Toward unified molecular surveillance of RSV: A proposal for genotype definition

Autores
Goya, Stephanie; Galiano, Mónica; Nauwelaers, Inne; Trento, Alfonsina; Openshaw, Peter J.; Mistchenko, Alicia Susana; Zambon, Maria; Viegas, Mariana
Año de publicación
2020
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: Human respiratory syncytial virus (RSV) is classified into antigenic subgroups A and B. Thirteen genotypes have been defined for RSV-A and 20 for RSV-B, without any consensus on genotype definition. Methods: We evaluated clustering of RSV sequences published in GenBank until February 2018 to define genotypes by using maximum likelihood and Bayesian phylogenetic analyses and average p-distances. Results: We compared the patterns of sequence clustering of complete genomes; the three surface glycoproteins genes (SH, G, and F, single and concatenated); the ectodomain and the 2nd hypervariable region of G gene. Although complete genome analysis achieved the best resolution, the F, G, and G-ectodomain phylogenies showed similar topologies with statistical support comparable to complete genome. Based on the widespread geographic representation and large number of available G-ectodomain sequences, this region was chosen as the minimum region suitable for RSV genotyping. A genotype was defined as a monophyletic cluster of sequences with high statistical support (≥80% bootstrap and ≥0.8 posterior probability), with an intragenotype p-distance ≤0.03 for both subgroups and an intergenotype p-distance ≥0.09 for RSV-A and ≥0.05 for RSV-B. In this work, the number of genotypes was reduced from 13 to three for RSV-A (GA1-GA3) and from 20 to seven for RSV-B (GB1-GB7). Within these, two additional levels of classification were defined: subgenotypes and lineages. Signature amino acid substitutions to complement this classification were also identified. Conclusions: We propose an objective protocol for RSV genotyping suitable for adoption as an international standard to support the global expansion of RSV molecular surveillance.
Fil: Goya, Stephanie. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Galiano, Mónica. Public Health England; Reino Unido
Fil: Nauwelaers, Inne. Imperial College London; Reino Unido
Fil: Trento, Alfonsina. Instituto de Investigación Hospital 12 de Octubre; España
Fil: Openshaw, Peter J.. Imperial College London; Reino Unido
Fil: Mistchenko, Alicia Susana. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas; Argentina
Fil: Zambon, Maria. Public Health England; Reino Unido
Fil: Viegas, Mariana. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Materia
AVERAGE GENETIC DISTANCE
GENOTYPES
GLOBAL MOLECULAR SURVEILLANCE
HUMAN ORTHOPNEUMOVIRUS
HUMAN RESPIRATORY SYNCYTIAL VIRUS
LINEAGES
PHYLOGENETIC ANALYSIS
SUBGENOTYPES
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/168183
Acceder
id CONICETDig_d5694c1b62de74fe5a340c3f5c8ae226
oai_identifier_str oai:ri.conicet.gov.ar:11336/168183
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Toward unified molecular surveillance of RSV: A proposal for genotype definitionGoya, StephanieGaliano, MónicaNauwelaers, InneTrento, AlfonsinaOpenshaw, Peter J.Mistchenko, Alicia SusanaZambon, MariaViegas, MarianaAVERAGE GENETIC DISTANCEGENOTYPESGLOBAL MOLECULAR SURVEILLANCEHUMAN ORTHOPNEUMOVIRUSHUMAN RESPIRATORY SYNCYTIAL VIRUSLINEAGESPHYLOGENETIC ANALYSISSUBGENOTYPEShttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Background: Human respiratory syncytial virus (RSV) is classified into antigenic subgroups A and B. Thirteen genotypes have been defined for RSV-A and 20 for RSV-B, without any consensus on genotype definition. Methods: We evaluated clustering of RSV sequences published in GenBank until February 2018 to define genotypes by using maximum likelihood and Bayesian phylogenetic analyses and average p-distances. Results: We compared the patterns of sequence clustering of complete genomes; the