Genetic diversification patterns in swine influenza A virus (H1N2) in vaccinated and nonvaccinated animals

Influenza A viruses (IAVs) are characterized by having a segmented genome, low proofreading polymerases, and a wide host range. Consequently, IAVs are constantly evolving in nature causing a threat to animal and human health. In 2009 a new human pandemic IAV strain arose in Mexico because of a reass...

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Autores: López-Valiñas, Álvaro, Valle González, Marta, Pérez, Marta, Darji, Ayub|||0000-0002-0967-3303, Chiapponi, Chiara|||0000-0001-8808-4680, Ganges, Llilianne|||0000-0002-8644-3560, Segalés Coma, Joaquim|||0000-0002-1539-7261, Núñez, J. Ignacio|||0000-0001-9890-7695
Tipo de recurso: artículo
Fecha de publicación:2023
País:España
Institución:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:284272
Acceso en línea:https://ddd.uab.cat/record/284272
https://dx.doi.org/urn:doi:10.3389/fcimb.2023.1258321
Access Level:acceso abierto
Palabra clave:Swine influenza virus
Viral evolution
Vaccination
NGS
Quasispecies
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spelling Genetic diversification patterns in swine influenza A virus (H1N2) in vaccinated and nonvaccinated animalsLópez-Valiñas, ÁlvaroValle González, MartaPérez, MartaDarji, Ayub|||0000-0002-0967-3303Chiapponi, Chiara|||0000-0001-8808-4680Ganges, Llilianne|||0000-0002-8644-3560Segalés Coma, Joaquim|||0000-0002-1539-7261Núñez, J. Ignacio|||0000-0001-9890-7695Swine influenza virusViral evolutionVaccinationNGSQuasispeciesInfluenza A viruses (IAVs) are characterized by having a segmented genome, low proofreading polymerases, and a wide host range. Consequently, IAVs are constantly evolving in nature causing a threat to animal and human health. In 2009 a new human pandemic IAV strain arose in Mexico because of a reassortment between two strains previously circulating in pigs; Eurasian "avian-like" (EA) swine H1N1 and "human-like" H1N2, highlighting the importance of swine as adaptation host of avian to human IAVs. Nowadays, although of limited use, a trivalent vaccine, which include in its formulation H1N1, H3N2, and, H1N2 swine IAV (SIAV) subtypes, is one of the most applied strategies to reduce SIAV circulation in farms. Protection provided by vaccines is not complete, allowing virus circulation, potentially favoring viral evolution. The evolutionary dynamics of SIAV quasispecies were studied in samples collected at different times from 8 vaccinated and 8 nonvaccinated pigs, challenged with H1N2 SIAV. In total, 32 SIAV genomes were sequenced by next-generation sequencing, and subsequent variant-calling genomic analysis was carried out. Herein, a total of 364 de novo single nucleotide variants (SNV) were found along all genetic segments in both experimental groups. The nonsynonymous substitutions proportion found was greater in vaccinated animals suggesting that H1N2 SIAV was under positive selection in this scenario. The impact of each substitution with an allele frequency greater than 5% was hypothesized according to previous literature, particularly in the surface glycoproteins hemagglutinin and neuraminidase. The H1N2 SIAV quasispecies evolution capacity was evidenced, observing different evolutionary trends in vaccinated and nonvaccinated animals. 22023-01-0120232023-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/284272https://dx.doi.org/urn:doi:10.3389/fcimb.2023.1258321reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengAgencia Estatal de Investigación https://doi.org/10.13039/501100011033 AGL2016-75280-RMinisterio de Ciencia e Innovación https://doi.org/10.13039/501100004837 FPI2017open accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:2842722026-06-06T12:50:31Z
dc.title.none.fl_str_mv Genetic diversification patterns in swine influenza A virus (H1N2) in vaccinated and nonvaccinated animals
title Genetic diversification patterns in swine influenza A virus (H1N2) in vaccinated and nonvaccinated animals
spellingShingle Genetic diversification patterns in swine influenza A virus (H1N2) in vaccinated and nonvaccinated animals
López-Valiñas, Álvaro
Swine influenza virus
Viral evolution
Vaccination
NGS
Quasispecies
