Genomic Epidemiology and Heterogeneity of SRLV in Italy from 1998 to 2019

Molecular Characterization of Small Ruminant Lentiviruses in Sheep and Goats: A Systematic Review

Small ruminant lentiviruses (SRLVs) are responsible for chronic and progressive multisystemic clinical forms, which significantly reduce flocks' productivity and have a considerable economic impact on the small ruminant industry. Due to the increase in genetic analysis studies and the potential for misclassification of certain strains, owing to the high genetic variability of these viruses, a systematic review was deemed necessary. This review explores the types of matrices used for molecular detection and phylogenetic studies, the genomic regions selected as targets, and the software utilized for phylogenetic analysis, assessing the geographical distribution of identified genotypes and subgenotypes over time. A thorough comparison of the diagnostic approaches highlights the strengths and limitations of each method, identifying gaps that need to be addressed. Additionally, recombination events and compartmentalization are examined to provide an updated, detailed, and comprehensive overview of SRLV phylogenesis.

The herd-level prevalence of caprine arthritis-encephalitis and genetic characteristics of small ruminant lentivirus in the Lithuanian goat population

Caprine arthritis-encephalitis (CAE) is a progressive disease of goats caused by small ruminant lentivirus (SRLV) and is considered as one of the most important threats for goat farming in developed countries. The disease prevalence has never been investigated in the Lithuanian goat population. Therefore, a descriptive cross-sectional study was carried out in 2021-2022 to determine if SRLV infection was present in the Lithuanian goat population and, in the case of a positive result, to estimate the true herd-level prevalence of SRLV infection and specify genotypes and subtypes of SRLV responsible for the infection. Thirty goat herds counting >5 adult goats were randomly selected and, in each herd, a representative sample of adult goats was blood-sampled and tested serologically for SRLV infection using a commercial ELISA. The herd was considered infected if at least one goat tested positive and the true herd-level prevalence of SRLV infection was estimated using the Bayesian approach. Seropositive animals were found in 17 / 30 herds (57 %; 95 % confidence interval: 39 %, 73 %). The true herd-level prevalence was 56 % (95 % credible interval: 36 %, 76 %). In 10 / 17 seropositive herds whose owners consented for resampling of seropositive goats, 1-5 seropositive goats were tested using the nested real-time PCR (nRT-PCR). Goats from 9 seropositive herds tested positive in the nRT-PCR: in 4 herds for genotype A, in 4 herds for genotype B, and in 1 herd - 2 goats for genotype B and 1 goat for genotype A. From each of 9 nRT-PCR-positive herds, 1 PCR product of each genotype was sequenced using Sanger method and the phylogenic tree was constructed using the neighbor-joining method in the Molecular Evolutionary Genetics Analysis software. Four herds turned out to be infected with B1 subtype (91 % identity with the prototypic strain), 3 herds with A2 subtype (90 %-92 % identity), and a herd with mixed infection was infected with B1 (91 % identity) and A2 subtype (90 % identity). In one herd, the only seropositive goat was found to be infected with the strain most closely related to the A1 subtype (80 % identity). This study shows for the first time that SRLV infection is present and widespread in the Lithuanian goat population and both classical SRLV genotypes, represented by quite typical subtypes A2 and B1, appear to be responsible for the infection.

First Molecular Characterization of Small Ruminant Lentiviruses in Hungarian Goat Population

In 2023, a molecular study was conducted on the Hungarian goat population to determine genotypes and subtypes of small ruminant lentiviruses (SRLV) infecting these herds. Ten goat herds seropositive for SRLV infection according to a serosurvey conducted earlier in Hungary were selected, and 135 adult goats (>1 year old) were blood sampled. The two-stage nested real-time PCR (nRT-PCR) was used to detect proviral DNA of SRLV and distinguish between two main viral genotypes (A and B). PCR products were submitted for Sanger dideoxy sequencing, and phylogenetic and molecular evolutionary analyses were conducted on the 200-250 bp-long proviral DNA sequences from the end of long terminal repeat (LTR) region and beginning of gag gene using the MEGA11 software. Reference strains included strains most identical to Hungarian sequences according to the Standard Nucleotide BLAST and prototypic strains for the relevant genotypes and subtypes. Proviral DNA of SRLV was detected in goats from all ten tested herds. A single SRLV genotype was detected in 6 herds-genotype A in three herds and B also in three herds. In four herds, mixed infection with genotypes A and B was confirmed. In total, 110/135 seropositive goats tested positive in the nRT-PCR (81.5%): 49/110 goats (44.5%) for genotype A, 54/110 goats (49.1%) for genotype B, and 7/110 goats (6.4%) for both genotypes. Hungarian sequences belonged to subtypes A1/A18, A2, and subtype B1. This is the first study which shows that Hungarian goats are infected by SRLV belonging to both genotypes A and B.

