Transcriptome Analysis for Genes Associated with Small Ruminant Lentiviruses Infection in Goats of Carpathian Breed

Small ruminant lentiviruses (SRLV) are economically important viral pathogens of sheep and goats. SRLV infection may interfere in the innate and adaptive immunity of the host, and genes associated with resistance or susceptibility to infection with SRLV have not been fully recognized. The presence of animals with relatively high and low proviral load suggests that some host factors are involved in the control of virus replication. To better understand the role of the genes involved in the host response to SRLV infection, RNA sequencing (RNA-seq) method was used to compare whole gene expression profiles in goats carrying both a high (HPL) and low (LPL) proviral load of SRLV and uninfected animals. Data enabled the identification of 1130 significant differentially expressed genes (DEGs) between control and LPL groups: 411 between control and HPL groups and 1434 DEGs between HPL and LPL groups. DEGs detected between the control group and groups with a proviral load were found to be significantly enriched in several gene ontology (GO) terms, including an integral component of membrane, extracellular region, response to growth factor, inflammatory and innate immune response, transmembrane signaling receptor activity, myeloid differentiation primary response gene 88 (MyD88)-dependent toll-like receptor signaling pathway as well as regulation of cytokine secretion. Our results also demonstrated significant deregulation of selected pathways in response to viral infection. The presence of SRLV proviral load in blood resulted in the modification of gene expression belonging to the toll-like receptor signaling pathway, the tumor necrosis factor (TNF) signaling pathway, the cytokine-cytokine receptor interaction, the phagosome, the Ras signaling pathway, the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) (PI3K-Akt) signaling pathway and rheumatoid arthritis. It is worth mentioning that the most predominant in all pathways were genes represented by toll-like receptors, tubulins, growth factors as well as interferon gamma receptors. DEGs detected between LPL and HPL groups were found to have significantly enriched regulation of signaling receptor activity, the response to toxic substances, nicotinamide adenine dinucleotide (NADH) dehydrogenase complex assembly, cytokine production, vesicle, and vacuole organization. In turn, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway tool classified DEGs that enrich molecular processes such as B and T-cell receptor signaling pathways, natural killer cell-mediated cytotoxicity, Fc gamma R-mediated phagocytosis, toll-like receptor signaling pathways, TNF, mammalian target of rapamycin (mTOR) signaling and forkhead box O (Foxo) signaling pathways, etc. Our data indicate that changes in SRLV proviral load induced altered expression of genes related to different biological processes such as immune response, inflammation, cell locomotion, and cytokine production. These findings provide significant insights into defense mechanisms against SRLV infection. Furthermore, these data can be useful to develop strategies against SRLV infection by selection of animals with reduced SRLV proviral concentration that may lead to a reduction in the spread of the virus.

Analysis of the antibody response to an immunodominant epitope of the envelope glycoprotein of a lentivirus and its diagnostic potential

The envelope glycoprotein of small ruminant lentiviruses (SRLV) is a major target of the humoral immune response and contains several linear B-cell epitopes. We amplified and sequenced the genomic segment encoding the SU5 antigenic site of the envelope glycoprotein of several SRLV field isolates. With synthetic peptides based on the deduced amino acid sequences of SU5 in an enzyme-linked immunosorbent assay (ELISA), we have (i) proved the immunodominance of this region regardless of its high variability, (ii) defined the epitopes encompassed by SU5, (iii) illustrated the rapid and peculiar kinetics of seroconversion to this antigenic site, and (iv) shown the rapid and strong maturation of the avidity of the anti-SU5 antibody. Finally, we demonstrated the modular diagnostic potential of SU5 peptides. Under Swiss field conditions, the SU5 ELISA was shown to detect the majority of infected animals and, when applied in a molecular epidemiological context, to permit rapid phylogenetic classification of the infecting virus.

Development of a semi-nested PCR using degenerate primers for the generic detection of small ruminant lentivirus proviral DNA

A PCR assay was developed for the reliable detection of small ruminant lentivirus (SRLV) proviral DNA. The method involved the use of degenerate deoxyinosine-substituted primers and a second semi-nested PCR step that increased the polyvalency and sensitivity of the detection, respectively. Primers were designed from the pol gene conserved motifs of 85 SRLV isolates and were evaluated using different SRLV isolates together with Maedi-Visna virus (MVV) and caprine arthritis-encephalitis virus (CAEV) reference strains. The method successfully detected SRLV proviral DNA in total DNA extracts originating from whole blood samples, separated peripheral blood mononuclear cells (PBMCs) and tissue cultures. The semi-nested PCR was compared with the agar gel immunodiffusion test and proved to be highly sensitive, specific and capable of detecting many SRLV variants in infected or suspect animals. Therefore, it would be useful in the diagnosis of natural SRLV infections, in eradication programs and epidemiological studies. Whole blood samples can be used directly, thus alleviating the need for PBMC separation, and thereby enables a simple, fast and cost-effective analysis of a large number of samples.

