title: Reconstruction of the evolutionary dynamics of the A(H1N1)pdm09 influenza virus in Italy during the pandemic and post-pandemic phases.
abstract: The aim of this study was to reconstruct the evolutionary dynamics of the A(H1N1)pdm09 influenza virus in Italy during two epidemic seasons (2009/2010 and 2010/2011) in the light of the forces driving the evolution of the virus. Nearly six thousands respiratory specimens were collected from patients with influenza-like illness within the framework of the Italian Influenza Surveillance Network, and the A(H1N1)pdm09 hemagglutinin (HA) gene was amplified and directly sequenced from 227 of these. Phylodynamic and phylogeographical analyses were made using a Bayesian Markov Chain Monte Carlo method, and codon-specific positive selection acting on the HA coding sequence was evaluated. The global and local phylogenetic analyses showed that all of the Italian sequences sampled in the post-pandemic (2010/2011) season grouped into at least four highly significant Italian clades, whereas those of the pandemic season (2009/2010) were interspersed with isolates from other countries at the tree root. The time of the most recent common ancestor of the strains circulating in the pandemic season in Italy was estimated to be between the spring and summer of 2009, whereas the Italian clades of the post-pandemic season originated in the spring of 2010 and showed radiation in the summer/autumn of the same year; this was confirmed by a Bayesian skyline plot showing the biphasic growth of the effective number of infections. The local phylogeography analysis showed that the first season of infection originated in Northern Italian localities with high density populations, whereas the second involved less densely populated localities, in line with a gravity-like model of geographical dispersion. Two HA sites, codons 97 and 222, were under positive selection. In conclusion, the A(H1N1)pdm09 virus was introduced into Italy in the spring of 2009 by means of multiple importations. This was followed by repeated founder effects in the post-pandemic period that originated specific Italian clades.
authors.affiliation: Dipartimento di Scienze Cliniche e Biomediche Luigi Sacco, Sezione di Malattie Infettive, Università degli Studi di Milano, Milan, Italy. gianguglielmo.zehender@unimi.it
authors.forename: Gianguglielmo
authors.initials: G
authors.lastname: Zehender
authors.forename: Elena
authors.initials: E
authors.lastname: Pariani
authors.forename: Antonio
authors.initials: A
authors.lastname: Piralla
authors.forename: Alessia
authors.initials: A
authors.lastname: Lai
authors.forename: Elena
authors.initials: E
authors.lastname: Gabanelli
authors.forename: Alberto
authors.initials: A
authors.lastname: Ranghiero
authors.forename: Erika
authors.initials: E
authors.lastname: Ebranati
authors.forename: Antonella
authors.initials: A
authors.lastname: Amendola
authors.forename: Giulia
authors.initials: G
authors.lastname: Campanini
authors.forename: Francesca
authors.initials: F
authors.lastname: Rovida
authors.forename: Massimo
authors.initials: M
authors.lastname: Ciccozzi
authors.forename: Massimo
authors.initials: M
authors.lastname: Galli
authors.forename: Fausto
authors.initials: F
authors.lastname: Baldanti
authors.forename: Alessandro Remo
authors.initials: AR
authors.lastname: Zanetti
mesh_terms: D019943:Amino Acid Substitution; D001499:Bayes Theorem; D019143:Evolution, Molecular; D005838:Genotype; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000145:classification / Q000235:genetics*; D007251:Influenza, Human / Q000453:epidemiology; D007558:Italy / Q000453:epidemiology; D008969:Molecular Sequence Data; D058873:Pandemics; D010802:Phylogeny; D058974:Phylogeography; D012641:Selection, Genetic
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus