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Imboumy-Limoukou RK, Biteghe-Bi-Essone JC, Lendongo Wombo JB, Lekana-Douki SE, Rougeron V, Ontoua SS, Oyegue-Liabagui LS, Mbani Mpega Ntigui CN, Kouna LC, Lekana-Douki JB. Detection of Plasmodium falciparum in Saliva and Stool Samples from Children Living in Franceville, a Highly Endemic Region of Gabon. Diagnostics (Basel) 2023; 13:3271. [PMID: 37892092 PMCID: PMC10606300 DOI: 10.3390/diagnostics13203271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 10/29/2023] Open
Abstract
Due to the difficulty of obtaining blood samples, which is the invasive method that is currently used for the detection of Plasmodium spp., alternative diagnostic sampling methods that are effective and non-invasive are needed, particularly for long-term studies. Saliva and stool samples from malaria-infected individuals contain trace amounts of Plasmodium DNA and therefore could be used as alternatives. Malaria was screened using rapid diagnosis tests and confirmed via microscopy. Nested PCR tests targeting the Plasmodium falciparum-specific STEVOR gene were performed for blood, saliva and stool samples that were positive for malaria. Three hundred sixty-seven (367) children were enrolled and eighty (22.22%) were confirmed to be positive for malaria. Matched blood, saliva and stool samples were available for 35 children. By using blood smears as the gold standard for the diagnosis of malaria, our study indicates that Plasmodium DNA was more detectable in blood (100%) than in saliva (22.86%) and stools (14.29%). Applying qPCR to the STEVOR gene to detect Plasmodium falciparum DNA in saliva and stool samples cannot be considered as an alternative to the current malaria detection processes using blood specimens.
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Affiliation(s)
- Roméo Karl Imboumy-Limoukou
- Unité Evolution Epidémiologie et Résistance Parasitaire (UNEEREP), Centre International de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon; (J.-C.B.-B.-E.); (J.B.L.W.); (S.-S.O.); (L.S.O.-L.); (C.N.M.M.N.); (L.C.K.); (J.-B.L.-D.)
| | - Jean-Claude Biteghe-Bi-Essone
- Unité Evolution Epidémiologie et Résistance Parasitaire (UNEEREP), Centre International de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon; (J.-C.B.-B.-E.); (J.B.L.W.); (S.-S.O.); (L.S.O.-L.); (C.N.M.M.N.); (L.C.K.); (J.-B.L.-D.)
| | - Judicael Boris Lendongo Wombo
- Unité Evolution Epidémiologie et Résistance Parasitaire (UNEEREP), Centre International de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon; (J.-C.B.-B.-E.); (J.B.L.W.); (S.-S.O.); (L.S.O.-L.); (C.N.M.M.N.); (L.C.K.); (J.-B.L.-D.)
- Laboratoire de Biologie Moléculaire et Cellulaire (LABMC), Université des Sciences et Techniques de Masuku, Franceville BP 943, Gabon
| | - Sonia Etenna Lekana-Douki
- Unité des Maladies Virales Emergentes (UMVE), Centre International de Recherches Médicales de Franceville, Franceville BP 769, Gabon;
| | - Virginie Rougeron
- MIVEGEC, IRD, CNRS, University of Montpellier, 34900 Montpellier, France;
| | - Steede-Seinnat Ontoua
- Unité Evolution Epidémiologie et Résistance Parasitaire (UNEEREP), Centre International de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon; (J.-C.B.-B.-E.); (J.B.L.W.); (S.-S.O.); (L.S.O.-L.); (C.N.M.M.N.); (L.C.K.); (J.-B.L.-D.)
- Ecole Doctoral Régional en Infectiologie Tropical, Franceville BP 876, Gabon
| | - Lydie Sandrine Oyegue-Liabagui
- Unité Evolution Epidémiologie et Résistance Parasitaire (UNEEREP), Centre International de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon; (J.-C.B.-B.-E.); (J.B.L.W.); (S.-S.O.); (L.S.O.-L.); (C.N.M.M.N.); (L.C.K.); (J.-B.L.-D.)
- Ecole Doctoral Régional en Infectiologie Tropical, Franceville BP 876, Gabon
| | - Cherone Nancy Mbani Mpega Ntigui
- Unité Evolution Epidémiologie et Résistance Parasitaire (UNEEREP), Centre International de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon; (J.-C.B.-B.-E.); (J.B.L.W.); (S.-S.O.); (L.S.O.-L.); (C.N.M.M.N.); (L.C.K.); (J.-B.L.-D.)
- Ecole Doctoral Régional en Infectiologie Tropical, Franceville BP 876, Gabon
| | - Lady Charlène Kouna
- Unité Evolution Epidémiologie et Résistance Parasitaire (UNEEREP), Centre International de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon; (J.-C.B.-B.-E.); (J.B.L.W.); (S.-S.O.); (L.S.O.-L.); (C.N.M.M.N.); (L.C.K.); (J.-B.L.-D.)
| | - Jean-Bernard Lekana-Douki
- Unité Evolution Epidémiologie et Résistance Parasitaire (UNEEREP), Centre International de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon; (J.-C.B.-B.-E.); (J.B.L.W.); (S.-S.O.); (L.S.O.-L.); (C.N.M.M.N.); (L.C.K.); (J.-B.L.-D.)
