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Phadungsombat J, Nakayama EE, Shioda T. Unraveling Dengue Virus Diversity in Asia: An Epidemiological Study through Genetic Sequences and Phylogenetic Analysis. Viruses 2024; 16:1046. [PMID: 39066210 PMCID: PMC11281397 DOI: 10.3390/v16071046] [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: 05/31/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Dengue virus (DENV) is the causative agent of dengue. Although most infected individuals are asymptomatic or present with only mild symptoms, severe manifestations could potentially devastate human populations in tropical and subtropical regions. In hyperendemic regions such as South Asia and Southeast Asia (SEA), all four DENV serotypes (DENV-1, DENV-2, DENV-3, and DENV-4) have been prevalent for several decades. Each DENV serotype is further divided into multiple genotypes, reflecting the extensive diversity of DENV. Historically, specific DENV genotypes were associated with particular geographical distributions within endemic regions. However, this epidemiological pattern has changed due to urbanization, globalization, and climate change. This review comprehensively traces the historical and recent genetic epidemiology of DENV in Asia from the first time DENV was identified in the 1950s to the present. We analyzed envelope sequences from a database covering 16 endemic countries across three distinct geographic regions in Asia. These countries included Bangladesh, Bhutan, India, Maldives, Nepal, Pakistan, and Sri Lanka from South Asia; Cambodia, Laos, Myanmar, Thailand, and Vietnam from Mainland SEA; and Indonesia, the Philippines, Malaysia, and Singapore from Maritime SEA. Additionally, we describe the phylogenetic relationships among DENV genotypes within each serotype, along with their geographic distribution, to enhance the understanding of DENV dynamics.
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Affiliation(s)
| | | | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; (J.P.); (E.E.N.)
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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.
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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
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Nash D, Ellmen I, Knapp JJ, Menon R, Overton AK, Cheng J, Lynch MDJ, Nissimov JI, Charles TC. A Novel Tiled Amplicon Sequencing Assay Targeting the Tomato Brown Rugose Fruit Virus (ToBRFV) Genome Reveals Widespread Distribution in Municipal Wastewater Treatment Systems in the Province of Ontario, Canada. Viruses 2024; 16:460. [PMID: 38543825 PMCID: PMC10974707 DOI: 10.3390/v16030460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 05/23/2024] Open
Abstract
Tomato Brown Rugose Fruit Virus (ToBRFV) is a plant pathogen that infects important Solanaceae crop species and can dramatically reduce tomato crop yields. The ToBRFV has rapidly spread around the globe due to its ability to escape detection by antiviral host genes which confer resistance to other tobamoviruses in tomato plants. The development of robust and reproducible methods for detecting viruses in the environment aids in the tracking and reduction of pathogen transmission. We detected ToBRFV in municipal wastewater influent (WWI) samples, likely due to its presence in human waste, demonstrating a widespread distribution of ToBRFV in WWI throughout Ontario, Canada. To aid in global ToBRFV surveillance efforts, we developed a tiled amplicon approach to sequence and track the evolution of ToBRFV genomes in municipal WWI. Our assay recovers 95.7% of the 6393 bp ToBRFV RefSeq genome, omitting the terminal 5' and 3' ends. We demonstrate that our sequencing assay is a robust, sensitive, and highly specific method for recovering ToBRFV genomes. Our ToBRFV assay was developed using existing ARTIC Network resources, including primer design, sequencing library prep, and read analysis. Additionally, we adapted our lineage abundance estimation tool, Alcov, to estimate the abundance of ToBRFV clades in samples.
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Affiliation(s)
- Delaney Nash
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
- Metagenom Bio Life Science Inc., Waterloo, ON N2L 5V4, Canada
| | - Isaac Ellmen
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
- Metagenom Bio Life Science Inc., Waterloo, ON N2L 5V4, Canada
| | - Jennifer J. Knapp
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
| | - Ria Menon
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
| | - Alyssa K. Overton
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
| | - Jiujun Cheng
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
- Metagenom Bio Life Science Inc., Waterloo, ON N2L 5V4, Canada
| | - Michael D. J. Lynch
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
- Metagenom Bio Life Science Inc., Waterloo, ON N2L 5V4, Canada
| | - Jozef I. Nissimov
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
| | - Trevor C. Charles
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (I.E.); (J.J.K.); (R.M.); (A.K.O.); (J.C.); (M.D.J.L.); (J.I.N.); (T.C.C.)
- Metagenom Bio Life Science Inc., Waterloo, ON N2L 5V4, Canada
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4
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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.
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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
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5
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Bergmann F, Holicki CM, Michel F, Bock S, Scuda N, Priemer G, Kenklies S, Siempelkamp T, Skuballa J, Sauerwald C, Herms L, Muluneh A, Peters M, Hlinak A, Groschup MH, Sadeghi B, Ziegler U. Reconstruction of the molecular evolution of Usutu virus in Germany: Insights into virus emersion and circulation. PLoS Negl Trop Dis 2023; 17:e0011203. [PMID: 37782665 PMCID: PMC10569574 DOI: 10.1371/journal.pntd.0011203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 10/12/2023] [Accepted: 09/07/2023] [Indexed: 10/04/2023] Open
Abstract
Usutu virus (USUV) is a mosquito-borne flavivirus that is widely distributed in southern and central Europe. The zoonotic virus circulates primarily between birds and mosquitoes, can, however, in rare cases infect other mammals including humans. In the past, USUV has been repeatedly associated with mass mortalities in birds, primarily blackbirds and owls. Birds commonly succumb either due to the peracute nature of the infection or due to severe encephalitis. In Germany, USUV has spread rapidly since its first detection in 2010 in mosquitoes under the presence of susceptible host and vector species. Nonetheless, there is to date limited access to whole genome sequences resulting in the absence of in-depth phylogenetic and phylodynamic analyses. In this study, 118 wild and captive birds were sequenced using a nanopore sequencing platform with prior target enrichment via amplicons. Due to the high abundancy of Europe 3 and Africa 3 in Germany an ample quantity of associated whole genome sequences was generated and the most recent common ancestor could be determined for each lineage. The corresponding clock phylogeny revealed an introduction of USUV Europe 3 and Africa 3 into Germany three years prior to their first isolation in the avifauna in 2011 and 2014, respectively. Based on the clustering and temporal history of the lineages, evidence exists for the genetic evolution of USUV within Germany as well as new introductions thereof into the country.
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Affiliation(s)
- Felicitas Bergmann
- Institute of Novel and Emerging Infectious Disease, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Cora M. Holicki
- Institute of Novel and Emerging Infectious Disease, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Friederike Michel
- Institute of Novel and Emerging Infectious Disease, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Sabine Bock
- Berlin-Brandenburg State Laboratory, Frankfurt (Oder), Germany
| | - Nelly Scuda
- Bavarian Health and Food Safety Authority, Erlangen, Germany
| | - Grit Priemer
- State Office of Agriculture, Food Safety and Fisheries Mecklenburg-Vorpommern (LALLF), Rostock, Germany
| | - Susanne Kenklies
- State Office for Consumer Protection Saxony-Anhalt (LAV), Stendal, Germany
| | - Timo Siempelkamp
- Thuringian State Office for Consumer Protection, Bad Langensalza, Germany
| | - Jasmin Skuballa
- State Institute for Chemical and Veterinary Analysis Karlsruhe, Karlsruhe, Germany
| | - Claudia Sauerwald
- Department of Veterinary Medicine, Hessian State Laboratory, Gießen, Germany
| | - Louise Herms
- Lower Saxony State Office for Consumer Protection and Food Safety (LAVES), Hannover, Germany
| | - Aemero Muluneh
- Saxon State Laboratory of Health and Veterinary Affairs, Dresden, Germany
| | - Martin Peters
- Chemical and Veterinary Investigation Office (CVUA), Arnsberg, Germany
| | - Andreas Hlinak
- Berlin-Brandenburg State Laboratory, Frankfurt (Oder), Germany
| | - Martin H. Groschup
- Institute of Novel and Emerging Infectious Disease, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- German Center of Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Greifswald-Insel Riems, Germany
| | - Balal Sadeghi
- Institute of Novel and Emerging Infectious Disease, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Ute Ziegler
- Institute of Novel and Emerging Infectious Disease, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- German Center of Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Greifswald-Insel Riems, Germany
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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.
