Genetic diversity of Bovine Viral Diarrhea Virus in cattle in France between 2018 and 2020

Abstract

Bovine Viral Diarrhea Virus (BVDV) is one of the main pathogens that affects ruminants worldwide, generating significant economic losses. Like other RNA viruses, BVDV is characterized by a high genetic variability, generating the emergence of new variants, and increasing the risk of new outbreaks. The last report on BVDV genotypes in France was in 2008, since which there have been no new information. The goal of this study is to determine the genetic diversity of BVDV strains currently circulating in France. To this aim, samples of cattle were taken from different departments that are part of the main areas of livestock production during the years 2018 to 2020. Using the partial sequence of the 5'UTR region of the viral genome, we identified and classified 145 samples corresponding to Pestivirus A and one sample corresponding to Pestivirus D. For the Pestivirus A samples, the 1e, 1b, 1d, and 1l genotypes, previously described in France, were identified. Next, the 1r and 1s genotypes, not previously described in the country, were detected. In addition, a new genotype was identified and was tentatively assigned as 1x genotype. These results indicate an increase in the genetic diversity of BVDV in France.

Keywords: Bovine Viral Diarrhea Virus; France; cattle; genetic diversity; genotype.

Figure 1

Map of the geographic distribution of the collection sites of the 146 samples included in the study. In pink the departments from which the samples have been collected.

Figure 2

Phylogenetic tree of Pestivirus A genotypes circulating in France. Phylogenetic tree based on the BVDV 5′UTR fragment, using the Maximum Likelihood method and the two-parameter Kimura model (17). Reference strains were used for each known species/genotype. The GenBank accession number is indicated. Field strains described in this study are identified by the GenBank accession number (Table 1). The asterisk identifies the samples that correspond to the new 1x genotype.

Figure 3

Sequence Identity Matrix of 1x strains compared with currently known Pestivirus A genotypes. Values generated from the 221-bp alignment of the 5′UTR segment. Sequences belonging to 1x genotype were compared with 24 reference strains of BVDV (one per known genotype).