猪瘟病毒编码区基因选择压力及重组分析
摘要
We detected the selection pressure and recombination of all 50 strains Classical Swine Fever Virus (CSFV) available complete coding region, based on the maximum likelihood estimation and six algorithms within Recombinant Detect Program 3.44, to provide the first complete overview of the evolution of CSFV. The results showed the overall <italic>ω </italic>(nonsynonymous/synonymous) of 12 proteins under one-radio model were all lower than 1, indicating that the selection pressure of CSFV was subject to strong purifying selection. Among the 12 proteins, NS3, NS4A and NS4B proteins underwent the stronger purifying selection; meanwhile Npro, E<sup>rns</sup>, E1, E2 and NS5A proteins were detected the positive selection sites, underwent the stonger positive selection, indicating that the adaptive evolution of CSFV were related to the host immune response. Furthermore, 4 putative recombination virus strains, and the newly found HCLV/99, ALD and SWH, were detected in 50 sample sequences by recombination analysis. The proteins related to the genome recombination were involved in the immunity and virulence of CSFV, and the recombination changed the phylogenetic tree branch of recombination strain. However, the recombination loci were detected in most proteins except NS3, NS4A and NS4B proteins which processed the shorter genetic distance. Our research suggested that the mutation and recombination under the selection pressure of the host immune system promoted the evolution of coding region in CSFV. These studies would provide the foundation for vaccine targets and the more and more complex situation of CSFV epidemiological research.