Genome-Wide Diversity of Zika Virus
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10362/137472 |
Resumo: | The Zika virus (ZIKV) disease caused a public health emergency of international concern that started in February 2016. The overall number of ZIKV-related cases increased until November 2016, after which it declined sharply. While the evaluation of the potential risk and impact of future arbovirus epidemics remains challenging, intensified surveillance efforts along with a scale-up of ZIKV whole-genome sequencing provide an opportunity to understand the patterns of genetic diversity, evolution, and spread of ZIKV. However, a classification system that reflects the true extent of ZIKV genetic variation is lacking. Our objective was to characterize ZIKV genetic diversity and phylodynamics, identify genomic footprints of differentiation patterns, and propose a dynamic classification system that reflects its divergence levels. We analysed a curated dataset of 762 publicly available sequences spanning the full-length coding region of ZIKV from across its geographical span and collected between 1947 and 2021. The definition of genetic groups was based on comprehensive evolutionary dynamics analyses, which included recombination and phylogenetic analyses, within- and between-group pairwise genetic distances comparison, detection of selective pressure, and clustering analyses. Evidence for potential recombination events was detected in a few sequences. However, we argue that these events are likely due to sequencing errors as proposed in previous studies. There was evidence of strong purifying selection, widespread across the genome, as also detected for other arboviruses. A total of 50 sites showed evidence of positive selection, and for a few of these sites, there was amino acid (AA) differentiation between genetic clusters. Two main genetic clusters were defined, ZA and ZB, which correspond to the already characterized ‘African’ and ‘Asian’ genotypes, respectively. Within ZB, two subgroups, ZB.1 and ZB.2, represent the Asiatic and the American (and Oceania) lineages, respectively. ZB.1 is further subdivided into ZB.1.0 (a basal Malaysia sequence sampled in the 1960s and a recent Indian sequence), ZB.1.1 (South-Eastern Asia, Southern Asia, and Micronesia sequences), and ZB.1.2 (very similar sequences from the outbreak in Singapore). ZB.2 is subdivided into ZB.2.0 (basal American sequences and the sequences from French Polynesia, the putative origin of South America introduction), ZB.2.1 (Central America), and ZB.2.2 (Caribbean and North America). This classification system does not use geographical references and is flexible to accommodate potential future lineages. It will be a helpful tool for studies that involve analyses of ZIKV genomic variation and its association with pathogenicity and serve as a starting point for the public health surveillance and response to on-going and future epidemics and to outbreaks that lead to the emergence of new variants. |
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Genome-Wide Diversity of Zika VirusExploring Spatio-Temporal Dynamics to Guide a New Nomenclature ProposalGeneticsVirologyInfectious DiseasesEcology, Evolution, Behavior and SystematicsSDG 3 - Good Health and Well-beingThe Zika virus (ZIKV) disease caused a public health emergency of international concern that started in February 2016. The overall number of ZIKV-related cases increased until November 2016, after which it declined sharply. While the evaluation of the potential risk and impact of future arbovirus epidemics remains challenging, intensified surveillance efforts along with a scale-up of ZIKV whole-genome sequencing provide an opportunity to understand the patterns of genetic diversity, evolution, and spread of ZIKV. However, a classification system that reflects the true extent of ZIKV genetic variation is lacking. Our objective was to characterize ZIKV genetic diversity and phylodynamics, identify genomic footprints of differentiation patterns, and propose a dynamic classification system that reflects its divergence levels. We analysed a curated dataset of 762 publicly available sequences spanning the full-length coding region of ZIKV from across its geographical span and collected between 1947 and 2021. The