title: Genetic characterization and evolution of H1N1pdm09 after circulation in a swine farm.
abstract: Following the emergence of the A(H1N1)pdm09 in humans, this novel influenza virus was reverse transmitted from infected people to swine population worldwide. In this study we investigated the molecular evolution of A(H1N1)pdm09 virus identified in pigs reared in a single herd. Nasal swabs taken from pigs showing respiratory distress were tested for influenza type A and A(H1N1)pdm09 by real-time RT-PCR assays. Virus isolation from positive samples was attempted by inoculation of nasal swabs samples into specific pathogen free embryonated chicken eggs (ECE) and complete genome sequencing was performed on virus strains after replication on ECE or from original swab sample. The molecular analysis of hemagglutinin (HA) showed, in four of the swine influenza viruses under study, a unique significant amino acid change, represented by a two-amino acid insertion at the HA receptor binding site. Phylogenetic analysis of HA, neuraminidase, and concatenated internal genes revealed a very similar topology, with viruses under study forming a separate cluster, branching outside the A(H1N1)pdm09 isolates recognized until 2014. The emergence of this new cluster of A(H1N1)pdm09 in swine raises further concerns about whether A(H1N1)pdm09 with new molecular characteristics will become established in pigs and potentially transmitted to humans.
authors.affiliation: Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
authors.forename: Arianna
authors.initials: A
authors.lastname: Boni
authors.affiliation: Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
authors.forename: Gabriele
authors.initials: G
authors.lastname: Vaccari
authors.affiliation: Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
authors.forename: Livia
authors.initials: L
authors.lastname: Di Trani
authors.affiliation: Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
authors.forename: Guendalina
authors.initials: G
authors.lastname: Zaccaria
authors.affiliation: Dipartimento di Virologia, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Via A. Bianchi 9, 25124 Brescia, Italy.
authors.forename: Giovanni Loris
authors.initials: GL
authors.lastname: Alborali
authors.affiliation: Dipartimento di Virologia, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Via A. Bianchi 9, 25124 Brescia, Italy.
authors.forename: Davide
authors.initials: D
authors.lastname: Lelli
authors.affiliation: Dipartimento di Virologia, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Via A. Bianchi 9, 25124 Brescia, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Cordioli
authors.affiliation: Dipartimento di Virologia, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Via A. Bianchi 9, 25124 Brescia, Italy.
authors.forename: Ana Maria
authors.initials: AM
authors.lastname: Moreno
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics; D000818:Animals; D019143:Evolution, Molecular; D016679:Genome, Viral; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics*; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics* / Q000472:pathogenicity; D007251:Influenza, Human / Q000235:genetics* / Q000821:virology; D009439:Neuraminidase / Q000235:genetics*; D058873:Pandemics; D010802:Phylogeny; D013552:Swine / Q000821:virology
chemical_list: C543345:H1N1 virus hemagglutinin; D019267:Hemagglutinin Glycoproteins, Influenza Virus; D009439:Neuraminidase