Molecular Characterization of the env Gene of Bovine Leukemia Virus in Cattle from Pakistan with NGS-Based Evidence of Virus Heterogeneity

Abstract

Characterization of the global genetic diversity of the bovine leukemia virus (BLV) is an ongoing international research effort. Up to now BLV sequences have been classified into eleven distinct genotypes. Although BLV genotyping and molecular analysis of field isolates were reported in many countries, there is no report describing BLV genotypes present in cattle from Pakistan. In this study we examined 27 env gene sequences from BLV-infected cattle coming from four farms located in Khyber Pakhtunkwa, Gilgit Baltisan and Punjab provinces. Phylogenetic analyses revealed the classification of Pakistani sequences into genotypes G1 and G6. The alignment with the FLK-BLV sequence revealed the presence of 45 mutations, namely, seven in genotype G1 and 33 in genotype G6. Five mutations were found in both, G1 and G6 genotypes. Twelve amino acid substitutions were found in the analyzed sequences, of which only one P264S was specific for sequences from Pakistan. Furthermore, a certain degree of nucleotide heterogeneity was identified by NGS. These results highlight the need for further study on the importance of genetic variability of BLV, especially in the context of its pathogenicity and potential effect on serological detection.

Bovine Leukaemia Virus: Current Epidemiological Circumstance and Future Prospective

“…These glycoproteins play an important role in the viral life cycle because they contain the recognition site required for viral entry and they mediate cell fusion [41]. The env gene shows a genetic polymorphism that may be useful in phylogenetic studies and classifications of BLV isolates, as confirmed by several studies [42]. The nucleotide sequence and amino acid composition of the env gene are useful genomic markers of BLV for the study of its distribution and to reveal the presence of different genotypes that correlate with geographic origin [32,43].…”

“…Genotype 10 is prevalent in China, Vietnam, Thailand, and Myanmar [33,[45][46][47][48][49]. Genotype 4 was present at some countries from North America, South America, Africa, and Asia [42,50]. Genotype 11 are recorded in China [51] and G6 genotype has been found in South American countries, such as Argentina, Brazil, Peru, Paraguay, and Bolivia [48,52], as well as Asian countries such as the Philippines, Thailand [53], and India [54].…”

Tracing Viral Transmission and Evolution of Bovine Leukemia Virus through Long Read Oxford Nanopore Sequencing of the Proviral Genome

“…Historically, the majority of BLV phylogenetic analyses is based solely on the env gene sequences alone (18)(19)(20) [20][21][22]. Analysis of the env gene sequences extracted from the ONT reads within this study (Figure 5) identified only six different nucleotide substitutions which were synonymous at the amino acid level.…”

“…Without availability of effective treatment or vaccination programs, effective herd management practices to break the chain of transmission is critical. Various transmission routes of BLV have been reported [19][20][21][22][23], but it has been challenging to find direct evidence to prove vertical transmission of the virus. We sought to develop a tool to accurately analyze the majority of the proviral BLV genome to aid in the detection of transmission among United States dairy farms.…”

“…Ten different genotypes have been identified so far based on the variations within the env gene and whole genome analysis via tiled PCR based NGS sequencing [20,21]. Previous studies agree that BLV genotypes associate with the global geographical origin [21,22]. However, it is precarious to draw on international BLV genetic relationships based on short and conserved genomic regions, like the env gene.…”