1
|
Hill V, Cleemput S, Fonseca V, Tegally H, Brito AF, Gifford R, Tran VT, Kien DTH, Huynh T, Yacoub S, Dieng I, Ndiaye M, Balde D, Diagne MM, Faye O, Salvato R, Wallau GL, Gregianini TS, Godinho FMS, Vogels CBF, Breban MI, Leguia M, Jagtap S, Roy R, Hapuarachchi C, Mwanyika G, Giovanetti M, Alcantara LCJ, Faria NR, Carrington CVF, Hanley KA, Holmes EC, Dumon W, de Oliveira T, Grubaugh ND. A new lineage nomenclature to aid genomic surveillance of dengue virus. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.16.24307504. [PMID: 38798319 PMCID: PMC11118645 DOI: 10.1101/2024.05.16.24307504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Dengue virus (DENV) is currently causing epidemics of unprecedented scope in endemic settings and expanding to new geographical areas. It is therefore critical to track this virus using genomic surveillance. However, the complex patterns of viral genomic diversity make it challenging to use the existing genotype classification system. Here we propose adding two sub-genotypic levels of virus classification, named major and minor lineages. These lineages have high thresholds for phylogenetic distance and clade size, rendering them stable between phylogenetic studies. We present an assignment tool to show that the proposed lineages are useful for regional, national and sub-national discussions of relevant DENV diversity. Moreover, the proposed lineages are robust to classification using partial genome sequences. We provide a standardized neutral descriptor of DENV diversity with which we can identify and track lineages of potential epidemiological and/or clinical importance. Information about our lineage system, including methods to assign lineages to sequence data and propose new lineages, can be found at: dengue-lineages.org.
Collapse
Affiliation(s)
- Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Vagner Fonseca
- Department of Exact and Earth Sciences, University of the State of Bahia, Salvador, Brazil
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Robert Gifford
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- MRC-University of Glasgow Centre for Virus Research, Bearsden, Glasgow, UK
| | - Vi Thuy Tran
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Tuyen Huynh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Sophie Yacoub
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Idrissa Dieng
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mignane Ndiaye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Diamilatou Balde
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Moussa M Diagne
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oumar Faye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Richard Salvato
- Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (CDCT/CEVS/SES-RS), Rio Grande do Sul, Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference, Hamburg, Germany
- National Reference Center for Tropical Infectious Diseases. Bernhard, Hamburg, Germany
| | - Tatiana S Gregianini
- Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (CDCT/CEVS/SES-RS), Rio Grande do Sul, Brazil
| | - Fernanda M S Godinho
- Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (CDCT/CEVS/SES-RS), Rio Grande do Sul, Brazil
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mariana Leguia
- Genomics Laboratory, Pontificia Universidad Católica del Peru, Lima, Peru
| | - Suraj Jagtap
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Rahul Roy
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, Karnataka, India
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, Karnataka, India
| | | | - Gaspary Mwanyika
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Applied Sciences, Mbeya University of Science and Technology (MUST), Mbeya, Tanzania
| | - Marta Giovanetti
- Department of Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, Italy
- Instituto René Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Climate Amplified Diseases and Epidemics (CLIMADE), Minas Gerais, Brazil
| | - Luiz C J Alcantara
- Instituto René Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Climate Amplified Diseases and Epidemics (CLIMADE), Minas Gerais, Brazil
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Christine V F Carrington
- Department of Preclinical Sciences, The University of the West Indies, St. Augustine Campus, St. Augustine, Trinidad and Tobago
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | | | - 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
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| |
Collapse
|
2
|
Dieng I, Talla C, Barry MA, Gaye A, Balde D, Ndiaye M, Kane M, Sagne SN, Diagne MM, Diop B, Diallo B, Sall AA, Faye O, Sow A, Fall G, Loucoubar C, Faye O. The Spatiotemporal Distribution and Molecular Characterization of Circulating Dengue Virus Serotypes/Genotypes in Senegal from 2019 to 2023. Trop Med Infect Dis 2024; 9:32. [PMID: 38393121 PMCID: PMC10891755 DOI: 10.3390/tropicalmed9020032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/09/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
Dengue virus is becoming a major public health threat worldwide, principally in Africa. From 2016 to 2020, 23 outbreaks were reported in Africa, principally in West Africa. In Senegal, dengue outbreaks have been reported yearly since 2017. Data about the circulating serotypes and their spatial and temporal distribution were limited to outbreaks that occurred between 2017 and 2018. Herein, we describe up-to-date molecular surveillance of circulating DENV serotypes in Senegal between 2019 to 2023 and their temporal and spatial distribution around the country. For this purpose, suspected DENV-positive samples were collected and subjected to dengue detection and serotyping using RT-qPCR methods. Positive samples were used for temporal and spatial mapping. A subset of DENV+ samples were then sequenced and subjected to phylogenetic analysis. Results show a co-circulation of three DENV serotypes with an overall predominance of DENV-3. In terms of abundance, DENV-3 is followed by DENV-1, with scarce cases of DENV-2 from February 2019 to February 2022. Interestingly, data show the extinction of both serotype 1 and serotype 2 and the only circulation of DENV-3 from March 2022 to February 2023. At the genotype level, the analysis shows that sequenced strains belong to same genotype as previously described: Senegalese DENV-1 strains belong to genotype V, DENV-2 strains to the cosmopolitan genotype, and DENV-3 strains to Genotype III. Interestingly, newly obtained DENV 1-3 sequences clustered in different clades within genotypes. This co-circulation of strains belonging to different clades could have an effect on virus epidemiology and transmission dynamics. Overall, our results highlight DENV serotype replacement by DENV-3, accompanied by a wider geographic distribution, in Senegal. These results highlight the importance of virus genomic surveillance and call for further viral fitness studies using both in vitro and in vivo models, as well as in-depth phylogeographic studies to uncover the virus dispersal patterns across the country.
