Genetic distribution of bovine viral diarrhea virus in free-living cattle in China

Abstract

Abstract According to sequencing of the 5’ untranslated region (5’UTR) in viral genome, five strains of bovine viral diarrhea virus (BVDV) isolated from different provinces in China were genetically typed. The phylogenetic tree for BVDV 5’UTR displays that the isolated strain 22AH-1 is clustered into the genotype 1c clade, the strain 22-Gansu-F2 is clustered into the genotype 2a clade, the strains 22Anhui-7, 22-Sichuan-B8 and 22-Gansu-F3 are clustered into the genotype 2d clade. Depending on principal component analysis for synonymous codon usage pattern, BVDV strains generally exhibit the genotype-specific model. Although most synonymous codons are selected at the highly variable levels, the strongly suppressive usages focus on synonymous codons containing CG dinucleotides in all BVDV strains. Moreover, the plot of ENC value vs. GC3 content obviously shows that apart from nucleotide usage at highly variable patterns derived from mutation pressure, strong selective forces caused by natural selection mediate synonymous codon usage pattern of BVDV. Taken together, the related results give new insight into multiple selective forces acting on synonymous codon usage beyond nucleotide usage variation during BVDV evolutionary pathway.