Identification and characterization of linear epitopes of monoclonal antibodies against the capsid proteins of small ruminant lentiviruses

Maedi-visna virus (MVV) and caprine arthritis encephalitis virus (CAEV) are members of a group of genetically highly homologous lentiviruses collectively referred to as small ruminant lentiviruses (SRLVs). SRLVs can infect sheep, goats and other small ruminants, causing multisystemic disease with progressive and persistent inflammatory changes, severely reducing animal productivity and impeding animal trade. The capsid protein of SRLVs, p28, is highly conserved among strains and is a commonly used marker for the detection of SRLVs. In this study, two monoclonal antibodies (mAbs), designated G8F7 and A10C12, against p28 were generated using a recombinant p28 protein expressed in Escherichia coli as an immunogen. Functional analysis showed that these two monoclonal antibodies could be used in iELISA, immunofluorescence assays (IFA) and western blot assays to detect p28 or Gag precursor proteins of SRLVs. Two linear epitopes, 61GNRAQKELIQGKLNEEA77 (E61-77) and 187CQKQMDRVLGTRVQQATVEEKMQACR212 (E187-212), which are recognized by G8F7 and A10C12, respectively, were identified through truncation of the GST-fused p28. Amino acid sequence alignment showed that the epitope E61-77 is conserved among SRLVs, with a dominant mutation site (K72R) that does not disrupt recognition by G8F7. E187-212 was found to exhibit variability among SRLVs, but the majority of mutant epitopes are recognized by A10C12, with the exception of a mutant epitope from an isolate with undefined subtypes from Ovis aries, which was not recognized. These findings may facilitate future study of SRLVs and promote the development of methods for the detection of these viruses.

Circulation of small ruminant lentivirus in endangered goat and sheep breeds of Southern Italy

According to the Domestic Animal Diversity Information System (DAD-IS) of the FAO, Italy has one of the largest numbers of local small ruminant breeds among European countries. In Southern Italy, namely the Campania Region, Bagnolese and Laticauda sheep breeds and Cilentana goat breeds are considered endangered according to the DAD-IS. Conservation of endangered animal breeds is a goal of the European Union (EU). However, the role of infectious diseases as risk factors for endangered breeds has rarely been considered. Small ruminant lentiviruses (SRLV) infect sheep and goats, causing slow-progressive, persistent, and debilitating diseases that can lead to animal death and productivity loss. In this study, we investigated the presence of SRLV in Bagnolese, Laticauda, and Cilentana breeds using a commercial ELISA in parallel with an in-house ELISA. The results of the two tests were in good agreement (Cohen Kappa 0.84, 95 % CI = 0.76-0.93). Discrepancies between the two tests were resolved using western blotting. In total, 430 samples were tested (248 Bagnolese, 125 Laticauda, and 57 Cilentana). The apparent prevalence rates were 12.5 %, 6.4 %, and 1.7 % in Bagnolese, Laticauda, and Cilentana, respectively. In the molecular analysis of 11 proviral partial sequences, subtypes B2 and A24 were identified in two Bagnolese herds. Owing to the beneficial role of sheep and goat breeding in marginal areas, it is important to screen the entire population and implement control/eradication of SRLV infections in conjunction with each conservation program.

