Sequencing and phylogenetic analysis of gp51 gene of bovine leukaemia virus in Iranian isolates

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

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.

Detection and molecular characterization of bovine leukemia virus in various regions of Iran

Purpose. Bovine leukemia virus (BLV) infects cattle worldwide, imposing an economic impact on the dairy cattle industry. The purpose of this study was to evaluate the molecular epidemiology of BLV in Iran.Methodology. Blood samples taken from 280 cows aged over 2 years old from 13 provinces of Iran were used for leukocyte count and blocking ELISA. Genomic DNA was extracted from the peripheral blood leukocytes of BLV-infected samples and fetal lamb kidney cells to perform PCR of partial env, rex and tax genes and long-terminal-repeat region. The PCR products were sequenced, the phylogenetic tree of each gene was constructed, and nucleotide and amino acid sequence pair distances were calculated.Results. The frequency of BLV infection was 32.8 % among animals and was 80 % among provinces. In BLV seropositive animals, the rate of persistent lymphocytosis was 36.9 %. The constructed phylogenetic trees showed the presence of two BLV genotypes (1 and 4) in Iranian strains. As previous studies, our results showed that the env gene was more variable than previously thought, the Rex protein could withstand more amino acid changes compared to the Tax protein, and no significant differences were observed in average changes of the nucleotide of these genes between clinical stages.Conclusions. Our data indicates an increase in the frequency of this infection in Iran. This is the first study report of the presence of BLV genotype 4 in Iranian farms. These findings may have an important role in the control and prevention of BLV infection in Iran and other countries.

Heterogeneity determination of bovine leukemia virus genome in Santa Catarina state, Brazil

ABSTRACT: Bovine leukemia virus (BLV) is a member of Retroviridae family, genus Deltaretrovirus, and the main viral agent responsible for economic loses in dairy herds. Some studies have been carried out about BLV genotypes, and at least seven genotypes were found out in samples of different regions of the world. The objective of this study was to identify BLV samples from seropositive dairy cattle in Santa Catarina state, Brazil, using molecular techniques. Blood samples were collected (454) from dairy cattle from 31 different farms, and serology using agar gel immunodiffusion test (AGID) was performed. After that, 191 seropositive samples were submitted to DNA extraction, and in 77 samples the polymerase chain reaction (PCR) for amplification of a 440 bp fragment of the env gene was performed. Nineteen DNA samples were subjected to restriction fragment length polymorphism (RFLP) analysis by digestion of the PCR fragment by five restriction endonucleases - BamHI, HaeIII, Tru9I, TaqI, and MwoI. It was found 42% seropositive animals (191/454) and 68% positives of the farms (21/31). The PCR showed 80.5% (62/77) of animals positive. The RFLP analysis identified five different genotypes dispersed by Santa Catarina state, with the highest prevalence for genotype X (47.4%). Overall, our results identified the viral genotypes present in dairy cattle and the prevalence of new variants in representative farms from Santa Catarina state.

Molecular Characterization of Bovine Leukaemia Virus (BLV) Strains Reveals Existence of Genotype 6 in Cattle in India with evidence of a new subgenotype

Bovine leukaemia virus (BLV) causes enzootic leucosis in cattle and is prevalent worldwide. Although recent studies have shown that BLV strains can be classified into 10 distinct genotypes, no information is available regarding the BLV genotype prevalent in cattle in India. To determine the genetic variability in BLV, in this study, 118 adult dairy cows from three states of India were screened for BLV infection by env gp51-specific ELISA and nested PCR. Of the 33 cows found positive by both PCR and ELISA, 10 selected BLV strains were subjected to molecular characterization. Phylogenetic analyses of partial and full-length env gp51 gene sequences of Indian BLV strains and other geographical diverse BLV strains representing all the 10 genotypes revealed that Indian strains belonged to BLV genotype 6. Although Indian strains showed close genetic proximity with the strains circulating in South America, they were classified into a new subgenotype within genotype 6. Alignment of deduced amino acid sequences in gp51 demonstrated substitutions mainly in conformational epitope G, neutralizing domain 2 and linear epitope D, with a novel mutation (threonine to alanine at residue 252) found in D-epitope of all the Indian BLV strains. Although serological evidence of BLV infection in India has been reported earlier, this study on molecular characterization of BLV strains established the existence of BLV genotype 6 in India. Additionally, the results of this study highlight the importance of genetic analysis of geographically diverse BLV strains to understand BLV global genetic diversity and further studies are required to determine BLV genetic diversity and extent of BLV infection in cattle in India.

