Infect Genet Evol

. 2021 Sep 3;105067.
doi: 10.1016/j.meegid.2021.105067. Online ahead of print.
Evolutionary perspectives and adaptation dynamics of human seasonal influenza viruses from 2009 to 2019: An insight from codon usage

Zhipeng Zhang 1 , Fucheng Guo 2 , Ayan Roy 3 , Jinjin Yang 4 , Wen Luo 4 , Xuejuan Shen 1 , David M Irwin 5 , Rui-Ai Chen 6 , Yongyi Shen 7



The annually recurrent seasonal influenza viruses, namely, influenza A viruses (H1N1/pdm2009 and H3N2) and influenza B viruses, contribute substantially to human disease burden. Elucidation of host adaptation, population dynamics and evolutionary patterns of these viruses contribute to better control of current epidemic situation and bolster efforts towards pandemic preparedness. Present study has been addressed at unraveling the signatures of codon usage and dinucleotide distribution of these seasonal influenza viruses associating with their fitness and ongoing adaptive evolution in human population. Thorough analysis of codon usage adaptation revealed that H3N2 has been exhibited best adapted to human cellular system, which correlate with its highest epidemic intensity as compared with the other seasonal influenza viruses. CpG dinucleotide was found to be strongly avoided among the seasonal influenza viruses with more restraint among influenza B viruses than influenza A viruses, and might be accounted to the strategy of the viral pathogens in evading human immune signals. Dynamic scenes of ongoing evolution in codon usage and elimination of CpG motif among the viruses, which correlate with their distinct host adaption state, signifying the marked impact of selective force operational on the viral genomes, aimed at proficient circulation, enhanced fitness and successful infective manifestations in humans.

Keywords: Codon adaptation index; Codon usage; CpG dinucleotide; Evolutionary analysis; Host adaptation; Seasonal influenza viruses.