Application of PCR technique in diagnosis of small ruminant lentivirus infection in sheep and goats

Detection of small ruminant lentiviruses (SRLVs) in sheep and goats usually relies on serological testing. In this study, we evaluated semi-nested PCR and nested PCR techniques applied as a diagnostic tool for detection of maedi-visna virus (MVV) and caprine arthritis-encephalitis virus (CAEV) in naturally infected sheep and goats, respectively. The examination of 193 ovine and 85 caprine serum samples by the ELISA revealed the presence of specific antibodies in 133 (69%) and 18 (21.2%) animals, respectively. Presence of proviral DNA was manifested in 103 (53.4%) sheep and 12 (14.2%) goats. Despite the relatively lower sensitivity of PCR, the fact of detection of proviral DNA in 19 out of 60 ovine samples and 7 out of 67 caprine samples collected from animals previously negative by ELISA was noteworthy. In conclusion, the data demonstrated that combinations of both ELISA and PCR might afford optimal detection of SRLVs infection.

First partial characterisation of small ruminant lentiviruses from Greece

Small ruminant lentivirus (SRLV) infections are widespread in Greece, but SRLVs have never been isolated and characterized. In this study, we present the sequence of a 574-nucleotide (191-amino acid) region of the gag gene of SRLV strains from four sheep and one goat from a single geographic area of Greece. All five sequences appeared to be closely related at both nucleotide (2.1-14.2% variation) and deduced amino acid (1.6-4.2% variation) level. Greek SRLV strains were closer to ovine prototypic strains (average divergence 16.8%) than to the caprine strain CAEV-Co (21% divergence). By amino acid composition, the Greek SRLVs were on the average more than twice as distant from CAEV-Co as from other ovine strains. Phylogenetic analysis suggested that Greek strains segregate into a unique group, separate from, but related to, other ovine prototype sequences.

Seven new ovine progressive pneumonia virus (OPPV) field isolates from Dubois Idaho sheep comprise part of OPPV clade II based on surface envelope glycoprotein (SU) sequences

Seven new ovine progressive pneumonia virus (OPPV) field isolates were derived from colostrum and milk of 10 naturally OPPV-infected sheep from the US Sheep Experiment Station in Dubois, Idaho, USA. Sixteen sequences of the surface envelope glycoprotein (SU) from these seven Dubois OPPV field isolates and SU sequence from OPPV WLC1 were obtained, aligned with published SRLV SU sequences, and analyzed using phylogenetic analysis using parsimony (PAUP). Percent nucleotide identity in SU was greater than 95.8% among clones from individual Dubois OPPVs and ranged from 85.5 to 93.8% between different Dubois OPPV clones. SU sequences from Dubois OPPVs and WLC1 OPPV had significantly higher percent nucleotide identity to SU sequences from the North American OPPVs (85/34 and S93) than caprine-arthritis encephalitis virus (CAEVs) or MVVs. PAUP analysis also showed that SU sequences from the Dubois OPPVs and OPPV WLC1 grouped with other North American OPPVs (85/34 and S93) with a bootstrap value of 100 and formed one OPPV clade II group. In addition, Dubois and WLC1 SU amino acid sequences had significantly higher identity to SU sequences from North American OPPVs than CAEV or MVV. These data indicate that the seven new Dubois OPPV field isolates along with WLC1 OPPV are part of the OPPV clade II and are distinct from CAEVs and MVVs.

Phylogenetic analysis and reclassification of caprine and ovine lentiviruses based on 104 new isolates: evidence for regular sheep-to-goat transmission and worldwide propagation through livestock trade

We performed a phylogenetic analysis of caprine and ovine lentiviruses using long sequences in gag and pol of 104 new Swiss isolates and six available corresponding database sequences. Forty-five isolates, forming five sequence clusters, were unclassifiable by the present classification. Pairwise DNA distance analysis indicated different categories of relatedness, requiring a new classification system. We propose four principal sequence groups, A-D, which differ by 25-37%. Groups A and B are further divided into subtypes which differ by 15-27%. Group D and four of the seven group A subtypes, A3, A4, A5 and A7, are formed by new Swiss isolates. Molecular epidemiology revealed that Swiss B1 strains differed no more from French, Brazilian or US strains than from each other, suggesting virus propagation through international livestock trade. Furthermore, infection of goats by subtypes A3 or A4 was significantly associated with documented contact with sheep, which also harbor these subtypes, thus indicating regularly occurring sheep-to-goat transmission.

