Reconstruction of the evolutionary dynamics of A(H3N2) influenza viruses circulating in Italy from 2004 to 2012

Erika Ebranati, Elena Pariani, Antonio Piralla, Monica Gozalo-Margüello, Carla Veo, Laura Bubba, Antonella Amendola, Massimo Ciccozzi, Massimo Galli, Alessandro Remo Zanetti, Fausto Baldanti, Gianguglielmo Zehender

Research output: Contribution to journalArticle

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Abstract

Background. Influenza A viruses are characterised by their rapid evolution, and the appearance of point mutations in the viral hemagglutinin (HA) domain causes seasonal epidemics. The A (H3N2) virus has higher mutation rate than the A(H1N1) virus. The aim of this study was to reconstruct the evolutionary dynamics of the A(H3N2) viruses circulating in Italy between 2004 and 2012 in the light of the forces driving viral evolution. Methods. Phylodinamic analyses were made using a Bayesian method, and codon-specific positive selection acting on the HA coding sequence was evaluated. Results. Global and local phylogenetic analyses showed that the Italian strains collected between 2004 and 2012 grouped into five significant Italian clades that included viral sequences circulating in different epidemic seasons. The time of the most recent common ancestor (tMRCA) of the tree root was between May and December 2003. The tMRCA estimates of the major clades suggest that the origin of a new viral strain precedes the effective circulation of the strain in the Italian population by 6-31 months, thus supporting a central role of global migration in seeding the epidemics in Italy. The study of selection pressure showed that four codons were under positive selection, three of which were located in antigenic sites. Analysis of population dynamics showed the alternation of periods of exponential growth followed by a decrease in the effective number of infections corresponding to epidemic and inter-epidemic seasons. Conclusions. Our analyses suggest that a complex interaction between the immune status of the population, migrations, and a few selective sweeps drive the influenza A(H3N2) virus evolution. Our findings suggest the possibility of the year-round survival of local strains even in temperate zones, a hypothesis that warrants further investigation.

Original languageEnglish
Article numbere0137099
JournalPLoS One
Volume10
Issue number9
DOIs
Publication statusPublished - Sep 2 2015

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H3N2 Subtype Influenza A Virus
Orthomyxoviridae
Viruses
Influenza A virus
Human Influenza
Italy
hemagglutinins
codons
Codon
ancestry
Viral Hemagglutinins
H1N1 Subtype Influenza A Virus
Population dynamics
Bayes Theorem
Hemagglutinins
Population Dynamics
Mutation Rate
point mutation
Bayesian theory
temperate zones

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Ebranati, E., Pariani, E., Piralla, A., Gozalo-Margüello, M., Veo, C., Bubba, L., ... Zehender, G. (2015). Reconstruction of the evolutionary dynamics of A(H3N2) influenza viruses circulating in Italy from 2004 to 2012. PLoS One, 10(9), [e0137099]. https://doi.org/10.1371/journal.pone.0137099

Reconstruction of the evolutionary dynamics of A(H3N2) influenza viruses circulating in Italy from 2004 to 2012. / Ebranati, Erika; Pariani, Elena; Piralla, Antonio; Gozalo-Margüello, Monica; Veo, Carla; Bubba, Laura; Amendola, Antonella; Ciccozzi, Massimo; Galli, Massimo; Zanetti, Alessandro Remo; Baldanti, Fausto; Zehender, Gianguglielmo.

In: PLoS One, Vol. 10, No. 9, e0137099, 02.09.2015.

Research output: Contribution to journalArticle

Ebranati, E, Pariani, E, Piralla, A, Gozalo-Margüello, M, Veo, C, Bubba, L, Amendola, A, Ciccozzi, M, Galli, M, Zanetti, AR, Baldanti, F & Zehender, G 2015, 'Reconstruction of the evolutionary dynamics of A(H3N2) influenza viruses circulating in Italy from 2004 to 2012', PLoS One, vol. 10, no. 9, e0137099. https://doi.org/10.1371/journal.pone.0137099
Ebranati, Erika ; Pariani, Elena ; Piralla, Antonio ; Gozalo-Margüello, Monica ; Veo, Carla ; Bubba, Laura ; Amendola, Antonella ; Ciccozzi, Massimo ; Galli, Massimo ; Zanetti, Alessandro Remo ; Baldanti, Fausto ; Zehender, Gianguglielmo. / Reconstruction of the evolutionary dynamics of A(H3N2) influenza viruses circulating in Italy from 2004 to 2012. In: PLoS One. 2015 ; Vol. 10, No. 9.
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