Genetic and antigenic characterization of small ruminant lentiviruses circulating in Poland

First Report of SNPs Detection in TMEM154 Gene in Sheep from Poland and Their Association with SRLV Infection Status

Small ruminant lentiviruses (SRLVs) infect sheep, causing a multiorganic disease called maedi-visna or ovine progressive pneumonia, which significantly affects the production and welfare of sheep, generating serious economic losses. Although not all infected animals develop fully symptomatic disease, they constantly spread the virus in the flock. Since the infection is incurable and no vaccine is available, another approach is necessary to control SRLV infections. In recent years, an alternative for culling infected animals has become the approach based on identifying genetic markers for selecting SRLV-resistant individuals. Recent reports revealed several candidates, including gene encoding transmembrane protein 154 (TMEM154). Several single nucleotide polymorphisms (SNPs) are found within this gene in sheep of different breeds, but only some can be considered as resistant markers. This study aimed to investigate the presence of single polymorphic sites in TMEM154 gene in sheep of selected Polish flocks and assess their association with the infection and proviral load in the context of susceptibility to SRLV infection. In total 107 sheep, representing three breeds, were screened for their SRLV infection status by serological and PCR testing. All these animals were also genotyped to characterize the presence of SNPs in TMEM154 gene and estimate their potential of being the SRLV-resistance marker. The frequency of identified alleles differed among breeds. Moreover, the positive association between TMEM154 genotype and SRLV status was found for E35K polymorphism and two polymorphic sites in 5'UTR in one of analyzed breed. However, when the relationship between SNPs and SRLV proviral load was analyzed, five had a strong association, considering the whole population of tested sheep. Presented data, for the first time, identified the presence of SNPs in TMEM154 gene in sheep housed in Polish flocks and suggested that selecting SRLV-resistant animals based on this analysis might be possible, but further validation in a larger group of sheep is required.

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.

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.

Comparison of serological and molecular methods for differentiation between genotype A and genotype B strains of small ruminant lentiviruses

Introduction

Small ruminant lentiviruses (SRLV) cause multisystemic, degenerative and chronic disease in sheep and goats. There are five genotypes (A, B, C, D and E), of which A and B are the most widespread. The purpose of this study was to evaluate the serotyping efficiency of the Eradikit SRLV Genotyping ELISA and the molecular typing efficiency of a newly developed nested real-time PCR targeting the long terminal repeat-gag (LTR-gag) region using samples from animals infected with subtypes of SRLV known to circulate in Poland.

Material and Methods

A total of 97 sera samples taken from 34 sheep and 63 goats were immunoassayed, and 86 DNA samples from 31 sheep and 55 goats were tested with the PCR. All ruminants were infected with known SRLV strains of the A1, A5, A12, A13, A16, A17, A18, A23, A24, A27, B1 and B2 subtypes.

Results

A total of 69 (80.2%, 95% confidence interval 71.6%-88.8%) out of 86 tested samples gave positive results in the PCR. In 17 out of the 86 (19.8%) samples, no proviral DNA of SRLV was detected. The differentiation between MVV (genotype A) and CAEV (genotype B) by PCR matched the predating phylogenetic analysis invariably. No cross-reactivity was observed. On the other hand, the proportion of samples genotyped the same by the older phylogenetic analysis and the Eradikit SRLV Genotyping ELISA was 42.3%. The test was unable to classify 40.2% of samples, and 17.5% of sera were incorrectly classified.

Conclusion

Our results showed that the Eradikit SRLV genotyping kit is not a reliable method for predicting SRLV genotype, while the nested real-time PCR based on the LTR-gag region did prove to be, at least for genotypes A and B.

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.

Genetic Characterization of Small Ruminant Lentiviruses Isolated from Dairy Sheep in Greece

The high genetic heterogeneity of small ruminant lentiviruses (SRLV) renders the genetic characterization of the circulating strains crucial for the epidemiological investigation and the designation of effective diagnostic tools. In Greece, research data regarding the genetic diversity of the circulating SRLV strains is scarce, hindering the implementation of efficient surveillance and control programs. The objective of the study was to genetically characterize SRLV strains isolated from intensive dairy sheep farms in Greece and evaluate the variability of the immunodominant regions of the capsid protein. For this reason, a total of 12 SRLV-infected animals from four intensive dairy sheep farms with purebred Chios and Lacaune ewes were used for the amplification and sequencing of an 800 bp gag-pol fragment. The phylogenetic analyses revealed a breed-related circulation of strains; Chios ewes were infected with strains belonging exclusively to a separate group of genotype A, whereas strains belonging to subtype B2 were isolated from Lacaune ewes. Immunodominant epitopes of capsid protein were quite conserved among the strains of the same genotype, except for the Major Homology Region which showed some unique mutations with potential effects on viral evolution. The present study contributes to the extension of the current knowledge regarding the genetic diversity of SRLV strains circulating in sheep in Greece. However, broader genetic characterization studies are warranted for the exploration of possible recombinant events and the more comprehensive classification of the circulating strains.

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.

Isolation and Identification of Caprine Arthritis Encephalitis Virus from Animals in the Republic of Mordovia

This article presents the results of virological and genetic studies of an isolate of caprine arthritis encephalitis (CAE) virus from the republic of Mordovia, Russian Federation. The isolate was found during monitoring studies of goat blood samples for the viral genome, and the presence of antibodies to lentiviruses was detected. According to the recommendation of the OIE, the positive result of PCR was confirmed with nucleotide sequencing. It was found that the obtained nucleotide sequence is identical to the genome of small ruminant lentiviruses presented in the GenBank database. Phylogenetic analysis showed that the isolate "Mordovia-2018" was included in the same cluster with an isolate from the Tver region of the Russian Federation detected in 2008. The sequence of the fragment of the env-gene of the isolate from the republic of Mordovia is available in GenBank under the number MN186380.1. To isolate the virus, a fraction of peripheral blood monocyte cells from the animal's blood was added to a monolayer of lamb synovial membrane cell culture, and ten passages were carried out. The first manifestations of the cytopathic effect were observed after the third passage on the eighth day of cultivation in the form of single large cells of irregular shape with 5-7 nuclei. At the seventh passage, multiple syncytium with 7-12 nuclei were observed. At subsequent passage levels, the formation of syncytium containing more than 10-14 nuclei was observed.

In vitro antiviral effect of ethanolic extracts from Azadirachta indica and Melia azedarach against goat lentivirus in colostrum and milk

This study aimed to evaluate, in vitro, the use of leaf extracts of Azadirachta indica (A. indica) and Melia azedarach (M. azedarach) as antivirals against caprine lentivirus (CLV) in colostrum and milk of goat nannies. These were collected from eight individuals and infected with the standard strain of CLV. Samples were then subdivided into aliquots and treated with 150 µg/mL of crude extract, and with ethyl acetate and methanol fractions for 30, 60, and 90 min. Next, somatic cells from colostrum and milk were co-cultured with cells from the ovine third eyelid. After this step, viral titers of the supernatants collected from treatments with greater efficacy in co-culture were assessed. The organic ethyl acetate fractions of both plants at 90 min possibly inhibited the viral activity of CLV by up to a thousandfold in colostrum. In milk, this inhibition was up to 800 times for the respective Meliaceae. In conclusion, the ethanolic fraction of ethyl acetate from both plants demonstrated efficacy against CLV in samples from colostrum and milk when subjected to treatment, which was more effective in colostrum.