Characterisation of an Irish caprine lentivirus strain--SRLV phylogeny revisited

Small ruminant lentiviruses (SRLV), i.e. caprine arthritis-encephalitis virus (CAEV) (which infects goats) and maedi-visna virus (MVV) (which infects sheep) are two closely related lentiviruses but the relationship between goat and sheep lentiviruses has not been clearly established. To better understand their genetic relationship, we reinvestigated the phylogeny of SRLV using new sequences from an Irish and a Norwegian strain together with sequences available from databases. The phylogenetic analyses were carried out on the gag, pol and env fragments using four methods: neighbor-joining (NJ), Fitch and Margoliash (Fitch), Fitch and Wagner parsimony (Pars) and maximum likelihood (ML). The tree topologies were consistent whether derived from any of the four methods or any of the gene fragments, but the phylogenetic analyses in the pol and env regions were more informative than in the gag region. The Tamura-Nei model with variable rates across sites (described by a gamma distribution) provides a more accurate description of SRLV evolution than simple methods. The newly described Irish lentivirus strain, which was isolated from a goat, was closely related to the lentivirus that infects sheep: MVV. The novel Norwegian CAEV strain belonged to a cluster specific to the CAEV strains from Norway. Together, both data confirm the previously reported subdivision of the different SRLV strains into six clades. The caprine and ovine lentivirus sequences are interspersed in phylogenetic trees, supporting the existence of cross-species transmission. Nevertheless, the transmission of an ovine lentivirus to a goat could trigger the emergence of some goat-adapted phylums. Our new sequences confirm the complex situation in SRLV phylogeny but more sequences are needed to elucidate more precisely the relationship between SRLV.

Conserved sequence motifs involving the tat reading frame of Brazilian caprine lentiviruses indicate affiliations to both caprine arthritis-encephalitis virus and visna-maedi virus

The sequence variation in small ruminant lentiviruses from Brazilian herds of milking goats was sampled in a representative region of the pol gene and in a region including the entire tat open reading frame. Clones were amplified from cDNA derived from virus produced in vitro using primers targetting conserved sequences of the pol gene. Iterative sequencing of clones indicated that animals from two herds in the Minas Gerais area were infected by a caprine arthritis-encephalitis virus (CAEV)-like virus and that individual animals carried variant virus populations. Sequences derived from an infected goat from a herd in Pernambuco showed no nucleic acid variation and were distant from the CAEV-type sequence but marginally closer to ovine visna-maedi virus (VMV) sequences. Sequences amplified from a region including the tat gene, amplified with a common upstream primer within the vif coding region and different downstream primers because of the local divergence between CAEV- and VMV-type sequences, confirmed the affiliation of the Minas Gerais sequences to CAEV and indicated that the Pernambuco isolate was indeed related to VMV, which had not previously been reported to cause natural caprine infection. The overlap between the vif and tat open reading frames clearly distinguished between CAEV-like small ruminant lentiviruses, which shared eight common nucleotides, and the VMV group, where the overlap was reduced to a single base; the final adenine of the vif terminator (TAA) is the initial adenine of the presumptive tat initiator codon. This may be useful for epizoological tracing of the origin of outbreaks.

Differential replication of ovine lentivirus in endothelial cells cultured from different tissues

Blood-brain barrier dysfunction has been postulated to be important in the pathogenesis of HIV dementia. This study used an in vitro model of the blood-brain barrier to determine the effects of ovine lentivirus (OvLV) infection on endothelial cells. The replication of two American OvLV isolates and two lcelandic OvLV isolates in pure cultures of endothelial cells isolated from brain was compared to replication in endothelial cells from adipose, lung, and aorta. Inoculation with the two American isolates resulted in 100 times greater reverse transcriptase (RT) activity in supernatant of the microvascular endothelial cells (brain, lung, and adipose) than in the macrovascular endothelial cells (aorta). Conversely, inoculation with the two lcelandic isolates resulted in 100 times higher RT activity in aortic, lung, and adipose endothelial cells than in the brain endothelial cells. Transmission electron microscopy of the brain capillary endothelial cells infected with the American isolates revealed polarized viral budding from the lateral cell membrane and a loss of tight junctions. Replication of OvLV in brain capillary endothelial cells could play a role in the pathogenesis of lentiviral encephalitis by altering blood-brain barrier integrity.

