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.
Highlights
In March 2009, a novel swine-derived A(H1N1) influenza virus – A(H1N1)pdm09 – emerged in Mexico and started spreading across the globe, prompting the World Health Organisation (WHO) to raise the level of influenza pandemic alert to phase 6 (WHO – available at: http://www.who.int/csr/disease/swineflu/ en/)
The maximum likelihood and Bayesian analyses of the global data set of 561 A(H1N1)pdm09 isolates (227 from Italy and 334 from all over the world) showed that the Italian isolates clustered into five significant groups
The clusters included a total of 136 isolates, representing 59.9% of the Italian isolates and 100% of those of the post-pandemic season (2010/2011), whereas the isolates of the pandemic season (2009/2010) were interspersed with sequences from other countries (Figure 1)
Summary
In March 2009, a novel swine-derived A(H1N1) influenza virus – A(H1N1)pdm09 – emerged in Mexico and started spreading across the globe, prompting the World Health Organisation (WHO) to raise the level of influenza pandemic alert to phase 6 (WHO – available at: http://www.who.int/csr/disease/swineflu/ en/). Despite the rapidity with which the virus reached a large number of countries in the world, its transmission was initially sustained only in a subset of countries, the USA and temperate countries in the southern hemisphere in which winter influenza transmission was ongoing and a full A(H1N1)pdm influenza epidemic was observed. The pandemic strain quickly became the predominant circulating influenza virus and replaced seasonal strains in most countries. A second epidemic wave was recorded during the post-pandemic period (November 2010–March 2011) during which the influenza A(H1N1)pdm virus was responsible for the majority of infections
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