Genetic and antigenic characterization of Brazilian SRLV strains: Natural small ruminant interspecies transmission from mixed herds

Cross-species transmission events and mixed infection of small ruminant lentiviruses (SRLVs) were studied in seven goats and two sheep from three small ruminant mixed flocks from Northeast and Southeast Brazil. Genetic and antigenic analyses with gag/env genes and ELISA multiepitope SU1/SU5 recombinant antigens were carried out, respectively. The genetic analysis of gag and env sequences showed high viral diversity in both species, MVV-like (subtype A1) and CAEV-like B1 in goats, and CAEV-like (subtype B1) in sheep, revealing SRLV interspecies transmission from sheep to goats and vice versa in Brazilian farms. Two Brazilian caprine lentiviruses were segregated in two new genetic clades based on gag analyses, which suggests a new classification into heterogenic genotype A. Furthermore, goat isolates were grouped into subtype A1 and B1 clusters. Cross-reactive antibodies were detected in goats using ELISA with a recombinant antigen carrying SU1 and SU5 immunodominant epitopes; the results showed anti-CAEV and MVV antibodies in goats and anti-CAEV antibodies in sheep. This result can be associated with the high divergence in the V4 region due to SRLV variability. All results confirm cross-species infection of SRLV in Brazilian mixed herds.

The Prevalence of Histopathological Features of Pneumonia in Goats with Symptomatic Caprine Arthritis-Encephalitis

Chronic interstitial pneumonia (CIP) is a main pathology of sheep infected with small ruminant lentivirus (SRLV). Caprine arthritis-encephalitis (CAE) is caused by the same pathogen; however, the presence of CIP has been only occasionally reported in SRLV-infected goats. We carried out a cross-sectional study to determine the prevalence of histopathological lesions indicative of CIP in goats with symptomatic CAE, and to investigate whether CIP was associated with a higher prevalence of other types of pneumonia (purulent bronchopneumonia, fibrinous pleuropneumonia) or bacterial infections. Lung specimens and bronchial swabs were collected for histopathological and bacteriological examination, respectively, from 116 goats from a CAE-affected herd. All goats were euthanized due to severe clinical signs of CAE. The goats were seropositive for SRLV infection in two different ELISAs and the presence of SRLV antigen in the lung tissue was confirmed by immunohistochemistry. Histopathologically, pneumonia of any type was confirmed in 82 goats (70.7%) and CIP was present in 67 goats (57.8%). In most goats, the severity of the histopathological features of pneumonia was mild. Bacteria were detected in bronchial swabs from 73 goats (62.9%). CIP proved to be significantly positively linked to the occurrence of purulent bronchopneumonia (p < 0.001), fibrinous pleuropneumonia (p = 0.001), and of the infection of lungs with bacteria capable of causing pneumonia (p = 0.050). The causal character of these associations should be considered and warrants further investigation.

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.

Molecular Characterization of Small Ruminant Lentiviruses in Polish Mixed Flocks Supports Evidence of Cross Species Transmission, Dual Infection, a Recombination Event, and Reveals the Existence of New Subtypes within Group A

Small ruminant lentiviruses (SRLVs) are a group of highly divergent viruses responsible for global infection in sheep and goats. In a previous study we showed that SRLV strains found in mixed flocks in Poland belonged to subtype A13 and A18, but this study was restricted only to the few flocks from Małopolska region. The present work aimed at extending earlier findings with the analysis of SRLVs in mixed flocks including larger numbers of animals and flocks from different part of Poland. On the basis of gag and env sequences, Polish SRLVs were assigned to the subtypes B2, A5, A12, and A17. Furthermore, the existence of a new subtypes, tentatively designed as A23 and A24, were described for the first time. Subtypes A5 and A17 were only found in goats, subtype A24 has been detected only in sheep while subtypes A12, A23, and B2 have been found in both sheep and goats. Co-infection with strains belonging to different subtypes was evidenced in three sheep and two goats originating from two flocks. Furthermore, three putative recombination events were identified within gag and env SRLVs sequences derived from three sheep. Amino acid (aa) sequences of immunodominant epitopes in CA protein were well conserved while Major Homology Region (MHR) had more alteration showing unique mutations in sequences of subtypes A5 and A17. In contrast, aa sequences of surface glycoprotein exhibited higher variability confirming type-specific variation in the SU5 epitope. The number of potential N-linked glycosylation sites (PNGS) ranged from 3 to 6 in respective sequences and were located in different positions. The analysis of LTR sequences revealed that sequences corresponding to the TATA box, AP-4, AML-vis, and polyadenylation signal (poly A) were quite conserved, while considerable alteration was observed in AP-1 sites. Interestingly, our results revealed that all sequences belonging to subtype A17 had unique substitution T to A in the fifth position of TATA box and did not have a 11 nt deletion in the R region which was noted in other sequences from Poland. These data revealed a complex picture of SRLVs population with ovine and caprine strains belonging to group A and B. We present strong and multiple evidence of dually infected sheep and goats in mixed flocks and present evidence that these viruses can recombine in vivo.

Serological, Molecular and Culture-Based Diagnosis of Lentiviral Infections in Small Ruminants

Small ruminant lentiviruses (SRLVs) infections lead to chronic diseases and remarkable economic losses undermining health and welfare of animals and the sustainability of farms. Early and definite diagnosis of SRLVs infections is the cornerstone for any control and eradication efforts; however, a "gold standard" test and/or diagnostic protocols with extensive applicability have yet to be developed. The main challenges preventing the development of a universally accepted diagnostic tool with sufficient sensitivity, specificity, and accuracy to be integrated in SRLVs control programs are the genetic variability of SRLVs associated with mutations, recombination, and cross-species transmission and the peculiarities of small ruminants' humoral immune response regarding late seroconversion, as well as intermittent and epitope-specific antibody production. The objectives of this review paper were to summarize the available serological and molecular assays for the diagnosis of SRLVs, to highlight their diagnostic performance emphasizing on advantages and drawbacks of their application, and to discuss current and future perspectives, challenges, limitations and impacts regarding the development of reliable and efficient tools for the diagnosis of SRLVs infections.

Does Small Ruminant Lentivirus Infection in Goats Predispose to Bacterial Infection of the Mammary Gland? A Preliminary Study

Simple Summary

The health and functionality of the mammary gland are important factors in animal welfare and milk production. Inflammation of the udder is associated with reduced milk yield and dairy product quality. Even though mastitis is usually caused by bacterial, fungal, or algae infections, some studies have suggested that infection with small ruminant lentivirus (SRLV), causing caprine arthritis-encephalitis (CAE), can also cause mastitis in small ruminants. Its pathophysiology is not, however, fully understood. Therefore, the aim of this study was to determine whether seropositive goats were more susceptible to bacterial infections of the udder than uninfected goats. A higher prevalence of pathogenic bacteria was identified only in seropositive goats in the 5th or further lactation. This indicates that a relationship may exist between a long-lasting SRLV infection and decreased resistance of the udder to bacterial infections, even though the seropositive goats enrolled in this study had no clinical signs of CAE.