- Département de Parasitologie-Mycologie, Université des Sciences de la Santé, Libreville BP 4008, Gabon
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2
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Ndjangangoye NK, Lekana-Douki SE, Oyegue-Liabagui SL, Kouna LC, Ndong Ndong KA, Onanga R, Lekana-Douki JB. Molecular Prevalence of Diarrheal Pathogens in Children with Acute Diarrhea in Southeastern Gabon. Am J Trop Med Hyg 2023; 108:829-836. [PMID: 36848891 PMCID: PMC10077015 DOI: 10.4269/ajtmh.22-0378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/12/2022] [Indexed: 03/01/2023] Open
Abstract
Diarrheal diseases are a major cause of morbidity and mortality in infants and young children, particularly in sub-Saharan countries. In Gabon, there are few data on the prevalence of diarrheal pathogens in children. The aim of this study was to assess the prevalence of diarrheal pathogens in children with diarrhea in southeastern Gabon. Stool samples (n = 284) from Gabonese children 0 to 15 years of age with acute diarrhea were analyzed using polymerase chain reaction targeting 17 diarrheal pathogens. At least one pathogen was detected in 75.7% of samples (n = 215). Coinfection with multiple pathogens was observed in 44.7% of patients (n = 127). Diarrheagenic Escherichia coli was the most commonly detected pathogen (30.6%, n = 87), followed by adenovirus (26.4%, n = 75), rotavirus (16.9%, n = 48), Shigella sp. (16.5%, n = 47), Giardia duodenalis (14.4%, n = 41), norovirus GII (7.0%, n = 20), sapovirus (5.6%, n = 16), Salmonella enterica (4.9%, n = 14), astrovirus (4.6%, n = 13), Campylobacter jejuni/coli (4.6%, n = 13), bocavirus (2.8%, n = 8), and norovirus GI (2.8%, n = 8). Our study provides useful information on the possible causes of diarrheal diseases affecting children in southeastern Gabon. A similar study with a control group of healthy children is needed to assess the burden of the disease attributed to each pathogen.
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Affiliation(s)
- Nal Kennedy Ndjangangoye
- Unité d’Evolution, Epidémiologie et Résistances Parasitaires, Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
- Unité Émergence des Maladies Virales, Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
- Ecole Doctorale Régionale d’Afrique Centrale en Infectiologie Tropicale, Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | - Sonia Etenna Lekana-Douki
- Unité Émergence des Maladies Virales, Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Sandrine Lydie Oyegue-Liabagui
- Unité d’Evolution, Epidémiologie et Résistances Parasitaires, Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
- Ecole Doctorale Régionale d’Afrique Centrale en Infectiologie Tropicale, Université des Sciences et Techniques de Masuku, Franceville, Gabon
- Département de Biologie, Faculté des Sciences, Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | - Lady Charlene Kouna
- Unité d’Evolution, Epidémiologie et Résistances Parasitaires, Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Kerry Ance Ndong Ndong
- Unité d’Evolution, Epidémiologie et Résistances Parasitaires, Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Richard Onanga
- Unité de Recherche et d’Analyses Médicales, Laboratoire de Bactériologie, Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Jean Bernard Lekana-Douki
- Unité d’Evolution, Epidémiologie et Résistances Parasitaires, Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
- Département de Parasitologie-Mycologie Médecine Tropicale, Faculté de Médecine, Université des Sciences de la Santé, Libreville, Gabon
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3
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Fischer C, Maponga TG, Yadouleton A, Abílio N, Aboce E, Adewumi P, Afonso P, Akorli J, Andriamandimby SF, Anga L, Ashong Y, Beloufa MA, Bensalem A, Birtles R, Boumba ALM, Bwanga F, Chaponda M, Chibukira P, Chico RM, Chileshe J, Chongwe G, Cissé A, D'Alessandro U, de Lamballerie XN, de Morais JFM, Derrar F, Dia N, Diarra Y, Doumbia L, Drosten C, Dussart P, Echodu R, Eggers Y, Eloualid A, Faye O, Feldt T, Frühauf A, Halatoko A, Ilouga PV, Ismael N, Jambou R, Jarju S, Kamprad A, Katowa B, Kayiwa J, King'wara L, Koita O, Lacoste V, Lagare A, Landt O, Lekana-Douki SE, Lekana-Douki JB, Iipumbu E, Loemba H, Lutwama J, Mamadou S, Maman I, Manyisa B, Martinez PA, Matoba J, Mhuulu L, Moreira-Soto A, Mwangi J, N'dilimabaka N, Nassuna CA, Ndiath MO, Nepolo E, Njouom R, Nourlil J, Nyanjom SG, Odari EO, Okeng A, Ouoba JB, Owusu M, Donkor IO, Phadu KK, Phillips RO, Preiser W, Ruhanya V, Salah F, Salifou S, Sall AA, Sylverken AA, Tagnouokam-Ngoupo PA, Tarnagda Z, Tchikaya FO, Tufa TB, Drexler JF. Retraction. Science 2022; 378:1284-1285. [PMID: 36537892 DOI: 10.1126/science.adg2821] [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] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Carlo Fischer
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Tongai Gibson Maponga
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa
| | - Anges Yadouleton
- Laboratoire dés fievres hemorragiques virales de Cotonou, Akpakpa, Benin
| | - Nuro Abílio
- Instituto Nacional de Saúde, Maputo, Mozambique
| | | | - Praise Adewumi
- Laboratoire dés fievres hemorragiques virales de Cotonou, Akpakpa, Benin
| | - Pedro Afonso
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Jewelna Akorli
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Latifa Anga
- Institut Pasteur du Maroc, Casablanca, Morocco
| | - Yvonne Ashong
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Aicha Bensalem
- Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria
| | - Richard Birtles
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda.,School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Anicet Luc Magloire Boumba
- Faculty of Health Sciences, Marien Ngouabi University, Pointe-Noire, Congo.,Molecular Diagnostic Laboratory HDL, Pointe-Noire, Congo
| | - Freddie Bwanga
- MBN Clinical Laboratories, Kampala, Uganda.,Makerere University College of Health Sciences, Kampala, Uganda
| | - Mike Chaponda
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Paradzai Chibukira
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | | | - Justin Chileshe