A Combined Approach for the Characterization of Small Ruminant Lentivirus Strains Circulating in the Islands and Mainland of Greece

Small ruminant lentiviruses are a group of viruses infecting goat and sheep worldwide. These viruses exhibit an extraordinary degree of genetic and antigenic variability that severely influence in vivo and in vitro features, as well as diagnostic test results. Small ruminant farming is the most important animal farming business in Greece, with a high impact on the Greek primary economy. Although SRLV infection and its impact on animal production are well established in the country, little is known about the circulating SRLV strains and their prevalence. The aim of this study was to characterize SRLVs circulating in Greece with a combined serological and molecular approach, using the bulk milk matrix collected from 60 farms in different municipalities. This study allowed us to estimate a seroprevalence of around 52% at the herd level. The B1, B2 and A3 subtypes and a novel A viral cluster were identified. Moreover, the amplicon sequencing method allowed us to identify more than one viral subtype in a sample. These results again confirm the high variability of these viruses and highlight the importance of the constant monitoring of viral evolution, in particular in antigens of diagnostic interest.

Serological and Molecular Characterization of Small Ruminant Lentiviruses in Morocco

Recent studies that investigated the origins of SRLV strains offered new insights into their distribution among domestic ruminants. The aim of the study was to investigate SRLV circulation in Morocco. A total of 51 farms were selected in different geographical locations and tested by screening and genotyping ELISA. Whole blood was used for DNA extraction and nested gag PCR. The sample size allowed for an estimation of prevalence lower than 20% (CI 95%). Surprisingly, a large proportion of screening-positive samples were not correctly serotyped. Sanger and NGS amplicon sequencing approaches allowed us to obtain new sequences even from difficult-to-amplify samples. The serological data support the evidence of an intrinsic difficulty of SRLV to spread, likely due to management practices. The low rate of success by genotyping ELISA led us to suppose that divergent strains might have escaped from diagnostic tools, as partially confirmed by the evidence of an A subtype carrying a mismatch in serotyping epitope. The sequence analysis revealed the circulation of novel B and recombinant A/B subtypes. This study highlights the importance of monitoring viral sequences and their evolution to develop specific diagnostic tests, particularly in countries where control measures are in place.

The genetic variability of small-ruminant lentiviruses and its impact on tropism, the development of diagnostic tests and vaccines and the effectiveness of control programmes

Introduction

Maedi-visna virus and caprine arthritis encephalitis virus are two closely related lentiviruses which cause multisystemic, progressive and persistent infection in goats and sheep. Because these viruses frequently cross the species barrier, they are considered to be one genetic group called small-ruminant lentiviruses (SRLV). They have in vivo tropism mainly for monocytes and macrophages and organ tropism with unknown mechanisms. Typical clinical signs are pneumonia in sheep, arthritis in goats, and mastitis in both species. Infection with SRLV cannot currently be treated or prevented, and control programmes are the only approaches to avoiding its spread. These programmes rely mainly on annual serological testing and elimination of positive animals. However, the high genetic and antigenic variability of SRLV complicate their early and definitive diagnosis. The objective of this review is to summarise the current knowledge of SRLV genetic variation and its implications for tropism, the development of diagnostic tests and vaccines and the effectiveness of control and eradication programmes.

Material and Methods

Subject literature was selected from the PubMed and the Google Scholar databases.

Results

The high genetic diversity of SRLV affects the performance of diagnostic tools and therefore control programmes. For the early and definitive diagnosis of SRLV infection, a combination of serological and molecular tests is suggested. Testing by PCR can also be considered for sub-yearling animals. There are still significant gaps in our knowledge of the epidemiology, immunology and biology of SRLV and their impact on animal production and welfare.

Conclusion

This information may aid selection of the most effective SRLV spread reduction measures.

First Molecular Characterization of Small Ruminant Lentiviruses Detected in Romania

Small ruminant lentiviruses (SRLVs) are a group of retroviruses that cause multisystem chronic diseases in goats and sheep and lead to production losses in these animals, negatively affecting animal health and welfare. Although molecular characterization of SRLV field isolates has been performed in many countries, there is currently no information on SRLV genotypes circulating in sheep and goats in Romania. Therefore, the main objective of this study was to conduct a molecular and phylogenetic analysis of SRLVs from Romania and determine the degree of genetic relatedness of the obtained sequences to other known SRLV reference strains. A total of 81 sheep lung tissue samples and 41 sheep lung lymph node samples were tested using nested real-time PCR, and samples positive for real-time PCR were used to amplify an 800 bp gag-pol fragment and an overlapping 625 bp fragment of the gag gene. Pairwise DNA distance and phylogenetic analysis showed that the Romanian SRLV strains were closely related to the A2 and A3 strains based on gag-pol sequences and to the A3 and A17 subtypes based on gag sequences. No recombination events were found. Our results revealed that the Romanian sequences have similar epitope patterns to other existing subtypes, although E/K and R/K mutations in epitope 3 were found only in the Romanian sequences, which may have potential value in serological diagnosis. This study is the first report on the genetic characterization of SRLV strains circulating in Romania and provides new information on SRLV heterogeneity. Further detailed studies should be conducted to better understand the divergence of SRLV Romanian strains.