Abstract

The aim of this study was to determine whether asymptomatic small ruminant lentivirus seropositive (SRLV-SP) goats were more susceptible to bacterial infection of the udder when lactating by comparing the presence and species of pathogenic bacteria in their milk with the values for seronegative goats (SRLV-SN). Milk samples were collected during morning milking on days 20, 40, 60, 150, and 210 of lactation for three consecutive years and subjected to bacteriological examination. Staphylococcus caprae and S. xylosus were the most frequent strains identified in both SRLV-SP and SRLV-SN goats. The prevalence of pathogenic bacteria was the highest in the 1st lactation, regardless of SRLV status. Moreover, the prevalence of pathogenic bacteria was significantly higher in SRLV-SP goats, but only those in the 5th or further lactation (p = 0.010). This suggests a relationship between long-lasting SRLV infection and susceptibility to bacterial infections of the udder.

Caprine Arthritis Encephalitis Virus Disease Modelling Review

Simple Summary

Mathematical modelling is used in disease studies to assess their economical impacts, as well as to better understand the epidemiological dynamics of the biological and environmental factors associated with disease spreading. For an incurable disease such as Caprine Arthritis Encephalitis, this knowledge is extremely valuable. However, the application of modelling techniques to study this disease has not been significantly explored in the literature. The purpose of the present work was to review the published studies, highlighting their scope, strengths and limitations, as well to provide ideas for future modelling approaches for this disease. The reviewed studies were divided into two major themes. The first is epidemiological modelling, which use mathematical models which equations describe the disease dynamics over time. Inside this group, the articles differ in considering or not considering the sexual transmission component. The second major theme is statistical modelling, which correlates the disease with biological and environmental factors to quantify its risks and impacts. Inside this group, the articles include models for dairy production, for risk factors of the disease and for Caprine Arthritis Encephalitis being a risk factor for other diseases. Finally, the present work concludes with further suggestions for modelling studies on Caprine Arthritis Encephalitis.

Abstract

Mathematical modelling is used in disease studies to assess the economical impacts of diseases, as well as to better understand the epidemiological dynamics of the biological and environmental factors that are associated with disease spreading. For an incurable disease such as Caprine Arthritis Encephalitis (CAE), this knowledge is extremely valuable. However, the application of modelling techniques to CAE disease studies has not been significantly explored in the literature. The purpose of the present work was to review the published studies, highlighting their scope, strengths and limitations, as well to provide ideas for future modelling approaches for studying CAE disease. The reviewed studies were divided into the following two major themes: Mathematical epidemiological modelling and statistical modelling. Regarding the epidemiological modelling studies, two groups of models have been addressed in the literature: With and without the sexual transmission component. Regarding the statistical modelling studies, the reviewed articles varied on modelling assumptions and goals. These studies modelled the dairy production, the CAE risk factors and the hypothesis of CAE being a risk factor for other diseases. Finally, the present work concludes with further suggestions for modelling studies on CAE.

Diagnostic accuracy of three commercial immunoenzymatic assays for small ruminant lentivirus infection in goats performed on individual milk samples

Caprine arthritis-encephalitis (CAE) caused by small ruminant lentivirus (SRLV) infection is one of the most widespread and devastating diseases of goats. Serological methods, mainly immunoenzymatic assays (ELISA), are the mainstay of CAE diagnostics. Even though blood is still the most commonly tested material, animal welfare issues and increasing costs of veterinary service prompt the development of serological methods based on milk testing. Several different types of ELISAs for CAE are available on the market. All of them perform well on serum, however their diagnostic accuracy for testing milk has not been so far compared. Therefore, we carried out the study in 5 dairy goat herds in Poland whose previous epidemiological situation regarding CAE was known. Paired serum and milk samples were collected from all adult females (n = 420) and tested with 3 commercial ELISAs - indirect ELISA based on the whole-virus antigen (wELISA), indirect ELISA based on the recombined transmembrane and capsid protein (TM/CA-ELISA), and competitive ELISA based on the surface glycoprotein (SU-ELISA). Milk was tested as lactoserum at dilution of 1/2 in wELISA and TM/CA-ELISA, and undiluted in SU-ELISA. The true status of goats was based on the composite reference standard comprising the results of all three ELISAs done on serum and the true prevalence of SRLV infection in the herd of origin. 243 (57.9 %) goats were classified as truly positive and 177 (42.1 %) goats as truly negative. Diagnostic accuracy was evaluated using the area under the ROC curve (AUROC) as well as sensitivity (Se) and specificity (Sp) for a range of cut-off values. AUROC was 98.8 % (CI 95 %: 97.5 %, 100 %) for wELISA, 97.9 % (CI 95 %: 96.5 %, 99.2 %) for TM/CA-ELISA, and 91.7 % (CI 95 %: 88.9 %, 94.5 %) for SU-ELISA. At the cut-off values recommended by the manufacturers both indirect ELISAs were highly sensitive (89.3 % and 91.4 %, respectively) and highly specific (98.3 % and 95.5 %, respectively), whereas SU-ELISA had only moderate Se (71.2 %) at comparably high Sp (96.6 %). Nevertheless, the optimal cut-off values were lower than those recommended by manufacturers for serum - sample-to-positive control serum ratio (S/P%) of 10 % for wELISA, S/P% of 80 % for TM/CA-ELISA, and percentage inhibition of 23 % for SU-ELISA. Concluding, the study shows that wELISA and TM/CA-ELISA may be interchangeably used for testing individual goat milk samples for SRLV infection. Diagnostic sensitivity and specificity of these ELISAs appear not to be lower on milk than on serum. SU-ELISA is considerably less sensitive on milk samples than indirect ELISAs.

Molecular Characterization of Small Ruminant Lentiviruses of Subtype A5 Detected in Naturally Infected but Clinically Healthy Goats of Carpathian Breed

Small ruminant lentiviruses (SRLVs) are widespread in sheep and goats in Poland, and several subtypes were identified and molecularly characterized up to date. This is the first study that characterizes the molecular properties of A5 strains of SRLV detected in naturally infected, but clinically healthy, Carpathian goats. Segments from three genomic regions (gag, env, and LTR) were analyzed. Genetic distance, pairwise comparison, and phylogenetic analysis revealed that Polish SRLV A5 sequences are closely related to the Swiss and German A5 sequences suggesting a common origin. The epidemiological linkage was identified particularly between the small ruminants of Germany and Poland. Amino acid sequences of immunodominant regions in CA protein were well-conserved within analyzed strains; however, they showed some remarkable changes like substitution (D) to (E), at position 90 in Major Homology Region (MHR) and (T) to (S), at position 141 in epitope 3. In contrast, aa sequences of surface glycoprotein exhibited the highest variability confirming type-specific variation in SU5 epitope. Two deletions in the U3 region of A5 strains were noted: One (8 nt) located near the 5′ end of the U3 region and the other (29 nt) located in the central region of U3. Additionally, all A5 strains had specific deletion (10 nt) in the R region. Furthermore, we did not find a correlation between copies of the CAAAT motif and clinical manifestation in infected animals. These data showed some remarkable features in the viral genome of A5 strains, which may be related to the attenuated phenotype in vivo, characterized by the lack of any clinical signs in infected goats. Certainly, more studies are required to support the hypothesis that these A5 viruses are of low pathogenicity for goats. We want to focus our future studies on the analysis of the whole genomes of these isolates and their biological properties, as well as on clinicopathological studies of goats infected by A5 SRLV, aiming to clarify the pathogenic potential of these viruses.