three surface glycoproteins genes (SH, G, and F, single and concatenated); the ectodomain and the 2nd hypervariable region of G gene. Although complete genome analysis achieved the best resolution, the F, G, and G-ectodomain phylogenies showed similar topologies with statistical support comparable to complete genome. Based on the widespread geographic representation and large number of available G-ectodomain sequences, this region was chosen as the minimum region suitable for RSV genotyping. A genotype was defined as a monophyletic cluster of sequences with high statistical support (≥80% bootstrap and ≥0.8 posterior probability), with an intragenotype p-distance ≤0.03 for both subgroups and an intergenotype p-distance ≥0.09 for RSV-A and ≥0.05 for RSV-B. In this work, the number of genotypes was reduced from 13 to three for RSV-A (GA1-GA3) and from 20 to seven for RSV-B (GB1-GB7). Within these, two additional levels of classification were defined: subgenotypes and lineages. Signature amino acid substitutions to complement this classification were also identified. Conclusions: We propose an objective protocol for RSV genotyping suitable for adoption as an international standard to support the global expansion of RSV molecular surveillance.Fil: Goya, Stephanie. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Galiano, Mónica. Public Health England; Reino UnidoFil: Nauwelaers, Inne. Imperial College London; Reino UnidoFil: Trento, Alfonsina. Instituto de Investigación Hospital 12 de Octubre; EspañaFil: Openshaw, Peter J.. Imperial College London; Reino UnidoFil: Mistchenko, Alicia Susana. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas; ArgentinaFil: Zambon, Maria. Public Health England; Reino UnidoFil: Viegas, Mariana. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaWiley Blackwell Publishing, Inc2020-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/168183Goya, Stephanie; Galiano, Mónica; Nauwelaers, Inne; Trento, Alfonsina; Openshaw, Peter J.; et al.; Toward unified molecular surveillance of RSV: A proposal for genotype definition; Wiley Blackwell Publishing, Inc; Influenza And Other Respiratory Viruses; 14; 3; 5-2020; 274-2851750-26401750-2659CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/10.1111/irv.12715info:eu-repo/semantics/altIdentifier/doi/10.1111/irv.12715info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T14:26:56Zoai:ri.conicet.gov.ar:11336/168183instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-15 14:26:57.234CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Toward unified molecular surveillance of RSV: A proposal for genotype definition
title Toward unified molecular surveillance of RSV: A proposal for genotype definition
spellingShingle Toward unified molecular surveillance of RSV: A proposal for genotype definition
Goya, Stephanie
AVERAGE GENETIC DISTANCE
GENOTYPES
GLOBAL MOLECULAR SURVEILLANCE
HUMAN ORTHOPNEUMOVIRUS
HUMAN RESPIRATORY SYNCYTIAL VIRUS
LINEAGES
PHYLOGENETIC ANALYSIS
SUBGENOTYPES
title_short Toward unified molecular surveillance of RSV: A proposal for genotype definition
title_full Toward unified molecular surveillance of RSV: A proposal for genotype definition
title_fullStr Toward unified molecular surveillance of RSV: A proposal for genotype definition
title_full_unstemmed Toward unified molecular surveillance of RSV: A proposal for genotype definition
title_sort Toward unified molecular surveillance of RSV: A proposal for genotype definition
dc.creator.none.fl_str_mv Goya, Stephanie
Galiano, Mónica
Nauwelaers, Inne
Trento, Alfonsina
Openshaw, Peter J.
Mistchenko, Alicia Susana
Zambon, Maria
Viegas, Mariana
author Goya, Stephanie
author_facet Goya, Stephanie
Galiano, Mónica
Nauwelaers, Inne
Trento, Alfonsina
Openshaw, Peter J.
Mistchenko, Alicia Susana
Zambon, Maria
Viegas, Mariana
author_role author
author2 Galiano, Mónica
Nauwelaers, Inne
Trento, Alfonsina
Openshaw, Peter J.