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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.)
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7
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de Carvalho Marques B, Sacchetto L, Banho CA, Estofolete CF, Dourado FS, da Silva Cândido D, Dutra KR, da Silva Salles FC, de Jesus JG, Sabino EC, Faria NR, Nogueira ML. Genetic differences of dengue virus 2 in patients with distinct clinical outcome. Braz J Microbiol 2023; 54:1411-1419. [PMID: 37178262 PMCID: PMC10485208 DOI: 10.1007/s42770-023-01006-1] [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: 02/13/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
The genetic diversity of the dengue virus is characterized by four circulating serotypes, several genotypes, and an increasing number of existing lineages that may have differences in the potential to cause epidemics and disease severity. Accurate identification of the genetic variability of the virus is essential to identify lineages responsible for an epidemic and understanding the processes of virus spread and virulence. Here, we characterize, using portable nanopore genomic sequencing, different lineages of dengue virus 2 (DENV-2) detected in 22 serum samples from patients with and without dengue warning signs attended at Hospital de Base of São José do Rio Preto (SJRP) in 2019, during a DENV-2 outbreak. Demographic, epidemiological, and clinical data were also analyzed. The phylogenetic reconstruction and the clinical data showed that two lineages belonging to the American/Asian genotype of DENV-2-BR3 and BR4 (BR4L1 and BR4L2)-were co-circulating in SJRP. Although preliminary, these results indicate no specific association between clinical form and phylogenetic clustering at the virus consensus sequence level. Studies with larger sample sizes and which explore single nucleotide variants are needed. Therefore, we showed that portable nanopore genome sequencing could generate quick and reliable sequences for genomic surveillance to monitor viral diversity and its association with disease severity as an epidemic unfolds.
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Affiliation(s)
- Beatriz de Carvalho Marques
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | - Lívia Sacchetto
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | - Cecília Artico Banho
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | - Cássia Fernanda Estofolete
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | - Fernanda Simões Dourado
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | | | - Karina Rocha Dutra
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | | | - Jaqueline Góes de Jesus
- Instituto de Medicina Tropical da Faculdade de Medicina - Universidade de São Paulo, São Paulo, Brazil
| | - Ester Cerdeira Sabino
- Instituto de Medicina Tropical da Faculdade de Medicina - Universidade de São Paulo, São Paulo, Brazil
| | - Nuno Rodrigues Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Instituto de Medicina Tropical da Faculdade de Medicina - Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil.
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA.
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Gutierrez B, da Silva Candido D, Bajaj S, Rodriguez Maldonado AP, Ayala FG, Rodriguez MDLLT, Rodriguez AA, Arámbula CW, González ER, Martínez IL, Díaz-Quiñónez JA, Pichardo MV, Hill SC, Thézé J, Faria NR, Pybus OG, Preciado-Llanes L, Reyes-Sandoval A, Kraemer MUG, Escalera-Zamudio M. Convergent trends and spatiotemporal patterns of Aedes-borne arboviruses in Mexico and Central America. PLoS Negl Trop Dis 2023; 17:e0011169. [PMID: 37672514 PMCID: PMC10506721 DOI: 10.1371/journal.pntd.0011169] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 09/18/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND Aedes-borne arboviruses cause both seasonal epidemics and emerging outbreaks with a significant impact on global health. These viruses share mosquito vector species, often infecting the same host population within overlapping geographic regions. Thus, comparative analyses of the virus evolutionary and epidemiological dynamics across spatial and temporal scales could reveal convergent trends. METHODOLOGY/PRINCIPAL FINDINGS Focusing on Mexico as a case study, we generated novel chikungunya and dengue (CHIKV, DENV-1 and DENV-2) virus genomes from an epidemiological surveillance-derived historical sample collection, and analysed them together with longitudinally-collected genome and epidemiological data from the Americas. Aedes-borne arboviruses endemically circulating within the country were found to be introduced multiple times from lineages predominantly sampled from the Caribbean and Central America. For CHIKV, at least thirteen introductions were inferred over a year, with six of these leading to persistent transmission chains. For both DENV-1 and DENV-2, at least seven introductions were inferred over a decade. CONCLUSIONS/SIGNIFICANCE Our results suggest that CHIKV, DENV-1 and DENV-2 in Mexico share evolutionary and epidemiological trajectories. The southwest region of the country was determined to be the most likely location for viral introductions from abroad, with a subsequent spread into the Pacific coast towards the north of Mexico. Virus diffusion patterns observed across the country are likely driven by multiple factors, including mobility linked to human migration from Central towards North America. Considering Mexico's geographic positioning displaying a high human mobility across borders, our results prompt the need to better understand the role of anthropogenic factors in the transmission dynamics of Aedes-borne arboviruses, particularly linked to land-based human migration.
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Affiliation(s)
- Bernardo Gutierrez
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Darlan da Silva Candido
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Sumali Bajaj
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | | | - Fabiola Garces Ayala
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - María de la Luz Torre Rodriguez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - Adnan Araiza Rodriguez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - Claudia Wong Arámbula
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - Ernesto Ramírez González
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - Irma López Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - José Alberto Díaz-Quiñónez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
- Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Pachuca de Soto, Mexico
| | - Mauricio Vázquez Pichardo
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, México
| | - Sarah C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Julien Thézé
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Genès-Champanelle, France
| | - Nuno R Faria
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, United Kingdom
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Lorena Preciado-Llanes
- Nuffield Department of Medicine/Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Arturo Reyes-Sandoval
- Nuffield Department of Medicine/Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Instituto Politécnico Nacional (IPN), Av. Luis Enrique Erro s/n., Unidad Adolfo López Mateos, Mexico City, Mexico
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9
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Sebastião CS, Sacomboio E, Francisco NM, Paixão J, Cassinela EK, de Vasconcelos JN, Pimentel V, Morais J. Demographic characteristics and risk factors related to high blood pressure among healthy blood donors from Luanda, Angola: A retrospective study. Health Sci Rep 2023; 6:e1300. [PMID: 37305153 PMCID: PMC10248479 DOI: 10.1002/hsr2.1300] [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: 02/24/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/13/2023] Open
Abstract
Background and Aims Hypertension is a public health concern, mainly in resource-limited countries. We investigated the characteristics and risk factors related to high blood pressure in healthy blood donors from, Luanda, the capital city of Angola. Methods This was a retrospective study that included 343 healthy donors from December 2019 to September 2020. Results The mean age was 32 ± 9 years. Men represented 93% of the population. Mean systolic blood pressure (SBP) was 131 ± 12.3 mmHg (ranging from 100 to 160 mmHg) and diastolic blood pressure (DBP) was 80.1 ± 9.72 mmHg (from 56.0 to 100 mmHg). DBP was related to age and gender (p < 0.05). About 7.3% of the donors had high-pressure (>140/90 mmHg). Age between 20 and 40 years (odds ratio [OR]: 2.52, p = 0.043), women (OR: 1.87, p = 0.548), nonurbanized areas (OR: 0.39, p = 0.067), high educational level (OR: 0.76, p = 0.637), employed (OR: 0.49, p = 0.491), voluntary donors (OR: 0.87, p = 0.799), blood group B (OR: 2.06, p = 0.346), and Rh- (OR: 0.26, p = 0.104), were potentially related with high-pressure. The high-pressure cases increased from December 2019 (4%) to September 2020 (28%) (p = 0.019). Conclusion We showed high pressure among the healthy blood donors population. Demographic characteristics, ABO/Rh blood group, and year period are features that should be considered in cardiovascular disease control strategies. Biological and nonbiological features related to blood pressure changes should be considered for further studies in the Angolan population.
