Bayesian phylogenetic analysis of the influenza-A virus genomes isolated in Tunisia, and determination of potential recombination events

Abstract

The influenza-A virus (IAV) causes seasonal epidemics and presents a pandemic risk with the possibility of genetic re-assortment, allowing the emergence of new strains. The evolution of IAVes is done most often by relatively frequent re-assortment between gene segments, but the hypothesis of their evolution by recombination between RNA segments has not been justified to this date. Here, we examine this hypothesis by Bayesian phylogenetic analysis, to test if recombination events have occurred between genomic RNA segments. Different IAV subtypes are observed in co-circulation in Tunisia, which increases the probability of occurrence of double infections. Mixed infections are a prerequisite for recombination between co-infecting of viral strains.The aim of this work, and since understanding the evolutionary dynamics of IAV is essential for controlling human and avian influenza, phylogenetic analyzes (Bayesian approach) have been carried out for IAV strains isolated in Tunisia, to study their co-evolutionary history, trends, and possible recombination models.A set of IAV nucleic sequences, isolated in Tunisia from 2009 to 2013 (n = 102) were used in this study. These genomic segments encode various influenza A proteins. These viral strains studied were isolated following the 2009 H1N1 pandemic.The analyzes identified two large distinct groups of viral sequences and different subgroups. Assuming a relaxed molecular clock model (uncorrelated exponential (uced)) in a Bayesian coalescence approach and a constant effective time demographic history model (Coalescent: constant size), the substitution rate was estimated at 1.356 × 10−3 substitutions/site/year for segment 4 (haemagglutinin HA gene). Consistent estimates of the age of the most recent Common Ancestor (MRCA) were obtained for the different subgroups, the MRCA ages of the two viral populations corresponding to segment 4 and segment 6 (neuraminidase gene NA) of the genome are estimated at 443.737 years and 501.159 years respectively. A detailed phylogenetic study of the HA gene was performed. The incongruous phylogenetic models deduced for the three genomic subgroups studied corresponding to this gene were indicative of recombination events between the different subpopulations. The detection of these relative signals indicating the presence of recombination events can be considered as proof that recombination seems to play a role, even a small one, in the evolution of (IAV). Reliable recombination sites have been located with statistical significance between H3, H1 and H9 subtypes. MRCA age estimates of recombinants phylogenetic clades indicate directional gene transfers from the H1 and H9 populations to the H3 population, and from H1 and H3 to the H9 population, and their co-divergences during the study period.