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Gershom Chongwe
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Assana Cissé
- Laboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso
| | - Umberto D'Alessandro
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | | | | | - Fawzi Derrar
- Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria
| | - Ndongo Dia
- Institut Pasteur de Dakar (IPD), Dakar, Senegal
| | - Youssouf Diarra
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Lassina Doumbia
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Christian Drosten
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany.,German Centre for Infection Research (DZIF), associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Richard Echodu
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda
| | - Yannik Eggers
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | | | - Torsten Feldt
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Anna Frühauf
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | | | | | | | - Ronan Jambou
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | - Sheikh Jarju
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Antje Kamprad
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Ben Katowa
- Macha Research Trust, Choma, Zambia.,School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - John Kayiwa
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Leonard King'wara
- National Public Health Reference Laboratory, Ministry of Health, Nairobi, Kenya
| | - Ousmane Koita
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | | | - Adamou Lagare
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | | | | | | | - Etuhole Iipumbu
- School of Medicine, University of Namibia, Windhoek, Namibia
| | - Hugues Loemba
- Molecular Diagnostic Laboratory HDL, Pointe-Noire, Congo.,Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Santou Mamadou
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | | | - Brendon Manyisa
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | - Pedro A Martinez
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Japhet Matoba
- Macha Research Trust, Choma, Zambia.,School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Lusia Mhuulu
- School of Medicine, University of Namibia, Windhoek, Namibia
| | - Andres Moreira-Soto
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Judy Mwangi
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda.,School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Nadine N'dilimabaka
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Mamadou Ousmane Ndiath
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Emmanuel Nepolo
- School of Medicine, University of Namibia, Windhoek, Namibia
| | | | | | - Steven Ger Nyanjom
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Eddy Okoth Odari
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | | | | | - Michael Owusu
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Irene Owusu Donkor
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Karabo Kristen Phadu
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa
| | - Richard Odame Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa.,National Health Laboratory Service Tygerberg Business Unit, Cape Town, South Africa
| | - Vurayai Ruhanya
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | | | | | | | - Augustina Angelina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana.,Department of Theoretical and Applied Biology, KNUST, Kumasi, Ghana
| | | | - Zekiba Tarnagda
- Laboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso
| | | | - Tafese Beyene Tufa
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany.,German Centre for Infection Research (DZIF), associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany
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4
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N’dilimabaka N, Mounguegui DM, Lekana-Douki SE, Yattara MK, Obame-Nkoghe J, Longo-Pendy NM, Koumba IPK, Mve-Ella OLB, Moukouama SK, Dzembo CE, Bolo LY, Biyie-Bi-Ngoghe P, Mangouka GL, Nzenze JR, Lekana-Douki JB. Biochemical and hematological factors associated with COVID-19 severity among Gabonese patients: A retrospective cohort study. Front Cell Infect Microbiol 2022; 12:975712. [PMID: 36619758 PMCID: PMC9816336 DOI: 10.3389/fcimb.2022.975712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
The COVID-19 disease presents a large range of clinical manifestations and includes asymptomatic, mild, and severe cases. The level of severity is related to parameters associated with immunity, genetics, and biochemistry. Africa shows one of the lowest COVID-19 fatality rates but very few data on the biochemical markers of COVID-19 in patients and the factors associated with disease severity are available for the continent. In Gabon, the COVID-19 fatality rate is only 0.63% but almost no data on biomarkers in COVID-19 patients have been published. Both the number of COVID-19 cases and the mortality rate reported in Africa in general, and in Gabon in particular, are lower than in non-African countries. As such, understanding the factors associated with disease severity in Gabonese patients is a crucial step to better understand the disease in the African context and prepare for future COVID-19 waves and other epidemics of emerging diseases. Here, we compared biochemical and hematological markers among 753 Gabonese COVID-19 patients with asymptomatic (184/753), mild/moderate (420/753), and severe/critical (149/753) forms of the disease using an Analysis of Variance (ANOVA) or a Kruskal-Wallis (KW) test. We modeled these parameters together with comorbidities, age, and sex to predict factors associated with disease severity by using a "binomial generalized linear model" utilizing the "package" stats of R software version 4.0.2. Our results showed that almost all the biochemical and hematological parameters (except creatinine, phosphorus, D-dimers, platelets, and monocytes) varied according to disease severity. However, age and the dysfunction of organs like the kidney, liver, and lung together with the decrease of electrolytes (chloride, potassium, and sodium) are the best predictors of disease severity in Gabonese patients.