Multi-Platform Detection of Small Ruminant Lentivirus Antibodies and Provirus as Biomarkers of Production Losses

Small ruminant lentiviruses (SRLVs) are endemic in most areas of Europe, causing a chronic infection and a multisystemic disease affecting the udder, carpal joints, lungs, and central nervous system. Due to the lack of treatments and protective vaccination strategies, infection control is focused on the identification of infected animals through serological or molecular techniques. However, antigenic and genetic heterogeneity of SRLVs represent a clear drawback for diagnosis. Infected animals may present lower animal production parameters such as birth weight or milk production and quality, depending on productive systems considered and, likely, to the diagnostic method applied. In this study, four sheep flocks dedicated to dairy or meat production were evaluated using three different ELISA and two PCR strategies to classify animal population according to SRLV infection status. Productive parameters were recorded along one whole lactation or reproductive period and compared between positive and negative animals. SRLV was present in 19% of the total population, being unequally distributed in the different flocks. Less than half of the infected animals were detected by a single diagnostic method, highlighting the importance of combining different diagnostic techniques. Statistical analysis employing animal classification using all the diagnostic methods associated lambing size, lamb weight at birth, and daily weight gain with SRLV infection status in meat flocks. Milk production, somatic cell count, fat, and protein content in the milk were associated with SRLV infection in dairy flocks, to a greater extent in the flock showing higher seroprevalence. A multi-platform SRLV diagnostic strategy was useful for ensuring correct animal classification, thus validating downstream studies investigating production traits.

Phylogenetic Analysis of Belgian Small Ruminant Lentiviruses Supports Cross Species Virus Transmission and Identifies New Subtype B5 Strains

Small ruminant lentiviruses (SRLV) are a group of highly divergent viruses responsible for global and fatal infections in sheep and goats. Since the current phylogenetic classification of these viruses was proposed in 2004, it nowadays consists out of 5 genotypes and 28 subtypes. In support of our national SRLV control program, we performed the genetic characterization of SRLV strains circulating in the Belgian sheep and goat population. Fourteen sheep and 9 goat strains were sequenced in the gag-pol and pol regions using the method described by Shah. Most SRLV strains from sheep and goats belonged to prototype A1 and B1 subtypes, respectively. We, however, also found indications for cross-species transmission of SRLV strains between sheep and goats and vice versa, and identified a new subtype designated as B5. An in-depth analysis of the current SRLV phylogeny revealed that many subtypes have been defined over the years based on limited sequence information. To keep phylogeny as a useful tool, we advocate to apply more rigorous sequencing standards to ensure the correct classification of current and new emerging strains. The genetic characterization of Belgian SRLV strains will help in the development of appropriate diagnostic tools to assist the national control program.

Phylogenetic analysis of small ruminant lentiviruses in Germany and Iran suggests their expansion with domestic sheep

Small ruminant lentiviruses (SRLVs) are found in sheep in Germany and Iran. SRLVs have been classified into four genotypes: A-C and E. Genotype A has been subdivided into 20 subtypes. Previous studies suggested that, first, the ancestors of genotype A are those SRLVs found in Turkey, second, the evolution of SRLVs is related to the domestication process, and, third, SRLV infection was first observed in sheep in Iceland and the source of that infection was a flock imported from Germany. This study generated, for the first time, partial SRLV sequence data from German and Iranian sheep, enhancing our knowledge of the genetic and evolutionary relationships of SRLVs, and their associations with the domestication process. Based on 54 SRLV sequences from German and Iranian sheep, our results reveal: (1) SRLV subtypes A4, A5, A11, A16 and A21 (new) are found in German sheep and A22 (new) in Iranian sheep. (2) Genotype A has potentially an additional ancestor (A22), found in Iran, Lebanon and Jordan. (3) Subtype A22 is likely an old version of SRLVs. (4) The transmission routes of some SRLVs are compatible with domestication pathways. (5) This study found no evidence of Icelandic subtype A1 in German sheep.

Seroprevalence of small ruminant lentivirus (SRLV) infection in wild cervids in Poland

Small ruminant lentiviruses (SRLV) are widespread amongst domesticated sheep and goats worldwide. Infection of wild ruminants in close contact with affected domesticated small ruminants has been proposed as an actor in SRLV epidemiology, but studies are limited. The aim of this study was to estimate the apparent (AP) and estimated prevalence (EP) of exposure to SRLV infection in wild ruminants from Poland. Samples originating from 198 free-living cervids comprising 142 European red deer and 56 roe deer were serologically tested using a multi-epitope recombinant antigen ELISA representing subtypes A1, A13, B1, and B2 of SRLV and a commercial ELISA test. The estimated prevalence of SRLV infection was estimated using the Bayesian approach with models that adjusted for the misclassification of animals because of a small population and lack of sampling method, the imperfect performance of the ELISAs and because sera of different species were tested. The calculated estimated prevalence ranged from 5.3 % (95 % CI 0.3, 12.5) to 24.6 % (95 % CI 3.3, 38.5) for the ELISA with multi-epitope antigens while estimated prevalence using the commercial ELISA was 2.5 % (95 % CI 0.2, 6.6). These results may suggest the existence of a new SRLV reservoir in Poland and highlight the importance of surveilling and controlling SRLV infection in domestic and wild ruminants sharing pasture areas.

Compartmentalization of Subtype A17 of Small Ruminant Lentiviruses between Blood and Colostrum in Infected Goats Is Not Exclusively Associated to the env Gene

The compartmentalization of small ruminant lentiviruses (SRLVs) subtype A17 was analyzed in colostrum and peripheral blood leukocyte cells of three naturally infected goats. This study aimed to analyze heterogeneity of the SRLV env (V4V5) gene, which encodes neutralizing epitopes of SU glycoprotein, the gag gene encoding capsid protein (CA), and LTR, a noncoding region, responsible for determination of cell tropism. Compartmentalization was assessed using six established tree or distance-based methods, including permutation test to determine statistical significance. We found statistical evidence of compartmentalization between blood and colostrum in all infected goats although phylogenetic evidence of such compartmentalization was not obvious. Our study demonstrated that compartmentalization is not exclusively specific to the env gene, as we revealed that gag and LTR sequences are also compartmentalized between blood and colostrum. The work also confirms the combined use of different methods as essential for reliable determination of intrahost viral compartmentalization. Identifying and characterizing distinct viral subpopulations and the genetic evolution of SRLV in specific anatomical sites enhances our overall understanding of SRLV pathogenesis, immune control, and particularly virus transmission.