definition of genetic groups was based on comprehensive evolutionary dynamics analyses, which included recombination and phylogenetic analyses, within- and between-group pairwise genetic distances comparison, detection of selective pressure, and clustering analyses. Evidence for potential recombination events was detected in a few sequences. However, we argue that these events are likely due to sequencing errors as proposed in previous studies. There was evidence of strong purifying selection, widespread across the genome, as also detected for other arboviruses. A total of 50 sites showed evidence of positive selection, and for a few of these sites, there was amino acid (AA) differentiation between genetic clusters. Two main genetic clusters were defined, ZA and ZB, which correspond to the already characterized ‘African’ and ‘Asian’ genotypes, respectively. Within ZB, two subgroups, ZB.1 and ZB.2, represent the Asiatic and the American (and Oceania) lineages, respectively. ZB.1 is further subdivided into ZB.1.0 (a basal Malaysia sequence sampled in the 1960s and a recent Indian sequence), ZB.1.1 (South-Eastern Asia, Southern Asia, and Micronesia sequences), and ZB.1.2 (very similar sequences from the outbreak in Singapore). ZB.2 is subdivided into ZB.2.0 (basal American sequences and the sequences from French Polynesia, the putative origin of South America introduction), ZB.2.1 (Central America), and ZB.2.2 (Caribbean and North America). This classification system does not use geographical references and is flexible to accommodate potential future lineages. It will be a helpful tool for studies that involve analyses of ZIKV genomic variation and its association with pathogenicity and serve as a starting point for the public health surveillance and response to on-going and future epidemics and to outbreaks that lead to the emergence of new variants.Instituto de Higiene e Medicina Tropical (IHMT)Global Health and Tropical Medicine (GHTM)TB, HIV and opportunistic diseases and pathogens (THOP)RUNSeabra, Sofia GLibin, Pieter J. K.Theys, KristofZhukova, AnnaPotter, Barney INebenzahl-guimaraes, HannaGorbalenya, Alexander ESidorov, Igor A.Pimentel, VictorPingarilho, MartaDe Vasconcelos, Ana T. R.Dellicour, SimonKhouri, RicardoGascuel, OlivierVandamme, Anne-miekeBaele, GuyCuypers, LizeAbecasis, Ana B2022-05-05T22:35:55Z2022-03-292022-03-29T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10362/137472eng2057-1577PURE: 43072903https://doi.org/10.1093/ve/veac029info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T05:14:57Zoai:run.unl.pt:10362/137472Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:48:50.767369Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Genome-Wide Diversity of Zika Virus Exploring Spatio-Temporal Dynamics to Guide a New Nomenclature Proposal |
title |
Genome-Wide Diversity of Zika Virus |
spellingShingle |
Genome-Wide Diversity of Zika Virus Seabra, Sofia G Genetics Virology Infectious Diseases Ecology, Evolution, Behavior and Systematics SDG 3 - Good Health and Well-being |
title_short |
Genome-Wide Diversity of Zika Virus |
title_full |
Genome-Wide Diversity of Zika Virus |
title_fullStr |
Genome-Wide Diversity of Zika Virus |
title_full_unstemmed |
Genome-Wide Diversity of Zika Virus |
title_sort |
Genome-Wide Diversity of Zika Virus |
author |
Seabra, Sofia G |
author_facet |
Seabra, Sofia G Libin, Pieter J. K. Theys, Kristof Zhukova, Anna Potter, Barney I Nebenzahl-guimaraes, Hanna Gorbalenya, Alexander E Sidorov, Igor A. Pimentel, Victor Pingarilho, Marta De Vasconcelos, Ana T. R. Dellicour, Simon Khouri, Ricardo Gascuel, Olivier Vandamme, Anne-mieke Baele, Guy Cuypers, Lize Abecasis, Ana B |
author_role |
author |
author2 |
Libin, Pieter J. K. Theys, Kristof Zhukova, Anna Potter, Barney I Nebenzahl-guimaraes, Hanna Gorbalenya, Alexander E Sidorov, Igor A. Pimentel, Victor Pingarilho, Marta De Vasconcelos, Ana T. R. Dellicour, Simon Khouri, Ricardo Gascuel, Olivier Vandamme, Anne-mieke Baele, Guy Cuypers, Lize Abecasis, Ana B |
author2_role |
author author author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Instituto de Higiene e Medicina Tropical (IHMT) Global Health and Tropical Medicine (GHTM) TB, HIV and opportunistic diseases and pathogens (THOP) RUN |
dc.contributor.author.fl_str_mv |