Envelope glycoprotein nucleotide sequence and genetic characterization of North American ovine lentiviruses

Ovine lentiviruses (OvLV) resemble human immunodeficiency viruses in genomic organization, viral heterogeneity, and spectrum of cytophenotypic expression. To gain a better understanding of the relationship of North American OvLV isolates with other characterized OvLV strains, the complete DNA nucleotide sequence of the env region of a highly lytic (rapid/high) OvLV strain (85/34) was determined and compared with the sequence of amplicons within env of three other OvLV strains of varying cytophenotype and isolated from the same flock of sheep. LTR and pol regions also were compared among these strains. The env region of 85/34 was 986 codons in length and the reported nucleotide sequence showed features shared by other OvLV including heavy glycosylation and conserved and hypervariable regions within the surface membrane protein region. Phylogenetic analyses of regions within LTR, reverse transcriptase, and env grouped the four virus strains together and similar to the maedi-visna OvLV strains, including visna virus, South African ovine maedi visna virus, and EV1 (British OvLV isolate), but they were distinct from caprine arthritis encephalitis virus.

Immortalization of caprine fibroblasts permissive for replication of small ruminant lentiviruses

OBJECTIVE

To establish immortalized caprine fibroblastic cell lines permissive for replication of small ruminant lentiviruses.

ANIMALS

Carpal synovial membrane explants collected aseptically from a surgically delivered fetus of a lentivirus-seronegative goat.

PROCEDURE

Immortalization of goat embryonic fibroblasts was performed by DNA transfection with plasmids coding for simian virus 40 large T antigen. The generated cell lines were phenotypically characterized. Cytogenetics, growth pattern, and sensitivity to viral infection were studied.

RESULTS

3 cell lines, designated TIGEF, mMTSV-54, and mMTSV-93, were generated. They had a more rapid doubling time than did fibroblasts from which they were derived, and retained morphologic and phenotypic fibroblastic characteristics. They were immortalized but not transformed because tumor formation was not promoted after their s.c. injection into athymic nude mice. The 3 cell lines were susceptible to caprine arthritis-encephalitis virus and visna-maedi virus infections, and supported a complete virus replication cycle.

CONCLUSIONS

Cultured caprine fibroblastic cells were immortalized, using simian virus 40 large T antigen. The TIGEF, mMTSV-54, and mMTSV-93 immortalized cell lines were permissive to in vitro small ruminant lentivirus replication.

CLINICAL RELEVANCE

Because lentivirus detection, as well as detailed studies of host-lentivirus interactions, are hampered by differences in viral susceptibility of each primary culture, permanent cell lines are essential tools for such analysis.

Genomic heterogeneity of small ruminant lentiviruses: existence of heterogeneous populations in sheep and of the same lentiviral genotypes in sheep and goats

We have recently shown that French small ruminant lentiviruses (SRLV) from sheep are more similar to Caprine Arthritis Encephalitis Virus (CAEV) than to visna maedi virus (VMV) in a conserved region of the pol gene. To extend these results, we have examined sequences from a variable region of the env gene in French SRLV. We found that they were nearly equally distant from both CAEV and VMV strains, suggesting a considerable divergence since the initial introduction of the virus. Analysis of separate clones from individual animals showed that some carry a population of variant viruses. The study of further pol gene sequences from both goats and sheep suggests that viral variants show little or no host species specificity. A phylogenetic tree of pol gene sequences confirmed the presence of a novel genotype of SRLV in France.

Sequence analysis and transcriptional activity of the LTR of OLV-CU1, a North American ovine lentivirus

Although ovine lentiviruses have been described in the United States since the early part of this century, North American strains of sheep lentiviruses remain relatively uncharacterized at the molecular level. The LTR of a North American ovine lentivirus, OLV-CU1, was found to be closely related at the molecular and functional levels to visna virus, the Icelandic ovine lentivirus. Sequence analysis of the LTR revealed high identity to other ovine and caprine lentiviruses in key regulatory elements of the upstream promoter region (-25 to -115). However, the R region of the LTR was much less homologous. Transcriptional control of OLV-CU1 in transient transcriptional assays required a conserved putative AP-4 region and possibly an AP-1 like element in the upstream promoter region for moderate to high levels of transcription, much like visna virus. In contrast to visna virus, the downstream region beyond the transcriptional start site was required for virus-specific transactivation.

