1
|
Toure CT, Dieng I, Sankhe S, Kane M, Dia M, Mhamadi M, Ndiaye M, Faye O, Sall AA, Diagne MM, Faye O. Genomic Characterization of a Bataï Orthobunyavirus, Previously Classified as Ilesha Virus, from Field-Caught Mosquitoes in Senegal, Bandia 1969. Viruses 2024; 16:261. [PMID: 38400037 PMCID: PMC10892164 DOI: 10.3390/v16020261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/06/2023] [Accepted: 12/14/2023] [Indexed: 02/25/2024] Open
Abstract
Bataï virus (BATV), belonging to the Orthobunyavirus genus, is an emerging mosquito-borne virus with documented cases in Asia, Europe, and Africa. It causes various symptoms in humans and ruminants. Another related virus is Ilesha virus (ILEV), which causes a range of diseases in humans and is mainly found in African countries. This study aimed to genetically identify and characterize a BATV strain previously misclassified as ILEV in Senegal. The strain was reactivated and subjected to whole genome sequencing using an Illumina-based approach. Genetic analyses and phylogeny were performed to assess the evolutionary relationships. Genomic analyses revealed a close similarity between the Senegal strain and the BATV strains UgMP-6830 from Uganda. The genetic distances indicated high homology. Phylogenetic analysis confirmed the Senegal strain's clustering with BATV. This study corrects the misclassification, confirming the presence of BATV in West Africa. This research represents the first evidence of BATV circulation in West Africa, underscoring the importance of genomic approaches in virus classification. Retrospective sequencing is crucial for reevaluating strains and identifying potential public health threats among neglected viruses.
Collapse
Affiliation(s)
- Cheikh Talibouya Toure
- Virology Department, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP. 220, Dakar 12000, Senegal; (C.T.T.); (I.D.); (S.S.); (M.K.); (M.D.); (M.M.); (M.N.); (O.F.); (A.A.S.); (O.F.)
- Department of Animal Biology, Faculty of Science, University Cheikh Anta Diop, BP. 5005, Dakar 10700, Senegal
| | - Idrissa Dieng
- Virology Department, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP. 220, Dakar 12000, Senegal; (C.T.T.); (I.D.); (S.S.); (M.K.); (M.D.); (M.M.); (M.N.); (O.F.); (A.A.S.); (O.F.)
| | - Safietou Sankhe
- Virology Department, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP. 220, Dakar 12000, Senegal; (C.T.T.); (I.D.); (S.S.); (M.K.); (M.D.); (M.M.); (M.N.); (O.F.); (A.A.S.); (O.F.)
| | - Mouhamed Kane
- Virology Department, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP. 220, Dakar 12000, Senegal; (C.T.T.); (I.D.); (S.S.); (M.K.); (M.D.); (M.M.); (M.N.); (O.F.); (A.A.S.); (O.F.)
| | - Moussa Dia
- Virology Department, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP. 220, Dakar 12000, Senegal; (C.T.T.); (I.D.); (S.S.); (M.K.); (M.D.); (M.M.); (M.N.); (O.F.); (A.A.S.); (O.F.)
| | - Moufid Mhamadi
- Virology Department, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP. 220, Dakar 12000, Senegal; (C.T.T.); (I.D.); (S.S.); (M.K.); (M.D.); (M.M.); (M.N.); (O.F.); (A.A.S.); (O.F.)
- Department of Animal Biology, Faculty of Science, University Cheikh Anta Diop, BP. 5005, Dakar 10700, Senegal
| | - Mignane Ndiaye
- Virology Department, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP. 220, Dakar 12000, Senegal; (C.T.T.); (I.D.); (S.S.); (M.K.); (M.D.); (M.M.); (M.N.); (O.F.); (A.A.S.); (O.F.)
