Comparative phylogenetic analysis of Siberian isolates of bovine pestiviruses

Abstract

The results of comparative phylogenetic analysis of 52 isolates of bovine pestiviruses of three species circulating among highly productive dairy cattle in Siberia, as well as those present in the samples of commercial fetal serum, transfected cell culture lines and live vaccines on four genes: Npro, Erns, E1 and E2 are presented. The obtained data were compared with the results of the 5'UTR gene sequencing obtained earlier. The results confirmed the circulation in Siberia of eleven subtypes of BVDV-1 (a,b,c,d,f,g,i,j, k,p,r), three subtypes of BVDV-2 (a,b,c) and one BVDV -3(a). The genetic profiles of the isolates for the 5'UTR, Npro, Erns and E1 genes matched completely. The exceptions were three BVDV-1a isolates (R/FBS/96, N/MDBK/08 and SA/FBS/08) detected in infected cell cultures that clustered in a clade formed by BVDV-1j reference sequences. The remaining isolates previously shown to have 100% sequence identity of the 5'UTR had nucleotide sequence similarities of the Npro, Erns, E1, and E2 genes ranging from 96-99%, which also implies that they are closely related. The results of the BVDV-2 isolates sequencing showed a complete correspondence with the genome sequences identified in the previous studies. Comparative sequencing also confirmed the circulation of H Italian-Brazilian pestivirus isolates (BVBD-3a) in Siberia, but all the isolates were divided into two subclades. The first included the isolates isolated from fetal sera and cell cultures, while the second included those isolated from the vaccines and internal organs of diseased animals during outbreaks in farms. The genetic diversity of bovine pestiviruses, their origin and variability are discussed.