A new genotype of bovine leukemia virus in South America identified by NGS-based whole genome sequencing and molecular evolutionary genetic analysis

Abstract

BackgroundBovine leukemia virus (BLV) is a member of retroviridae family, together with human T cell leukemia virus types 1 and 2 (HTLV-1 and -2) belonging to the genes deltaretrovirus, and infects cattle worldwide. Previous studies have classified the env sequences of BLV provirus from different geographic locations into eight genetic groups. To investigate the genetic variability of BLV in South America, we performed phylogenetic analyses of whole genome and partial env gp51 sequences of BLV strains isolated from Peru, Paraguay and Bolivia, for which no the molecular characteristics of BLV have previously been published, and discovered a novel BLV genotype, genotype-9, in Bolivia.ResultsIn Peru and Paraguay, 42.3 % (139/328) and over 50 % (76/139) of samples, respectively, were BLV positive. In Bolivia, the BLV infection rate was up to 30 % (156/507) at the individual level. In Argentina, 325/420 samples were BLV positive, with a BLV prevalence of 77.4 % at the individual level and up to 90.9 % at herd level. By contrast, relatively few BLV positive samples were detected in Chile, with a maximum of 29.1 % BLV infection at the individual level. We performed phylogenetic analyses using two different approaches, maximum likelihood (ML) tree and Bayesian inference, using 35 distinct partial env gp51 sequences from BLV strains isolated from Peru, Paraguay, and Bolivia, and 74 known BLV strains, representing eight different BLV genotypes from various geographical locations worldwide. The results indicated that Peruvian and Paraguayan BLV strains were grouped into genotypes-1, -2, and -6, while those from Bolivia were clustered into genotypes-1, -2, and -6, and a new genotype, genotype-9. Interestingly, these results were confirmed using ML phylogenetic analysis of whole genome sequences obtained by next generation sequencing of 25 BLV strains, assigned to four different genotypes (genotypes-1, -2, -6, and -9) from Peru, Paraguay, and Bolivia. Comparative analyses of complete genome sequences clearly showed some specific substitutions, in both structural and non-structural BLV genes, distinguishing the novel genotype-9 from known genotypes.ConclusionsOur results demonstrate widespread BLV infection in South American cattle and the existence of a new BLV genotype-9 in Bolivia. We conclude that at least seven BLV genotypes (genotypes-1, -2, -4, -5, -6, -7, and -9) are circulating in South America.Electronic supplementary materialThe online version of this article (doi:10.1186/s12977-016-0239-z) contains supplementary material, which is available to authorized users.

Characterization of new RNA polymerase III and RNA polymerase II transcriptional promoters in the Bovine Leukemia Virus genome

“…Our analyses revealed the presence of a putative BRE (nt 29–35, nt 1 defined as the first nucleotide of the 3′LTR in antisense orientation), and overlapping MTE (nt 94–105)/DPE (nt 100–104) motifs, that are both conserved in the nine different BLV genetic groups51.…”

Genetic diversity of bovine leukemia virus worldwide

“…-2, -6 and -9 in Bolivia (Polat et al 2016a), genotype-1, -2, and -6 in samples from Peru and Paraguay (Polat et al 2016a), and genotype-1 in Uruguay (Moratorio et al 2010).…”

“…Fortunately, Japanese group constructed phylogenetic tree to classify BLV genotypes by using full length BLV genome sequences (G-1, -2, and -4) stored in a database, along with newly identified sequences of BLV strains (G-6, -9 and -10); they then showed clear stratification of BLV genotypes with very high bootstrap values (Polat et al 2016a;Polat et al 2016b) (Figure 6). …”

“…Comparison of full amino acid sequences derived from complete genome sequences of available BLV genotypic strains (G-1, -2, -4, -6, -9, and -10) revealed that, even though amino acid substitutions were shared among different genotypes, each harbored genotype-specific amino acid substitutions in both the structural and non-structural genes (Polat et al 2016a;Polat et al 2016b) (summarized in Figure 7). Genotype-1 is the consensus sequence and is the most conserved genotype; it harbors two distinct amino Env, I130V in Tax, I36V in R3, and H27R and F45S in G4.…”

First Molecular Characterization of Bovine Leukemia Virus Infections in the Caribbean

“…Based on env sequences, various genetic groupings have been described [9–16]. In 2009, Rodriguez et al [17] used new and existing sequence data to differentiate BLV into seven genotypes and subsequently three new genotypes were described in Croatia [18], Bolivia [19], Eastern Europe and Siberia [20], Thailand [21] and Myanmar [22] to bring the total number of described genotypes to 10. Although BLV has been described on all continents, there is little information on BLV infections in the Caribbean region.…”