Collapse
Affiliation(s)
- Idrissa Dieng
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Cheikh Talla
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Mamadou Aliou Barry
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Aboubacry Gaye
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Diamilatou Balde
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Mignane Ndiaye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Mouhamed Kane
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Samba Niang Sagne
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Moussa Moise Diagne
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Boly Diop
- Direction of Prevention, Ministry of Health, Dakar 220, Senegal
| | - Boubacar Diallo
- Department of Public Health, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Amadou Alpha Sall
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Ousmane Faye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Abdourahmane Sow
- Department of Public Health, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Gamou Fall
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Oumar Faye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| |
Collapse
|
3
|
Levine ZC, Sene A, Mkandawire W, Deme AB, Ndiaye T, Sy M, Gaye A, Diedhiou Y, Mbaye AM, Ndiaye IM, Gomis J, Ndiop M, Sene D, Faye Paye M, MacInnis BL, Schaffner SF, Park DJ, Badiane AS, Colubri A, Ndiaye M, Sy N, Sabeti PC, Ndiaye D, Siddle KJ. Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing. Nat Commun 2024; 15:747. [PMID: 38272885 PMCID: PMC10810818 DOI: 10.1038/s41467-024-44800-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/04/2024] [Indexed: 01/27/2024] Open
Abstract
The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical metadata in a cross-sectional study of febrile patients and healthy controls in a low malaria burden area. Using 16S and untargeted sequencing, we detected viral, bacterial, or eukaryotic pathogens in 23% (38/163) of NMFI cases. Bacteria were the most common, with relapsing fever Borrelia and spotted fever Rickettsia found in 15.5% and 3.8% of cases, respectively. Four viral pathogens were found in a total of 7 febrile cases (3.5%). Sequencing also detected undiagnosed Plasmodium, including one putative P. ovale infection. We developed a logistic regression model that can distinguish Borrelia from NMFIs with similar presentation based on symptoms and vital signs (F1 score: 0.823). These results highlight the challenge and importance of improved diagnostics, especially for Borrelia, to support diagnosis and surveillance.
Collapse
Affiliation(s)
- Zoë C Levine
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston, MA, USA
- Harvard/MIT MD-PhD Program, Boston, MA, USA
| | - Aita Sene
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Winnie Mkandawire
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Awa B Deme
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Tolla Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Mouhamad Sy
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Amy Gaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Younouss Diedhiou
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Amadou M Mbaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Ibrahima M Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Jules Gomis
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Médoune Ndiop
- Programme National de lutte contre le Paludisme, Ministère de la Santé, Dakar Fann, Senegal
| | - Doudou Sene
- Programme National de lutte contre le Paludisme, Ministère de la Santé, Dakar Fann, Senegal
| | | | - Bronwyn L MacInnis
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Stephen F Schaffner
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Daniel J Park
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aida S Badiane
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Andres Colubri
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Mouhamadou Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal
| | - Ngayo Sy
- Service de Lutte Anti Parasitaire, Thies, Senegal
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Daouda Ndiaye
- Department of Parasitology, Cheikh Anta Diop University Dakar, Dakar, Senegal.
- Centre International de Recherche et de Formation en Génomique Appliquée et de la Surveillance Sanitaire, Dakar, Senegal.
| | - Katherine J Siddle
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.
