基于遗传演化和密码子分析探究猪伪狂犬病病毒gD基因流行与变异特点OA

To understand the current epidemic status and variation characteristics of porcine pseudorabies virus(PRV)in China,150 full-length gD gene sequences of swine-derived PRV from China were aligned and trimmed,followed by phylogenetic analysis,gene flow analysis,selection pressure analysis,genetic distance analysis,and codon usage analysis.The results showed that PRV could be divided into genotypes Ⅰ and Ⅱ based on the gD gene sequence,and the currently prevalent PRV strains in China were predominantly genotype Ⅱ variant strains of subtype 2.2.The coefficient of genetic differentiation between genotype Ⅰ and genotype Ⅱ populations was 0.510 38,and the gene flow index was 0.24 for both.The ratio of nonsynonymous to synonymous substitution rates(dN/dS)was 1.67(0.010/0.006)for genotype Ⅰ,and 0.33(0.001/0.003)and 1.00(0.001/0.001)for subtypes 2.1 and 2.2,respectively.Genetic distances within genotypes were low,with genotype 2.2 showing the smallest values(0.001 for nucleotide genetic distance and 0.003 for amino acid genetic distance).Among groups,the largest nucleotide genetic distance was observed between genotype Ⅰ and subtype 2.1(0.012),whereas the smallest was between subtypes 2.1 and 2.2(0.004).The effective number of codons(ENC)was similar among the three genotypes/subtypes(genotype Ⅰ,subtype 2.1,and subtype 2.2),being 31.03,31.28,and 31.25,respectively.A total of 28 high-frequency codons were identified,all ending with G or C.In the ENC-plot,three genotypes/subtypes were located below the standard curve.Genotype Ⅰ showed a strong codon usage bias(correlation coefficient=1.000),whereas subtype 2.2 showed an extremely weak bias(correlation coefficient=0.004).These results indicate that PRV strains circulating in China are predominantly genotype Ⅱ,with significant genetic differentiation among populations.Their evolution is mainly influenced by neutral mutations and random factors,with high GC content and codon usage bias predominantly driven by mutational pressure.These findings provide a reference for the prevention and control of PRV in China.