Genetic Diversity of the LTR Region of Polish SRLVs and Its Impact on the Transcriptional Activity of Viral Promoters

A long terminal repeat (LTR) plays an indispensable role in small ruminant lentivirus (SRLV) gene expression. In this study, we present the LTR sequence of Polish SRLVs representing different subtypes, and analyzed their impact on SRLV promoter activity, as measured in transient transfection assays. Although certain nucleotide motifs (AML(vis), TATA box and the polyadenylation site (AATAAA)) were conserved across sequences, numerous mutations within the LTR sequences have been identified. Single nucleotide polymorphisms (SNPs) were detected in both regulatory (AP-1, AP-4, Stat and Gas) and non-regulatory sequences, and subtype-specific genetic diversity in the LTR region of Polish SRLVs was observed. In vitro assays demonstrated subtype-specific functional differences between the LTR regions of distinct SRLV subtypes. Our results revealed that the promoter activity of Polish strains was lower (1.64-10.8-fold) than that noted for the K1514 reference strain; however, the differences in most cases were not statistically significant. The lowest promoter activity was observed for strains representing subtype A5 (mean 69.067) while the highest promoter activity was observed for strain K1514 representing subtype A1 (mean 373.48). The mean LTR activities of strains representing subtypes A12, A17, A23, A18 and A24 were 91.22, 137.21, 178.41, 187.05 and 236.836, respectively. The results of the inter-subtype difference analysis showed that the promoter activity of strains belonging to subtype A5 was significantly lower than that for subtype A12 strains (1.32-fold; p < 0.00). The promoter activities of the A5 strain were 1.98-fold and 2.58-fold less active than that of the A17 and A23 strains, and the promoter activities of A12 strains were 1.955 and 1.5 times lower than the promoter activity of A23 and A17 strains, respectively. Furthermore, the promoter activity of A17 strains was 1.3 lower than the promoter activity of A23 strains. Our findings suggest that subtype-specific genetic diversity, mainly in the transcription factor's binding sites, has an impact on their transcriptional activity, producing a distinct activity pattern for the subtypes. This study provides new information that is important for better understanding the function of the SRLV LTR. However, further research including more strains and subtypes as well as other cell lines is needed to confirm these findings.

Alternative Molecular Tools for the Fight against Infectious Diseases of Small Ruminants: Native Sicilian Sheep Breeds and Maedi-Visna Genetic Susceptibility

Simple Summary

Local breeds represent a precious reservoir of genetic diversity, crucial to adapting to environmental and climate changes and reacting to evolving diseases. In Sicily, four native dairy breeds, namely Valle del Belìce, Comisana, Barbaresca, and Pinzirita, have adapted to low-input farming systems and semiarid environments, having an essential role in producing high-quality milk and typical dairy products. Maedi-visna (MV) is one of the most important chronic diseases affecting the sheep sector worldwide, causing production losses. Different target genes play an important role in immunity and in genetic resilience to MV, such as TMEM154, TLR9, MYD88, and CCR5. A major host genetic component to sheep MV susceptibility was identified in the ovine TMEM154 gene. Animals with either of TMEM154 haplotypes that encode glutamate at position 35 (E35) of the protein are at higher risk of MV infection than those homozygous with lysine at position 35 (K35). In the tested Sicilian breeds, animals carrying the allele E35 showed a greater risk of being serologically positive. Comisana, Barbaresca, and Pinzirita breeds showed a good frequency of the protective allele K35, whilst a high frequency of risk allele was found in the Valle del Belìce breed, related to the selection strategies addressed to obtain a productive dairy sheep. Our results highlight the importance of the preservation of autochthonous breeds as a reservoir of natural resistance against infectious disease.