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Affiliation(s)
- Cruz S. Sebastião
- Instituto Nacional de Investigação em Saúde (INIS)LuandaAngola
- Centro de Investigação em Saúde de Angola (CISA)CaxitoAngola
- Instituto de Ciências da Saúde (ICISA)LuandaAngola
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT)LisbonPortugal
| | - Euclides Sacomboio
- Instituto Nacional de Investigação em Saúde (INIS)LuandaAngola
- Instituto de Ciências da Saúde (ICISA)LuandaAngola
- Centro de Estudos, Investigação Cientifica e Pós‐graduação (CEIP)LuandaAngola
| | | | - Joana Paixão
- Instituto Nacional de Investigação em Saúde (INIS)LuandaAngola
| | - Edson K. Cassinela
- Centro de Estudos, Investigação Cientifica e Pós‐graduação (CEIP)LuandaAngola
- Centro Nacional de Investigação Científica (CNIC)LuandaAngola
| | - Jocelyne Neto de Vasconcelos
- Instituto Nacional de Investigação em Saúde (INIS)LuandaAngola
- Centro de Investigação em Saúde de Angola (CISA)CaxitoAngola
| | - Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT)LisbonPortugal
| | - Joana Morais
- Instituto Nacional de Investigação em Saúde (INIS)LuandaAngola
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT)LisbonPortugal
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Dieng I, Ndiaye M, Ndione MHD, Sankhe S, Diagne MM, Sagne SN, Gaye A, Balde D, Barry A, Fall G, Sall AA, Loucoubar C, Faye O, Faye O. Molecular characterization of circulating Dengue virus 2 during an outbreak in Northern Senegal's Saint-Louis region in 2018. J Med Virol 2023; 95:e28347. [PMID: 36424699 DOI: 10.1002/jmv.28347] [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: 12/20/2021] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
Globally, 390 million people are at risk of dengue infection and over the past 50 years, the virus incidence increased thirty-fold. In Senegal, an unprecedented occurrence of outbreaks and sporadic cases have been noticed since 2017. In October 2018, an outbreak of Dengue virus 2 (DENV-2) was reported in the north of Senegal affecting multiple areas including Saint-Louis, Richard Toll, and Rosso which are located at the border with Mauritania. Of these 173 blood specimen samples collected from patients, 27 were positive for dengue by quantitative reverse transcription PCR (qRT-PCR), and eight were serologically confirmed to be positive for DENV immunoglobulin M (IgM). Serotyping using qRT-PCR reveals that isolates were positive for DENV-2. A subset of DENV-2 positive samples was selected and subjected to whole-genome sequencing followed by phylogenetic analysis. Analysis of six nearly complete genome sequences revealed that the isolates belong to the cosmopolitan genotype and are closely related to the Mauritanian strains detected between 2017 and 2018 and those detected in many West African countries such as Burkina Faso or Cote d'Ivoire. Our results suggest a transboundary circulation of the DENV-2 cosmopolitan genotype between Senegal and Mauritania and call for a need for coordinated surveillance of arboviruses between these two countries. Interestingly, a high level of homology between West African isolates highlights endemicity and calls for the set-up of subregional viral genomic surveillance which will lead to a better understanding of viral dynamics, transmission, and spread across Africa.
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Affiliation(s)
- 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
| | - Marie Henriette Dior Ndione
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Safietou Sankhe
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Moussa Moïse Diagne
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Samba Niang Sagne
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Aboubacry Gaye
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Diamilatou Balde
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Aliou Barry
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Gamou Fall
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou Alpha Sall
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oumar Faye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ousmane Faye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
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11
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Oladipo HJ. Dengue virus and SARS-CoV-2 Co-infection dynamics: An emerging threat among African countries. Ann Med Surg (Lond) 2022; 82:104398. [PMID: 36035770 PMCID: PMC9394095 DOI: 10.1016/j.amsu.2022.104398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 01/08/2023] Open
Abstract
The rising circulation of the vector borne disease such as dengue fever amidst the COVID-19 pandemic in African countries is on the rise, which pose a significant public health threat. In this article, we discussed the co-infection of dengue virus (DENV) (the causative agent of dengue fever) and SARS-CoV-2 (the causative agents of COVID-19) as well as the associated risk factors involved. Our review highlights that the continuous increase in the incidence and disease mortality from the co-infection of dengue Virus and SARS-CoV-2 is as result of inadequate surveillance and limited testing centers. Second, the overlapping clinical features and indistinguishable symptoms from both infections is a major challenge. Third, lack of scientific prudence among stakeholders has played a significant impact on how to contain these diseases. Therefore, there is a need to reassess research priorities in understanding the risk factors involved from the coinfection. Also, the development of accurate point-of-care diagnostics for COVID-19 and dengue fever coupled with community-based health intervention programs is highly essential for control. In Africa, the incidence and disease mortality rate from the co-infection of dengue fever and COVID- 19 is on the rise due to inadequate surveillance and limited testing centers. Overlapping clinical features and lack of scientific prudence among stakeholders have played a significant impact on how to contain these infectious diseases. Research priorities need to be reassessed with focus on understanding risk factors involved. Development of accurate point-of-care diagnostics and community-based health intervention programs for both infection is highly essential for control.
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Affiliation(s)
- Habeebullah Jayeola Oladipo
- Corresponding author. Faculty of Pharmaceutical Sciences, University of Ilorin, P.M.B. 1515, Ilorin, 240003, Nigeria.
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12
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Sebastião CS, Neto Z, Jandondo D, Mirandela M, Morais J, Brito M. Dengue virus among HIV-infected pregnant women attending antenatal care in Luanda, Angola: An emerging public health concern. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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13
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Neto Z, Martinez PA, Hill SC, Jandondo D, Thézé J, Mirandela M, Aguiar RS, Xavier J, dos Santos Sebastião C, Cândido ALM, Vaz F, Castro GR, Paixão JP, Loman NJ, Lemey P, Pybus OG, Vasconcelos J, Faria NR, de Morais J. Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017-2019. PLoS Negl Trop Dis 2022; 16:e0010255. [PMID: 35584153 PMCID: PMC9166355 DOI: 10.1371/journal.pntd.0010255] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/03/2022] [Accepted: 02/11/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The transmission patterns and genetic diversity of dengue virus (DENV) circulating in Africa remain poorly understood. Circulation of the DENV serotype 1 (DENV1) in Angola was detected in 2013, while DENV serotype 2 (DENV2) was detected in 2018. Here, we report results from molecular and genomic investigations conducted at the Ministry of Health national reference laboratory (INIS) in Angola on suspected dengue cases detected between January 2017 and February 2019. METHODS A total of 401 serum samples from dengue suspected cases were collected in 13 of the 18 provinces in Angola. Of those, 351 samples had complete data for demographic and epidemiological analysis, including age, gender, province, type of residence, clinical symptoms, as well as dates of onset of symptoms and sample collection. RNA was extracted from residual samples and tested for DENV-RNA using two distinct real time RT-PCR protocols. On-site whole genome nanopore sequencing was performed on RT-PCR+ samples. Bayesian coalescent models were used to estimate date and origin of outbreak emergence, as well as population growth rates. RESULTS Molecular screening showed that 66 out of 351 (19%) suspected cases were DENV-RNA positive across 5 provinces in Angola. DENV RT-PCR+ cases were detected more frequently in urban sites compared to rural sites. Of the DENV RT-PCR+ cases most were collected within 6 days of symptom onset. 93% of infections were confirmed by serotype-specific RT-PCR as DENV2 and 1 case (1.4%) was confirmed as DENV1. Six CHIKV RT-PCR+ cases were also detected during the study period, including 1 co-infection of CHIKV with DENV1. Most cases (87%) were detected in Luanda during the rainy season between April and October. Symptoms associated with severe dengue were observed in 11 patients, including 2 with a fatal outcome. On-site nanopore genome sequencing followed by genetic analysis revealed an introduction of DENV2 Cosmopolitan genotype (also known as DENV2-II genotype) possibly from India in or around October 2015, at least 1 year before its detection in the country. Coalescent models suggest relatively moderately rapid epidemic growth rates and doubling times, and a moderate expansion of DENV2 in Angola during the studied period. CONCLUSION This study describes genomic, epidemiological and demographic characteristic of predominately urban transmission of DENV2 in Angola. We also find co-circulation of DENV2 with DENV1 and CHIKV and report several RT-PCR confirmed severe dengue cases in the country. Increasing dengue awareness in healthcare professional, expanding the monitorization of arboviral epidemics across the country, identifying most common mosquito breeding sites in urban settings, implementing innovative vector control interventions and dengue vaccination campaigns could help to reduce vector presence and DENV transmission in Angola.