| |
Collapse
|
4
|
Agbodzi B, Sado Yousseu FB, Nemg Simo FB, Kumordjie S, Yeboah C, Mosore MT, Bentil RE, Coatsworth HG, Attram N, Nimo-Paintsil S, Fox AT, Bonney JHK, Ampofo W, Dinglasan RR, Sanders T, Wiley MR, Demanou M, Letizia AG. Whole genome sequencing of outbreak strains from 2017 to 2018 reveals an endemic clade of dengue 1 virus in Cameroon. Emerg Microbes Infect 2023; 12:2281352. [PMID: 37933502 PMCID: PMC10732222 DOI: 10.1080/22221751.2023.2281352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 11/04/2023] [Indexed: 11/08/2023]
Abstract
Dengue fever is expanding as a global public health threat including countries within Africa. For the past few decades, Cameroon has experienced sporadic cases of arboviral infections including dengue fever. Here, we conducted genomic analyses to investigate the origin and phylogenetic profile of Cameroon DENV-1 outbreak strains and predict the impact of emerging therapeutics on these strains. Bayesian and maximum-likelihood phylogenetic inference approaches were employed in virus evolutionary analyses. An in silico analysis was performed to assess the divergence in immunotherapeutic and vaccine targets in the new genomes. Six complete DENV-1 genomes were generated from 50 samples that met a clinical definition for DENV infection. Phylogenetic analyses revealed that the strains from the current study belong to a sub-lineage of DENV-1 genotype V and form a monophyletic taxon with a 2012 strain from Gabon. The most recent common ancestor (TMRCA) of the Cameroon and Gabon strains was estimated to have existed around 2008. Comparing our sequences to the vaccine strains, 19 and 15 amino acid (aa) substitutions were observed in the immuno-protective prM-E protein segments of the Dengvaxia® and TetraVax-DV-TV003 vaccines, respectively. Epitope mapping revealed mismatches in aa residues at positions E155 and E161 located in the epitope of the human anti-DENV-1 monoclonal antibody HMAb 1F4. The new DENV strains constitute a conserved genomic pool of viruses endemic to the Central African region that needs prospective monitoring to track local viral evolution. Further work is needed to ascertain the performance of emerging therapeutics in DENV strains from the African region.
Collapse
Affiliation(s)
- Bright Agbodzi
- U.S. Naval Medical Research Unit EURAFCENT, Accra, Ghana
| | | | | | | | - Clara Yeboah
- U.S. Naval Medical Research Unit EURAFCENT, Accra, Ghana
| | | | | | - Heather G. Coatsworth
- Department of Infectious Diseases & Immunology and Emerging Pathogens Institute, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Naiki Attram
- U.S. Naval Medical Research Unit EURAFCENT, Accra, Ghana
| | | | - Anne T. Fox
- U.S. Naval Medical Research Unit EURAFCENT, Accra, Ghana
| | - Joseph H. K. Bonney
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - William Ampofo
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Rhoel R. Dinglasan
- Department of Infectious Diseases & Immunology and Emerging Pathogens Institute, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Terrel Sanders
- U.S. Naval Medical Research Unit EURAFCENT, Accra, Ghana
| | - Michael R. Wiley
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | | | | |
Collapse
|
5
|
Dieng I, Balde D, Talla C, Camara D, Barry MA, Sagne SN, Gueye K, Dia CAKM, Sambe BS, Fall G, Sall AA, Faye O, Loucoubar C, Faye O. Molecular Evolution of Dengue Virus 3 in Senegal between 2009 and 2022: Dispersal Patterns and Implications for Prevention and Therapeutic Countermeasures. Vaccines (Basel) 2023; 11:1537. [PMID: 37896941 PMCID: PMC10610876 DOI: 10.3390/vaccines11101537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Dengue fever is the most prevalent arboviral disease worldwide. Dengue virus (DENV), the etiological agent, is known to have been circulating in Senegal since 1970, though for a long time, virus epidemiology was restricted to the circulation of sylvatic DENV-2 in south-eastern Senegal (the Kedougou region). In 2009 a major shift was noticed with the first urban epidemic, which occurred in the Dakar region and was caused by DENV-3. Following the notification by Senegal, many other West African countries reported DENV-3 epidemics. Despite these notifications, there are scarce studies and data about the genetic diversity and molecular evolution of DENV-3 in West Africa. Using nanopore sequencing, phylogenetic, and phylogeographic approaches on historic strains and 36 newly sequenced strains, we studied the molecular evolution of DENV-3 in Senegal between 2009 and 2022. We then assessed the impact of the observed genetic diversity on the efficacy of preventive countermeasures and vaccination by mapping amino acid changes against vaccine strains. The results showed that the DENV-3 strains circulating in Senegal belong to genotype III, similarly to strains from other West African countries, while belonging to different clades. Phylogeographic analysis based on nearly complete genomes revealed three independent introduction events from Asia and Burkina Faso. Comparison of the amino acids in the CprM-E regions of genomes from the Senegalese strains against the vaccine strains revealed the presence of 22 substitutions (7 within the PrM and 15 within the E gene) when compared to CYD-3, while 23 changes were observed when compared to TV003 (6 within the PrM and 17 within the E gene). Within the E gene, most of the changes compared to the vaccine strains were located in the ED-III domain, which is known to be crucial in neutralizing antibody production. Altogether, these data give up-to-date insight into DENV-3 genomic evolution in Senegal which needs to be taken into account in future vaccination strategies. Additionally, they highlight the importance of the genomic epidemiology of emerging pathogens in Africa and call for the implementation of a pan-African network for genomic surveillance of dengue virus.