Abstract

Maedi-visna (MV) is a disease caused by small ruminant lentiviruses. It is included in the list of notifiable terrestrial animal diseases due to economic losses and animal welfare harm in the sheep sector. To date, control programs remain the onliest approach to avoiding infection. The allelic variant p.Glu35Lys (E35K) of the TMEM154 gene has been strongly associated with host vulnerability to MV illness. The present study aimed to investigate the association of TMEM154 E35K allele frequencies with MV susceptibility in native Sicilian sheep breeds. More than 400 animals from 14 local sheep were serologically tested and genotyped for the TMEM154 E35K polymorphism. The local breeds displayed different values of MV seroprevalence, with the lowest antibody prevalence in Barbaresca and Pinzirita breeds. TMEM154 protective allele (K35) was less frequent than the risk allele (E35) in Valle del Belìce breed, whereas the other three breeds showed a more balanced alleles distribution. A positive association between seroprevalence and genotype was found in the entire sample set. The risk of infection resulted in more than 3-fold times as high in sheep with EK and EE genotype compared to the KK genotype. Our data could be helpful in establishing selection breeding programs aimed at reducing MV infection in Sicilian sheep farming and encouraging the breeding of native breeds.

Molecular Characterization of Small Ruminant Lentiviruses Isolated from Polish Goats with Arthritis

Previous studies revealed that the small ruminant lentivirus (SRLV) population in Poland is highly heterogeneous. All SRLVs detected from Polish sheep and goats so far have belonged to subtypes B1, B2, A1, A5, A12, A13, A16, A17, A18, A23 and A24. However, all characterized strains originated from asymptomatic animals. This is the first study that characterizes the molecular properties of SRLVs isolated from different organs of six arthritic goats. Segments from three genomic regions (gag, LTR and env) were analyzed. In addition, we quantified the SRLV proviral load in the blood and different organs and examined its association with different degrees of histopathological lesions. All sequences obtained from the goats involved in this study were homogeneous, showing an average degree of variability of 4.8%, 3.7% and 8.8% for gag, LTR and env, respectively. Phylogenetic analysis revealed that the sequences from the analyzed goats were clustered within SRLVs group A and formed a new subtype within this group, tentatively named A27. The histopathological examination of the lung, mammary gland, synovial membranes of joints and brain of the analyzed goats revealed evidence of inflammatory processes associated with SRLV infection, which was confirmed by positive immunohistochemistry assays. No significant correlation was observed between histological features and alterations in the sequences from different tissues. No tissue-specific signature pattern was identified. It was shown that animals with a higher proviral load showed more lesion severity in various SRLV-affected tissues, indicating a positive association between these two parameters. Our results also revealed differences in the SRLV load between animals even though the sequences derived from all of the goats were closely related, suggesting that host factors may restrict and control viral replication. This study provides new information about SRLV variants isolated from arthritic goats; however, more studies, including the isolation and characterization of biological properties of these viruses, should be performed to evaluate their pathogenic potential.

Genetic Characterization of Small Ruminant Lentiviruses (SRLVs) Circulating in Naturally Infected Sheep in Central Italy

Small ruminant lentiviruses (SRLVs) represent a very heterogeneous group of ss-RNA viruses that infect sheep and goats worldwide. They cause important, deleterious effects on animal production and limit the animal trade. SRLVs show a high genetic variability due to high mutation rate and frequent recombination events. Indeed, five genotypes (A–E) and several subtypes have been detected. The aim of this work was to genetically characterize SRLVs circulating in central Italy. On this basis, a phylogenetic study on the gag-pol genetic region of 133 sheep, collected from 19 naturally infected flocks, was conducted. In addition, to evaluate the frequency of mutation and the selective pressure on this region, a WebLogo 3 analysis was performed, and the dN/dS ratio was computed. The results showed that 26 samples out of 133 were clustered in genotype A and 106 samples belonged to genotype B, as follows: A9 (n = 8), A11 (n = 10), A24 (n = 7), B1 (n = 2), B2 (n = 59), and B3 (n = 45). No recombination events were found. Mutations were localized mainly in the VR-2 region, and the dN/dS ratio of 0.028 indicated the existence of purifying selection. Since the genetic diversity of SRLVs could make serological identification difficult, it is important to perform molecular characterization to ensure a more reliable diagnosis, to maintain flock health status, and for the application of local and national control programs.