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Affiliation(s)
- Zoraima Neto
- Instituto Nacional de Investigação em Saúde (INIS), Ministry of Health, Luanda, Angola
| | - Pedro A. Martinez
- Instituto Nacional de Investigação em Saúde (INIS), Ministry of Health, Luanda, Angola
| | - Sarah C. Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Domingos Jandondo
- Instituto Nacional de Investigação em Saúde (INIS), Ministry of Health, Luanda, Angola
| | - Julien Thézé
- Université Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Marinela Mirandela
- Instituto Nacional de Investigação em Saúde (INIS), Ministry of Health, Luanda, Angola
| | - Renato Santana Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Joilson Xavier
- Laboratório de Genética Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Filipa Vaz
- Instituto Nacional de Investigação em Saúde (INIS), Ministry of Health, Luanda, Angola
- World Health Organization Angola, Luanda, Angola
| | - Gisel Reyes Castro
- Instituto Nacional de Investigação em Saúde (INIS), Ministry of Health, Luanda, Angola
| | - Joana Paula Paixão
- Instituto Nacional de Investigação em Saúde (INIS), Ministry of Health, Luanda, Angola
| | - Nicholas J. Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Jocelyne Vasconcelos
- Instituto Nacional de Investigação em Saúde (INIS), Ministry of Health, Luanda, Angola
| | - Nuno Rodrigues Faria
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom
| | - Joana de Morais
- Instituto Nacional de Investigação em Saúde (INIS), Ministry of Health, Luanda, Angola
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14
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Diallo D, Diouf B, Gaye A, NDiaye EH, Sene NM, Dia I, Diallo M. Dengue vectors in Africa: A review. Heliyon 2022; 8:e09459. [PMID: 35620619 PMCID: PMC9126922 DOI: 10.1016/j.heliyon.2022.e09459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/04/2021] [Accepted: 05/12/2022] [Indexed: 11/25/2022] Open
Abstract
Dengue fever is a mosquito-borne-disease of growing public health importance in Africa. The continuous increase of number and frequency of outbreaks of dengue fever, especially in urban area in Africa underline the need to review the current data available on vectors involved in dengue virus transmission in Africa. Here, we summarized the available data on vectors involved in the transmission of dengue virus in the sylvatic and urban environments, vertical transmission, vector competence studies, and vector control strategies used in Africa. The virus was isolated mainly from Aedes furcifer, Ae. luteocephalus, and Ae. taylori in the sylvatic environment and from Ae. aegypti and Ae. albopictus in the urban areas. Prospective and urgently needed studies on vectors biology, behavior, and alternative control strategies are suggested.
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Affiliation(s)
- Diawo Diallo
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP 220, Dakar, Senegal
| | - Babacar Diouf
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP 220, Dakar, Senegal
| | - Alioune Gaye
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP 220, Dakar, Senegal
| | - El Hadji NDiaye
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP 220, Dakar, Senegal
| | - Ndeye Marie Sene
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP 220, Dakar, Senegal
| | - Ibrahima Dia
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP 220, Dakar, Senegal
| | - Mawlouth Diallo
- Pôle de Zoologie Médicale, Institut Pasteur de Dakar, 36 Avenue Pasteur, BP 220, Dakar, Senegal
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15
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Sebastião CS, Gaston C, Paixão JP, Sacomboio ENM, Neto Z, de Vasconcelos JN, Morais J. Coinfection between SARS-CoV-2 and vector-borne diseases in Luanda, Angola. J Med Virol 2022; 94:366-371. [PMID: 34546584 PMCID: PMC8662186 DOI: 10.1002/jmv.27354] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/16/2021] [Accepted: 09/18/2021] [Indexed: 11/26/2022]
Abstract
Co-epidemics happening simultaneously can generate a burden on healthcare systems. The co-occurrence of SARS-CoV-2 with vector-borne diseases (VBD), such as malaria and dengue in resource-limited settings represents an additional challenge to the healthcare systems. Herein, we assessed the coinfection rate between SARS-CoV-2 and VBD to highlight the need to carry out an accurate diagnosis and promote timely measures for these infections in Luanda, the capital city of Angola. This was a cross-sectional study conducted with 105 subjects tested for the SARS-CoV-2 and VBD with a rapid detection test in April 2021. The participants tested positive for SARS-CoV-2 (3.80%), malaria (13.3%), and dengue (27.6%). Low odds related to testing positivity to SARS-CoV-2 or VBD were observed in participants above or equal to 40 years (odds ratio [OR]: 0.60, p = 0.536), while higher odds were observed in male (OR: 1.44, p = 0.392) and urbanized areas (OR: 3.78, p = 0.223). The overall co-infection rate between SARS-CoV-2 and VBD was 11.4%. Our findings showed a coinfection between SARS-CoV-2 with malaria and dengue, which could indicate the need to integrate the screening for VBD in the SARS-CoV-2 testing algorithm and the adjustment of treatment protocols. Further studies are warranted to better elucidate the relationship between COVID-19 and VBD in Angola.
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Affiliation(s)
- Cruz S. Sebastião
- Instituto Nacional de Investigação em Saúde (INIS)LuandaAngola
- Centro de Investigação em Saúde de Angola (CISA)CaxitoAngola
- Instituto Superior de Ciências da Saúde (ISCISA)Universidade Agostinho Neto (UAN)LuandaAngola
| | | | | | - Euclides N. M. Sacomboio
- Instituto Nacional de Investigação em Saúde (INIS)LuandaAngola
- Instituto Superior de Ciências da Saúde (ISCISA)Universidade Agostinho Neto (UAN)LuandaAngola
| | - Zoraima Neto
- Instituto Nacional de Investigação em Saúde (INIS)LuandaAngola
| | - Jocelyne Neto de Vasconcelos
- Instituto Nacional de Investigação em Saúde (INIS)LuandaAngola
- Centro de Investigação em Saúde de Angola (CISA)CaxitoAngola
| | - Joana Morais
- Instituto Nacional de Investigação em Saúde (INIS)LuandaAngola
- Faculdade de MedicinaUniversidade Agostinho NetoLuandaAngola
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16
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Sebastião CS, Parimbelli P, Mendes M, Sacomboio E, Morais J, de Vasconcelos JN, Brito M. Prevalence and Risk Factors of SARS-CoV-2 Infection among Parturients and Newborns from Luanda, Angola. Pathogens 2021; 10:1494. [PMID: 34832649 PMCID: PMC8624220 DOI: 10.3390/pathogens10111494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/29/2021] [Accepted: 11/08/2021] [Indexed: 12/05/2022] Open
Abstract
SARS-CoV-2 emerged in China in December 2019, creating a massive public health concern. Although previous studies have identified SARS-CoV-2 in pregnant women, the possibility of transmission to newborns remains uncertain. Herein, we investigated SARS-CoV-2 infection and risk factors among parturients and newborns. This was a cross-sectional study carried out with 3633 parturients from Luanda, Angola, between January and April 2021, with an age ranging from 13 to 48 years. SARS-CoV-2 infection of the parturients was further confirmed with RT-PCR after COVID-19 Ag Rapid Testing. About 0.4% of parturients tested positive on the day of delivery. Surprisingly, parturients from urbanized areas (OR: 0.18, p = 0.025) had a low chance of infection. None of the newborns tested positive in the first 24 h after birth, while one (9.1%, 1/10) of the newborns tested positive with pharyngeal swabs seven days after birth. However, whether the case was due to vertical transmission from mother to child remains to be confirmed. The mother's residence, education level, antenatal follow-up, and delivery category were related to SARS-CoV-2 transmission (p < 0.05). Our findings showed a relatively low SARS-CoV-2 infection from parturients to newborns, regardless of the severity of the maternal disease. Furthermore, these findings are an early assessment of COVID-19 cases in late pregnancy, which could indicate the need for intensive management of SARS-CoV-2 infection among parturients in Angola. Further studies are needed on the consequences of SARS-CoV-2 among pregnant women and neonates from Angola.