- Department of Animal Biology, Faculty of Science, University Cheikh Anta Diop, BP. 5005, Dakar 10700, Senegal
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP. 220, Dakar 12000, Senegal; (C.T.T.); (I.D.); (S.S.); (M.K.); (M.D.); (M.M.); (M.N.); (O.F.); (A.A.S.); (O.F.)
| | - Amadou Alpha Sall
- Virology Department, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP. 220, Dakar 12000, Senegal; (C.T.T.); (I.D.); (S.S.); (M.K.); (M.D.); (M.M.); (M.N.); (O.F.); (A.A.S.); (O.F.)
| | - Moussa Moise Diagne
- Virology Department, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP. 220, Dakar 12000, Senegal; (C.T.T.); (I.D.); (S.S.); (M.K.); (M.D.); (M.M.); (M.N.); (O.F.); (A.A.S.); (O.F.)
| | - Oumar Faye
- Virology Department, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP. 220, Dakar 12000, Senegal; (C.T.T.); (I.D.); (S.S.); (M.K.); (M.D.); (M.M.); (M.N.); (O.F.); (A.A.S.); (O.F.)
| |
Collapse
|
2
|
Diouf B, Gaye A, Dieng I, Diagne CT, Ndiaye EH, Mhamadi M, Gueye A, Ndiaye O, Sene NM, Sy FA, Faye O, Dia I, Weaver SC, Diallo M, Diallo D. Dengue 1 outbreak in Rosso, northern Senegal, October 2021: entomologic investigations. J Med Entomol 2024; 61:222-232. [PMID: 37703355 PMCID: PMC10784780 DOI: 10.1093/jme/tjad126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023]
Abstract
Senegal has experienced periodic epidemics of dengue in urban areas with increased incidence in recent years. However, few data are available on the local ecology of the epidemic vectors. In October 2021, a dengue outbreak was reported in northern Senegal to the Institute Pasteur de Dakar. Entomologic investigations then were undertaken to identify the areas at risk of transmission and to identify the vector(s). Adult mosquitoes were collected indoors and outdoors at selected households, while containers with water were inspected for mosquito larvae. All the Aedes aegypti (L.) collected were tested for dengue virus NS1 protein using a rapid diagnostic test (RDT), and positive samples were confirmed by real-time RT-PCR. The qRT-PCR positive samples were subjected to whole genome sequencing using Nanopore technology. The majority of the larvae-positive containers (83.1%) were used for water storage. The Breteau and Container indices exceeded the WHO-recommended thresholds for the risk of dengue virus transmission except at 2 localities. Ae. aegypti, the only reputed dengue vector, was collected resting indoors as well as outdoors and biting during the day and night. The NS1 protein was detected in 22 mosquito pools, including one pool of females emerging from field-collected larvae. All NS1-positive results were confirmed by RT-PCR. Virus serotyping showed that the outbreak was caused by DENV-1. This study demonstrates the need for continuous control of adult and aquatic stages of Ae. aegypti to prevent future dengue epidemics in Senegal. RDTs appear to be a promising tool for dengue diagnostics and surveillance.
Collapse
Affiliation(s)
- Babacar Diouf
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Alioune Gaye
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Idrissa Dieng
- Pôle de Virologie, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Cheikh Tidiane Diagne
- Pôle de Virologie, Institut Pasteur de Dakar, Dakar 220, Senegal
- DIATROPIX, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - El Hadj Ndiaye
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Moufid Mhamadi
- Pôle de Virologie, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Assiyatou Gueye
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Oumar Ndiaye
- Pôle de Virologie, Institut Pasteur de Dakar, Dakar 220, Senegal
- DIATROPIX, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Ndeye Marie Sene
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Faty Amadou Sy
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Oumar Faye
- Pôle de Virologie, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Ibrahima Dia
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Scott C Weaver
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Mawlouth Diallo
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Diawo Diallo
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, Dakar 220, Senegal
| |
Collapse
|
3
|
Mhamadi M, Mencattelli G, Gaye A, Ndiaye EH, Sow AA, Faye M, Ndione MHD, Diagne MM, Mhamadi M, Faye O, Weidmann M, Faye O, Diallo M, Diagne CT. Rapid On-Site Detection of Arboviruses by a Direct RT-qPCR Assay. Biosensors (Basel) 2023; 13:1035. [PMID: 38131795 PMCID: PMC10741549 DOI: 10.3390/bios13121035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 12/23/2023]
Abstract
Arthropod-borne diseases currently constitute a source of major health concerns worldwide. They account for about 50% of global infectious diseases and cause nearly 700,000 deaths every year. Their rapid increase and spread constitute a huge challenge for public health, highlighting the need for early detection during epidemics, to curtail the virus spread, and to enhance outbreak management. Here, we compared a standard quantitative polymerase chain reaction (RT-qPCR) and a direct RT-qPCR assay for the detection of Zika (ZIKV), Chikungunya (CHIKV), and Rift Valley Fever (RVFV) viruses from experimentally infected-mosquitoes. The direct RT-qPCR could be completed within 1.5 h and required 1 µL of viral supernatant from homogenized mosquito body pools. Results showed that the direct RT-qPCR can detect 85.71%, 89%, and 100% of CHIKV, RVFV, and ZIKV samples by direct amplifications compared to the standard method. The use of 1:10 diluted supernatant is suggested for CHIKV and RVFV direct RT-qPCR. Despite a slight drop in sensitivity for direct PCR, our technique is more affordable, less time-consuming, and provides a better option for qualitative field diagnosis during outbreak management. It represents an alternative when extraction and purification steps are not possible because of insufficient sample volume or biosecurity issues.