Mistchenko, Alicia Susana
Zambon, Maria
Viegas, Mariana
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv AVERAGE GENETIC DISTANCE
GENOTYPES
GLOBAL MOLECULAR SURVEILLANCE
HUMAN ORTHOPNEUMOVIRUS
HUMAN RESPIRATORY SYNCYTIAL VIRUS
LINEAGES
PHYLOGENETIC ANALYSIS
SUBGENOTYPES
topic AVERAGE GENETIC DISTANCE
GENOTYPES
GLOBAL MOLECULAR SURVEILLANCE
HUMAN ORTHOPNEUMOVIRUS
HUMAN RESPIRATORY SYNCYTIAL VIRUS
LINEAGES
PHYLOGENETIC ANALYSIS
SUBGENOTYPES
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Background: Human respiratory syncytial virus (RSV) is classified into antigenic subgroups A and B. Thirteen genotypes have been defined for RSV-A and 20 for RSV-B, without any consensus on genotype definition. Methods: We evaluated clustering of RSV sequences published in GenBank until February 2018 to define genotypes by using maximum likelihood and Bayesian phylogenetic analyses and average p-distances. Results: We compared the patterns of sequence clustering of complete genomes; the three surface glycoproteins genes (SH, G, and F, single and concatenated); the ectodomain and the 2nd hypervariable region of G gene. Although complete genome analysis achieved the best resolution, the F, G, and G-ectodomain phylogenies showed similar topologies with statistical support comparable to complete genome. Based on the widespread geographic representation and large number of available G-ectodomain sequences, this region was chosen as the minimum region suitable for RSV genotyping. A genotype was defined as a monophyletic cluster of sequences with high statistical support (≥80% bootstrap and ≥0.8 posterior probability), with an intragenotype p-distance ≤0.03 for both subgroups and an intergenotype p-distance ≥0.09 for RSV-A and ≥0.05 for RSV-B. In this work, the number of genotypes was reduced from 13 to three for RSV-A (GA1-GA3) and from 20 to seven for RSV-B (GB1-GB7). Within these, two additional levels of classification were defined: subgenotypes and lineages. Signature amino acid substitutions to complement this classification were also identified. Conclusions: We propose an objective protocol for RSV genotyping suitable for adoption as an international standard to support the global expansion of RSV molecular surveillance.
Fil: Goya, Stephanie. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Galiano, Mónica. Public Health England; Reino Unido
Fil: Nauwelaers, Inne. Imperial College London; Reino Unido
Fil: Trento, Alfonsina. Instituto de Investigación Hospital 12 de Octubre; España
Fil: Openshaw, Peter J.. Imperial College London; Reino Unido
Fil: Mistchenko, Alicia Susana. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas; Argentina
Fil: Zambon, Maria. Public Health England; Reino Unido
Fil: Viegas, Mariana. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description Background: Human respiratory syncytial virus (RSV) is classified into antigenic subgroups A and B. Thirteen genotypes have been defined for RSV-A and 20 for RSV-B, without any consensus on genotype definition. Methods: We evaluated clustering of RSV sequences published in GenBank until February 2018 to define genotypes by using maximum likelihood and Bayesian phylogenetic analyses and average p-distances. Results: We compared the patterns of sequence clustering of complete genomes; the three surface glycoproteins genes (SH, G, and F, single and concatenated); the ectodomain and the 2nd hypervariable region of G gene. Although complete genome analysis achieved the best resolution, the F, G, and G-ectodomain phylogenies showed similar topologies with statistical support comparable to complete genome. Based on the widespread geographic representation and large number of available G-ectodomain sequences, this region was chosen as the minimum region suitable for RSV genotyping. A genotype was defined as a monophyletic cluster of sequences with high statistical support (≥80% bootstrap and ≥0.8 posterior probability), with an intragenotype p-distance ≤0.03 for both subgroups and an intergenotype p-distance ≥0.09 for RSV-A and ≥0.05 for RSV-B. In this work, the number of genotypes was reduced from 13 to three for RSV-A (GA1-GA3) and from 20 to seven for RSV-B (GB1-GB7). Within these, two additional levels of classification were defined: subgenotypes and lineages. Signature amino acid substitutions to complement this classification were also identified. Conclusions: We propose an objective protocol for RSV genotyping suitable for adoption as an international standard to support the global expansion of RSV molecular surveillance.
publishDate 2020
dc.date.none.fl_str_mv 2020-05
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/168183
Goya, Stephanie; Galiano, Mónica; Nauwelaers, Inne; Trento, Alfonsina; Openshaw, Peter J.; et al.; Toward unified molecular surveillance of RSV: A proposal for genotype definition; Wiley Blackwell Publishing, Inc; Influenza And Other Respiratory Viruses; 14; 3; 5-2020; 274-285
1750-2640
1750-2659
CONICET Digital
CONICET
url http://hdl.handle.net/11336/168183
identifier_str_mv Goya, Stephanie; Galiano, Mónica; Nauwelaers, Inne; Trento, Alfonsina; Openshaw, Peter J.; et al.; Toward unified molecular surveillance of RSV: A proposal for genotype definition; Wiley Blackwell Publishing, Inc; Influenza And Other Respiratory Viruses; 14; 3; 5-2020; 274-285
1750-2640
1750-2659
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/10.1111/irv.12715
info:eu-repo/semantics/altIdentifier/doi/10.1111/irv.12715
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Wiley Blackwell Publishing, Inc
publisher.none.fl_str_mv Wiley Blackwell Publishing, Inc
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.22299

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