{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T14:54:40Z","timestamp":1775919280277,"version":"3.50.1"},"reference-count":91,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2021,10,16]],"date-time":"2021-10-16T00:00:00Z","timestamp":1634342400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100014440","name":"Ministerio de Ciencia, innovaci\u00f3n y universidades","doi-asserted-by":"publisher","award":["AGL2016-75280_R"],"award-info":[{"award-number":["AGL2016-75280_R"]}],"id":[{"id":"10.13039\/100014440","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Influenza viruses represent a continuous threat to both animal and human health. The 2009 H1N1 A influenza pandemic highlighted the importance of a swine host in the adaptation of influenza viruses to humans. Nowadays, one of the most extended strategies used to control swine influenza viruses (SIVs) is the trivalent vaccine application, whose formulation contains the most frequently circulating SIV subtypes H1N1, H1N2, and H3N2. These vaccines do not provide full protection against the virus, allowing its replication, evolution, and adaptation. To better understand the main mechanisms that shape viral evolution, here, the SIV intra-host diversity was analyzed in samples collected from both vaccinated and nonvaccinated animals challenged with the H1N1 influenza A virus. Twenty-eight whole SIV genomes were obtained by next-generation sequencing, and differences in nucleotide variants between groups were established. Substitutions were allocated along all influenza genetic segments, while the most relevant nonsynonymous substitutions were allocated in the NS1 protein on samples collected from vaccinated animals, suggesting that SIV is continuously evolving despite vaccine application. Moreover, new viral variants were found in both vaccinated and nonvaccinated pigs, showing relevant substitutions in the HA, NA, and NP proteins, which may increase viral fitness under field conditions.<\/jats:p>","DOI":"10.3390\/v13102087","type":"journal-article","created":{"date-parts":[[2021,10,18]],"date-time":"2021-10-18T13:59:52Z","timestamp":1634565592000},"page":"2087","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Identification and Characterization of Swine Influenza Virus H1N1 Variants Generated in Vaccinated and Nonvaccinated, Challenged Pigs"],"prefix":"10.3390","volume":"13","author":[{"given":"\u00c1lvaro","family":"L\u00f3pez-Vali\u00f1as","sequence":"first","affiliation":[{"name":"Centre de Recerca en Sanitat Animal (CReSA), Institut de Recerca en Tecnologies Agroalimentaries (IRTA), 08193 Barcelona, Spain"},{"name":"OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0214-6348","authenticated-orcid":false,"given":"Marta","family":"Sister\u00e9-Or\u00f3","sequence":"additional","affiliation":[{"name":"Centre de Recerca en Sanitat Animal (CReSA), Institut de Recerca en Tecnologies Agroalimentaries (IRTA), 08193 Barcelona, Spain"},{"name":"OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0968-7713","authenticated-orcid":false,"given":"Sergi","family":"L\u00f3pez-Serrano","sequence":"additional","affiliation":[{"name":"Centre de Recerca en Sanitat Animal (CReSA), Institut de Recerca en Tecnologies Agroalimentaries (IRTA), 08193 Barcelona, Spain"},{"name":"OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laura","family":"Baioni","sequence":"additional","affiliation":[{"name":"OIE Reference Laboratory for Swine Influenza Virus, Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia-Romagna, 25124 Brescia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ayub","family":"Darji","sequence":"additional","affiliation":[{"name":"Centre de Recerca en Sanitat Animal (CReSA), Institut de Recerca en Tecnologies Agroalimentaries (IRTA), 08193 Barcelona, Spain"},{"name":"OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8808-4680","authenticated-orcid":false,"given":"Chiara","family":"Chiapponi","sequence":"additional","affiliation":[{"name":"OIE Reference Laboratory for Swine Influenza Virus, Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia-Romagna, 25124 Brescia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1539-7261","authenticated-orcid":false,"given":"Joaquim","family":"Segal\u00e9s","sequence":"additional","affiliation":[{"name":"Centre de Recerca en Sanitat Animal (CReSA), Institut de Recerca en Tecnologies Agroalimentaries (IRTA), 08193 Barcelona, Spain"},{"name":"OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Barcelona, Spain"},{"name":"Departament de Sanitat i Anatomia Animals, Universitat Aut\u00f2noma de Barcelona, Bellaterra, 08193 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8644-3560","authenticated-orcid":false,"given":"Llilianne","family":"Ganges","sequence":"additional","affiliation":[{"name":"Centre de Recerca en Sanitat Animal (CReSA), Institut de Recerca en Tecnologies Agroalimentaries (IRTA), 08193 Barcelona, Spain"},{"name":"OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Barcelona, Spain"},{"name":"OIE Reference Laboratory for Classical Swine Fever Virus, IRTA-CReSA, 08193 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9890-7695","authenticated-orcid":false,"given":"Jos\u00e9 I.","family":"N\u00fa\u00f1ez","sequence":"additional","affiliation":[{"name":"Centre de Recerca en Sanitat Animal (CReSA), Institut de Recerca en Tecnologies Agroalimentaries (IRTA), 08193 Barcelona, Spain"},{"name":"OIE 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