Impact of the subclinical small ruminant lentivirus infection of female goats on the litter size and the birth body weight of kids

A longitudinal study was conducted in a single dairy goat herd to investigate the relationship between subclinical small ruminant lentivirus (SRLV) infection in does and litter size (LS) or birth body weight of kids (BW). Each year kids born to seropositive and seronegative does were weighed before the first consumption of colostrum. LS and BW of each kid were recorded. BW was significantly negatively linked to LS (p = 0.006) - singletons weighed (mean ± SD) 4.20 ± 0.67 kg, twins - 3.75 ± 0.62 kg, and triplets and quadruplets - 3.38 ± 0.47 kg. Male kids were significantly heavier than female kids in twin litters (3.97 ± 0.53 kg vs. 3.52 ± 0.60 kg; p < 0.001) and triplet or quadruplet litters (3.62 ± 0.40 kg vs. 3.17 ± 0.43 kg; p < 0.001). However, BW of male and female kids from singleton litters did not differ (4.31 ± 0.71 kg vs. 4.07 ± 0.65 kg; p = 0.154). Then, two mixed models were developed to assess the relationship between LS (mixed Poisson log linear regression model) or BW (mixed linear model) and SRLV infection in the doe, controlling for potential confounders such as the effect of an individual doe, year in which the parturition took place, parity and kid's sex. Neither LS nor BW proved to be significantly associated with SRLV infection (p = 0.788 and p = 0.214, respectively). On this basis it was concluded that LS and BW were not affected by the subclinical SRLV infection of a doe.

Molecular analysis of small-ruminant lentiviruses in Polish flocks reveals the existence of a novel subtype in sheep

Small-ruminant lentivirus (SRLV) infections are widespread in Poland, and circulation of subtypes A1, A12, A13, A16, A17, B1 and B2 has been documented. The aim of this study was to characterize the SRLV strains circulating in sheep and goats in mixed flocks in the Malopolska region, where the highest seroprevalence has been detected. Phylogenetic analysis revealed that most of the isolates from sheep belonged to subtype A13, suggesting that this subtype may be predominant in the Malopolska region. Furthermore, the existence of a new subtype, tentatively designated as A18, was described for the first time. This work extends the current knowledge on the distribution of SRLV subtypes in sheep and goats in Poland and provides further information on the genetic diversity of SRLV. The new data are important for both epidemiological studies and eradication programs and provide insight into the evolution of SRLV.

Small ruminant lentiviruses in goats in southern Italy: Serological evidence, risk factors and implementation of control programs

Small ruminant lentiviruses (SRLVs) can drastically affect milk production in goat flocks and only an early detection can control and prevent their spread. Since SRLVs are responsible for persistent infections, antibody screening is the most valuable tool to identify infected animals. ELISA is recommended as the election test both for its sensitivity and for its ability to detect low antibody titers, thus identifying infected animals earlier than agar gel immunodiffusion (AGID). In the present study, an investigation was conducted to assess the SRLV seroprevalence in goat flocks in southern Italy and a transversal comparative study was carried out through the analysis of the possible risk factors influencing SRLV spread. A total of 4800 sera from 1060 flocks were analyzed and overall seroprevalences of 18,64% and 51,69% at animal and herd levels, respectively, were observed. Both the region and the herd production systems were able to affect seroprevalence, differently from the herd size, probably because the mean number of goats per herd is low and the semi-intensive management is similar regardless of the dimensional class of each herd. In particular, meat producing herds showed the higher seroprevalence, as a result of the poor sanitation and low animal monitoring in comparison to milk producing herds, where animals are managed twice daily and the relationship between dams and kids is checked to guarantee an adequate quantitative/qualitative milk yield. In the absence of vaccines or effective treatments, health preventive management and seroepidemiological investigations are the only successful approach to restrict SRLV spread as observed in countries were official/voluntary control programs are carried out.

Relationship between the dissemination of small ruminant lentivirus infection in goat herds and opinion of farmers on the occurrence of arthritis

Small ruminant lentivirus (SRLV) infection manifests itself mainly with chronic progressive arthritis affecting mainly carpal joints. The data from serological and questionnaire surveys were retrospectively analyzed to determine how the dissemination of SRLV infection in the herd influenced farmer's subjective opinion on the occurrence of swelling of carpal joints (considered as a proxy of arthritis). Between 1996 and 2017 153 different Polish dairy goat herds counting at least 20 adult goats were serologically screened for CAE and their owners were asked about their opinion on the occurrence of arthritis (never, rarely, often). Of them 73 SRLV-seropositive herds, in which true seroprevalence had been estimated, were included in the analysis. The ordinal logistic regression model was developed to determine the relationship between the true within-herd seroprevalence and the probability that the farmer would observe arthritis in the herd never, rarely or often. True within-herd seroprevalence ranged from 0.2% to 100% with the median of 34.6%. Farmers declared not to have observed arthritis in 40 (54.8%) herds, to have seen it rarely in 9 (12.3%) of herds, and to have observed it often in 24 (32.9%) of herds. The model proved that the probability of observing goats with carpal arthritis in the herd was significantly linked to the true within-herd seroprevalence (OR = 1.058, CI 95% from 1.037 to 1.078; p<0.001), but this relationship was not linear and SRLV infection proved to remain unapparent to farmers even when a considerable part of the herd had already become infected. Concluding, the study shows that when the farmer realizes that goats in the herd suffer from arthritis, SRLV infection is almost certainly already widespread in the herd.

Sheep infection by caprine lentivirus

SUMMARY The objective of this study was to demonstrate iatrogenic transmission of small ruminant lentivirus (SRLV) from goats to sheep and horizontal transmission between sheep. The study was conducted on a farm with separate goat and sheep rearing, and animals were monitored for lentivirus occurrence by clinical examination and testing by immunoblotting (IB), agar gel immunodiffusion (AGID), and nested polymerase chain reaction (nPCR). Positive results had not been observed in the sheep flock until this study. Conversely, virus positive dairy goats were known. For this reason, the farm performed the caprine arthritis-encephalitis (CAE) control program. The study was designed with a sheep group that presented positive animals for SRLV by nPCR. It was verified that three newborn animals in this group were rejected by their mothers and consequently received milk from the goat herd. These three animals remained with another 20 sheep of the same age, totaling 23 animals. After one year, during monitoring, 11 of the 23 animals in the group presented positive results in the nPCR and three demonstrated seroconversion by IB. Of the animals that had received goat milk, two had positive results in the nPCR and IB. The 11 animals positive in the nPCR were followed and it was verified that five animals did not present further positive results in the nPCR, nor seroconversion; two continued presenting positive results in the nPCR but were negative in the IB and AGID and four were positive in the nPCR, IB, and AGID. Thus, it was possible to demonstrate iatrogenic interspecific infection and the occurrence of horizontal caprine lentivirus transmission among sheep.

