title: Genome plasticity of triple-reassortant H1N1 influenza A virus during infection of vaccinated pigs.
abstract: To gain insight into the evolution of influenza A viruses (IAVs) during infection of vaccinated pigs, we experimentally infected a 3-week-old naive pig with a triple-reassortant H1N1 IAV and placed the seeder pig in direct contact with a group of age-matched vaccinated pigs (n = 10). We indexed the genetic diversity and evolution of the virus at an intra-host level by deep sequencing the entire genome directly from nasal swabs collected at two separate samplings during infection. We obtained 13 IAV metagenomes from 13 samples, which included the virus inoculum and two samples from each of the six pigs that tested positive for IAV during the study. The infection produced a population of heterogeneous alleles (sequence variants) that was dynamic over time. Overall, 794 polymorphisms were identified amongst all samples, which yielded 327 alleles, 214 of which were unique sequences. A total of 43 distinct haemagglutinin proteins were translated, two of which were observed in multiple pigs, whereas the neuraminidase (NA) was conserved and only one dominant NA was found throughout the study. The genetic diversity of IAVs changed dynamically within and between pigs. However, most of the substitutions observed in the internal gene segments were synonymous. Our results demonstrated remarkable IAV diversity, and the complex, rapid and dynamic evolution of IAV during infection of vaccinated pigs that can only be appreciated with repeated sampling of individual animals and deep sequence analysis.
authors.affiliation: College of Veterinary Medicine, University of Minnesota Saint Paul, Minnesota, USA.
authors.forename: Andres
authors.initials: A
authors.lastname: Diaz
authors.affiliation: Department of Biology University of Utah, South Lake City, Utah, USA.
authors.forename: Shinichiro
authors.initials: S
authors.lastname: Enomoto
authors.affiliation: College of Veterinary Medicine, University of Minnesota Saint Paul, Minnesota, USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Romagosa
authors.affiliation: College of Veterinary Medicine, University of Minnesota Saint Paul, Minnesota, USA.
authors.forename: Srinand
authors.initials: S
authors.lastname: Sreevatsan
authors.affiliation: Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA.
authors.forename: Martha
authors.initials: M
authors.lastname: Nelson
authors.affiliation: College of Veterinary Medicine, University of Minnesota Saint Paul, Minnesota, USA.
authors.forename: Marie
authors.initials: M
authors.lastname: Culhane
authors.affiliation: College of Veterinary Medicine, University of Minnesota Saint Paul, Minnesota, USA.
authors.forename: Montserrat
authors.initials: M
authors.lastname: Torremorell
mesh_terms: D000483:Alleles; D000818:Animals; D019143:Evolution, Molecular; D014644:Genetic Variation; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics* / Q000254:growth & development / Q000276:immunology / Q000302:isolation & purification; D054892:Metagenome; D008969:Molecular Sequence Data; D009297:Nasal Mucosa / Q000276:immunology / Q000821:virology; D009976:Orthomyxoviridae Infections / Q000276:immunology / Q000821:virology*; D012367:RNA, Viral / Q000235:genetics; D016865:Reassortant Viruses / Q000235:genetics* / Q000254:growth & development / Q000276:immunology / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D013552:Swine; D014764:Viral Proteins / Q000235:genetics
chemical_list: D012367:RNA, Viral; D014764:Viral Proteins