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Affiliation(s)
- Cruz S. Sebastião
- Centro de Investigação em Saúde de Angola (CISA), Caxito, Angola; (C.S.S.); (J.N.d.V.)
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola; (E.S.); (J.M.)
- Instituto Superior de Ciências da Saúde (ISCISA), Universidade Agostinho Neto (UAN), Luanda, Angola
| | - Paolo Parimbelli
- Maternidade Lucrécia Paim, Ministério da Saúde, Luanda, Angola; (P.P.); (M.M.)
| | - Manuela Mendes
- Maternidade Lucrécia Paim, Ministério da Saúde, Luanda, Angola; (P.P.); (M.M.)
| | - Euclides Sacomboio
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola; (E.S.); (J.M.)
- Instituto Superior de Ciências da Saúde (ISCISA), Universidade Agostinho Neto (UAN), Luanda, Angola
| | - Joana Morais
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola; (E.S.); (J.M.)
- Faculdade de Medicina, Universidade Agostinho Neto, Luanda, Angola
| | | | - Miguel Brito
- Centro de Investigação em Saúde de Angola (CISA), Caxito, Angola; (C.S.S.); (J.N.d.V.)
- Health and Technology Research Center, Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, 1990-096 Lisboa, Portugal
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17
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Alfsnes K, Eldholm V, Gaunt MW, de Lamballerie X, Gould EA, Pettersson JHO. Tracing and tracking the emergence, epidemiology and dispersal of dengue virus to Africa during the 20th century. One Health 2021; 13:100337. [PMID: 34746356 PMCID: PMC8551533 DOI: 10.1016/j.onehlt.2021.100337] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/15/2021] [Accepted: 10/15/2021] [Indexed: 12/02/2022] Open
Abstract
The four mosquito-borne dengue virus serotypes (DENV1–DENV4) cause a high burden of disease throughout the tropical and sub-tropical regions of the world. Nevertheless, their precise epidemiological history in Africa, including when and where they originated and were distributed during the 20th century, remains unclear stressing the need for One Health focused research. Accordingly, we conducted a time-scaled molecular epidemiological reconstruction using publicly available and newly sequenced dengue virus genomes of African origin representing all four serotypes to deduce the most likely temporal and spatial transmission routes of each DENV serotype from their ancestral regions to, within and from Africa. Our analyses suggest that during the 20th century, serotypes DENV1–DENV3 were introduced to Africa from South East Asia on multiple occasions. The earliest evidence recorded indicates introduction of DENV2 during the early-1940s and of DENV1 during the mid-1940s to Western Africa from South East Asia. The analysis also implies an early introduction of DENV4 during the mid-1940s to Western Africa, alongside DENV1, probably originating in South East Asia. Establishment of DENV3 in Africa appears to have occurred later in the 1960s, apparently originating from South East Asia. However, with the re-establishment of DENV in the Americas, following the cessation of the PAHO mosquito control programme during the mid-20th century, evidence of introductions of DENV1 and DENV2 from the Americas to Western Africa was also observed. The data also identify intra-regional circulation of DENV, but also inter-regional dispersal of all four serotypes within Africa, which has led to a high degree of geographical overlap among serotypes. It is also noteworthy that DENV from both Eastern and Western Africa, have been introduced into Central Africa but there is no support for the converse relationship. For serotypes DENV1–DENV3, we observed probable exports from within established African DENV clusters (≥2 sequences) primarily to Eastern and Southern Asia. Collectively, our findings support the view that all DENV serotypes, apart from DENV4, have been introduced on multiple occasions to Africa, primarily originating from South East Asia, and subsequently to neighbouring regions within Africa.
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Affiliation(s)
- Kristian Alfsnes
- Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Vegard Eldholm
- Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Michael W Gaunt
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Xavier de Lamballerie
- UMR "Unité des Virus Emergents", Aix-Marseille Université-IRD 190-Inserm 1207-IHU Méditerranée Infection, Marseille, France.,APHM Public Hospitals of Marseille, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Ernest A Gould
- UMR "Unité des Virus Emergents", Aix-Marseille Université-IRD 190-Inserm 1207-IHU Méditerranée Infection, Marseille, France
| | - John H-O Pettersson
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden.,Public Health Agency of Sweden, Solna, Sweden.,Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, Australia
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18
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Dieng I, Diagne MM, Ndione MHD, Hedible BG, Diop M, Adjoguoua EV, Sylla Y, Kadjo H, Loucoubar C, Sall AA, Faye O, Faye O. Dengue virus serotype 2 imported case from Côte d'Ivoire to Senegal, 2017. Transbound Emerg Dis 2021; 69:3035-3040. [PMID: 34270171 DOI: 10.1111/tbed.14239] [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: 12/09/2020] [Revised: 07/05/2021] [Accepted: 07/12/2021] [Indexed: 11/28/2022]
Abstract
Dengue fever is the most common arboviral infection worldwide. Its epidemiology in Africa is not yet fully understood due to the lack of awareness, the presence of other dengue-like febrile diseases, and insufficient laboratory capabilities. This paper reports on the import of dengue virus serotype 2 case from Côte d'Ivoire to Senegal in West Africa. Phylogenetic analysis based on full-length genome sequence revealed that the isolate clustered with strains of cosmopolitan genotypes from the Burkina Faso outbreak in 2016 and those from the ongoing dengue fever outbreak in Côte d'Ivoire. This suggests a possible spread of strains from the Burkina Faso outbreak to other West African countries including Côte d'Ivoire and Senegal.
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Affiliation(s)
- Idrissa Dieng
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Moussa Moïse Diagne
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Marie Henriette Dior Ndione
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Boris Gildas Hedible
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mamadou Diop
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Edgard Valéry Adjoguoua
- Departement des virus épidemiques, Institut Pasteur de Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Yahaya Sylla
- Departement des virus épidemiques, Institut Pasteur de Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Herve Kadjo
- Departement des virus épidemiques, Institut Pasteur de Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou Alpha Sall
- 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
| | - Ousmane Faye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
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19
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Evolution, heterogeneity and global dispersal of cosmopolitan genotype of Dengue virus type 2. Sci Rep 2021; 11:13496. [PMID: 34188091 PMCID: PMC8241877 DOI: 10.1038/s41598-021-92783-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023] Open
Abstract
Dengue virus type 2 (DENV-2) contributes substantially to the dengue burden and dengue-related mortality in the tropics and sub-tropics. DENV-2 includes six genotypes, among which cosmopolitan genotype is the most widespread. The present study investigated the evolution, intra-genotype heterogeneity and dispersal of cosmopolitan genotype to understand unique genetic characteristics that have shaped the molecular epidemiology and distribution of cosmopolitan lineages. The spatial analysis demonstrated a wide geo-distribution of cosmopolitan genotype through an extensive inter-continental network, anchored in Southeast Asia and Indian sub-continent. Intra-genotype analyses using 3367 envelope gene sequences revealed six distinct lineages within the cosmopolitan genotype, namely the Indian sub-continent lineage and five other lineages. Indian sub-continent lineage was the most diverged among six lineages and has almost reached the nucleotide divergence threshold of 6% within E gene to qualify as a separate genotype. Genome wide amino acid signatures and selection pressure analyses further suggested differences in evolutionary characteristics between the Indian sub-continent lineage and other lineages. The present study narrates a comprehensive genomic analysis of cosmopolitan genotype and presents notable genetic characteristics that occurred during its evolution and global expansion. Whether those characteristics conferred a fitness advantage to cosmopolitan genotype in different geographies warrant further investigations.
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20
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Genomic investigation of a dengue virus outbreak in Thiès, Senegal, in 2018. Sci Rep 2021; 11:10321. [PMID: 33990632 PMCID: PMC8121849 DOI: 10.1038/s41598-021-89070-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/16/2021] [Indexed: 12/23/2022] Open
Abstract
Dengue virus is a major and rapidly growing public health concern in tropic and subtropic regions across the globe. In late 2018, Senegal experienced its largest dengue virus outbreak to date, covering several regions. However, little is known about the genetic diversity of dengue virus (DENV) in Senegal. Here we report complete viral genomes from 17 previously undetected DENV cases from the city of Thiès. In total we identified 19 cases of DENV in a cohort of 198 individuals with fever collected in October and November 2018. We detected 3 co-circulating serotypes; DENV 3 was the most frequent accounting for 11/17 sequences (65%), 4 (23%) were DENV2 and 2 (12%) were DENV1. Sequences were most similar to recent sequences from West Africa, suggesting ongoing local circulation of viral populations; however, detailed inference is limited by the scarcity of available genomic data. We did not find clear associations with reported clinical signs or symptoms, highlighting the importance of testing for diagnosing febrile diseases. Overall, these findings expand the known range of DENV in Senegal, and underscore the need for better genomic characterization of DENV in West Africa.