Genetic Characterization and Phylogenetic Analysis of Small Ruminant Lentiviruses Detected in Spanish Assaf Sheep with Different Mammary Lesions

Small Ruminant Lentiviruses (SRLVs) are widespread in many countries and cause economically relevant, slow, and persistent diseases in sheep and goats. Monitoring the genetic diversity of SRLVs is useful to improve the diagnostic tools used in the eradication programs. In this study, SRLVs detected in Spanish Assaf sheep with different grades of lymphoproliferative mastitis were sequenced. Genetic characterization showed that most samples belonged to type A and were closer to Spanish SRLV isolates previously classified as A2/A3. Four samples belonged to subtype B2 and showed higher homology with Italian B2 strains than with Spanish B2 isolates. Amino acid sequences of immuno-dominant epitopes in the gag region were very conserved while more alterations were found in the LTR sequences. No significant correlations were found between grades of mastitis and alterations in the sequences although samples with similar histological features were phylogenetically closer to each other. Broader genetic characterization surveys in samples with different grades of SRLV-lesions are required for evaluating potential correlations between SRLV sequences and the severity of diseases.

Decline of maternal antibodies to small ruminant lentivirus in goat kids

We carried out this study to determine for how long small ruminant lentivirus (SRLV)-specific antibodies can be detected by three commercial ELISA kits in goat kids after suckling infected does in field conditions. Forty-one kids born to SRLV-seropositive asymptomatic does were blood sampled prior to colostrum consumption, and then weekly for 6 months in total. The sera were screened with three commercial ELISA kits: whole-virus ELISA (wELISA), recombinant transmembrane and capsid antigen ELISA (TM/CA-ELISA), and surface antigen ELISA (SU-ELISA). All but one kid were seronegative in all three ELISAs right after birth. At the age of 1 week all kids turned seropositive in wELISA, 39 kids (95%) in TM/CA-ELISA, and 35 kids (85%) in SU-ELISA. All seropositive kids turned seronegative in wELISA by the 15th week, and in SU-ELISA by the 19th week (median of 8 weeks in both ELISA), whereas in TM/CA-ELISA five kids (13% of 39 initially seropositive) were still seropositive at the age of 6 months (median of 11 weeks). Antibody levels at the age of 1 week proved significantly linked to the duration of maternal antibodies in all three ELISAs and could be employed to predict for how long maternal antibodies would remain detectable.

Epidemiological survey in single-species flocks from Poland reveals expanded genetic and antigenic diversity of small ruminant lentiviruses

Small ruminant lentivirus (SRLV) infections are widespread in Poland and circulation of subtypes A1, A12, A13, B1 and B2 was detected. The present work aimed at extending previous study based on the analysis of a larger number of animals from single-species flocks. Animals were selected for genetic analysis based on serological reactivity towards a range of recombinant antigens derived from Gag and Env viral proteins. Phylogenetic analysis revealed the existence of subtypes B2 and A12 in both goats and sheep and subtypes A1 and B1 in goats only. In addition, two novel subtypes, A16 and A17, were found in goats. Co-infections with strains belonging to different subtypes within A and B groups were detected in 1 sheep and 4 goats originating from four flocks. Although the reactivity of serum samples towards the recombinant antigens confirmed immunological relatedness between Gag epitopes of different subtypes and the cross-reactive nature of Gag antibodies, eleven serum samples failed to react with antigens representing all subtypes detected up-to-date in Poland, highlighting the limitations of the serological diagnosis. These data showed the complex nature of SRLV subtypes circulating in sheep and goats in Poland and the need for improving SRLV-related diagnostic capacity.

Bayesian estimation of seroprevalence of small ruminant lentiviruses in sheep from Poland

In Poland, no systematic survey of ruminant lentiviruses (SRLVs) infection was performed, neither at the national nor at the regional level and only limited knowledge exists on the prevalence of SRLVs among sheep. The aim of the present study was to establish the true prevalence of SRLVs infection in sheep from Poland at the animal and herd-levels. The blood samples used for this study were the fraction of samples collected by Veterinary Inspection during an official sampling for the national monitoring program for brucellosis. Under this program the animals and herds were randomly selected using the data available from ARMA (Agency for Restructuring and Modernisation of Agriculture). The sampling unit was the herd and the target population included at least 5% of sheep, over 6 months old, from each of 16 voievodships (provinces) of Poland. Two-stage cluster sampling design was performed in this study offering the possibility to determine the prevalence of SRLVs infection, when only a fraction of herds and a fraction of animals in the herds are tested. In total, 8233 sheep serum samples coming from 832 herds were tested by indirect ELISA. 1474 (17.9%) samples were positive and 261 (31.4%) herds with at least one seropositive animals were identified. The overall true prevalence estimated by the Bayesian framework was 9.3% (95% CI 6.8, 11.3) and 33.3% (95% CI 26.5, 38.2) on the animal and herd level, respectively. Large variation in the animal and herd prevalence between the voivodships was observed. True prevalence on the herd level varied from 0.0% (95% CI 0.0, 0.0) to 71.6% (95% CI 67.6, 75.9) whereas true prevalence on the animal level ranged from 0.0% (95% CI 0.0, 0.0) to 55.3% (95% CI 50.0, 61.2). The true prevalence of SRLVs infection at animal and herd level increased according to herd size as was proved by posterior probabilities (POPR).

Risk factors associated with small ruminant lentivirus infection in eastern Poland sheep flocks

An analysis of the risk factors for ovine lentivirus infection was performed in sheep flocks located throughout the central-eastern region of Poland. Here, we report the infection details for 98 flocks with a total of 6470 ewes, 15 sheep breeds. The identification of infected animals and a review of the epidemiological status of each flock were based on an evaluation of serological tests performed on collected blood serum samples. Blood for examination was obtained from 2925 ewes of the 98 flocks under observation. Specific antibodies for Maedi Visna Virus (MVV) were detected via ELISA. Data illustrating the conditions at each sheep farm were obtained through questionnaires completed by farmers, as well as observations, measurements, and breeding records that were available. These observations were used to assess risk factors contributing to small ruminant lentivirus (SRLV) infection in sheep flocks. It was found that both sheep flock size and the type of management system had a significant effect on the increased risk of lentiviral infection. In addition, we demonstrate that there is a significant (p<0.0001) relationship between the occurrence of mastitis (OR 2.01, CI: 1.55-2.61) and diarrhea (OR 4.22, CI: 3.30-5.39) with SRLV infection in the observed sheep. Additionally, the infection rate of the animals translated directly to an impaired physical condition. Notably, the risk of infection could potentially be reduced if sheep producers are further acquainted with SRLV detection and invoke a control program based on diagnostic tests. Moreover, marketing approval should be granted for solely SRLV-seronegative animals.