title_short Genetic diversification patterns in swine influenza A virus (H1N2) in vaccinated and nonvaccinated animals
title_full Genetic diversification patterns in swine influenza A virus (H1N2) in vaccinated and nonvaccinated animals
title_fullStr Genetic diversification patterns in swine influenza A virus (H1N2) in vaccinated and nonvaccinated animals
title_full_unstemmed Genetic diversification patterns in swine influenza A virus (H1N2) in vaccinated and nonvaccinated animals
title_sort Genetic diversification patterns in swine influenza A virus (H1N2) in vaccinated and nonvaccinated animals
dc.creator.none.fl_str_mv López-Valiñas, Álvaro
Valle González, Marta
Pérez, Marta
Darji, Ayub|||0000-0002-0967-3303
Chiapponi, Chiara|||0000-0001-8808-4680
Ganges, Llilianne|||0000-0002-8644-3560
Segalés Coma, Joaquim|||0000-0002-1539-7261
Núñez, J. Ignacio|||0000-0001-9890-7695
author López-Valiñas, Álvaro
author_facet López-Valiñas, Álvaro
Valle González, Marta
Pérez, Marta
Darji, Ayub|||0000-0002-0967-3303
Chiapponi, Chiara|||0000-0001-8808-4680
Ganges, Llilianne|||0000-0002-8644-3560
Segalés Coma, Joaquim|||0000-0002-1539-7261
Núñez, J. Ignacio|||0000-0001-9890-7695
author_role author
author2 Valle González, Marta
Pérez, Marta
Darji, Ayub|||0000-0002-0967-3303
Chiapponi, Chiara|||0000-0001-8808-4680
Ganges, Llilianne|||0000-0002-8644-3560
Segalés Coma, Joaquim|||0000-0002-1539-7261
Núñez, J. Ignacio|||0000-0001-9890-7695
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Swine influenza virus
Viral evolution
Vaccination
NGS
Quasispecies
topic Swine influenza virus
Viral evolution
Vaccination
NGS
Quasispecies
description Influenza A viruses (IAVs) are characterized by having a segmented genome, low proofreading polymerases, and a wide host range. Consequently, IAVs are constantly evolving in nature causing a threat to animal and human health. In 2009 a new human pandemic IAV strain arose in Mexico because of a reassortment between two strains previously circulating in pigs; Eurasian "avian-like" (EA) swine H1N1 and "human-like" H1N2, highlighting the importance of swine as adaptation host of avian to human IAVs. Nowadays, although of limited use, a trivalent vaccine, which include in its formulation H1N1, H3N2, and, H1N2 swine IAV (SIAV) subtypes, is one of the most applied strategies to reduce SIAV circulation in farms. Protection provided by vaccines is not complete, allowing virus circulation, potentially favoring viral evolution. The evolutionary dynamics of SIAV quasispecies were studied in samples collected at different times from 8 vaccinated and 8 nonvaccinated pigs, challenged with H1N2 SIAV. In total, 32 SIAV genomes were sequenced by next-generation sequencing, and subsequent variant-calling genomic analysis was carried out. Herein, a total of 364 de novo single nucleotide variants (SNV) were found along all genetic segments in both experimental groups. The nonsynonymous substitutions proportion found was greater in vaccinated animals suggesting that H1N2 SIAV was under positive selection in this scenario. The impact of each substitution with an allele frequency greater than 5% was hypothesized according to previous literature, particularly in the surface glycoproteins hemagglutinin and neuraminidase. The H1N2 SIAV quasispecies evolution capacity was evidenced, observing different evolutionary trends in vaccinated and nonvaccinated animals.
publishDate 2023
dc.date.none.fl_str_mv 2
2023-01-01
2023
2023-01-01
dc.type.none.fl_str_mv Article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://ddd.uab.cat/record/284272
https://dx.doi.org/urn:doi:10.3389/fcimb.2023.1258321
url https://ddd.uab.cat/record/284272
https://dx.doi.org/urn:doi:10.3389/fcimb.2023.1258321
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Agencia Estatal de Investigación https://doi.org/10.13039/501100011033 AGL2016-75280-R
Ministerio de Ciencia e Innovación https://doi.org/10.13039/501100004837 FPI2017
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Dipòsit Digital de Documents de la UAB
instname:Universitat Autònoma de Barcelona
instname_str Universitat Autònoma de Barcelona
reponame_str Dipòsit Digital de Documents de la UAB
collection Dipòsit Digital de Documents de la UAB
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