Computational analysis of envelope glycoproteins from diverse geographical isolates of bovine leukemia virus identifies highly conserved peptide motifs

BACKGROUND

Bovine leukemia virus (BLV) is a deltaretrovirus infecting bovine B cells and causing enzootic bovine leucosis. The SU or surface subunit, gp51, of its envelope glycoprotein is involved in receptor recognition and virion attachment. It contains the major neutralizing and CD4+ and CD8+ T cell epitopes found in naturally infected animals. In this study, we aimed to determine global variation and conservation within gp51 in the context of developing an effective global BLV vaccine.

RESULTS

A total of 256 sequences extracted from the NCBI database and collected in different parts of the world, were studied to identify conserved segments along the env gene sequences that encode the gp51 protein. Using the MEME server and the conserved DNA Region module for analysis within DnaSP, we identified six conserved segments, referred to as A-F, and five semi-conserved segments, referred to as G-K. The amino acid conservation ranged from 98.8 to 99.8% in conserved segments A to F, while segments G to K had 89.6-95.2% conserved amino acid sequence. Selection analysis of individual segments revealed that residues of conserved segments had undergone purifying selection, whereas, particular residues in the semi-conserved segments are currently undergoing positive selection, specifically at amino acid positions 48 in segment K, 74 in segment G, 82 in segment I, 133 and 142 in segment J, and residue 291 in segment H. Each of the codons for these six residues contain the most highly variable nucleotides within their respective semi-conserved segments.

CONCLUSIONS

The data described here show that the consensus amino acid sequence constitutes a strong candidate from which a global vaccine can be derived for use in countries where eradication by culling is not economically feasible. The most conserved segments overlap with amino acids in known immunodeterminants, specifically in epitopes D-D', E-E', CD8+ T-cell epitopes, neutralizing domain 1 and CD4+ T-cell epitopes. Two of the segments reported here represent unique segments that do not overlap with previously identified antigenic determinants. We propose that evidence of positive selection in some residues of the semi-conserved segments suggests that their variation is involved in viral strategy to escape immune surveillance of the host.

Molecular characterization of bovine leukemia virus from Moldovan dairy cattle

Bovine leukemia virus (BLV) is the causative agent of enzootic bovine leukosis (EBL), a disease that has worldwide distribution. Whilst it has been eradicated in most of Western Europe and Scandinavia, it remains a problem in other regions, particularly Eastern Europe and South America. For this study, in 2013, 24 cattle from three farms in three regions of Moldova were screened by ELISA and nested PCR. Of these cattle, 14 which were PCR positive, and these were molecularly characterized based on the nucleotide sequence of the env gene and the deduced amino acid sequence of the encoded gp51 protein. Our results demonstrated a low level of genetic variability (0-2.9%) among BLV field strains from Moldova, in contrast to that observed for other retroviruses, including human immunodeficiency virus (HIV) (20-38%) Mason IL (Trudy vologod moloch Inst 146–164, 1970) and equine infectious anemia virus (EIAV) (~40%) Willems L et al (AIDS Res Hum Retroviruses 16(16):1787–1795, 2000), where the envelope gene exhibits high levels of variation Polat M et al (Retrovirology 13(1):4, 2016). Sequence comparisons and phylogenetic analysis revealed that BLV genotype 7 (G7) is predominant in Moldova and that the BLV population in Moldovan cattle is a mixture of at least three new sub-genotypes: G7D, G7E and G4C. Neutrality tests revealed that negative selection was the major force operating upon the 51-kDa BLV envelope surface glycoprotein subunit gp51, although one positively selected site within conformational epitope G was detected in the N-terminal part of gp51. Furthermore, two functional domains, linear epitope B and the zinc-binding domain, were found to have an elevated ratio of nonsynonymous to synonymous codon differences. Together, these data suggest that the evolutionary constraints on epitopes G and B and the zinc-binding domains of gp51 differ from those on the other domains, with a tendency towards formation of homogenous genetic groups, which is a common concept of global BLV diversification during virus transmission that may be associated with genetic drift.