Genome-Wide Search for Host Association Factors during Ovine Progressive Pneumonia Virus Infection

Ovine progressive pneumonia virus (OPPV) is an important virus that causes serious diseases in sheep and goats with a prevalence of 36% in the USA. Although OPPV was discovered more than half of a century ago, little is known about the infection and pathogenesis of this virus. In this report, we used RNA-seq technology to conduct a genome-wide probe for cellular factors that are associated with OPPV infection. A total of approximately 22,000 goat host genes were detected of which 657 were found to have been significantly up-regulated and 889 down-regulated at 12 hours post-infection. In addition to previously known restriction factors from other viral infections, a number of factors which may be specific for OPPV infection were uncovered. The data from this RNA-seq study will be helpful in our understanding of OPPV infection, and also for further study in the prevention and intervention of this viral disease.

Identification and characterization of an emerging small ruminant lentivirus circulating recombinant form (CRF)

The molecular epidemiology of small ruminant lentiviruses (SRLVs) is constantly changing due to animal movements, cross species transmission and because of their rapid evolutionary rate. This study reports a comprehensive genetic and phylogenetic analysis based on consensus gag and pol sequences covering 3kb of the SRLV genome from small ruminants in Québec, Canada. A group of strains obtained from goats originating from different flocks, segregated in a unique clade distinct from currently known SRLV groups. Genetic dissection of the gag gene from these strains revealed that it originated as a result of a recombination event between parental strains currently circulating in small ruminants of the country. Following HIV nomenclature, we propose to call this group of strains, circulating recombinant form 1 SRLV, or CRF01_AB SRLV. In addition, the study confirms the existence of genetically distinct and homogeneous populations of SRLVs infecting sheep and goats housed in single species flocks.

Immunogenetics of small ruminant lentiviral infections

The small ruminant lentiviruses (SRLV) include the caprine arthritis encephalitis virus (CAEV) and the Maedi-Visna virus (MVV). Both of these viruses limit production and can be a major source of economic loss to producers. Little is known about how the immune system recognizes and responds to SRLVs, but due to similarities with the human immunodeficiency virus (HIV), HIV research can shed light on the possible immune mechanisms that control or lead to disease progression. This review will focus on the host immune response to HIV-1 and SRLV, and will discuss the possibility of breeding for enhanced SRLV disease resistance.

Small ruminant macrophage polarization may play a pivotal role on lentiviral infection

Small ruminant lentiviruses (SRLV) infect the monocyte/macrophage lineage inducing a long-lasting infection affecting body condition, production and welfare of sheep and goats all over the world. Macrophages play a pivotal role on the host’s innate and adaptative immune responses against parasites by becoming differentially activated. Macrophage heterogeneity can tentatively be classified into classically differentiated macrophages (M1) through stimulation with IFN-γ displaying an inflammatory profile, or can be alternatively differentiated by stimulation with IL-4/IL-13 into M2 macrophages with homeostatic functions. Since infection by SRLV can modulate macrophage functions we explored here whether ovine and caprine macrophages can be segregated into M1 and M2 populations and whether this differential polarization represents differential susceptibility to SRLV infection. We found that like in human and mouse systems, ovine and caprine macrophages can be differentiated with particular stimuli into M1/M2 subpopulations displaying specific markers. In addition, small ruminant macrophages are plastic since M1 differentiated macrophages can express M2 markers when the stimulus changes from IFN-γ to IL-4. SRLV replication was restricted in M1 macrophages and increased in M2 differentiated macrophages respectively according to viral production. Identification of the infection pathways in macrophage populations may provide new targets for eliciting appropriate immune responses against SRLV infection.

Development and validation of TaqMan probe based real time PCR assays for the specific detection of genotype A and B small ruminant lentivirus strains

BACKGROUND

Small ruminant lentiviruses (SRLV) are members of the Retroviridae family and infect goats and sheep worldwide. Detection of specific antibodies using AGID and ELISA is the most commonly used means of diagnosing SRLV infection. The most frequent molecular method for detecting the provirus genome is PCR, using peripheral blood leucocytes as target cells. Real time PCR has also recently been used. The aim of this study was to develop a real time PCR for detection of SRLV in order to improve molecular diagnostics of SRLV infections in sheep and goats.

RESULTS

Two new real time PCR assays using TaqMan probes for the specific detection of genotype A (MVV assay) and genoptype B (CAEV assay) SRLV strains and differentiation between them were developed and validated at both analytical and diagnostic levels following MIQE guidelines. The validation results showed that the new real time PCR is 100% specific, with a reliable limit of detection of 26 (CAEV assay) and 72 (MVV assay) plasmid DNA copies, while compared to ELISA the diagnostic sensitivity of both assays was 79% when tested with Slovenian SRLV field samples. Intra-assay and inter-assay coefficients of variation showed overall good repeatability and reproducibility of the new real time PCR assays, except for the highest dilutions.

CONCLUSIONS

Two new TaqMan probe based real time PCR assays for the specific detection of genotype A and B SRLV strains and differentiation between them were developed and validated. They can serve as an additional tool for confirming infection with SRLV and may also be useful for early detection of infected animals prior to seroconversion.

Small ruminant lentivirus genetic subgroups associate with sheep TMEM154 genotypes

Small ruminant lentiviruses (SRLVs) are prevalent in North American sheep and a major cause of production losses for the U.S. sheep industry. Sheep susceptibility to SRLV infection is influenced by genetic variation within the ovine transmembrane 154 gene (TMEM154). Animals with either of two distinct TMEM154 haplotypes that both encode glutamate at position 35 of the protein (E35) are at greater risk of SRLV infection than those homozygous with a lysine (K35) haplotype. Prior to this study, it was unknown if TMEM154 associations with infection are influenced by SRLV genetic subgroups. Accordingly, our goals were to characterize SRLVs naturally infecting sheep from a diverse U.S. Midwestern flock and test them for associations with TMEM154 E35K genotypes. Two regions of the SRLV genome were targeted for proviral amplification, cloning, sequence analysis, and association testing with TMEM154 E35K genotypes: gag and the transmembrane region of env. Independent analyses of gag and env sequences showed that they clustered in two subgroups (1 and 2), they were distinct from SRLV subtypes originating from Europe, and that subgroup 1 associated with hemizygous and homozygous TMEM154 K35 genotypes and subgroup 2 with hemi- and homozygous E35 genotypes (gag p < 0.001, env p = 0.01). These results indicate that SRLVs in the U.S. have adapted to infect sheep with specific TMEM154 E35K genotypes. Consequently, both host and SRLV genotypes affect the relative risk of SRLV infection in sheep.

