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

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.