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Affiliation(s)
- Nadine N’dilimabaka
- Unité Emergence des Maladies Virales, Département de Virologie, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon,Département de Biologie, Faculté des Sciences, Université des Sciences et Techniques de Masuku (USTM), Franceville, Gabon,*Correspondence: Nadine N’dilimabaka,
| | | | - Sonia Etenna Lekana-Douki
- Unité Emergence des Maladies Virales, Département de Virologie, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Judicaël Obame-Nkoghe
- Département de Biologie, Faculté des Sciences, Université des Sciences et Techniques de Masuku (USTM), Franceville, Gabon,Unité Écologie des Systèmes Vectoriels (ESV), Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Neil Michel Longo-Pendy
- Unité Écologie des Systèmes Vectoriels (ESV), Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Ingrid Precilya Koumba Koumba
- Unité Emergence des Maladies Virales, Département de Virologie, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Octavie Lauris Banga Mve-Ella
- Unité Emergence des Maladies Virales, Département de Virologie, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Schedy Koumba Moukouama
- Unité Emergence des Maladies Virales, Département de Virologie, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Cresh Emelya Dzembo
- Unité Emergence des Maladies Virales, Département de Virologie, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Lauriane Yacka Bolo
- Unité Emergence des Maladies Virales, Département de Virologie, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | | | | | - Jean-Raymond Nzenze
- Site Coronavirus, Hôpital d’Instruction des Armes d’Akanda, Libreville-Nord, Gabon
| | - Jean-Bernard Lekana-Douki
- Unité Evolution Epidémiologie et Résistances Parasitaires (UNEEREP), Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon,Département de Parasitologie-Mycologie Médecine Tropicale, Faculté de Médecine, Université des Sciences de la Sante, Libreville, Gabon
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5
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Fischer C, Maponga TG, Yadouleton A, Abílio N, Aboce E, Adewumi P, Afonso P, Akorli J, Andriamandimby SF, Anga L, Ashong Y, Beloufa MA, Bensalem A, Birtles R, Boumba ALM, Bwanga F, Chaponda M, Chibukira P, Chico RM, Chileshe J, Chongwe G, Cissé A, D'Alessandro U, de Lamballerie XN, de Morais JFM, Derrar F, Dia N, Diarra Y, Doumbia L, Drosten C, Dussart P, Echodu R, Eggers Y, Eloualid A, Faye O, Feldt T, Frühauf A, Halatoko A, Ilouga PV, Ismael N, Jambou R, Jarju S, Kamprad A, Katowa B, Kayiwa J, King'wara L, Koita O, Lacoste V, Lagare A, Landt O, Lekana-Douki SE, Lekana-Douki JB, Iipumbu E, Loemba H, Lutwama J, Mamadou S, Maman I, Manyisa B, Martinez PA, Matoba J, Mhuulu L, Moreira-Soto A, Mwangi J, N Dilimabaka N, Nassuna CA, Ndiath MO, Nepolo E, Njouom R, Nourlil J, Nyanjom SG, Odari EO, Okeng A, Ouoba JB, Owusu M, Owusu Donkor I, Phadu KK, Phillips RO, Preiser W, Ruhanya V, Salah F, Salifou S, Sall AA, Sylverken AA, Tagnouokam-Ngoupo PA, Tarnagda Z, Tchikaya FO, Tufa TB, Drexler JF. RETRACTED: Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa. Science 2022; 378:eadd8737. [PMID: 36454863 DOI: 10.1126/science.add8737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection.
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Affiliation(s)
- Carlo Fischer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Tongai Gibson Maponga
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa
| | - Anges Yadouleton
- Laboratoire dés fievres hemorragiques virales de Cotonou, Akpakpa, Benin
| | - Nuro Abílio
- Instituto Nacional de Saúde, Maputo, Mozambique
| | | | - Praise Adewumi
- Laboratoire dés fievres hemorragiques virales de Cotonou, Akpakpa, Benin
| | - Pedro Afonso
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Jewelna Akorli
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Latifa Anga
- Institut Pasteur du Maroc, Casablanca, Morocco
| | - Yvonne Ashong
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Aicha Bensalem
- Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria
| | - Richard Birtles
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda.,School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Anicet Luc Magloire Boumba
- Faculty of Health Sciences, Marien Ngouabi University, Pointe-Noire, Congo.,Molecular Diagnostic Laboratory HDL, Pointe-Noire, Congo
| | - Freddie Bwanga
- MBN Clinical Laboratories, Kampala, Uganda.,Makerere University College of Health Sciences, Kampala, Uganda
| | - Mike Chaponda
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Paradzai Chibukira
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | | | - Justin Chileshe
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Gershom Chongwe
- Tropical Diseases Research Centre, Ndola Teaching Hospital, Ndola, Zambia
| | - Assana Cissé
- Laboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso
| | - Umberto D'Alessandro
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | | | | | - Fawzi Derrar
- Institut Pasteur of Algeria, National Influenza Centre, Sidi-Fredj, Algeria
| | - Ndongo Dia
- Institut Pasteur de Dakar (IPD), Dakar, Senegal
| | - Youssouf Diarra
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Lassina Doumbia
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Christian Drosten
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany.,German Centre for Infection Research (DZIF), associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Richard Echodu
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda
| | - Yannik Eggers
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | | | - Torsten Feldt
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Anna Frühauf
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | | | | | | | - Ronan Jambou
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | - Sheikh Jarju
