Molecular cloning and sequence analysis of VP6 gene of giant panda rotavirus strain CH-1

Abstract

Rotavirus (family Reoviridae) is the leading cause of severe gastroenteritis in human and animals worldwide. The genome of rotavirus comprises of 11 segments of dsRNA and encodes six structural proteins (VP1 to VP4, VP6 and VP7) and six non structural proteins (NSP1 to NSP6). VP6 is a group of antigen of rotavirus (according to the disparation of VP6, rotavirus is classified into seven groups: A to G), and the major structural protein of inner capsid particles (ICP), and also specific antigen of mucosa immunization that mediate specific immunological reaction. In this report, sequence analysis of VP6 gene of giant panda rotavirus was carried out. Full-length VP6 gene encoding for ICP of giant panda rotavirus was amplified by RT-PCR and the amplicons (1356 bp) were cloned and sequenced. Comparative sequence analysis revealed an open reading frame of 1194 nucleotides (nt) encoding a polypeptide of 397 amino acids (aa). Porcine and human rotaviruses VP6 were highly related giant panda rotavirus VP6 with sequence identity of 98.7 and 97% at the aa level, respectively. Further, they showed 62.9 to 95.1% sequence identity at the nt level with other species of rotavirus. Phylogenetic analysis also showed that giant panda rotavirus VP6 gene was closely related to porcine and human rotavirus. Together, these results may improve our understanding of the evolution, pathogenesis and functional studies of giant panda rotavirus, as well as contribute significantly to giant panda rotavirus research and possibly studies with other species rotaviruses.

Key words: Giant panda rotavirus, VP6 gene, molecular cloning, sequence analysis.