Collapse
Affiliation(s)
- Moufid Mhamadi
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Giulia Mencattelli
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Alioune Gaye
- Department of Medical Zoology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (A.G.); (E.H.N.)
| | - El Hadji Ndiaye
- Department of Medical Zoology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (A.G.); (E.H.N.)
| | - Aïssatou Aïcha Sow
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Martin Faye
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Marie Henriette Dior Ndione
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Moussa Moïse Diagne
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Moundhir Mhamadi
- DIATROPIX, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (M.M.); (M.D.)
| | - Ousmane Faye
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Manfred Weidmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 01968 Senftenberg, Germany;
| | - Oumar Faye
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Mawlouth Diallo
- DIATROPIX, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (M.M.); (M.D.)
| | - Cheikh Tidiane Diagne
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
- DIATROPIX, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (M.M.); (M.D.)
| |
Collapse
|
4
|
Badji A, Ndiaye M, Gaye A, Dieng I, Ndiaye EH, Dolgova AS, Mhamadi M, Diouf B, Dia I, Dedkov VG, Faye O, Diallo M. Detection of Crimean-Congo Haemorrhagic Fever Virus from Livestock Ticks in Northern, Central and Southern Senegal in 2021. Trop Med Infect Dis 2023; 8:317. [PMID: 37368735 DOI: 10.3390/tropicalmed8060317] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Crimean-Congo haemorrhagic fever virus (CCHFV) occurs sporadically in Senegal, with a few human cases each year. This active circulation of CCHFV motivated this study which investigated different localities of Senegal to determine the diversity of tick species, tick infestation rates in livestock and livestock infections with CCHFV. The samples were collected in July 2021 from cattle, sheep and goats in different locations in Senegal. Tick samples were identified and pooled by species and sex for CCHFV detection via RT-PCR. A total of 6135 ticks belonging to 11 species and 4 genera were collected. The genus Hyalomma was the most abundant (54%), followed by Amblyomma (36.54%), Rhipicephalus (8.67%) and Boophilus (0.75%). The prevalence of tick infestation was 92%, 55% and 13% in cattle, sheep and goats, respectively. Crimean-Congo haemorrhagic fever virus (CCHFV) was detected in 54/1956 of the tested pools. The infection rate was higher in ticks collected from sheep (0.42/1000 infected ticks) than those from cattle (0.13/1000), while all ticks collected from goats were negative. This study confirmed the active circulation of CCHFV in ticks in Senegal and highlights their role in the maintenance of CCHFV. It is imperative to take effective measures to control tick infestation in livestock to prevent future CCHFV infections in humans.
