title: Evolutionary trajectories of two distinct avian influenza epidemics: Parallelisms and divergences.
abstract: Influenza A virus can quickly acquire genetic mutations that may be associated with increased virulence, host switching or antigenic changes. To provide new insights into the evolutionary dynamics and the adaptive strategies of distinct avian influenza lineages in response to environmental and host factors, we compared two distinct avian influenza epidemics caused by the H7N1 and H7N3 subtypes that circulated under similar epidemiological conditions, including the same domestic species reared in the same densely populated poultry area for similar periods of time. The two strains appear to have experienced largely divergent evolution: the H7N1 viruses evolved into a highly pathogenic form, while the H7N3 did not. However, a more detailed molecular and evolutionary analysis revealed several common features: (i) the independent acquisition of 32 identical mutations throughout the entire genome; (ii) the evolution and persistence of two sole genetic groups with similar genetic characteristics; (iii) a comparable pattern of amino acid variability of the HA proteins during the low pathogenic epidemics; and (iv) similar rates of nucleotide substitutions. These findings suggest that the evolutionary trajectories of viruses with the same virulence level circulating in analogous epidemiological conditions may be similar. In addition, our deep sequencing analysis of 15 samples revealed that 17 of the 32 parallel mutations were already present at the beginning of the two epidemics, suggesting that fixation of these mutations may occur with different mechanisms, which may depend on the fitness gain provided by each mutation. This highlighted the difficulties in predicting the acquisition of mutations that can be correlated to viral adaptation to specific epidemiological conditions or to changes in virus virulence.
authors.affiliation: Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università, 10, Legnaro (PD), Italy. Electronic address: afusaro@izsvenezie.it.
authors.forename: Alice
authors.initials: A
authors.lastname: Fusaro
authors.affiliation: Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università, 10, Legnaro (PD), Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Tassoni
authors.affiliation: MRC-University of Glasgow Center for Virus Research, 464 Bearsden Road, Glasgow, United Kingdom.
authors.forename: Joseph
authors.initials: J
authors.lastname: Hughes
authors.affiliation: Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università, 10, Legnaro (PD), Italy.
authors.forename: Adelaide
authors.initials: A
authors.lastname: Milani
authors.affiliation: Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università, 10, Legnaro (PD), Italy.
authors.forename: Annalisa
authors.initials: A
authors.lastname: Salviato
authors.affiliation: Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università, 10, Legnaro (PD), Italy.
authors.forename: Alessia
authors.initials: A
authors.lastname: Schivo
authors.affiliation: MRC-University of Glasgow Center for Virus Research, 464 Bearsden Road, Glasgow, United Kingdom.
authors.forename: Pablo R
authors.initials: PR
authors.lastname: Murcia
authors.affiliation: Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università, 10, Legnaro (PD), Italy.
authors.forename: Lebana
authors.initials: L
authors.lastname: Bonfanti
authors.affiliation: Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università, 10, Legnaro (PD), Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Cattoli
authors.affiliation: Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università, 10, Legnaro (PD), Italy.
authors.forename: Isabella
authors.initials: I
authors.lastname: Monne
mesh_terms: D019943:Amino Acid Substitution; D000818:Animals; D058872:Epidemics; D019143:Evolution, Molecular; D005787:Gene Frequency; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000737:chemistry / Q000235:genetics; D057916:Influenza A Virus, H7N1 Subtype / Q000235:genetics*; D057920:Influenza A Virus, H7N3 Subtype / Q000235:genetics*; D005585:Influenza in Birds / Q000453:epidemiology / Q000821:virology*; D016013:Likelihood Functions; D010802:Phylogeny; D011200:Poultry / Q000821:virology; D011201:Poultry Diseases / Q000453:epidemiology / Q000821:virology*; D012641:Selection, Genetic
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus
keywords: Avian influenza virus; Deep sequencing; Evolutionary dynamics; H7 subtype; Molecular analysis; Parallel evolution