Abstract:

In order to understand the genetic stability and variation of RHDV RdRp gene, the RdRp gene of RHDV SCH04 strain and RHDV2 SCCN03 strain were cloned respectively in this study, then the gene sequences were compared and phylogenetic analysis was carried out. The bioinformatics analysis of RdRp was carried out by predicting the physical and chemical properties, signal peptides, transmembrane region, secondary structure, tertiary structure, phosphorylation and glycosylation modification sites of the coding protein. The results showed that the full length of RdRp gene sequences of the two strains were 1 548 bp, encoding 516 amino acids. The sequence similarity between GI.1 RHDV strains was 86.9%-99.9% and that between GI.2 RHDV strains was 91.3%-99.9%. The sequence similarity between GI.1 and GI.2 RHDV strains was 84.3-88.3%. SCH04 and SCCN03 strains belonged to GI.1a and GI.2 RHDV respectively, and the similarity of nucleotide sequence of RdRp gene between SCH04 and SCCN03 strains was 84.95%. There were 17 amino acid difference sites in coding protein, the amino acid sequence similarity was 96.71%. Both of them belong to stable proteins without signal peptides and transmembrane regions. There was no significant difference in molecular weight, isoelectric point, fat-soluble coefficient, average hydrophilic coefficient and instability coefficient. The proportions of α helix and β rotation of RdRp in SCH04 strain were slightly higher than those in SCCN03 strain (41.86% and 4.26%, respectively), while the proportions of extended chain and random curl in SCCN03 strain were slightly higher than those in SCH04 strain (12.79% and 43.41%, respectively). SCCN03 strain’s RdRp had 4 more phosphorylation sites and 1 more N-glycosylation site than SCH04 strain’s RdRp. The results showed that the nucleotide variation rate of RHDV RdRp gene among different types was large, and the variation range of GI.1 RHDV strain was larger than that of GI.2 RHDV strain. The amino acid sequence similarity of RHDV RdRp of SCH04 strain and SCCN03 strain is higher than that of nucleotide, the difference between secondary structure and advanced structure is small, and the inheritance is relatively stable. These results provide scientific reference for the molecular etiology of RHDV such as genetic evolution and biosynthesis.

Key words: rabbit hemorrhagic disease virus, RdRp, comparative analysis, bioinformatics analysis