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Antje Kamprad
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Ben Katowa
- Macha Research Trust, Choma, Zambia.,School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - John Kayiwa
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Leonard King'wara
- National Public Health Reference Laboratory, Ministry of Health, Nairobi, Kenya
| | - Ousmane Koita
- Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | | | - Adamou Lagare
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | | | | | | | - Etuhole Iipumbu
- School of Medicine, University of Namibia, Windhoek, Namibia
| | - Hugues Loemba
- Molecular Diagnostic Laboratory HDL, Pointe-Noire, Congo.,Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Santou Mamadou
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | | | - Brendon Manyisa
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | - Pedro A Martinez
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Japhet Matoba
- Macha Research Trust, Choma, Zambia.,School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Lusia Mhuulu
- School of Medicine, University of Namibia, Windhoek, Namibia
| | - Andres Moreira-Soto
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Judy Mwangi
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda.,School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Nadine N Dilimabaka
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Mamadou Ousmane Ndiath
- Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Emmanuel Nepolo
- School of Medicine, University of Namibia, Windhoek, Namibia
| | | | | | - Steven Ger Nyanjom
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Eddy Okoth Odari
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | | | | | - Michael Owusu
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Irene Owusu Donkor
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Karabo Kristen Phadu
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa
| | - Richard Odame Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa.,National Health Laboratory Service Tygerberg Business Unit, Cape Town, South Africa
| | - Vurayai Ruhanya
- National Virology Laboratory, Faculty of Medicine and Health Sciences, University of Zimbabwe, Avondale, Zimbabwe
| | | | | | | | - Augustina Angelina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana.,Department of Theoretical and Applied Biology, KNUST, Kumasi, Ghana
| | | | - Zekiba Tarnagda
- Laboratoire National de Référence-Grippes, Ouagadougou, Burkina Faso
| | | | - Tafese Beyene Tufa
- Hirsch Institute of Tropical Medicine, Asella, Ethiopia.,Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jan Felix Drexler
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany.,German Centre for Infection Research (DZIF), associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany
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Lekana-Douki SE, N'dilimabaka N, Levasseur A, Colson P, Andeko JC, Zong Minko O, Banga Mve-Ella O, Fournier PE, Devaux C, Ondo BM, Akombi FL, Yacka Mouele Bolo L, Ngonga Dikongo AM, Diané A, Mabika Mabika A, Mathouet JF, Dzembo C, Atiga NC, Mouity Matoumba A, Ndjangangoye NK, Bréchard L, Bedotto-Buffet M, Mangombi Pambou JB, Kandet Yattara M, Mbongo Nkama EA, Mintsa Ndong A, Adegnika AA, Raoult D, Fenollar F, Lekana-Douki JB. Screening and Whole Genome Sequencing of SARS-CoV-2 Circulating During the First Three Waves of the COVID-19 Pandemic in Libreville and the Haut-Ogooué Province in Gabon. Front Med (Lausanne) 2022; 9:877391. [PMID: 35655849 PMCID: PMC9152426 DOI: 10.3389/fmed.2022.877391] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/27/2022] [Indexed: 01/08/2023] Open
Abstract
Since the onset of the COVID-19 pandemic, the SARS-CoV-2 viral dynamics in Africa have been less documented than on other continents. In Gabon, a Central African country, a total number of 37,511 cases of COVID-19 and 281 deaths have been reported as of December 8, 2021. After the first COVID-19 case was reported on March 12, 2020, in the capital Libreville, the country experienced two successive waves. The first one, occurred in March 2020 to August 2020, and the second one in January 2021 to May 2021. The third wave began in September 2021 and ended in November 2021. In order to reduce the data gap regarding the dynamics of SARS-CoV-2 in Central Africa, we performed a retrospective genotyping study using 1,006 samples collected from COVID-19 patients in Gabon from 2020 to 2021. Using SARS-CoV-2 variant screening by Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) and whole genome sequencing (WGS), we genotyped 809 SARS-CoV-2 samples through qRT-PCR and identified to generated 291 new genomes. It allowed us to describe specific mutations and changes in the SARS-CoV-2 variants in Gabon. The qRT-PCR screening of 809 positive samples from March 2020 to September 2021 showed that 119 SARS-CoV-2 samples (14.7%) were classified as VOC Alpha (Pangolin lineage B.1.1.7), one (0.1%) was a VOC Beta (B.1.351), and 198 (24.5 %) were VOC Delta (B.1.617.2), while 491 samples (60.7%) remained negative for the variants sought. The B1.1 variant was predominant during the first wave while the VOC Alpha dominated the second wave. The B1.617.2 Delta variant is currently the dominant variant of the third wave. Similarly, the analysis of the 291 genome sequences indicated that the dominant variant during the first wave was lineage B.1.1, while the dominant variants of the second wave were lineages B.1.1.7 (50.6%) and B.1.1.318 (36.4%). The third wave started with the circulation of the Delta variant (B.1.617). Finally, we compared these results to the SARS-CoV-2 sequences reported in other African, European, American and Asian countries. Sequences of Gabonese SARS-CoV-2 strains presented the highest similarities with those of France, Belgium and neighboring countries of Central Africa, as well as West Africa.
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Affiliation(s)
| | - Nadine N'dilimabaka
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon.,Département de Biologie, Faculté des Sciences, Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | - Anthony Levasseur
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Philippe Colson
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Julia Cyrielle Andeko
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Ornella Zong Minko
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Octavie Banga Mve-Ella
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Christian Devaux
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,Centre National de la Recherche Scientifique (CNRS), Marseille, France
| | | | | | | | | | - Abdoulaye Diané
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Arsène Mabika Mabika
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Jenny Francine Mathouet
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Cresh Dzembo
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Nick Chenis Atiga
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Anicet Mouity Matoumba
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | | | | | | | | | | | | | | | - Ayola Akim Adegnika
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon.,Institute of Tropical Medecine, University of Tübingen and German Center for Infectious Research (DZIF), Tübingen, Germany
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Florence Fenollar
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Jean-Bernard Lekana-Douki
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon.,Département de Parasitologie-Mycologie Médecine Tropicale, Faculté de Médecine, Université des Sciences de la Sante, Libreville, Gabon
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N'dilimabaka N, Koumba Mavoungou D, Soami V, Bohou Kombila L, Mouguiama RM, Mondjo A, Mangombi Pambou JB, Ngoma JF, Ovengue FC, Alilangori TP, Koko J, Bitegue Methe L, Mboumba Mboumba H, Sima Zue A, Edjo Nkili G, Lekana-Douki SE, Maganga GD. Molecular analyses of human rabies virus associated with encephalitis in two children in Gabon. IJID Regions 2022; 2:180-183. [PMID: 35757081 PMCID: PMC9216393 DOI: 10.1016/j.ijregi.2022.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 10/25/2022]
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Lekana-Douki SE, Sir-Ondo-Enguier PN, Banga-Mve-Ella O, Imboumy-Limoukou RK, Maganga GD, Lekana-Douki JB, Berthet N. Epidemiology and molecular characterization of the re-emerging measles virus among children and adults in the Haut-Ogooue, Gabon. BMC Infect Dis 2019; 19:90. [PMID: 30683064 PMCID: PMC6347803 DOI: 10.1186/s12879-019-3731-y] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 01/16/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Measles is one of the most infectious diseases with a high mortality rate worldwide. It is caused by the measles virus (MeV) which is a single stranded RNA virus with genetic diversity based on the nucleoprotein gene, including 24 genotypes. In Gabon, several outbreaks occurred in the past few years, especially in 2016 in Libreville and Oyem. A surveillance network of infectious diseases highlighted a measles outbreak which occurred in the south of Gabon from April to June 2017. METHODS Clinical specimens of urine, blood, throat and nasal swabs were collected in the two main cities of the Haut-Ogooue province, Franceville and Moanda. Virological investigations based on real-time polymerase chain reaction for molecular diagnosis and conventional PCR for genotype identification were done. RESULTS Specimens were collected from 139 suspected measles patients. A total of 46 (33.1%) children and adults were laboratory-confirmed cases among which 16 (34.8%) were unvaccinated, 16 (34.8%) had received one dose, and 11 (23.9%) had received two doses of the measles vaccine. Phylogenetic analysis revealed that all the sequences of the nucleoprotein gene belonged to genotype B3. CONCLUSIONS Measles infection was more commonly confirmed among those with one recorded dose compared to suspect cases with none, unknown or two recorded doses. The molecular characterization of the strains showed the circulation of the B3 genotype which is endemic on the African continent, thirty years after the B2 genotype was described in an outbreak in Libreville, the capital of Gabon. These findings highlight that surveillance and molecular investigation of measles should be continued in Gabon.
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Affiliation(s)
- Sonia Etenna Lekana-Douki
- Unité Emergence des maladies virales, Centre International de Recherches Médicales de Franceville, 769 Franceville, BP Gabon
| | - Pater Noster Sir-Ondo-Enguier
- Unité Evolution Epidémiologie et Résistances Parasitaires (UNEEREP), Centre International de Recherches Médicales de Franceville, 769 Franceville, BP Gabon
| | - Octavie Banga-Mve-Ella
- Unité Emergence des maladies virales, Centre International de Recherches Médicales de Franceville, 769 Franceville, BP Gabon
| | - Romeo Karl Imboumy-Limoukou
- Unité Evolution Epidémiologie et Résistances Parasitaires (UNEEREP), Centre International de Recherches Médicales de Franceville, 769 Franceville, BP Gabon
| | - Gael D. Maganga
- Unité Emergence des maladies virales, Centre International de Recherches Médicales de Franceville, 769 Franceville, BP Gabon
| | - Jean-Bernard Lekana-Douki
- Unité Evolution Epidémiologie et Résistances Parasitaires (UNEEREP), Centre International de Recherches Médicales de Franceville, 769 Franceville, BP Gabon