Collapse
Affiliation(s)
- Idrissa Dieng
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (D.B.); (D.C.); (G.F.); (A.A.S.); (O.F.); (O.F.)
| | - Diamilatou Balde
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (D.B.); (D.C.); (G.F.); (A.A.S.); (O.F.); (O.F.)
| | - Cheikh Talla
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (C.T.); (M.A.B.); (S.N.S.); (C.L.)
| | - Diogop Camara
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (D.B.); (D.C.); (G.F.); (A.A.S.); (O.F.); (O.F.)
| | - Mamadou Aliou Barry
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (C.T.); (M.A.B.); (S.N.S.); (C.L.)
| | - Samba Niang Sagne
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (C.T.); (M.A.B.); (S.N.S.); (C.L.)
| | - Khadim Gueye
- EMBL’s European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK;
| | - Cheikh Abdou Khadre Mbacké Dia
- Department of Animal Biology, Faculty of Science et Technics, Université Cheikh Anta Diop de Dakar (UCAD), BP 5005 Fann, Dakar, Senegal; (C.A.K.M.D.); (B.S.S.)
| | - Babacar Souleymane Sambe
- Department of Animal Biology, Faculty of Science et Technics, Université Cheikh Anta Diop de Dakar (UCAD), BP 5005 Fann, Dakar, Senegal; (C.A.K.M.D.); (B.S.S.)
| | - Gamou Fall
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (D.B.); (D.C.); (G.F.); (A.A.S.); (O.F.); (O.F.)
| | - Amadou Alpha Sall
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (D.B.); (D.C.); (G.F.); (A.A.S.); (O.F.); (O.F.)
| | - Ousmane Faye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (D.B.); (D.C.); (G.F.); (A.A.S.); (O.F.); (O.F.)
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (C.T.); (M.A.B.); (S.N.S.); (C.L.)
| | - Oumar Faye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal; (D.B.); (D.C.); (G.F.); (A.A.S.); (O.F.); (O.F.)
| |
Collapse
|
6
|
Levine ZC, Sene A, Mkandawire W, Deme AB, Ndiaye T, Sy M, Gaye A, Diedhiou Y, Mbaye AM, Ndiaye I, Gomis J, Ndiop M, Sene D, Paye MF, MacInnis B, Schaffner SF, Park DJ, Badiane AS, Colubri A, Ndiaye M, Sy N, Sabeti PC, Ndiaye D, Siddle KJ. Improving diagnosis of non-malarial fevers in Senegal: Borrelia and the contribution of tick-borne bacteria. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.24.23294564. [PMID: 37662407 PMCID: PMC10473814 DOI: 10.1101/2023.08.24.23294564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical metadata from febrile patients and healthy controls in a low malaria burden area. Using 16S and unbiased sequencing, we detected viral, bacterial, or eukaryotic pathogens in 29% of NMFI cases. Bacteria were the most common, with relapsing fever Borrelia and spotted fever Rickettsia found in 15% and 3.7% of cases, respectively. Four viral pathogens were found in a total of 7 febrile cases (3.5%). Sequencing also detected undiagnosed Plasmodium, including one putative P. ovale infection. We developed a logistic regression model to distinguish Borrelia from NMFIs with similar presentation based on symptoms and vital signs. These results highlight the challenge and importance of improved diagnostics, especially for Borrelia, to support diagnosis and surveillance.
