Evolutionary analysis of human-origin influenza A virus (H3N2) genes associated with the codon usage patterns since 1993

Abstract

This study investigated genetic variations in eight major genes (hemagglutinin, HA; neuraminidase, NA; matrix protein, MP; non-structural protein, NS; nucleoprotein, NP; polymerase, PA; PA basic protein 1, PB1; and PA basic protein 2, PB2) of the influenza A virus subtype H3N2 (A/H3N2) to determine the evolutionary pattern in codon bias. A total of 6,881 sequences isolated between 1993 and 2010 were used. The relative synonymous codon usage (RSCU) and G+C% content at the three codon positions were analyzed by calculating the codon substitution patterns were analyzed by calculating the percentage of synonymously substituted codons (SSCs) and that of codons substituted to the same codon within each synonymous codon group (EMC) between 1993 and subsequent years. In the multivariate analysis of RSCU, we observed directional changes in HA, NA, PB1, and PB2, and these changes were significantly correlated with the variation in the G+C contents at the first (GC(1st)) and second (GC(2nd)) codon positions over time. These directional changes in HA and NA appear to affect their antigenic characteristics by altering their SSCs gradually, and NP, PA, PB1, and PB2 genes also continuously changed their substitution patterns by accumulating the decrements of EMC values over a long term. Our findings suggest that, in human populations, A/H3N2 viruses have gradually changed their SSCs in two external genes, HA and NA, and that these accumulated alteration patterns may result in the antigenic changes over time. Moreover, A/H3N2 viruses also appear to change synonymous codon usage patterns in NP, PA, PB1, and PB2 genes by accumulating decrements in EMCs within synonymous codon groups over time.