- Département de Parasitologie-Mycologie Médecine Tropicale, Faculté de Médecine, Université des Sciences de la Sante, 4009 Libreville, BP Gabon
| | - Nicolas Berthet
- Unité Emergence des maladies virales, Centre International de Recherches Médicales de Franceville, 769 Franceville, BP Gabon
- Centre National de Recherche Scientifique (CNRS) UMR3569, 25 rue du docteur Roux, Paris, France
- Institut Pasteur, Unité Environnement et risques infectieux, Cellule d’Intervention Biologique d’Urgence, 25 rue du docteur Roux, Paris, France
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Lekana-Douki SE, Behillil S, Enouf V, Leroy EM, Berthet N. Detection of human bocavirus-1 in both nasal and stool specimens from children under 5 years old with influenza-like illnesses or diarrhea in Gabon. BMC Res Notes 2018; 11:495. [PMID: 30029615 PMCID: PMC6053798 DOI: 10.1186/s13104-018-3605-1] [Citation(s) in RCA: 14] [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: 05/04/2018] [Accepted: 07/13/2018] [Indexed: 12/19/2022] Open
Abstract
Objective Human bocavirus (HBoV) is a viral pathogen which causes respiratory tract diseases and acute gastroenteritis worldwide. This virus mainly affected children under 5 years old. There is little information on HBoV in Gabon. Two first studies was conducted to determine the prevalence of respiratory and enteric viruses in children under 5 years old who visited health centers for influenza-like illness (ILI) or diarrhea in Gabon from March 2010 to June 2011. However, HBoV was not included in the screening. The aim of this retrospective study was to evaluate the prevalence and the HBoV genotype in children under 5 years old with ILI or diarrhea in Gabon. Results A total of 810 nasal swabs and 317 feces samples collected during the two first study were analyzed among which 32 (4.4%) and 7 (2.2%) were positive for HBoV respectively. While there were no significant differences in prevalence between age groups in children with ILI, all children with diarrhea were under 12 months of age. Moreover, 84.4 and 42.8% were diagnosed in co-infections with at least one other respiratory virus, or enteric viruses respectively. Finally, HBoV subtype 1 has been detected in both respiratory and gastrointestinal tracts with very low variability.
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Affiliation(s)
| | - Sylvie Behillil
- Unité de Génétique Moléculaire des Virus à ARN, Centre National de Référence des Virus des Infections Respiratoires, Institut Pasteur, 25 rue du docteur Roux, Paris, France.,Centre National de Recherche Scientifique (CNRS) UMR3569, 25 rue du docteur Roux, Paris, France
| | - Vincent Enouf
- Unité de Génétique Moléculaire des Virus à ARN, Centre National de Référence des Virus des Infections Respiratoires, Institut Pasteur, 25 rue du docteur Roux, Paris, France.,Centre National de Recherche Scientifique (CNRS) UMR3569, 25 rue du docteur Roux, Paris, France
| | - Eric M Leroy
- Centre International de Recherches Médicales de Franceville, BP 769, Franceville, Gabon.,UMR (IRD 224/CNRS 5290/UM1-UM2), Institut de Recherche pour le Développement, Montpellier, France
| | - Nicolas Berthet
- Centre International de Recherches Médicales de Franceville, BP 769, Franceville, Gabon.,Centre National de Recherche Scientifique (CNRS) UMR3569, 25 rue du docteur Roux, Paris, France.,Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, 25 rue du docteur Roux, Paris, France
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Lekana-Douki SE, Kombila-Koumavor C, Nkoghe D, Drosten C, Drexler JF, Leroy EM. Molecular epidemiology of enteric viruses and genotyping of rotavirus A, adenovirus and astrovirus among children under 5 years old in Gabon. Int J Infect Dis 2015; 34:90-5. [PMID: 25796432 DOI: 10.1016/j.ijid.2015.03.009] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVES This study aimed to determine the prevalence of enteric viruses causing gastroenteritis, and the circulating stains, in Gabonese children under five years old who visited health centers between March 2010 and June 2011. METHODS Stool specimens were collected and sent for analysis to CIRMF (Centre International de Recherches Médicales de Franceville). Stools were screened for six enteric viruses (rotavirus, adenovirus, norovirus I and II, sapovirus, human astrovirus) by means of a multiplex real-time reverse transcription polymerase chain reaction, and Rotavirus A, Adenovirus and Astrovirus were genotyped. RESULTS Among the 317 specimens analyzed, 193 (60.9%) were positive for at least one enteric virus. Rotavirus A (RVA) (27.1%) was the most frequently detected virus, followed by human Adenovirus (HAdV) (19.6%), Norovirus II (NoVs-II) (13.9%), Norovirus I (NoVs-I) (9.1%), Sapovirus (SaV) (9.5%) and human Astrovirus (HAstV) (6.3%). One-third of the 193 positive samples contained more than one virus. The most common Rotavirus A genotype was G6P[6]. Various HAdV serotypes were found. HAstV-1 was identified. CONCLUSIONS These findings improve our knowledge of circulating enteric viruses in Gabon. The emergence of unusual G6P[6] strain of rotavirus A, predominant, suggested a particular epidemiological surveillance of circulating rotavirus strains during the introduction of vaccination in Gabon.
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Affiliation(s)
| | | | - Dieudonné Nkoghe
- Centre International de Recherches Médicales de Franceville, BP 769 Franceville, Gabon; Ministère de la Santé Publique, BP 5978 Libreville, Gabon.
| | | | | | - Eric M Leroy
- Centre International de Recherches Médicales de Franceville, BP 769 Franceville, Gabon; UMR (IRD 224 /CNRS 5290 / UM1-UM2), Institut de Recherche pour le Développement, Montpellier, France.
