Giuseppe
Emeritus
[Source: PLoS ONE, full text: (LINK). Abstract, edited.]
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Reconstruction of the Evolutionary Dynamics of the A(H1N1)pdm09 Influenza Virus in Italy during the Pandemic and Post-Pandemic Phases
Gianguglielmo Zehender<SUP>1</SUP><SUP>*</SUP>, Elena Pariani<SUP>2</SUP><SUP>#</SUP>, Antonio Piralla<SUP>3</SUP><SUP>#</SUP>, Alessia Lai<SUP>1</SUP>, Elena Gabanelli<SUP>1</SUP>, Alberto Ranghiero<SUP>2</SUP>, Erika Ebranati<SUP>1</SUP>, Antonella Amendola<SUP>2</SUP>, Giulia Campanini<SUP>3</SUP>, Francesca Rovida<SUP>3</SUP>, Massimo Ciccozzi<SUP>4</SUP>, Massimo Galli<SUP>1</SUP>, Fausto Baldanti<SUP>3</SUP>, Alessandro Remo Zanetti<SUP>2</SUP>
<SUP></SUP>
1 Dipartimento di Scienze Cliniche e Biomediche ?Luigi Sacco?, Sezione di Malattie Infettive, Universit? degli Studi di Milano, Milan, Italy, 2 Dipartimento di Scienze Biomediche per la Salute, Universit? degli Studi di Milano, Milan, Italy, 3 Struttura Semplice Virologia Molecolare, Struttura Complessa Virologia e Microbiologia, Fondazione Istituto Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy, 4 Istituto Superiore di Sanit?, Dipartimento Malattie Infettive, Parassitarie ed Immunomediate, Rome, Italy
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.
Citation: Zehender G, Pariani E, Piralla A, Lai A, Gabanelli E, et al. (2012) Reconstruction of the Evolutionary Dynamics of the A(H1N1)pdm09 Influenza Virus in Italy during the Pandemic and Post-Pandemic Phases. PLoS ONE 7(11): e47517. doi:10.1371/journal.pone.0047517
Editor: Yi Guan, The University of Hong Kong, China
Received: June 20, 2012; Accepted: September 12, 2012; Published: November 9, 2012
Copyright: ? 2012 Zehender et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This study was supported by grants from Direzione Generale Sanit?, Regione Lombardia (Grant No. 5988, 30/6/2011), Ministero della Salute, Fondazione IRCCS Policlinico San Matteo, Ricerca Corrente (grant no. 80622), Progetto Cariplo 2012, Milan, Italy. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: gianguglielmo.zehender@unimi.it
# These authors contributed equally to this work.
-Gianguglielmo Zehender<SUP>1</SUP><SUP>*</SUP>, Elena Pariani<SUP>2</SUP><SUP>#</SUP>, Antonio Piralla<SUP>3</SUP><SUP>#</SUP>, Alessia Lai<SUP>1</SUP>, Elena Gabanelli<SUP>1</SUP>, Alberto Ranghiero<SUP>2</SUP>, Erika Ebranati<SUP>1</SUP>, Antonella Amendola<SUP>2</SUP>, Giulia Campanini<SUP>3</SUP>, Francesca Rovida<SUP>3</SUP>, Massimo Ciccozzi<SUP>4</SUP>, Massimo Galli<SUP>1</SUP>, Fausto Baldanti<SUP>3</SUP>, Alessandro Remo Zanetti<SUP>2</SUP>
<SUP></SUP>
1 Dipartimento di Scienze Cliniche e Biomediche ?Luigi Sacco?, Sezione di Malattie Infettive, Universit? degli Studi di Milano, Milan, Italy, 2 Dipartimento di Scienze Biomediche per la Salute, Universit? degli Studi di Milano, Milan, Italy, 3 Struttura Semplice Virologia Molecolare, Struttura Complessa Virologia e Microbiologia, Fondazione Istituto Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy, 4 Istituto Superiore di Sanit?, Dipartimento Malattie Infettive, Parassitarie ed Immunomediate, Rome, Italy
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.
Citation: Zehender G, Pariani E, Piralla A, Lai A, Gabanelli E, et al. (2012) Reconstruction of the Evolutionary Dynamics of the A(H1N1)pdm09 Influenza Virus in Italy during the Pandemic and Post-Pandemic Phases. PLoS ONE 7(11): e47517. doi:10.1371/journal.pone.0047517
Editor: Yi Guan, The University of Hong Kong, China
Received: June 20, 2012; Accepted: September 12, 2012; Published: November 9, 2012
Copyright: ? 2012 Zehender et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This study was supported by grants from Direzione Generale Sanit?, Regione Lombardia (Grant No. 5988, 30/6/2011), Ministero della Salute, Fondazione IRCCS Policlinico San Matteo, Ricerca Corrente (grant no. 80622), Progetto Cariplo 2012, Milan, Italy. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: gianguglielmo.zehender@unimi.it
# These authors contributed equally to this work.
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