:88-97. [PMID: 25404071 DOI: 10.4269/ajtmh.13-0617] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Sylvatic arboviruses have been isolated in Senegal over the last 50 years. The ecological drivers of the pattern and frequency of virus infection in these species are largely unknown. We used time series analysis and Bayesian hierarchical count modeling on a long-term arbovirus dataset to test associations between mosquito abundance, weather variables, and the frequency of isolation of dengue, yellow fever, chikungunya, and Zika viruses. We found little correlation between mosquito abundance and viral isolations. Rainfall was a negative predictor of dengue virus (DENV) isolation but a positive predictor of Zika virus isolation. Temperature was a positive predictor of yellow fever virus (YFV) isolations but a negative predictor of DENV isolations. We found slight interference between viruses, with DENV negatively associated with concurrent YFV isolation and YFV negatively associated with concurrent isolation of chikungunya virus. These findings begin to characterize some of the ecological associations of sylvatic arboviruses with each other and climate and mosquito abundance.
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Affiliation(s)
- Benjamin M Althouse
- Santa Fe Institute, Santa Fe, New Mexico; Department of Biology, New Mexico State University, Las Cruces, New Mexico; Institut Pasteur de Dakar, Dakar, Senegal; Office of Research and Sponsored Projects, University of Texas, El Paso, Texas; Tropical Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Kathryn A Hanley
- Santa Fe Institute, Santa Fe, New Mexico; Department of Biology, New Mexico State University, Las Cruces, New Mexico; Institut Pasteur de Dakar, Dakar, Senegal; Office of Research and Sponsored Projects, University of Texas, El Paso, Texas; Tropical Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Mawlouth Diallo
- Santa Fe Institute, Santa Fe, New Mexico; Department of Biology, New Mexico State University, Las Cruces, New Mexico; Institut Pasteur de Dakar, Dakar, Senegal; Office of Research and Sponsored Projects, University of Texas, El Paso, Texas; Tropical Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Amadou A Sall
- Santa Fe Institute, Santa Fe, New Mexico; Department of Biology, New Mexico State University, Las Cruces, New Mexico; Institut Pasteur de Dakar, Dakar, Senegal; Office of Research and Sponsored Projects, University of Texas, El Paso, Texas; Tropical Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Yamar Ba
- Santa Fe Institute, Santa Fe, New Mexico; Department of Biology, New Mexico State University, Las Cruces, New Mexico; Institut Pasteur de Dakar, Dakar, Senegal; Office of Research and Sponsored Projects, University of Texas, El Paso, Texas; Tropical Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Ousmane Faye
- Santa Fe Institute, Santa Fe, New Mexico; Department of Biology, New Mexico State University, Las Cruces, New Mexico; Institut Pasteur de Dakar, Dakar, Senegal; Office of Research and Sponsored Projects, University of Texas, El Paso, Texas; Tropical Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Diawo Diallo
- Santa Fe Institute, Santa Fe, New Mexico; Department of Biology, New Mexico State University, Las Cruces, New Mexico; Institut Pasteur de Dakar, Dakar, Senegal; Office of Research and Sponsored Projects, University of Texas, El Paso, Texas; Tropical Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Douglas M Watts
- Santa Fe Institute, Santa Fe, New Mexico; Department of Biology, New Mexico State University, Las Cruces, New Mexico; Institut Pasteur de Dakar, Dakar, Senegal; Office of Research and Sponsored Projects, University of Texas, El Paso, Texas; Tropical Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Scott C Weaver
- Santa Fe Institute, Santa Fe, New Mexico; Department of Biology, New Mexico State University, Las Cruces, New Mexico; Institut Pasteur de Dakar, Dakar, Senegal; Office of Research and Sponsored Projects, University of Texas, El Paso, Texas; Tropical Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Derek A T Cummings
- Santa Fe Institute, Santa Fe, New Mexico; Department of Biology, New Mexico State University, Las Cruces, New Mexico; Institut Pasteur de Dakar, Dakar, Senegal; Office of Research and Sponsored Projects, University of Texas, El Paso, Texas; Tropical Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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