Collapse
Affiliation(s)
- Aminata Badji
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Mignane Ndiaye
- Pôle de Virologie, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Alioune Gaye
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Idrissa Dieng
- Pôle de Virologie, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - El Hadji Ndiaye
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Anna S Dolgova
- St. Petersburg Pasteur Institute, Federal Service for Consumer Rights Protection and Human Well-Being Surveillance, St. Petersburg 190013, Russia
| | - Moufid Mhamadi
- Pôle de Virologie, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Babacar Diouf
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Ibrahima Dia
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Vladimir G Dedkov
- St. Petersburg Pasteur Institute, Federal Service for Consumer Rights Protection and Human Well-Being Surveillance, St. Petersburg 190013, Russia
| | - Oumar Faye
- Pôle de Virologie, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Mawlouth Diallo
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, Dakar 220, Senegal
| |
Collapse
|
5
|
Mhamadi M, Dieng I, Dolgova AS, Touré CT, Ndiaye M, Diagne MM, Faye B, Gladkikh AS, Dedkov VG, Sall AA, Faye O, Faye O. Whole Genome Sequencing Analysis of African Orthobunyavirus Isolates Reveals Naturally Interspecies Segments Recombinations between Bunyamwera and Ngari Viruses. Viruses 2023; 15:v15020550. [PMID: 36851764 PMCID: PMC9963518 DOI: 10.3390/v15020550] [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: 11/27/2022] [Revised: 02/04/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Bunyamwera virus is the prototype of the Bunyamwera serogroup, which belongs to the order Bunyavirales of the Orthobunyavirus genus in the Peribunyaviridae family. Bunyamwera is a negative-sense RNA virus composed of three segments S, M, and L. Genetic recombination is possible between members of this order as it is already documented. Additionally, it can lead to pathogenic or host range improvement, if it occurs with viruses of public health and agricultural importance such as Rift Valley fever virus and Crimea-Congo hemorrhagic fever virus. Here, we characterize five African Orthobunyavirus viruses from different geographical regions. Our results suggest that the five newly characterized strains are identified as Bunyamwera virus strains. Furthermore, two of the five strains sequenced in this study are recombinant strains, as fragments of their segments are carried by Ngari and Bunyamwera strains. Further investigations are needed to understand the functional impact of these recombinations.
Collapse
Affiliation(s)
- Moufid Mhamadi
- Virology Department, Institut Pasteur de Dakar, Dakar 12900, Senegal
- Parasitology Department, Université Cheikh Anta Diop de Dakar, Dakar 10700, Senegal
| | - Idrissa Dieng
- Virology Department, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Anna S. Dolgova
- Saint Petersburg Pasteur Institute, 197101 Saint Petersburg, Russia
- Correspondence: (A.S.D.); (O.F.)
| | | | - Mignane Ndiaye
- Virology Department, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | | | - Babacar Faye
- Parasitology Department, Université Cheikh Anta Diop de Dakar, Dakar 10700, Senegal
| | - Anna S. Gladkikh
- Saint Petersburg Pasteur Institute, 197101 Saint Petersburg, Russia
| | | | - Amadou Alpha Sall
- Virology Department, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Oumar Faye
- Virology Department, Institut Pasteur de Dakar, Dakar 12900, Senegal
- Correspondence: (A.S.D.); (O.F.)
| |
Collapse
|
6
|
Dieng I, Sagne SN, Ndiaye M, Barry MA, Talla C, Mhamadi M, Balde D, Toure CT, Diop B, Sall AA, Fall G, Loucoubar C, Faye O, Faye O. Detection of a human case of dengue virus 2 belonging to the sylvatic genotype during routine surveillance of fever in Kolda, Senegal, in 2021. Front Virol 2022. [DOI: 10.3389/fviro.2022.1050880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Dengue virus 2 (DENV-2) was detected in a febrile patient living in Saré Yoba in the Kolda region of southern Senegal. Phylogenetic analysis based on the full coding region revealed that the virus belongs to the DENV-2 sylvatic genotype and is closely related to a strain (JF260983/99.66% identity) detected in Spain in a tourist who traveled to Guinea-Bissau (which borders the Kolda region) in 2009. This highlights a potential recent under-reported circulation of sylvatic dengue in the southern part of Senegal and calls for reinforced integrated surveillance among humans, non-human primates, and arboreal mosquitoes through a one-health approach.
Collapse
|
7
|
Dieng I, Diallo A, Ndiaye M, Mhamadi M, Diagne MM, Sankhe S, Ndione MHD, Gaye A, Sagne SN, Heraud JM, Sall AA, Fall G, Loucoubar C, Faye O, Faye O. Full genome analysis of circulating DENV-2 in Senegal reveals a regional diversification into separate clades. J Med Virol 2022; 94:5593-5600. [PMID: 35879861 DOI: 10.1002/jmv.28027] [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: 02/10/2022] [Revised: 07/09/2022] [Accepted: 07/21/2022] [Indexed: 12/15/2022]
Abstract
To assess the genetic diversity of circulating dengue virus 2 (DENV-2) in Senegal, we analyzed nine newly generated complete genomes of strains isolated during the 2018 outbreaks and 06 sequences obtained in 2018 and 2019 from Thiès and Rosso, respectively. Phylogenetic analyses revealed that Senegalese strains belonged to the cosmopolitan genotype of DENV-2, but we observed intragenotype variability leading to a divergence in two clades associated with specific geographic distribution. We report two DENV-2 variants belonging to two distinct clades. Isolates from the "Northern clade" (n = 8) harbored three nonsynonymous mutations (V1183M, R1405K, P2266T) located respectively on NS2A, NS2B, and NS4A, while isolates from the "Western clade" (n = 7) had two nonsynonymous mutations (V1185E, V3214E) located respectively in the NS2A and NS5 genes. These findings call for phylogeographic analysis to investigate routes of introductions, dispersal patterns, and in-depth in vitro and functional study to elucidate the impact of observed mutations on viral fitness, spread, epidemiology, and pathology.