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Lekana-Douki SE, Nkoghe D, Drosten C, Ngoungou EB, Drexler JF, Leroy EM. Viral etiology and seasonality of influenza-like illness in Gabon, March 2010 to June 2011. BMC Infect Dis 2014; 14:373. [PMID: 25000832 PMCID: PMC4107952 DOI: 10.1186/1471-2334-14-373] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/30/2014] [Indexed: 12/13/2022] Open
Abstract
Background Surveillance of influenza-like illness (ILI) in Central Africa began only recently, and few data are therefore available on the circulation of influenza virus and other respiratory viruses. In Gabon, a Central African country, we established a surveillance network in four major towns in order to analyze cases of ILI among patients who visited health centers between March 2010 and June 2011, and to determine the viral etiology. Methods Nasal swabs were sent for analysis to the Centre International de Recherches Médicales de Franceville, where they were screened for 17 respiratory viruses in a multiplex real-time reverse transcription polymerase chain reaction for all pathogens according the following pairs: adenovirus/parainfluenza virus 4, respiratory syncytial virus/human metapneumovirus, parainfluenza virus 1/parainfluenza virus 2, pandemic influenza virus A/seasonal influenza virus A (H1N1, H3N2)/seasonal influenza virus B, human coronaviruses 229E/OC43, human coronaviruses NL63/HKU1, rhinovirus/human parechovirus, and enterovirus/parainfluenza virus 3. Results We analyzed a total of 1041 specimens, of which 639 (61%) were positive for at least one virus. Three-quarters of the patients were children under five years old. We therefore focused on this age group, in which 68.1% of patients were positive for at least one virus. The most common viruses were adenoviruses (17.5%), followed by parainfluenza viruses (PIVs) 1–4 (16.8%), enteroviruses (EV) (14.7%), respiratory syncytial virus (RSV) (13.5%), and influenza virus (11.9%). The prevalence of some viruses was subject to geographic and seasonal variations. One-third of positive samples contained more than one virus. Conclusions Like most studies in the world, the virus PIVs, EV, RSV, Influenza virus, HRV were predominant among children under five years old in Gabon. An exception is made for adenoviruses which have a high prevalence in our study. However adenoviruses can be detected in asymptomatic persons. These finding gave a better knowledge of the circulation and the seasonality of the viruses involved in ILI in Gabon.
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Affiliation(s)
| | | | | | | | | | - Eric M Leroy
- Centre International de Recherches Médicales de Franceville, BP 769 Franceville, Gabon.
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Lekana-Douki SE, Mouinga-Ondémé A, Nkoghe D, Drosten C, Drexler JF, Kazanji M, Leroy EM. Early introduction and delayed dissemination of pandemic influenza, Gabon. Emerg Infect Dis 2013; 19:644-7. [PMID: 23631999 PMCID: PMC3647404 DOI: 10.3201/eid1904.111925] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [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] [Indexed: 11/30/2022] Open
Abstract
Active surveillance in health care centers in Gabon during 2009–2011 detected 72 clinical cases of pandemic (H1N1) 2009 (pH1N1). We found that pH1N1 virus was introduced in mid-2009 but spread throughout the country in 2010. Thus, Gabon was also affected by pH1N1.
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Caron M, Lekana-Douki SE, Makuwa M, Obiang-Ndong GP, Biba O, Nkoghé D, Kazanji M. Prevalence, genetic diversity and antiretroviral drugs resistance-associated mutations among untreated HIV-1-infected pregnant women in Gabon, central Africa. BMC Infect Dis 2012; 12:64. [PMID: 22433277 PMCID: PMC3359209 DOI: 10.1186/1471-2334-12-64] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [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] [Received: 11/30/2011] [Accepted: 03/20/2012] [Indexed: 12/02/2022] Open
Abstract
Background In Africa, the wide genetic diversity of HIV has resulted in emergence of new strains, rapid spread of this virus in sub-Saharan populations and therefore spread of the HIV epidemic throughout the continent. Methods To determine the prevalence of antibodies to HIV among a high-risk population in Gabon, 1098 and 2916 samples were collected from pregnant women in 2005 and 2008, respectively. HIV genotypes were evaluated in 107 HIV-1-positive samples to determine the circulating subtypes of strains and their resistance to antiretroviral drugs (ARVs). Results The seroprevalences were 6.3% in 2005 and 6.0% in 2008. The main subtype was recombinant CRF02_AG (46.7%), followed by the subtypes A (19.6%), G (10.3%), F (4.7%), H (1.9%) and D (0.9%) and the complex recombinants CRF06_cpx (1.9%) and CRF11_cpx (1.9%); 12.1% of subtypes could not be characterized. Analysis of ARVs resistance to the protease and reverse transcriptase coding regions showed mutations associated with extensive subtype polymorphism. In the present study, the HIV strains showed reduced susceptibility to ARVs (2.8%), particularly to protease inhibitors (1.9%) and nucleoside reverse transcriptase inhibitors (0.9%). Conclusions The evolving genetic diversity of HIV calls for continuous monitoring of its molecular epidemiology in Gabon and in other central African countries.
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Affiliation(s)
- Mélanie Caron
- Unité de Rétrovirologie, Centre International de Recherches Médicales de Franceville, Franceville BP 769, Gabon
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