Genetic analysis of the PB1-F2 gene of equine influenza virus.

ABSTRACT

Amino acid and phylogenetic analysis showed that PB1-F2 of H7N7 and H3N8 equine influenza virus (EIV) evolved into two and nine clades, respectively. The PB1-F2 gene of H7N7 EIV strains isolated after 1973 was identified as being replaced by that of H3N8 EIV circulating simultaneously. All H7N7 EIV strains before 1973 contained PB1-F2 of 34 aa, while 90 aa after 1973. Meanwhile, most H3N8 EIV strains contained PB1-F2 of 90 or 81 aa. Evolutionary rate of PB1-F2 of H3N8 EIV was similar with that of PB1 in previous study. Meanwhile, PB1-F2 of H7N7 EIV evolved in significantly higher rate when compared with PB1-F2 of H3N8 EIV. Codon usage analysis revealed that PB1-F2 gene of EIV was less biased, which was identified as being determined by three main factors mutational bias, selection pressure, and gene length. Our studies first in details report the genetic evolution, evolutionary rate, and the factors influencing codon usage bias of PB1-F2 of EIV.