Collapse
Affiliation(s)
- Idrissa Dieng
- Virology Department, Arboviruses and Haemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou Diallo
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mignane Ndiaye
- Virology Department, Arboviruses and Haemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Moufid Mhamadi
- Virology Department, Arboviruses and Haemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Moussa Moïse Diagne
- Virology Department, Arboviruses and Haemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Safietou Sankhe
- Virology Department, Arboviruses and Haemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Marie Henriette Dior Ndione
- Virology Department, Arboviruses and Haemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Aboubacry Gaye
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Samba Niang Sagne
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Jean Michel Heraud
- Virology Department, Arboviruses and Haemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou Alpha Sall
- Virology Department, Arboviruses and Haemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Gamou Fall
- Virology Department, Arboviruses and Haemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cheikh Loucoubar
- Virology Department, Arboviruses and Haemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ousmane Faye
- Virology Department, Arboviruses and Haemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oumar Faye
- Virology Department, Arboviruses and Haemorrhagic Fever Viruses Unit, Institut Pasteur de Dakar, Dakar, Senegal
| |
Collapse
|
8
|
Mhamadi M, Badji A, Dieng I, Gaye A, Ndiaye EH, Ndiaye M, Mhamadi M, Toure CT, Barry A, Ndiaye O, Faye B, Ba FA, Diop B, Ndiaye M, Sagne SN, Fall G, Loucoubar C, Bovendo HF, Sall AA, Kobinger G, Faye O, Diallo M, Faye O. Multiple genotypes of Crimean-Congo Hemorrhagic Fever Virus detected in ticks during a one health survey in Agnam, Northeastern Senegal. Emerg Microbes Infect 2022; 11:2711-2714. [PMID: 36268900 DOI: 10.1080/22221751.2022.2136537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A Crimean-Congo Hemorrhagic Fever Virus (CCHFV) survey in Agnam (North Senegal) permits the detection of 3 isolates in ticks. These isolates belong genetically to multiple genotypes (I, II, III) and clustered with strains from Uganda, Sudan, Mauritania and Senegal. The role of ticks in CCHF emergence and widespread is highlighted.
Collapse
Affiliation(s)
- Moufid Mhamadi
- Institut Pasteur de Dakar, virology department, Senegal.,Université Cheikh Anta Diop de Dakar, parasitology department, Senegal
| | - Aminata Badji
- Institut Pasteur de Dakar, medical zoology department, Senegal
| | - Idrissa Dieng
- Institut Pasteur de Dakar, virology department, Senegal
| | - Alioune Gaye
- Institut Pasteur de Dakar, medical zoology department, Senegal
| | - El Hadji Ndiaye
- Institut Pasteur de Dakar, medical zoology department, Senegal
| | | | | | | | - Aliou Barry
- Institut Pasteur de Dakar, Epidemiology, Clinical Research and Data Science department, Senegal
| | - Oumar Ndiaye
- Institut Pasteur de Dakar, virology department, Senegal.,Institut Pasteur de Dakar, DIATROPIX, Senegal
| | - Babacar Faye
- Université Cheikh Anta Diop de Dakar, parasitology department, Senegal
| | - Fatimata Amadou Ba
- Microbiology, Immunology and Infectious Pathology Service, Department of Public Health and Environment, EISMV of Dakar, Senegal
| | - Boly Diop
- Ministry of Health and Social Action
| | | | - Samba Niang Sagne
- Institut Pasteur de Dakar, Epidemiology, Clinical Research and Data Science department, Senegal
| | - Gamou Fall
- Institut Pasteur de Dakar, virology department, Senegal
| | - Cheikh Loucoubar
- Institut Pasteur de Dakar, Epidemiology, Clinical Research and Data Science department, Senegal
| | | | | | - Gary Kobinger
- University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Ousmane Faye
- Institut Pasteur de Dakar, virology department, Senegal
| | - Mawlouth Diallo
- Institut Pasteur de Dakar, medical zoology department, Senegal
| | - Oumar Faye
- Institut Pasteur de Dakar, virology department, Senegal
| |
Collapse
|
9
|