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21
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Adelino TÉR, Giovanetti M, Fonseca V, Xavier J, de Abreu ÁS, do Nascimento VA, Demarchi LHF, Oliveira MAA, da Silva VL, de Mello ALES, Cunha GM, Santos RH, de Oliveira EC, Júnior JAC, de Melo Iani FC, de Filippis AMB, de Abreu AL, de Jesus R, de Albuquerque CFC, Rico JM, do Carmo Said RF, Silva JA, de Moura NFO, Leite P, Frutuoso LCV, Haddad SK, Martínez A, Barreto FK, Vazquez CC, da Cunha RV, Araújo ELL, de Oliveira Tosta SF, de Araújo Fabri A, Chalhoub FLL, da Silva Lemos P, de Bruycker-Nogueira F, de Castro Lichs GG, Zardin MCSU, Segovia FMC, Gonçalves CCM, Grillo ZDCF, Slavov SN, Pereira LA, Mendonça AF, Pereira FM, de Magalhães JJF, Dos Santos Júnior ADCM, de Lima MM, Nogueira RMR, Góes-Neto A, de Carvalho Azevedo VA, Ramalho DB, Oliveira WK, Macario EM, de Medeiros AC, Pimentel V, Holmes EC, de Oliveira T, Lourenço J, Alcantara LCJ. Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil. Nat Commun 2021; 12:2296. [PMID: 33863880 PMCID: PMC8052316 DOI: 10.1038/s41467-021-22607-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 03/17/2021] [Indexed: 12/17/2022] Open
Abstract
Brazil experienced a large dengue virus (DENV) epidemic in 2019, highlighting a continuous struggle with effective control and public health preparedness. Using Oxford Nanopore sequencing, we led field and classroom initiatives for the monitoring of DENV in Brazil, generating 227 novel genome sequences of DENV1-2 from 85 municipalities (2015-2019). This equated to an over 50% increase in the number of DENV genomes from Brazil available in public databases. Using both phylogenetic and epidemiological models we retrospectively reconstructed the recent transmission history of DENV1-2. Phylogenetic analysis revealed complex patterns of transmission, with both lineage co-circulation and replacement. We identified two lineages within the DENV2 BR-4 clade, for which we estimated the effective reproduction number and pattern of seasonality. Overall, the surveillance outputs and training initiative described here serve as a proof-of-concept for the utility of real-time portable sequencing for research and local capacity building in the genomic surveillance of emerging viruses.
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Affiliation(s)
- Talita Émile Ribeiro Adelino
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Vagner Fonseca
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joilson Xavier
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Álvaro Salgado de Abreu
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Valdinete Alves do Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | | | | | | | | | | | - Roselene Hans Santos
- Laboratório Central de Saúde Pública Dr. Milton Bezerra Sobral, Recife, Pernambuco, Brazil
| | | | | | - Felipe Campos de Melo Iani
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Ana Maria Bispo de Filippis
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - André Luiz de Abreu
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - Ronaldo de Jesus
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | | | - Jairo Mendez Rico
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil
| | | | - Joscélio Aguiar Silva
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - Noely Fabiana Oliveira de Moura
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - Priscila Leite
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - Lívia Carla Vinhal Frutuoso
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | | | | | | | | | | | - Emerson Luiz Lima Araújo
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | | | - Allison de Araújo Fabri
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Flávia Löwen Levy Chalhoub
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | | | | | | | | | | | - Luiz Augusto Pereira
- Laboratório Central de Saúde Pública Dr. Giovanni Cysneiros, Goiânia, Goiás, Brazil
| | - Ana Flávia Mendonça
- Laboratório Central de Saúde Pública Dr. Giovanni Cysneiros, Goiânia, Goiás, Brazil
| | | | | | | | | | - Rita Maria Ribeiro Nogueira
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Aristóteles Góes-Neto
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Dario Brock Ramalho
- Secretaria de Saúde do Estado de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | | | - Victor Pimentel
- Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - José Lourenço
- Department of Zoology, Peter Medawar Building, University of Oxford, Oxford, UK.
| | - Luiz Carlos Junior Alcantara
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil.
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22
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Sebastião CS, Neto Z, Martinez P, Jandondo D, Antonio J, Galangue M, de Carvalho M, David K, Miranda J, Afonso P, Inglês L, Carrelero RR, de Vasconcelos JN, Morais J. Sociodemographic characteristics and risk factors related to SARS-CoV-2 infection in Luanda, Angola. PLoS One 2021; 16:e0249249. [PMID: 33765102 PMCID: PMC7993870 DOI: 10.1371/journal.pone.0249249] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/10/2021] [Indexed: 01/07/2023] Open
Abstract
This study aimed to investigate the characteristics related to SARS-CoV-2 in Luanda, Angola. A total of 622 individuals were screened for SARS-CoV-2 from January to September 2020. Chi-square and logistic regression were used to identify the relationship between sociodemographic characteristics and SARS-CoV-2. Of the 622 tested, 14.3% tested positive. The infection rate was the same for both genders (14.3%). Individuals ≥40 years old, from non-urbanized areas, and healthcare professionals had a higher frequency of infection. The risk of infection was very high in individuals ≥60 years old (AOR: 23.3, 95% CI: 4.83-112), in women (AOR: 1.24, 95% CI: 0.76-2.04), in Luanda (AOR: 7.40, 95% CI: 1.64-33.4), and healthcare professionals (AOR: 1.27, 95% CI: 0.60-2.71), whereas a low risk was observed in individuals from urbanized areas (AOR: 0.44, 95% CI: 0.26-0.75). Our results suggest that Angolan authorities should implement a greater effort in non-urbanized areas and among healthcare professionals since when these individuals presented any indication for a COVID-19 test, such as fever/cough/myalgia, they were more likely to test positive for SARS-CoV-2 than having some other cause for symptoms.
