Who’s who in the Bovine viral diarrhea virus type 1 species: Genotypes L and R.

Highlights • Bovine isolates from Turkey reported as BVDV-1 R and L have been characterized as genotypes 1.14 and 1.16 according to PNS method. • They resulted separate clusters in the species, as demonstrated by phylogenetic analysis based on 5’-UTR and Npro regions. • Genotypes 1.14 and 1.16 - R and L - have been detected only in Turkey. • Other bovine isolates, identified with same genotype names L and R, were different from Turkish isolates and clustered as 1.12 and 1.20 by PNS. • Uncoherent nomenclature of homonymous strains should be corrected to avoid confusion in the taxonomy of the BVDV-1 species. Abstract The bovine viral diarrhea virus type 1 species is responsible for cosmopolitan diseases affecting cattle and other ruminants, with relevant impact on animal production. The species presents high genomic heterogeneity, with implications on control and prophylactic programs. Genomic traits of different genetic groups are often related to geographic origin. Atypical sequences have been reported from Pestivirus isolates originated from cattle in Turkey. Based on phylogenetic analysis of 5′ untranslated region and Npro and secondary structure analysis of the 5′-UTR RNA, Turkish isolates have been segregated in two distinct genotypes. Out of the twenty-three identified BVDV-1 genotypes, the Turkish clusters, named L and R or 1.16 and 1.14, according to palindromic nucleotide substitution genotyping method, represent genomic clusters so far, not described elsewhere, suggesting geographic segregation. In order to avoid confusion in the current taxonomy of the species, nomenclature of described homonymous genotypes, referred to different genomic clusters, should be corrected. [ABSTRACT FROM AUTHOR]