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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| Format: | Article |
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Frontiers Media S.A.
2023-09-01
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| Series: | Frontiers in Cellular and Infection Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fcimb.2023.1258321/full |
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| author | Álvaro López-Valiñas Álvaro López-Valiñas Álvaro López-Valiñas Marta Valle Marta Valle Marta Valle Marta Pérez Marta Pérez Marta Pérez Ayub Darji Ayub Darji Ayub Darji Chiara Chiapponi Llilianne Ganges Llilianne Ganges Llilianne Ganges Llilianne Ganges Joaquim. Segalés Joaquim. Segalés Joaquim. Segalés José I. Núñez José I. Núñez José I. Núñez |
| author_facet | Álvaro López-Valiñas Álvaro López-Valiñas Álvaro López-Valiñas Marta Valle Marta Valle Marta Valle Marta Pérez Marta Pérez Marta Pérez Ayub Darji Ayub Darji Ayub Darji Chiara Chiapponi Llilianne Ganges Llilianne Ganges Llilianne Ganges Llilianne Ganges Joaquim. Segalés Joaquim. Segalés Joaquim. Segalés José I. Núñez José I. Núñez José I. Núñez |
| author_sort | Álvaro López-Valiñas |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-11T23:59:30Z |
| format | Article |
| id | doaj.art-c992153c681043ec8d2ab0e16348c5e6 |
| institution | Directory Open Access Journal |
| issn | 2235-2988 |
| language | English |
| last_indexed | 2024-03-11T23:59:30Z |
| publishDate | 2023-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj.art-c992153c681043ec8d2ab0e16348c5e62023-09-18T05:45:32ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882023-09-011310.3389/fcimb.2023.12583211258321Genetic diversification patterns in swine influenza A virus (H1N2) in vaccinated and nonvaccinated animalsÁlvaro López-Valiñas0Álvaro López-Valiñas1Álvaro López-Valiñas2Marta Valle3Marta Valle4Marta Valle5Marta Pérez6Marta Pérez7Marta Pérez8Ayub Darji9Ayub Darji10Ayub Darji11Chiara Chiapponi12Llilianne Ganges13Llilianne Ganges14Llilianne Ganges15Llilianne Ganges16Joaquim. Segalés17Joaquim. Segalés18Joaquim. Segalés19José I. Núñez20José I. Núñez21José I. Núñez22IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Bellaterra, Barcelona, SpainUnitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Barcelona, SpainWOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, SpainIRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Bellaterra, Barcelona, SpainUnitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Barcelona, SpainWOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, SpainIRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Bellaterra, Barcelona, SpainUnitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Barcelona, SpainWOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, SpainIRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Bellaterra, Barcelona, SpainUnitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Barcelona, SpainWOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, SpainWOAH Reference Laboratory for Swine Influenza, Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia-Romagna, Brescia, ItalyIRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Bellaterra, Barcelona, SpainUnitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Barcelona, SpainWOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, SpainWOAH Reference Laboratory for Classical Swine Fever, IRTA-CReSA, Barcelona, SpainUnitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Barcelona, SpainWOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, SpainDepartament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Barcelona, SpainIRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Bellaterra, Barcelona, SpainUnitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Barcelona, SpainWOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona, SpainInfluenza 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.https://www.frontiersin.org/articles/10.3389/fcimb.2023.1258321/fullswine influenza virusviral evolutionvaccinationNGSquasispecies |
| spellingShingle | Álvaro López-Valiñas Álvaro López-Valiñas Álvaro López-Valiñas Marta Valle Marta Valle Marta Valle Marta Pérez Marta Pérez Marta Pérez Ayub Darji Ayub Darji Ayub Darji Chiara Chiapponi Llilianne Ganges Llilianne Ganges Llilianne Ganges Llilianne Ganges Joaquim. Segalés Joaquim. Segalés Joaquim. Segalés José I. Núñez José I. Núñez José I. Núñez Genetic diversification patterns in swine influenza A virus (H1N2) in vaccinated and nonvaccinated animals Frontiers in Cellular and Infection Microbiology swine influenza virus viral evolution vaccination NGS quasispecies |
| title | 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_short | 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 |
| topic | swine influenza virus viral evolution vaccination NGS quasispecies |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2023.1258321/full |
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