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Affiliation(s)
- Cruz S. Sebastião
- Centro de Investigação em Saúde de Angola, Caxito, Angola
- Instituto Nacional de Investigação em Saúde, Luanda, Angola
- Instituto Superior de Ciências da Saúde, Universidade Agostinho Neto, Luanda, Angola
| | - Zoraima Neto
- Instituto Nacional de Investigação em Saúde, Luanda, Angola
| | - Pedro Martinez
- Instituto Nacional de Investigação em Saúde, Luanda, Angola
| | | | - Janete Antonio
- Instituto Nacional de Investigação em Saúde, Luanda, Angola
| | | | | | | | - Julio Miranda
- Instituto Nacional de Investigação em Saúde, Luanda, Angola
| | - Pedro Afonso
- Instituto Nacional de Investigação em Saúde, Luanda, Angola
| | - Luzia Inglês
- Instituto Nacional de Investigação em Saúde, Luanda, Angola
| | | | - Jocelyne Neto de Vasconcelos
- Centro de Investigação em Saúde de Angola, Caxito, Angola
- Instituto Nacional de Investigação em Saúde, Luanda, Angola
| | - Joana Morais
- Instituto Nacional de Investigação em Saúde, Luanda, Angola
- Faculdade de Medicina, Universidade Agostinho Neto, Luanda, Angola
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23
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Hill SC, Vasconcelos J, Neto Z, Jandondo D, Zé-Zé L, Aguiar RS, Xavier J, Thézé J, Mirandela M, Micolo Cândido AL, Vaz F, Sebastião CDS, Wu CH, Kraemer MUG, Melo A, Schamber-Reis BLF, de Azevedo GS, Tanuri A, Higa LM, Clemente C, da Silva SP, da Silva Candido D, Claro IM, Quibuco D, Domingos C, Pocongo B, Watts AG, Khan K, Alcantara LCJ, Sabino EC, Lackritz E, Pybus OG, Alves MJ, Afonso J, Faria NR. Emergence of the Asian lineage of Zika virus in Angola: an outbreak investigation. THE LANCET. INFECTIOUS DISEASES 2020; 19:1138-1147. [PMID: 31559967 PMCID: PMC6892302 DOI: 10.1016/s1473-3099(19)30293-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 05/05/2019] [Accepted: 05/30/2019] [Indexed: 01/05/2023]
Abstract
Background Zika virus infections and suspected microcephaly cases have been reported in Angola since late 2016, but no data are available about the origins, epidemiology, and diversity of the virus. We aimed to investigate the emergence and circulation of Zika virus in Angola. Methods Diagnostic samples collected by the Angolan Ministry of Health as part of routine arboviral surveillance were tested by real-time reverse transcription PCR by the Instituto Nacional de Investigação em Saúde (Ministry of Health, Luanda, Angola). To identify further samples positive for Zika virus and appropriate for genomic sequencing, we also tested samples from a 2017 study of people with HIV in Luanda. Portable sequencing was used to generate Angolan Zika virus genome sequences from three people positive for Zika virus infection by real-time reverse transcription PCR, including one neonate with microcephaly. Genetic and mobility data were analysed to investigate the date of introduction and geographical origin of Zika virus in Angola. Brain CT and MRI, and serological assays were done on a child with microcephaly to confirm microcephaly and assess previous Zika virus infection. Findings Serum samples from 54 people with suspected acute Zika virus infection, 76 infants with suspected microcephaly, 24 mothers of infants with suspected microcephaly, 336 patients with suspected dengue virus or chikungunya virus infection, and 349 samples from the HIV study were tested by real-time reverse transcription PCR. Four cases identified between December, 2016, and June, 2017, tested positive for Zika virus. Analyses of viral genomic and human mobility data suggest that Zika virus was probably introduced to Angola from Brazil between July, 2015, and June, 2016. This introduction probably initiated local circulation of Zika virus in Angola that continued until at least June, 2017. The infant with microcephaly in whom CT and MRI were done had brain abnormalities consistent with congenital Zika syndrome and serological evidence for Zika virus infection. Interpretation Our analyses show that autochthonous transmission of the Asian lineage of Zika virus has taken place in Africa. Zika virus surveillance and surveillance of associated cases of microcephaly throughout the continent is crucial. Funding Royal Society, Wellcome Trust, Global Challenges Research Fund (UK Research and Innovation), Africa Oxford, John Fell Fund, Oxford Martin School, European Research Council, Departamento de Ciência e Tecnologia/Ministério da Saúde/National Council for Scientific and Technological Development, and Ministério da Educação/Coordenação de Aperfeicoamento de Pessoal de Nível Superior.
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Affiliation(s)
- Sarah C Hill
- Department of Zoology, University of Oxford, Oxford, UK
| | | | - Zoraima Neto
- Instituto Nacional de Investigação em Saúde, Ministry of Health, Luanda, Angola
| | - Domingos Jandondo
- Instituto Nacional de Investigação em Saúde, Ministry of Health, Luanda, Angola
| | - Líbia Zé-Zé
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Águas de Moura, Portugal; University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Lisbon, Portugal
| | - Renato Santana Aguiar
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Joilson Xavier
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Julien Thézé
- Department of Zoology, University of Oxford, Oxford, UK
| | - Marinela Mirandela
- Instituto Nacional de Investigação em Saúde, Ministry of Health, Luanda, Angola
| | | | - Filipa Vaz
- Instituto Nacional de Investigação em Saúde, Ministry of Health, Luanda, Angola
| | - Cruz Dos Santos Sebastião
- Instituto Nacional de Investigação em Saúde, Ministry of Health, Luanda, Angola; Instituto Superior de Ciências da Saúde, Universidade Agostinho Neto, Luanda, Angola
| | - Chieh-Hsi Wu
- Department of Statistics, University of Oxford, Oxford, UK
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK; Computational Epidemiology Lab, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Adriana Melo
- Instituto de Pesquisa Professor Joaquim Amorim Neto, Campina Grande, Brazil
| | | | | | - Amilcar Tanuri
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luiza M Higa
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | - Ingra M Claro
- Instituto de Medicina Tropical e Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | - Alexander G Watts
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada; BlueDot, Toronto, ON, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada; BlueDot, Toronto, ON, Canada; Department of Medicine, University of Toronto, Canada
| | - Luiz Carlos Junior Alcantara
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Laboratório de Flavivirus, IOC-Fundação Oswaldo Cruz/MS, Rio de Janeiro, Brazil
| | - Ester C Sabino
- Instituto de Medicina Tropical e Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Maria-João Alves
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Águas de Moura, Portugal
| | - Joana Afonso
- Instituto Nacional de Investigação em Saúde, Ministry of Health, Luanda, Angola.
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK.
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24
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de Jesus JG, Dutra KR, Sales FCDS, Claro IM, Terzian AC, Candido DDS, Hill SC, Thézé J, Torres C, D'Agostini TL, Felix AC, Reis AFN, Alcantara LCJ, de Abreu AL, Croda JH, de Oliveira WK, de Filipis AMB, Camis MDCRDS, Romano CM. Genomic detection of a virus lineage replacement event of dengue virus serotype 2 in Brazil, 2019. Mem Inst Oswaldo Cruz 2020; 115:e190423. [PMID: 32428189 PMCID: PMC7227788 DOI: 10.1590/0074-02760190423] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 04/06/2020] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Despite efforts to mitigate the impact of dengue virus (DENV) epidemics, the virus remains a public health problem in tropical and subtropical regions around the world. Most DENV cases in the Americas between January and July 2019 were reported in Brazil. São Paulo State in the southeast of Brazil has reported nearly half of all DENV infections in the country. OBJECTIVES To understand the origin and dynamics of the 2019 DENV outbreak. METHODS Here using portable nanopore sequencing we generated20 new DENV genome sequences from viremic patients with suspected dengue infection residing in two of the most-affected municipalities of São Paulo State, Araraquara and São José do Rio Preto. We conducted a comprehensive phylogenetic analysis with 1,630 global DENV strains to better understand the evolutionary history of the DENV lineages that currently circulate in the region. FINDINGS The new outbreak strains were classified as DENV2 genotype III (American/Asian genotype). Our analysis shows that the 2019 outbreak is the result of a novel DENV lineage that was recently introduced to Brazil from the Caribbean region. Dating phylogeographic analysis suggests that DENV2-III BR-4 was introduced to Brazil in or around early 2014, possibly from the Caribbean region. MAIN CONCLUSIONS Our study describes the early detection of a newly introduced and rapidly-expanding DENV2 virus lineage in Brazil.
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Affiliation(s)
| | - Karina Rocha Dutra
- Laboratório de Pesquisa em Virologia, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP, Brazil
| | | | - Ingra Morales Claro
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ana Carolina Terzian
- Laboratório de Pesquisa em Virologia, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP, Brazil
| | | | - Sarah C Hill
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Julien Thézé
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Celeste Torres
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Tatiana Lang D'Agostini
- Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica Professor Alexandre Vranjac, Secretaria de Estado da Saúde, São Paulo, SP, Brasil
| | - Alvina Clara Felix
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | | | - André L de Abreu
- Coordenação Geral de Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, DF, Brazil
| | - Júlio Hr Croda
- Coordenação Geral de Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, DF, Brazil
| | - Wanderson K de Oliveira
- Coordenação Geral de Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, DF, Brazil
| | - Ana Maria Bispo de Filipis
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | - Camila Malta Romano
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, SP, Brazil
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25
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Systematic Review of Important Viral Diseases in Africa in Light of the 'One Health' Concept. Pathogens 2020; 9:pathogens9040301. [PMID: 32325980 PMCID: PMC7238228 DOI: 10.3390/pathogens9040301] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 12/19/2022] Open
Abstract
Emerging and re-emerging viral diseases are of great public health concern. The recent emergence of Severe Acute Respiratory Syndrome (SARS) related coronavirus (SARS-CoV-2) in December 2019 in China, which causes COVID-19 disease in humans, and its current spread to several countries, leading to the first pandemic in history to be caused by a coronavirus, highlights the significance of zoonotic viral diseases. Rift Valley fever, rabies, West Nile, chikungunya, dengue, yellow fever, Crimean-Congo hemorrhagic fever, Ebola, and influenza viruses among many other viruses have been reported from different African countries. The paucity of information, lack of knowledge, limited resources, and climate change, coupled with cultural traditions make the African continent a hotspot for vector-borne and zoonotic viral diseases, which may spread globally. Currently, there is no information available on the status of virus diseases in Africa. This systematic review highlights the available information about viral diseases, including zoonotic and vector-borne diseases, reported in Africa. The findings will help us understand the trend of emerging and re-emerging virus diseases within the African continent. The findings recommend active surveillance of viral diseases and strict implementation of One Health measures in Africa to improve human public health and reduce the possibility of potential pandemics due to zoonotic viruses.