Collapse
Affiliation(s)
- Zoë C Levine
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston, MA, USA
- Harvard/MIT MD-PhD Program, Boston, MA, 02115, USA
| | - Aita Sene
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Winnie Mkandawire
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Awa B Deme
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Tolla Ndiaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Mouhamad Sy
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Amy Gaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Younouss Diedhiou
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Amadou M Mbaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Ibrahima Ndiaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Jules Gomis
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Médoune Ndiop
- Programme National de Lutte contre le Paludisme (PNLP), Ministère de la Santé, Dakar Fann, Senegal
| | - Doudou Sene
- Programme National de Lutte contre le Paludisme (PNLP), Ministère de la Santé, Dakar Fann, Senegal
| | | | - Bronwyn MacInnis
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Stephen F Schaffner
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Daniel J Park
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aida S Badiane
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Andres Colubri
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Mouhamadou Ndiaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Ngayo Sy
- Service de Lutte Anti Parasitaire, Thies, Senegal
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Daouda Ndiaye
- Centre International de recherche, de formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Katherine J Siddle
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| |
Collapse
|
7
|
Ndiaye O, Woolston K, Gaye A, Loucoubar C, Cocozza M, Fall C, Dia F, Adams ER, Samb M, Camara D, Sadio BD, Diagne CT, Weidmann M, Faye O, Fitchett JRA, Sall AA, Diagne CT. Laboratory Evaluation and Field Testing of Dengue NS1 and IgM/IgG Rapid Diagnostic Tests in an Epidemic Context in Senegal. Viruses 2023; 15:v15040904. [PMID: 37112887 PMCID: PMC10143717 DOI: 10.3390/v15040904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
In Senegal, the burden of dengue is increasing and expanding. As case management and traditional diagnostic techniques can be difficult to implement, rapid diagnostic tests (RDTs) deployed at point of care are ideal for investigating active outbreaks. The aim of this study was to evaluate the diagnostic performance of the Dengue NS1 and Dengue IgM/IgG RDTs on the serum/plasma samples in a laboratory setting and in the field. During laboratory evaluation, performance of the NS1 RDT was assessed using NS1 ELISA as the gold standard. Sensitivity and specificity were 88% [75–95%] and 100% [97–100%], respectively. Performance of the IgM/IG RDT was assessed using the IgM Antibody Capture (MAC) ELISA, indirect IgG, and PRNT as gold standards. The IgM and IgG test lines respectively displayed sensitivities of 94% [83–99%] and 70% [59–79%] and specificities of 91% [84–95%] and 91% [79–98%]. In the field, the Dengue NS1 RDT sensitivity and specificity was 82% [60–95%] and 75% [53–90%], respectively. The IgM and IgG test lines displayed sensitivities of 86% [42–100%] and 78% [64–88%], specificities of 85% [76–92%] and 55% [36–73%], respectively. These results demonstrate that RDTs are ideal for use in a context of high prevalence or outbreak setting and can be implemented in the absence of a confirmatory test for acute and convalescent patients.
Collapse
Affiliation(s)
- Oumar Ndiaye
- Diatropix Unit, Institut Pasteur de Dakar, Dakar BP 220, Senegal
- Virology Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal
| | - Kevin Woolston
- Global Access Diagnostics, Bedford Technology Park, Bedford MK44 2YA, Bedfordshire, UK
| | - Aboubacry Gaye
- Epidemiology Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal
| | - Cheikh Loucoubar
- Epidemiology Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal
| | - Michael Cocozza
- Global Access Diagnostics, Bedford Technology Park, Bedford MK44 2YA, Bedfordshire, UK
| | - Cheikh Fall
- Microbiology Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal
| | - Fatou Dia
- Diatropix Unit, Institut Pasteur de Dakar, Dakar BP 220, Senegal
- Virology Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal
| | - Emily R. Adams
- Global Access Diagnostics, Bedford Technology Park, Bedford MK44 2YA, Bedfordshire, UK
| | - Marième Samb
- Diatropix Unit, Institut Pasteur de Dakar, Dakar BP 220, Senegal
| | - Diogop Camara
- Virology Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal
| | | | - Cheikh T. Diagne
- Mivegec Infectious Diseases and Vector: Ecology, Genetics, Evolution and Control, Université Montpellier, IRD, CNRS, 34394 Montpellier, France
| | - Manfred Weidmann
- Institute of Microbiology and Virology, Medical School Brandenburg Theodor Fontane, D-01968 Senftenberg, Germany
| | - Oumar Faye
- Virology Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal
| | | | - Amadou Alpha Sall
- Virology Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal
| | - Cheikh Tidiane Diagne
- Diatropix Unit, Institut Pasteur de Dakar, Dakar BP 220, Senegal
- Virology Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal
| |
Collapse
|
8
|
Diagne CT, Dieng I, Faye O, Fall C, Barry MA, Diarra M, Ndiaye O, Dior Ndione MH, Ndiaye M, Diop B, Bousso A, Sall A, Fall G, Loucoubar C, Ba Y, Sall AA, Diallo M, Faye O. Co-circulation of dengue virus serotypes 1 and 3 in the Fatick region of senegal 2018. FRONTIERS IN VIROLOGY 2023. [DOI: 10.3389/fviro.2022.1009382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
On 10th September 2018, the Syndromic Sentinel Surveillance network that monitors febrile illnesses in all 14 regions of Senegal detected a peak of fever in the Fatick region. On 13 September 2018, 10 samples were sent to the WHO Collaborating Centre for Arboviruses and Viral Haemorrhagic Fevers at the Institut Pasteur de Dakar (IPD). Laboratory investigations revealed an epidemic of dengue 1 genotype V and dengue 3 genotype III. Fatick neighbors the Holy City of Touba where 3.5 million people from all over the word gather every year for the Grand Magal pilgrimage. This article discusses the impact of mass gatherings and their role in the recent introduction of dengue serotypes in Senegal. Dengue is now endemic in Senegal and across many countries in Africa, highlighting the need for early detection, control measures and prevention of severe dengue cases in highly connected urban settings.