First Molecular Characterization of Bovine Leukemia Virus Infections in the Caribbean

Bovine leukemia virus (BLV) is a retrovirus that causes enzootic bovine leucosis. To investigate the presence and genetic variability of BLV in the Caribbean for the first time, we preformed fluorescence resonance energy transfer (FRET)-PCR for the pol of BLV on DNA from whole blood of cattle from Dominica, Montserrat, Nevis and St. Kitts. Standard PCRs with primers for the env were used for phylogenetic analysis of BLV in positive animals. We found FRET-PCR positive cattle (12.6%, 41/325) on Dominica (5.2%; 4/77) and St. Kitts (19.2%; 37/193) but not on Montserrat (0%, 0/12) or Nevis (0%, 0/43). Positive animals were cows on farms where animals were raised intensively. Phylogenetic analysis using the neighbor-joining (NJ) method on partial and full-length env sequences obtained for strains from Dominica (n = 2) and St. Kitts (n = 5) and those available in GenBank (n = 90) (genotypes 1-10) revealed the Caribbean strains belonged to genotype 1 (98-100% sequence homology). Ours is the first molecular characterization of BLV infections in the Caribbean and the first description of genotype 1 in the region.

Sequencing and phylogenetic analysis of the gp51 gene from Korean bovine leukemia virus isolates

BACKGROUND

Bovine Leukemia virus (BLV) infection of cattle has been reported in Korea for more than three decades. However, to date, there have been few studies regarding Korean BLV since 1980s. Thus, the purpose of this study is to perform a diagnosis and molecular characterization of BLV strains circulating in Korea and to estimate genetic diversity of different genotypes of BLV.

METHOD

To investigate the distribution of BLV variants in the world and assess the evolutionary history of Korean BLV isolates, a comprehensive molecular analysis of the BLV env gp51 gene was conducted using recent worldwide BLV isolates. The isolates included 50 samples obtained from two cattle farms in southeastern Korea in 2014.

RESULTS

Sequence and phylogenetic analyses of partial 444-nt fragment sequences and complete gp51 sequences of BLV revealed eight distinct genotypes of BLV showing geographic distribution of the world. Most Korean BLV isolates were found to belong to genotype 1 which is a major genotype prevailed throughout the world, and only four isolates from one farm were classified as genotype 3 related to the US and Japan isolates. Analysis of amino acids of Korean BLV isolates showed several sequence substitutions in the leader peptide, conformational epitope, and neutralizing domain regions. The observations suggest the possibility of affecting on viral infectivity and formation.

CONCLUSION

Korean BLV isolates showed the close relationship to genotype 1 and 3. Further study to identify the diversity of BLV circulating in Korea is necessary with samples collected nationwide because this study is the first report of BLV genotype 3 being in circulation in Korea.

Interaction between Bovine leukemia virus (BLV) infection and age on telomerase misregulation

Bovine leukemia virus (BLV) is the causative agent of enzootic bovine leukosis (EBL). BLV can interact with telomerase and inhibits telomere shortening, contributing in leukemogenesis and tumour induction. The role of telomerase in BLV-induced lymphosarcoma and aging has been extensively studied. To date, the interaction of both BLV and aging on telomerase mis-regulation have, however, not been investigated. In the present study, telomerase activity in BLV positive and negative cows was compared over a wide range of ages (11-85 months). Lymphocyte counts were also measured in both BLV positive and negative groups. Telomerase activity was detected in all BLV infected animals with persistent lymphocytosis (PL), especially in older individuals. This study revealed that the cells undergo the natural telomerase shortening even in the presence of an existing viral infection. We also show that viral infection, especially during the PL phase of the disease, increases telomerase activity. A statistically significant interaction between age and viral infection was observed for telomere shortening during BLV infection. Older animals with BLV infection, especially those with persistent lymphocytosis or visible tumors, exhibited a sharp increase in telomerase activity. This study demonstrates that there is a significant interaction between BLV infection and telomerase up-regulation and lymphocytosis.