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26
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Genomic monitoring to understand the emergence and spread of Usutu virus in the Netherlands, 2016-2018. Sci Rep 2020; 10:2798. [PMID: 32071379 PMCID: PMC7029044 DOI: 10.1038/s41598-020-59692-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/31/2020] [Indexed: 12/22/2022] Open
Abstract
Usutu virus (USUV) is a mosquito-borne flavivirus circulating in Western Europe that causes die-offs of mainly common blackbirds (Turdus merula). In the Netherlands, USUV was first detected in 2016, when it was identified as the likely cause of an outbreak in birds. In this study, dead blackbirds were collected, screened for the presence of USUV and submitted to Nanopore-based sequencing. Genomic sequences of 112 USUV were obtained and phylogenetic analysis showed that most viruses identified belonged to the USUV Africa 3 lineage, and molecular clock analysis evaluated their most recent common ancestor to 10 to 4 years before first detection of USUV in the Netherlands. USUV Europe 3 lineage, commonly found in Germany, was less frequently detected. This analyses further suggest some extent of circulation of USUV between the Netherlands, Germany and Belgium, as well as likely overwintering of USUV in the Netherlands.
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27
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Kiselev D, Matsvay A, Abramov I, Dedkov V, Shipulin G, Khafizov K. Current Trends in Diagnostics of Viral Infections of Unknown Etiology. Viruses 2020; 12:E211. [PMID: 32074965 PMCID: PMC7077230 DOI: 10.3390/v12020211] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/27/2022] Open
Abstract
Viruses are evolving at an alarming rate, spreading and inconspicuously adapting to cutting-edge therapies. Therefore, the search for rapid, informative and reliable diagnostic methods is becoming urgent as ever. Conventional clinical tests (PCR, serology, etc.) are being continually optimized, yet provide very limited data. Could high throughput sequencing (HTS) become the future gold standard in molecular diagnostics of viral infections? Compared to conventional clinical tests, HTS is universal and more precise at profiling pathogens. Nevertheless, it has not yet been widely accepted as a diagnostic tool, owing primarily to its high cost and the complexity of sample preparation and data analysis. Those obstacles must be tackled to integrate HTS into daily clinical practice. For this, three objectives are to be achieved: (1) designing and assessing universal protocols for library preparation, (2) assembling purpose-specific pipelines, and (3) building computational infrastructure to suit the needs and financial abilities of modern healthcare centers. Data harvested with HTS could not only augment diagnostics and help to choose the correct therapy, but also facilitate research in epidemiology, genetics and virology. This information, in turn, could significantly aid clinicians in battling viral infections.
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Affiliation(s)
- Daniel Kiselev
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- I.M. Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - Alina Matsvay
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
| | - Ivan Abramov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Vladimir Dedkov
- Pasteur Institute, Federal Service on Consumers’ Rights Protection and Human Well-Being Surveillance, 197101 Saint-Petersburg, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - German Shipulin
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Kamil Khafizov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
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28
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Stubbs SCB, Blacklaws BA, Yohan B, Yudhaputri FA, Hayati RF, Schwem B, Salvaña EM, Destura RV, Lester JS, Myint KS, Sasmono RT, Frost SDW. Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia. Virol J 2020; 17:24. [PMID: 32054488 PMCID: PMC7020346 DOI: 10.1186/s12985-020-1294-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/29/2020] [Indexed: 12/15/2022] Open
Abstract
Background Dengue virus (DENV) infects hundreds of thousands of people annually in Indonesia. However, DENV sequence data from the country are limited, as samples from outbreaks must be shipped across long-distances to suitably equipped laboratories to be sequenced. This approach is time-consuming, expensive, and frequently results in failure due to low viral load or degradation of the RNA genome. Methods We evaluated a method designed to address this challenge, using the ‘Primal Scheme’ multiplex PCR tiling approach to rapidly generate short, overlapping amplicons covering the complete DENV coding-region, and sequencing the amplicons on the portable Nanopore MinION device. The resulting sequence data was assessed in terms of genome coverage, consensus sequence accuracy and by phylogenetic analysis. Results The multiplex approach proved capable of producing near complete coding-region coverage from all samples tested (\documentclass[12pt]{minimal}
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\begin{document}$$ \overline{x} $$\end{document}x¯ = 99.96%, n = 18), 61% of which could not be fully amplified using the current, long-amplicon PCR, approach. Nanopore-generated consensus sequences were found to be between 99.17–99.92% identical to those produced by high-coverage Illumina sequencing. Consensus accuracy could be improved by masking regions below 20X coverage depth (99.69–99.92%). However, coding-region coverage was reduced at this depth (\documentclass[12pt]{minimal}
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\begin{document}$$ \overline{x} $$\end{document}x¯ = 93.48%). Nanopore and Illumina consensus sequences generated from the same samples formed monophyletic clades on phylogenetic analysis, and Indonesian consensus sequences accurately clustered by geographical origin. Conclusion The multiplex, short-amplicon approach proved superior for amplifying DENV genomes from clinical samples, particularly when the virus was present at low concentrations. The accuracy of Nanopore-generated consensus sequences from these amplicons was sufficient for identifying the geographic origin of the samples, demonstrating that the approach can be a useful tool for identifying and monitoring DENV clades circulating in low-resource settings across Indonesia. However, the inaccuracies in Nanopore-generated consensus sequences mean that the approach may not be appropriate for higher resolution transmission studies, particularly when more accurate sequencing technologies are available.
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Affiliation(s)
- Samuel C B Stubbs
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK.
| | - Barbara A Blacklaws
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | | | | | - Rahma F Hayati
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Brian Schwem
- University of Philippines Manila, Manila, Philippines
| | | | | | - James S Lester
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Khin S Myint
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | - Simon D W Frost
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK.,The Alan Turing Institution, London, UK.,Present address: London School of Hygiene and Tropical Medicine, London, UK.,Microsoft Healthcare, Redmond, USA
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29
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Jia L, Jiang M, Wu K, Hu J, Wang Y, Quan W, Hao M, Liu H, Wei H, Fan W, Liu W, Hu R, Wang D, Li J, Chen J, Liu D. Nanopore sequencing of African swine fever virus. SCIENCE CHINA. LIFE SCIENCES 2020; 63:160-164. [PMID: 31701406 DOI: 10.1007/s11427-019-9828-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 09/16/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Lijia Jia
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengwei Jiang
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Ke Wu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juefu Hu
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yang Wang
- GrandOmics Biosciences, Beijing, 101312, China
| | | | - Mengchan Hao
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Haizhou Liu
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,African Swine Fever Regional Laboratory of China, Wuhan, 430071, China
| | - Wenhui Fan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenjun Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Rongliang Hu
- Institute of Military Veterinary Medicine, Academy of Military Medical Science, Changchun, 130122, China
| | - Depeng Wang
- GrandOmics Biosciences, Beijing, 101312, China.,NextOmics Biosciences, Wuhan, 430074, China
| | - Jing Li
- University of Chinese Academy of Sciences, Beijing, 100049, China. .,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jianjun Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China. .,Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China. .,African Swine Fever Regional Laboratory of China, Wuhan, 430071, China. .,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Di Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China. .,Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China. .,African Swine Fever Regional Laboratory of China, Wuhan, 430071, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
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