Phylogenetic analysis of small ruminant lentiviruses in mixed flocks: multiple evidence of dual infection and natural transmission of types A2 and B1 between sheep and goats

Previous molecular analyses of small ruminant lentivirus (SRLV) populations in single species herds in Quebec, Canada, have revealed a relatively simple structure where goats and sheep appeared exclusively infected with B1 and A2 subtypes respectively. The present work aimed at extending these earlier findings with the analysis of SRLVs in mixed flocks. Molecular analyses revealed a more complex picture of SRLV population structure in mixed herds compared to single species herds. Notably, phylogenetic analyses of long gag sequences strongly support transmission of A2 subtype from sheep to goats as well as transmission of B1 subtype from goats to sheep. Hence, this work uncovered for the first time natural transmission between sheep and goats of North American subtype A2. In addition, multiple evidences of mixed infection of sheep and goats with A2 and B1 subtypes were found. The data reported in this study reinforces the concept of a genetic continuum of SRLVs where strains are exchanged between sheep and goats under favourable conditions and in the absence of specific species barriers. Most interestingly, this study suggests that dual infection, which is a hallmark of the lentivirus paradigm HIV, may not be such rare events in small ruminants but may simply be understudied and underreported. Overall, the present data shows that sheep and goats in Canada can be infected with both SRLV A and B types, sometimes simultaneously, and that mixed flocks may represent a breeding ground for their evolution.

Small ruminant lentiviruses: genetic variability, tropism and diagnosis

Small ruminant lentiviruses (SRLV) cause a multisystemic chronic disease affecting animal production and welfare. SRLV infections are spread across the world with the exception of Iceland. Success in controlling SRLV spread depends largely on the use of appropriate diagnostic tools, but the existence of a high genetic/antigenic variability among these viruses, the fluctuant levels of antibody against them and the low viral loads found in infected individuals hamper the diagnostic efficacy. SRLV have a marked in vivo tropism towards the monocyte/macrophage lineage and attempts have been made to identify the genome regions involved in tropism, with two main candidates, the LTR and env gene, since LTR contains primer binding sites for viral replication and the env-encoded protein (SU ENV), which mediates the binding of the virus to the host's cell and has hypervariable regions to escape the humoral immune response. Once inside the host cell, innate immunity may interfere with SRLV replication, but the virus develops counteraction mechanisms to escape, multiply and survive, creating a quasi-species and undergoing compartmentalization events. So far, the mechanisms of organ tropism involved in the development of different disease forms (neurological, arthritic, pulmonary and mammary) are unknown, but different alternatives are proposed. This is an overview of the current state of knowledge on SRLV genetic variability and its implications in tropism as well as in the development of alternative diagnostic assays.

Diverse host–virus interactions following caprine arthritis-encephalitis virus infection in sheep and goats

Interspecies transmissions substantially contribute to the epidemiology of small ruminant lentiviruses (SRLVs), including caprine arthritis encephalitis virus (CAEV) and visna-maëdi virus. However, comprehensive studies of host–virus interactions during SRLV adaptation to the new host are lacking. In this study, virological and serological features were analysed over a 6 month period in five sheep and three goats experimentally infected with a CAEV strain. Provirus load at the early stage of infection was significantly higher in sheep than in goats. A broad antibody reactivity against the matrix and capsid proteins was detected in goats, whereas the response to these antigens was mostly type-specific in sheep. The humoral response to the major immunodominant domain of the surface unit glycoprotein was type-specific, regardless of the host species. These species-specific immune responses were then confirmed in naturally infected sheep and goats using sera from mixed flocks in which interspecies transmissions were reported. Taken together, these results provide evidence that SRLV infections evolve in a host-dependent manner, with distinct host–virus interactions in sheep and goats, and highlight the need to consider both SRLV genotypes in diagnosis, particularly in sheep.

First molecular characterization of visna/maedi viruses from naturally infected sheep in Turkey

Recent worldwide serological and genetic studies of small ruminant lentiviruses (SRLV) have led to the description of new genotypes and the development of new diagnostic tests. This study investigated the detection and molecular characterization of visna/maedi virus (VMV) infection in serum and blood samples from pure and mixed sheep breeds acquired from different regions in Turkey using ELISA and PCR techniques. The prevalence of VMV was 67.8 % by ELISA and/or LTR-PCR with both assays showing a medium level of agreement (kappa: 0.26; ± 0.038 CI). Positivity of VMV in sheep increased according to the age of the animal, although PCR positivity was higher than ELISA in young individuals. Phylogenetic analysis of 33 LTR sequences identified two distinct clades that were closely related to American and Greek LTR sequences. Phylogenetic analysis of 10 partial gag gene sequences identified A2, A3, A5, A9, A11 subtypes of genotype A SRLVs. In vitro culture of all isolates in fetal sheep lung cells (FSLC) showed a slow/low phenotype causing less or no lytic infection compared with infection with the WLC-1 American strain characterized by a rapid/highly lytic phenotype. Phylogenetic analysis revealed that Turkish VMV sequences preceded the establishment of American or Greek strains that were associated with the migration of sheep from the Middle East to Western Europe several centuries ago. This is the first study that describes Turkish VMV sequences with the molecular characterization of LTR and gag genes, and it strongly suggests that SRLV-genotype A originated in Turkey.

Risk factors associated with seropositivity to small ruminant lentiviruses in goat herds

Cross-sectional studies based on serological testing and questionnaires were conducted at 5-yr intervals (1996, 2002 and 2007) in goat breeding herds from Poland to determine true herd-level seroprevalence of caprine arthritis-encephalitis and the herd-level risk factors for seropositivity. Multivariable logistic regression models were developed for data from 1996 and the combined data from 2002 and 2007, separately. True herd-level seroprevalences in 1996, 2002 and 2007 were 30.8% (CI 95%: 20.5-41.0%), 65.7% and 71.9%, respectively. The import of goats from abroad was a risk factor only in 1996 (OR 13.6, CI 95%: 1.14-162). The presence of seropositive bucks in a herd was a risk factor in 1996 (OR 21, CI 95%: 1.89-233) and in 2002-2007 (OR 2.9, CI 95%: 1.04-8.4). Moreover, large herds (>30 does in 1996 or >100 does in 2002-2007) were more likely to be seropositive than smaller herds (OR=10.1, CI 95%: 2.17-46 in 1996 and OR 5.4, CI 95%: 1.11-26 in 2002-2007).

Phylogenetic analysis of small ruminant lentiviruses detected in Slovenia

Small ruminant lentiviruses (SRLV), which belong to the Retroviridae family, infect goats and sheep worldwide. The aim of this study was to characterize the SRLV strains circulating in Slovenia, by phylogenetic analysis of two genomic regions, 1.8 kb gag-pol fragment and 1.2kb pol fragment. The results of our study revealed that Slovenian SRLV strains are highly heterogeneous, with ovine strains belonging to genotype A and caprine strains to genotypes A and B. The closest relatives of sheep virus sequences from two flocks that clustered together (SLO 35, 36) were found to be in subtype A5. A cluster composed of four sheep virus sequences (SLO 31) was clearly divergent from all other subtypes in group A and could not be assigned to any of them. The virus sequences from one goat flock belonged solely to subtype B1, whereas virus sequences from more than one genotype were found to circulate within the other two goat flocks, belonging to subtype B1 (SLO 1 and SLO 37) and to genotype A (SLO 2 and 78-88 g). Two goat virus sequences (SLO 2) were found to belong to genotype A and could not be assigned to existing subtypes. One goat virus sequence (37-88 g) from flock 37 was clearly different from other sequences of this flock and was more closely related to genotype A sequences. We propose two new subtypes within genotype A, subtype A14 (SLO 2) and A15 (SLO 31).