Quasispecies and viral gene expression analysis of the influenza A virus H1N1 strains isolated from human, mallard duck and pig

Characterizing the mutational diversity of viruses can shed light on both intra-host and between-host evolutionary processes. In this study, we analyzed the transcriptome profiles of five different strains of Influenza A virus H1N1 isolated from humans, ducks, and pigs. We detected positive selection that led to the evolution and fixation of virus variants at the intra-host level. Among the strains studied, A/mallard/Balkhash/6304/2014 was the most affected by intra-host dynamics, with 143 substitutions, while A/Puerto Rico/8/34 (PR8) had the least, with only one substitution. A/California/04/09 had the highest frequency of distribution in the HA epitope sites. We also detected amino acid substitutions in immunodominant antigenic regions of A/WSN/1933, mallard, and swine influenza strains. We detected a total of 19 shared substitutions across both the inter-host and intra-host levels. The sequences of the different strains showed different patterns of gene expression. Phylogenetic trees constructed based on the HA and NA segments of the 26 GenBank isolates showed incongruences with other phylogenetic trees based on other IAV segments. We also identified amino acid changes in critical regions of the studied isolates, which could provide valuable information on the contingency of novel recombinants with different morphogenesis, infectivity, and behavior against antivirals. Our results show that influenza A viruses (IAVs) could potentially adapt more efficiently within their host organisms, mostly in wild birds. This underlines the importance of certain population characteristics, such as the elimination of genetic bottlenecks, as a means to expand their ability to infect new hosts.