Diagne MM, Ndione MHD, Gaye A, Barry MA, Diallo D, Diallo A, Mwakibete LL, Diop M, Ndiaye EH, Ahyong V, Diouf B, Mhamadi M, Diagne CT, Danfakha F, Diop B, Faye O, Loucoubar C, Fall G, Tato CM, Sall AA, Weaver SC, Diallo M, Faye O. Yellow Fever Outbreak in Eastern Senegal, 2020-2021. Viruses 2021; 13:v13081475. [PMID: 34452343 PMCID: PMC8402698 DOI: 10.3390/v13081475] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 01/07/2023] Open
Abstract
Yellow fever virus remains a major threat in low resource countries in South America and Africa despite the existence of an effective vaccine. In Senegal and particularly in the eastern part of the country, periodic sylvatic circulation has been demonstrated with varying degrees of impact on populations in perpetual renewal. We report an outbreak that occurred from October 2020 to February 2021 in eastern Senegal, notified and managed through the synergistic effort yellow fever national surveillance implemented by the Senegalese Ministry of Health in collaboration with the World Health Organization, the countrywide 4S network set up by the Ministry of Health, the Institut Pasteur de Dakar, and the surveillance of arboviruses and hemorrhagic fever viruses in human and vector populations implemented since mid 2020 in eastern Senegal. Virological analyses highlighted the implication of sylvatic mosquito species in virus transmission. Genomic analysis showed a close relationship between the circulating strain in eastern Senegal, 2020, and another one from the West African lineage previously detected and sequenced two years ago from an unvaccinated Dutch traveler who visited the Gambia and Senegal before developing signs after returning to Europe. Moreover, genome analysis identified a 6-nucleotide deletion in the variable domain of the 3′UTR with potential impact on the biology of the viral strain that merits further investigations. Integrated surveillance of yellow fever virus but also of other arboviruses of public health interest is crucial in an ecosystem such as eastern Senegal.
Collapse
Affiliation(s)
- Moussa Moïse Diagne
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
- Correspondence: ; Tel.: +221-77-405-9928
| | - Marie Henriette Dior Ndione
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| | - Alioune Gaye
- Zoology Medical Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (A.G.); (D.D.); (E.H.N.); (B.D.); (M.D.)
| | - Mamadou Aliou Barry
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.A.B.); (A.D.); (M.D.); (C.L.)
| | - Diawo Diallo
- Zoology Medical Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (A.G.); (D.D.); (E.H.N.); (B.D.); (M.D.)
| | - Amadou Diallo
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.A.B.); (A.D.); (M.D.); (C.L.)
| | - Lusajo L. Mwakibete
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; (L.L.M.); (V.A.); (C.M.T.)
| | - Mamadou Diop
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.A.B.); (A.D.); (M.D.); (C.L.)
| | - El Hadji Ndiaye
- Zoology Medical Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (A.G.); (D.D.); (E.H.N.); (B.D.); (M.D.)
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; (L.L.M.); (V.A.); (C.M.T.)
| | - Babacar Diouf
- Zoology Medical Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (A.G.); (D.D.); (E.H.N.); (B.D.); (M.D.)
| | - Moufid Mhamadi
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| | - Cheikh Tidiane Diagne
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| | - Fodé Danfakha
- Kedougou Medical Region, Ministry of Health, Kedougou 26005, Senegal;
| | - Boly Diop
- Prevention Department, Ministry of Health, Dakar 220, Senegal;
| | - Oumar Faye
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.A.B.); (A.D.); (M.D.); (C.L.)
| | - Gamou Fall
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| | - Cristina M. Tato
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; (L.L.M.); (V.A.); (C.M.T.)
| | - Amadou Alpha Sall
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| | - Scott C. Weaver
- World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Mawlouth Diallo
- Zoology Medical Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (A.G.); (D.D.); (E.H.N.); (B.D.); (M.D.)
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (M.H.D.N.); (M.M.); (C.T.D.); (O.F.); (G.F.); (A.A.S.); (O.F.)
| |
Collapse
|