Genetic diversity of Bovine Viral Diarrhea Virus from cattle in Chile between 2003 and 2007

Abstract

Background: Bovine Viral Diarrhea Virus causes significant economic losses in cattle. BVDV has high genomic diversity, with two species, BVDV-1 and BVDV-2, and at least twenty-one subgenotypes for BVDV-1 and four subgenotypes for BVDV-2. Vaccines are important tools to reduce the economic losses caused by this virus. However, vaccine strains must correspond to the antigenic profile of the viruses present in the region where the vaccine is applied. A restricted phylogenetic study with 14 viruses isolated from cattle between 1993 and 2001 showed that the genetic profile of BVDV in Chile consisted of viruses of both species and sub-genotypes 1a, 1b, 1c (currently 1j) and 2a. To determine more accurately the genetic profile of BVDV in Chile, in this study a larger number of viruses obtained from bovines between 2003 and 2007 were typed.

Results: The study was performed using partial sequences from the 5' noncoding region (5'UTR) and E2 coding region of the viral genome of thirty-five Chilean viruses isolated from geographic regions that have 84.6% of the Chilean cattle. All tested viruses belonged to species BVDV-1. Eighteen viruses belonged to BVDV-1j subgenotype (51.4%), twelve belonged to BVDV-1b (34.3%) and five belonged to BVDV-1a (14.3%). The Chilean BVDV-1j viruses showed low genetic diversity, both among themselves and with the BVDV-1j present in other regions of the world. This could be explained by a relatively recent introduction of this viral subgenotype in cattle, which agrees with its low geographical distribution worldwide. Otherwise, Chilean BVDV-1b viruses grouped into a single cluster, different even than the viruses present in Argentina and Brazil, countries geographically close to Chile, a process of local evolution that could generate antigenic differences between the Chilean viruses and the viruses used as vaccine strains.

Conclusions: The high presence of viruses of the BVDV-1j subgenotype, which show major antigenic differences with BVDV-1a and BVDV-1b subgenotypes used in the commercial vaccines, suggest that BVDV-1j viruses could be an emergent subgenotype of BVDV in cattle in South America and suggest evaluating an update of the vaccines used in Chile.

Keywords: 5’UTR; BVDV; Bovine viral diarrhea virus; E2; Genetic diversity; Pestivirus.

Fig. 1

Phylogenetic analysis of Chilean BVDV isolates based on partial 5’-Untranslated Region (5’UTR). The phylogenetic tree were prepared using the Maximum Likelihood method and numbers over branches indicate the percentage of 1000 bootstrap replicates that support each phylogenetic branch. The GenBak accession numbers are indicated after the name of the BVDV strains. The Chilean viruses of this study are marked with circles

Fig. 2

Phylogenetic analysis of Chilean BVDV isolates based on partial E2 coding region (E2). The phylogenetic tree was prepared using the Maximum Likelihood method and numbers over branches indicate the percentage of 1000 bootstrap replicates that support each phylogenetic branch. The GenBak accession numbers are after the name of the BVDV strains. The Chilean viruses of this study are marked with circles

Fig. 3

SDT matrix of pairwise identity scores generated by alignment of a 420 bp fragment of the E2 gene for 37 BVDV viruses. Each colored cell represents the percentage of identity between two nucleotide sequences, one horizontally and the other vertically, that intersect in the cell. A figure indicating the correspondence between pairwise identities and the colors is included

Fig. 4

Alignment of partial amino acid sequences of E2 of BVDV-1a, BVDV-1b and BVDV-1j subgenotypes of BVDV. The aligned sequences correspond to amino acids from 832 to 891. Dots represent identical amino acids to the standard sequence of the corresponding subgenotype (BVDV-1a: SD-1, BVDV-1b: CP7, and BVDV-1j: 190cp). Uppercase letters represent an amino acid substitution. Domain C (amino acids 843 to 870) is indicated