3.4 Analysis of sequence variation in the newly goat PRV strain
To further address the genetic characteristics of YNG strain, the major viral immune (gB , gC , and gD ) and virulence gene (gE and TK ) sequences were successfully amplified and sequenced. The findings revealed that the lengths of gB ,gC , gD , gE and TK genes of YNG strain were 2745 bp, 1464 bp, 1209 bp, 1737 bp, and 1023 bp, respectively (GenBank accession numbers: MW458931, MW392295, MW458932, MW458933, MW458934). Sequence analysis results also showed that there existed continuous nucleotides insertion encoding65AASTPAA71 in the gC gene in comparison to referring PRV strains in genotype I, such as Bartha and Becker strains (Fig. 4A ). Similarly, a 6-nucleotide deletion (encoding 278SP279) in the gDgene was identified in YNG strain relative to classical PRV strains (eg. Fa and Ea) prevalent in Chinese pig population before 2011, indicating that YNG strain is a PRV variant (Fig. 4B ). Compared with other referring variants, only few amino acid variations in gB gene of YNG strain were identified, while no amino acid variations of TK ,gC , and gD genes were found. Notably, compared to other PRV strains, a 3-nt deletion (encoding D at the position of 490) was found in the gE gene of YNG strain and another variant PRV strain (JX/CH/2016, Genbank number accession: MK806387) isolated in Guangdong province, China (Fig. 4C ).
To define the evolutionary position of YNG strain among numerous referring strains from different regions or hosts, gC andgE gene based phylogenetic trees were constructed, respectively (Fig. 4D&E ). The results demonstrated that all PRV strains prevalent in the world could be divided into two genotypes (genotype I and II), and the genotype II was composed of classical PRV strains prevalent before 2011 and variant PRV strains circulated after 2011 in China. Notably, most of PRV strains isolated from different hosts (pigs, dogs, wolves, sheep, foxes, human, etc.) prevalent in China, including YNG strain, belonging to the genotype II, presented a random distribution. Additionally, the phylogenetic position of YNG strain was closer to these of variant PRV strains than classical PRV strains, and far away from the traditional vaccine strains (such as Bartha) belonging to the genotype I.