Detection and molecular characterization of bovine leukemia virus in Philippine cattle

Bovine leukemia virus (BLV) is the etiological agent of enzootic bovine leukosis, which is the most common neoplastic disease of cattle. BLV infects cattle worldwide, imposing a severe economic impact on the dairy cattle industry. However, there are no comprehensive studies on the distribution of BLV in the Philippines, and the genetic characteristics of Philippine BLV strains are unknown. Therefore, the aim of this study was to detect BLV infections in the Philippines and determined their genetic variability. Blood samples were obtained from 1116 cattle from different farms on five Philippine islands, and BLV provirus was detected by BLV-CoCoMo-qPCR-2 and nested PCR targeting BLV long terminal repeats. Out of 1116 samples, 108 (9.7 %) and 54 (4.8 %) were positive for BLV provirus, as determined by BLV-CoCoMo-qPCR-2 and nested PCR, respectively. Of the five islands, Luzon Island showed the highest prevalence of BLV infection (23.1 %). Partial env gp51 genes from 43 samples, which were positive for BLV provirus by both methods, were sequenced for phylogenetic analysis. Phylogenetic analysis based on a 423-bp fragment of the env gene revealed that Philippine BLV strains clustered into either genotype 1 or genotype 6. Substitutions were mainly found in antigenic determinants, such as the CD4(+) T-cell epitope, the CD8(+) T-cell epitope, the second neutralizing domain, B and E epitopes, and these substitutions varied according to genotype. This study provides comprehensive information regarding BLV infection levels in the Philippines and documents the presence of two BLV genotypes, genotypes 1 and 6, in this population.

Detection of bovine leukemia virus in brains of cattle with a neurological syndrome: pathological and molecular studies

Bovine leukemia virus (BLV) was investigated in the central nervous system (CNS) of cattle with neurological syndrome. A total of 269 CNS samples were submitted to nested-PCR (BLV env gene gp51), and the viral genotypes were identified. The nested-PCR was positive in 4.8% (13/269) CNS samples, with 2.7% (2/74) presenting at histological examination lesions of nonpurulent meningoencephalitis (NPME), whereas 5.6% (11/195) not presenting NPME (P > 0.05). No samples presented lymphosarcoma. The PCR products (437 bp) were sequenced and submitted to phylogenetic analysis by neighbor-joining and maximum composite likelihood methods, and genotypes 1, 5, and 6 were detected, corroborating other South American studies. The genotype 6 barely described in Brazil and Argentina was more frequently detected in this study. The identity matrices showed maximum similarity (100%) among some samples of this study and one from Argentina (FJ808582), recovered from GenBank. There was no association among the genotypes and NPME lesions.

The molecular characterization of bovine leukaemia virus isolates from Eastern Europe and Siberia and its impact on phylogeny

Recent studies have shown that bovine leukemia virus (BLV) sequences can be classified into seven distinct genotypes based on full gp51 sequence. This classification was based on available sequence data that mainly represented the BLV population that is circulating in cattle from the US and South America. In order to aid with a global perspective inclusion of data from Eastern Europe is required. In this study we examined 44 BLV isolates from different geographical regions of Poland, Belarus, Ukraine, and Russia. Phylogenetic analysis based on a 444bp fragment of env gene revealed that most of isolates belonged to genotypes 4 and 7. Furthermore, we confirmed the existence of a new genotype, genotype 8, which was highly supported by phylogenetic computations. A significant number of amino acid substitutions were found in the sequences of the studied Eastern European isolates, of which 71% have not been described previously. The substitutions encompassed mainly the C-part of the CD4+ epitope, zinc binding peptide region, CD8+ T cell epitope, and overlapping linear epitope E. These observations highlight the use of sequence data to both elucidate phylogenetic relationships and the potential effect on serological detection of geographically diverse isolates.