Collapse
|
9
|
Dieng I, Fall C, Barry MA, Gaye A, Dia N, Ndione MHD, Fall A, Diop M, Sarr FD, Ndiaye O, Dieng M, Diop B, Diagne CT, Ndiaye M, Fall G, Sylla M, Faye O, Loucoubar C, Faye O, Sall AA. Re-Emergence of Dengue Serotype 3 in the Context of a Large Religious Gathering Event in Touba, Senegal. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:16912. [PMID: 36554793 PMCID: PMC9779395 DOI: 10.3390/ijerph192416912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Dengue virus (DENV) was detected in Senegal in 1979 for the first time. Since 2017, unprecedented frequent outbreaks of DENV were noticed yearly. In this context, epidemiological and molecular evolution data are paramount to decipher the virus diffusion route. In the current study, we focused on a dengue outbreak which occurred in Senegal in 2018 in the context of a large religious gathering with 263 confirmed DENV cases out of 832 collected samples, including 25 life-threatening cases and 2 deaths. It was characterized by a co-circulation of dengue serotypes 1 and 3. Phylogenetic analysis based on the E gene revealed that the main detected serotype in Touba was DENV-3 and belonged to Genotype III. Bayesian phylogeographic analysis was performed and suggested one viral introduction around 2017.07 (95% HPD = 2016.61-2017.57) followed by cryptic circulation before the identification of the first case on 1 October 2018. DENV-3 strains are phylogenetically related, with strong phylogenetic links between strains retrieved from Burkina Faso and other West African countries. These phylogenetic data substantiate epidemiological data of the origin of DENV-3 and its spread between African countries and subsequent diffusion after religious mass events. The study also highlighted the usefulness of a mobile laboratory during the outbreak response, allowing rapid diagnosis and resulting in improved patient management.
Collapse
Affiliation(s)
- Idrissa Dieng
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Cheikh Fall
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Mamadou Aliou Barry
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Aboubacry Gaye
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Ndongo Dia
- Respiratory Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Marie Henriette Dior Ndione
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Amary Fall
- Respiratory Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Mamadou Diop
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Fatoumata Diene Sarr
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Oumar Ndiaye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | | | - Boly Diop
- Ministry of Health, Dakar 16504, Senegal
| | - Cheikh Tidiane Diagne
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | | | - Gamou Fall
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | | | - Ousmane Faye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Oumar Faye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| | - Amadou Alpha Sall
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar 220, Senegal
| |
Collapse
|
10
|
Dieng I, Barry MA, Talla C, Sow B, Faye O, Diagne MM, Sene O, Ndiaye O, Diop B, Diagne CT, Fall G, Sall AA, Loucoubar C, Faye O. Analysis of a Dengue Virus Outbreak in Rosso, Senegal 2021. Trop Med Infect Dis 2022; 7:tropicalmed7120420. [PMID: 36548675 PMCID: PMC9781526 DOI: 10.3390/tropicalmed7120420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/19/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Senegal is hyperendemic for dengue. Since 2017, outbreaks have been noticed annually in many regions around the country, marked by the co-circulation of DENV1-3. On 8 October 2021, a Dengue virus outbreak in the Rosso health post (sentinel site of the syndromic surveillance network) located in the north of the country was notified to the WHO Collaborating Center for arboviruses and hemorrhagic fever viruses at Institut Pasteur de Dakar. A multidisciplinary team was then sent for epidemiological and virologic investigations. This study describes the results from investigations during an outbreak in Senegal using a rapid diagnostic test (RDT) for the combined detection of dengue virus non-structural protein 1 (NS1) and IgM/IgG. For confirmation, samples were also tested by real-time RT-PCR and IgM ELISA at the reference lab in Dakar. qRT-PCR positive samples were subjected to whole genome sequencing using nanopore technology. Virologic analysis scored 102 positives cases (RT-PCR, NS1 antigen detection and/or IgM) out of 173 enrolled patients; interestingly, virus serotyping showed that the outbreak was caused by the DENV-1, a serotype different from DENV-2 involved during the outbreak in Rosso three years earlier, indicating a serotype replacement. Nearly all field-tested NS1 positives samples were confirmed by qRT-PCR with a concordance of 92.3%. Whole genome sequencing and phylogenetic analysis of strains suggested a re-introduction in Rosso of a DENV-1 strain different to the one responsible for the outbreak in the Louga area five years before. Findings call for improved dengue virus surveillance in Senegal, with a wide deployment of DENV antigenic tests, which allow easy on-site diagnosis of suspected cases and early detection of outbreaks. This work highlights the need for continuous monitoring of circulating serotypes which is crucial for a better understanding of viral epidemiology around the country.