Seabra, Sofia G Libin, Pieter J. K. Theys, Kristof Zhukova, Anna Potter, Barney I Nebenzahl-guimaraes, Hanna Gorbalenya, Alexander E Sidorov, Igor A. Pimentel, Victor Pingarilho, Marta De Vasconcelos, Ana T. R. Dellicour, Simon Khouri, Ricardo Gascuel, Olivier Vandamme, Anne-mieke Baele, Guy Cuypers, Lize Abecasis, Ana B |
dc.subject.por.fl_str_mv |
Genetics Virology Infectious Diseases Ecology, Evolution, Behavior and Systematics SDG 3 - Good Health and Well-being |
topic |
Genetics Virology Infectious Diseases Ecology, Evolution, Behavior and Systematics SDG 3 - Good Health and Well-being |
description |
The Zika virus (ZIKV) disease caused a public health emergency of international concern that started in February 2016. The overall number of ZIKV-related cases increased until November 2016, after which it declined sharply. While the evaluation of the potential risk and impact of future arbovirus epidemics remains challenging, intensified surveillance efforts along with a scale-up of ZIKV whole-genome sequencing provide an opportunity to understand the patterns of genetic diversity, evolution, and spread of ZIKV. However, a classification system that reflects the true extent of ZIKV genetic variation is lacking. Our objective was to characterize ZIKV genetic diversity and phylodynamics, identify genomic footprints of differentiation patterns, and propose a dynamic classification system that reflects its divergence levels. We analysed a curated dataset of 762 publicly available sequences spanning the full-length coding region of ZIKV from across its geographical span and collected between 1947 and 2021. The definition of genetic groups was based on comprehensive evolutionary dynamics analyses, which included recombination and phylogenetic analyses, within- and between-group pairwise genetic distances comparison, detection of selective pressure, and clustering analyses. Evidence for potential recombination events was detected in a few sequences. However, we argue that these events are likely due to sequencing errors as proposed in previous studies. There was evidence of strong purifying selection, widespread across the genome, as also detected for other arboviruses. A total of 50 sites showed evidence of positive selection, and for a few of these sites, there was amino acid (AA) differentiation between genetic clusters. Two main genetic clusters were defined, ZA and ZB, which correspond to the already characterized ‘African’ and ‘Asian’ genotypes, respectively. Within ZB, two subgroups, ZB.1 and ZB.2, represent the Asiatic and the American (and Oceania) lineages, respectively. ZB.1 is further subdivided into ZB.1.0 (a basal Malaysia sequence sampled in the 1960s and a recent Indian sequence), ZB.1.1 (South-Eastern Asia, Southern Asia, and Micronesia sequences), and ZB.1.2 (very similar sequences from the outbreak in Singapore). ZB.2 is subdivided into ZB.2.0 (basal American sequences and the sequences from French Polynesia, the putative origin of South America introduction), ZB.2.1 (Central America), and ZB.2.2 (Caribbean and North America). This classification system does not use geographical references and is flexible to accommodate potential future lineages. It will be a helpful tool for studies that involve analyses of ZIKV genomic variation and its association with pathogenicity and serve as a starting point for the public health surveillance and response to on-going and future epidemics and to outbreaks that lead to the emergence of new variants. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-05-05T22:35:55Z 2022-03-29 2022-03-29T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10362/137472 |
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http://hdl.handle.net/10362/137472 |
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eng |
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eng |
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2057-1577 PURE: 43072903 https://doi.org/10.1093/ve/veac029 |
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info:eu-repo/semantics/openAccess |
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openAccess |
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application/pdf |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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