Detection and molecular characterization of bovine leukemia viruses from Jordan

Bovine leukemia virus (BLV) is distributed worldwide. BLV has many effects on the health status and productivity of infected animals and is a potential risk for humans. In this study, we aimed to investigate the presence of and genotype bovine leukemia viruses on Jordanian dairy farms. Nested PCR coupled with RFLP and direct sequencing of a partial fragment of the env gene were carried out. Two BLV genotypes were found, genotypes 1 and 6. These genotypes were identified by nested PCR-RFLP of 444 bp of the env gene by restriction digestion with HaeIII, Bcl I and Pvu II. However, BLV-Jordan-10 seems to represent an entirely new genotype in our phylogenetic analysis. The nucleotide sequence identity between these two Jordanian BLV genotypes (1 and 6) was 96.2 %. The nucleotide sequence identity between Jordanian BLV genotype 1 and other reference BLV genotype 1 strains ranged from 99 % to 99.5 %. The nucleotide sequence similarity of the Jordanian BLV genotype 6 to other BLV genotypes ranged from 90 % to 96.7 %. A neutralizing motif and CD8(+) T-cell epitope were found in the env protein of both Jordanian isolates. In this study, we documented the presence of two BLV genotypes (1 and 6) on Jordanian dairy farms.

Identification of a new genotype of bovine leukemia virus

To investigate the degree of genetic variability of bovine leukemia virus (BLV) strains circulating in Croatia, 29 isolates from the six largest dairy farms were examined by PCR for a segment of the gp51 env gene, followed by DNA sequencing and phylogenetic analysis. The nucleotide sequences were compared with other previously characterized BLV strains from different geographical areas, comprising all seven known BLV genotypes. The Croatian sequences showed six to eight nucleotide substitutions: six silent substitutions and two amino acid changes. Four of those substitutions were within epitopes. In comparison to the sequences of other BLV genotypes, our isolates showed the closest relationship to genotype 1 isolates PL-3252 (FJ808585) and AL-148 (FJ808573) from Argentina. The degree of variation between our sequences and those of genotype 1 was 0.2- 4.6 %. In phylogenetic trees based on 400-nt and 519-nt sequences, all of the Croatian sequences clustered separately from the other sequences, revealing a new genotype.

Preventive and therapeutic strategies for bovine leukemia virus: lessons for HTLV

Bovine leukemia virus (BLV) is a retrovirus closely related to the human T-lymphotropic virus type 1 (HTLV-1). BLV is a major animal health problem worldwide causing important economic losses. A series of attempts were developed to reduce prevalence, chiefly by eradication of infected cattle, segregation of BLV-free animals and vaccination. Although having been instrumental in regions such as the EU, these strategies were unsuccessful elsewhere mainly due to economic costs, management restrictions and lack of an efficient vaccine. This review, which summarizes the different attempts previously developed to decrease seroprevalence of BLV, may be informative for management of HTLV-1 infection. We also propose a new approach based on competitive infection with virus deletants aiming at reducing proviral loads.

Bovine leukemia virus can be classified into seven genotypes: evidence for the existence of two novel clades

Previous studies have classified the env sequences of bovine leukemia virus (BLV) provirus from different locations worldwide into between two and four genetic groupings. These different studies gave unique names to the identified groups and no study has yet integrated all the available sequences. Thus, we hypothesized that many of the different groups previously identified actually correspond to a limited group of genotypes that are unevenly distributed worldwide. To examine this hypothesis, we sequenced the env gene from 28 BLV field strains and compared these sequences to 46 env sequences that represent all the genetic groupings already identified. By using phylogenetic analyses, we recovered six clades, or genotypes, that we have called genotypes 1, 2, 3, 4, 5 and 6. Genotypes 1–5 have counterparts among the sequence groupings identified previously. One env sequence did not cluster with any of the others and was highly divergent when compared with the six genotypes identified here. Thus, an extra genotype, which we named 7, may exist. Similarity comparisons were highly congruent with phylogenetic analyses. Furthermore, our analyses confirmed the existence of geographical clusters.