Collapse
Affiliation(s)
- Idrissa Dieng
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institute Pasteur de Dakar, Dakar 220, Senegal
- Correspondence: ; Tel.: +221-76-1912447
| | - Mamadou Aliou Barry
- Epidemiology, Clinical Research and Data Science Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Cheikh Talla
- Epidemiology, Clinical Research and Data Science Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Bocar Sow
- Epidemiology, Clinical Research and Data Science Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Oumar Faye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Moussa Moise Diagne
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Ousseynou Sene
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Oumar Ndiaye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Boly Diop
- Ministry of Health, Direction of Prevention, Dakar 220, Senegal
| | - Cheikh Tidiane Diagne
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institute Pasteur de Dakar, Dakar 220, Senegal
- DIATROPIX, Institute Pasteur de Dakar, Dakar 12900, Senegal
| | - Gamou Fall
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Amadou Alpha Sall
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| | - Ousmane Faye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institute Pasteur de Dakar, Dakar 220, Senegal
| |
Collapse
|
11
|
Surveillance of arthropod-borne viruses in Benin, West Africa 2020-2021: detection of dengue virus 3 in Aedes aegypti (Diptera: Culicidae). Mil Med Res 2022; 9:64. [PMID: 36372882 PMCID: PMC9661747 DOI: 10.1186/s40779-022-00425-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/28/2022] [Indexed: 11/15/2022] Open
|
12
|
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] [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
|
13
|
Effectiveness of a New Self-Marking Technique in Aedes aegypti under Laboratory Conditions. INSECTS 2022; 13:insects13040379. [PMID: 35447821 PMCID: PMC9044741 DOI: 10.3390/insects13040379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 11/17/2022]
Abstract
In the implementation of mosquito control strategy programs using Sterile Insect Technique and other rear and release strategies, knowledge on the dispersion, competitiveness and survival of mosquitos is considered essential. To assess these parameters, marking techniques are generally used to differentiate colony mosquitoes from wild ones. Most of the existing mosquito marking methods require numerous manipulations that can impact their quality. In this study, we have developed a self-marking technique that can reduce the damage associated with mosquito handling. The marking technique consisted of adding fluorescent powder (DayGlo: A-17-N Saturn yellow) directly to the surface water of the receptacle containing Aedes aegypti male pupae. Different quantities of powder were used, and marking efficacy, powder persistence and mosquito survival were assessed. The results show a mean marking rate of 98 ± 1.61%, and the probability of marking increased significantly (p < 0.001) with increasing concentrations of fluorescent powder. Fluorescent powder persisted up to 20 days and did not induce a negative effect on mosquito survival (χ2 = 5.3, df = 7, p = 0.63). In addition, powder transfer did not occur between marked and unmarked populations. This marking method significantly reduces human intervention and mosquito handling during the marking process, improving the quality of marked mosquitoes used to assess SIT programs.
Collapse
|
14
|
Uncovering the Burden of Dengue in Africa: Considerations on Magnitude, Misdiagnosis, and Ancestry. Viruses 2022; 14:v14020233. [PMID: 35215827 PMCID: PMC8877195 DOI: 10.3390/v14020233] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 01/27/2023] Open
Abstract
Dengue is a re-emerging neglected disease of major public health importance. This review highlights important considerations for dengue disease in Africa, including epidemiology and underestimation of disease burden in African countries, issues with malaria misdiagnosis and co-infections, and potential evidence of genetic protection from severe dengue disease in populations of African descent. The findings indicate that dengue virus prevalence in African countries and populations may be more widespread than reported data suggests, and that the Aedes mosquito vectors appear to be increasing in dissemination and number. Changes in climate, population, and plastic pollution are expected to worsen the dengue situation in Africa. Dengue misdiagnosis is also a problem in Africa, especially due to the typical non-specific clinical presentation of dengue leading to misdiagnosis as malaria. Finally, research suggests that a protective genetic component against severe dengue exists in African descent populations, but further studies should be conducted to strengthen this association in various populations, taking into consideration socioeconomic factors that may contribute to these findings. The main takeaway is that Africa should not be overlooked when it comes to dengue, and more attention and resources should be devoted to this disease in Africa.