Recognition of ovine lentivirus gag gene products by serum from infected sheep

In order to localize the immunodominant regions, 12 ovine lentivirus (OLV) gag-coding gene fragments were cloned and expressed in Escherichia coli and then tested in a Western blot (WB) assay against a panel of sera collected from US and Italian OLV-infected sheep. The most immunoreactive regions were mapped to the amino-terminal of p25 and carboxyl-terminal of p14. In addition, we found that the reactivity pattern between US and Italian sheep was very similar, suggesting the antigenic domain between US and Italian isolates in the gag gene structures could be conserved. Given the broad immunoreactivity of the amino-terminal of p25, this region could serve as an ideal diagnostic antigen for the serological identification of OLV-infected sheep.

Genetic characterization of two phenotypically distinct North American ovine lentiviruses and their possible origin from caprine arthritis-encephalitis virus

Ovine and caprine lentiviruses are closely related genetically and antigenically although the diseases that these viruses cause in their respective host animals can vary greatly. In sheep, syndromes consist primarily of interstitial pneumonia with rare occurrences of arthritis and encephalitis, whereas in goats, the disease expresses mainly as arthritis in adult animals with rare cases of encephalitis in newborns. Experimentally, viruses from either sheep or goats can infect animals of the reciprocal species and many field strains of ovine lentivirus have biological properties similar to those of caprine viruses. However, a molecular correlation for the phenotypic differences between ovine and caprine lentivirus strains is unknown. To investigate this, we examined genetic characteristics of two phenotypically distinct North American ovine lentiviruses. Nucleotide sequence analysis of the envelope regions from virus strains 85/34 and 84/28 showed that despite significant biological differences, these viruses are closely related to each other and are genotypically more homologous to caprine arthritis-encephalitis virus (CAEV) than to visna virus of sheep. Furthermore, analysis of the nucleotide substitutions in their env regions indicated that when differences between the two ovine viruses and CAEV were found, the changes often resulted in nucleotides homologous with visna virus. These results suggest that the two field strains of ovine lentivirus may have originated from a cross-species infection of sheep by a CAEV-like virus and, evolution of their genomes toward that of ovine lentivirus may be reflective of adaptation of these viruses to the new ovine host.

Genome analysis of North American small ruminant lentiviruses by polymerase chain reaction and restriction enzyme analysis

The polymerase chain reaction (PCR) was used to amplify portions of the gag and env structural genes of 8 ovine and 1 caprine lentivirus isolates of North American origin. Three sets of primers were used to amplify p16, p25, and N'-gp40 gene fragments, and 1 set, annealing highly conserved portions of long terminal repeat (LTR) among small ruminant lentiviruses, was used as a positive control. Variable PCR amplification efficiency was observed. Different stringency conditions of hybridization with specific DNA probes were used to maximize detection of the PCR product. The p25 primers detected all strains, the gp40 primers detected 1 ovine and the caprine strain, and the p16 primers detected only 1 ovine isolate. All strains were detected by LTR primers. Restriction endonuclease analysis of 5 amplified p25 and 2 N'-gp40 gene fragments revealed extensive heterogeneity among these North American small ruminant lentiviruses.

Genomic heterogeneity in the pol region of ovine lentiviruses obtained from bronchoalveolar cells of infected sheep from France

In order to determine the genomic heterogeneity of ovine lentiviruses, we analysed eight isolates from naturally infected sheep from one geographical region of France. A 475 nt fragment in the region of the pol gene coding for reverse transcriptase was amplified by RT-PCR from RNA directly extracted from uncultured bronchoalveolar lavage cells. The resulting PCR fragments were analysed by restriction enzyme digestion, cloned in a TA vector and sequenced. Restriction enzyme analysis showed distinct patterns from the eight isolates, and sequencing showed them to be closely related in both nucleotide (2.3-8.1% variation) and deduced amino acid (0-6.2% variation) sequences. Their amino acid sequences differed from that of visna-maedi virus complete viral genome sequence K1514 by 12.5-15.3%, but from that of caprine arthritis encephalitis virus (CAEV) viral genome sequence Co by only 4.2-6.9%. Phylogenetic analysis showed that the French isolates form a group related to CAEV Co and distant from previously reported ovine lentivirus sequences from different origins.

Analysis of lentiviral genomic variation by denaturing gradient gel electrophoresis

Retroviruses are known for their genetic variability. In any infection, several genotypes usually exist within the host. We have used denaturing gradient gel electrophoresis to study genetic variation of ovine lentiviruses. Starting with viral DNA from cells infected in vitro, a portion of the envelope gene was amplified by PCR, and the products were analyzed by DGGE. With this technique we have been able to detect sequence variations between and within virus isolates and to show evolution of the predominant viral species upon in vivo passage.