Collapse
|
15
|
Fourié T, El Bara A, Dubot-Pérès A, Grard G, Briolant S, Basco LK, Ouldabdallahi Moukah M, Leparc-Goffart I. Emergence of dengue virus serotype 2 in Mauritania and molecular characterization of its circulation in West Africa. PLoS Negl Trop Dis 2021; 15:e0009829. [PMID: 34695119 PMCID: PMC8568173 DOI: 10.1371/journal.pntd.0009829] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 11/04/2021] [Accepted: 09/21/2021] [Indexed: 01/01/2023] Open
Abstract
The number of sporadic and epidemic dengue fever cases have reportedly been increasing in recent years in some West African countries, such as Senegal and Mali. The first epidemic of laboratory-confirmed dengue occurred in Nouakchott, the capital city of Mauritania situated in the Saharan desert, in 2014. On-site diagnosis of dengue fever was established using a rapid diagnostic test for dengue. In parallel, the presence of Aedes aegypti mosquitoes in the city was confirmed. The initial diagnosis was confirmed by RT-PCR, which showed that all samples from the 2014 dengue epidemic in Nouakchott were dengue virus serotype 2 (DENV-2). The whole genome or envelope protein gene of these strains, together with other DENV-2 strains obtained from travelers returning from West African countries to France between 2016 and 2019 (including two Mauritanian strains in 2017 and 2018), were sequenced. Phylogenetic analysis suggested a recent emergence of an epidemic strain from the cosmopolitan genotype belonging to West African cosmopolitan lineage II, which is genetically distinct from African sylvatic genotype. The origin of this DENV-2 lineage is still unknown, but our data seem to suggest a recent and rapid dispersion of the epidemic strain throughout the region. More complete genome sequences of West African DENV-2 are required for a better understanding of the dynamics of its circulation. Arboviral surveillance and outbreak forecasting are urgently needed in West Africa. In Africa, dengue viruses 1 to 4 are transmitted to primates by Aedes mosquitoes in a sylvatic cycle or an urban/epidemic cycle involving humans. Infection in humans may be asymptomatic or may range from mild flu-like illness to severe hemorrhagic fever. The dengue viruses have a pantropical distribution, mostly in urbanized areas where vectors have become well adapted. This report shows dengue can also emerge in desert areas, as seen for the first time in an outbreak in 2014 in Nouakchott, Mauritania, where climatic, environmental, and human behavioral changes favor the emergence of Aedes mosquitoes. Dengue virus 2 was found in multiple human samples collected during the outbreak. Genomic analysis of dengue virus 2 isolates from the Mauritanian outbreak and from infected travelers revealed the rapid emergence of a specific “West African epidemic strain” of the virus throughout West Africa during the last decade, which is distinct from other strains found elsewhere and from historical or sylvatic strains. More genomic data would help us understand the circulation of dengue virus in West Africa, to help forecast and mitigate outbreaks in this region.
Collapse
Affiliation(s)
- Toscane Fourié
- Unité des Virus Emergents (UVE), Aix Marseille Université - IRD 190—INSERM 1207, Marseille, France
- Institut de Recherche Biomédicale des Armées, Marseille, France
| | - Ahmed El Bara
- Institut National de Recherche en Santé Publique, Nouakchott, Mauritania
| | - Audrey Dubot-Pérès
- Unité des Virus Emergents (UVE), Aix Marseille Université - IRD 190—INSERM 1207, Marseille, France
| | - Gilda Grard
- Unité des Virus Emergents (UVE), Aix Marseille Université - IRD 190—INSERM 1207, Marseille, France
- Institut de Recherche Biomédicale des Armées, Marseille, France
| | - Sébastien Briolant
- Institut de Recherche Biomédicale des Armées, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU—Méditerranée Infection, Marseille, France
| | - Leonardo K. Basco
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU—Méditerranée Infection, Marseille, France
| | - Mohamed Ouldabdallahi Moukah
- Unité de Recherche Génomes et Milieux, Faculté des Sciences et Techniques, Université de Nouakchott Al-Aasriya, Nouakchott, Mauritania
- Initiative mauritanienne pour la lutte contre les maladies endémiques “MEDCINGO” Nouakchott, Mauritania
| | - Isabelle Leparc-Goffart
- Unité des Virus Emergents (UVE), Aix Marseille Université - IRD 190—INSERM 1207, Marseille, France
- Institut de Recherche Biomédicale des Armées, Marseille, France
- * E-mail:
| |
Collapse
|
16
|
Adam A, Jassoy C. Epidemiology and Laboratory Diagnostics of Dengue, Yellow Fever, Zika, and Chikungunya Virus Infections in Africa. Pathogens 2021; 10:pathogens10101324. [PMID: 34684274 PMCID: PMC8541377 DOI: 10.3390/pathogens10101324] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 11/30/2022] Open
Abstract
Arbovirus infections are widespread, and their disease burden has increased in the past decade. In Africa, arbovirus infections and fever with unknown etiology are common. Due to the lack of well-established epidemiologic surveillance systems and accurate differential diagnosis in most African countries, little is known about the prevalence of human arbovirus infections in Africa. The aim of this review is to summarize the available epidemiological data and diagnostic laboratory tools of infections with dengue, yellow fever, Zika, and chikungunya viruses, all transmitted by Aedes mosquitoes. Studies indicate that these arboviral infections are endemic in most of Africa. Surveillance of the incidence and prevalence of the infections would enable medical doctors to improve the diagnostic accuracy in patients with typical symptoms. If possible, arboviral diagnostic tests should be added to the routine healthcare systems. Healthcare providers should be informed about the prevalent arboviral diseases to identify possible cases.
Collapse
Affiliation(s)
- Awadalkareem Adam
- Correspondence: (A.A.); (C.J.); Tel.: +49-341-9714314 (C.J.); Fax: +49-341-9714309 (C.J.)
| | - Christian Jassoy
- Correspondence: (A.A.); (C.J.); Tel.: +49-341-9714314 (C.J.); Fax: +49-341-9714309 (C.J.)
| |
Collapse
|