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

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.

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.

Detection of small ruminant Lentivirus proviral DNA in red deer from Poland

Small ruminant lentiviruses (SRLVs) are widespread and infect goats and sheep. Several reports also suggest that SRLVs can infect wild ruminants. The presence of specific antibodies against SRLVs has been identified in wild ruminants from Poland, but no studies have been conducted to detect proviral DNA of SRLVs in these animals. Therefore, the purpose of this study was to examine samples from Polish wild ruminants to determine whether these animals can serve as reservoirs of SRLVs under natural conditions. A total of 314 samples were tested from red deer (n = 255), roe deer (n = 52) and fallow deer (n = 7) using nested real-time PCR. DNA from positive real-time PCR samples was subsequently used to amplify a CA fragment (625 bp) of the gag gene, a 1.2 kb fragment of the pol gene and an LTR-gag fragment. Three samples (0.95%) were positive according to nested real-time PCR using primers and probe specific for CAEV (SRLV group B). All the samples were negative for the primers and probe specific for MVV (SRLV A group). Only SRLV LTR-gag sequences were obtained from two red deer. Phylogenetic analysis revealed that these sequences were more closely related to CAEV than to MVV. Our results revealed that deer can carry SRLV proviral sequences and therefore may play a role in the epidemiology of SRLVs. To our knowledge, this is the first study describing SRLV sequences from red deer.

Small Ruminant Lentivirus Infection in Sheep and Goats in North Portugal: Seroprevalence and Risk Factors

Small ruminant lentiviruses (SRLVs) are transmitted among ovine and caprine species. This disease is a severe problem for small ruminant production, not only for animals' well-being but also for flocks' efficiency. The main aim of this research was to quantify the seroprevalence and associated risk factors for SRLV infection in the northern region of Portugal. Samples were collected from a total of 150 flocks, of which 129 (86.0%; 95% CI: 80.67%-91.33%) had at least one seropositive animal. Out of 2607 individual blood samples, 1074 (41.2%) were positive for SRLVs. Risk factors associated with SRLV infection were species (caprine), age (>2 years old), flock size (>100 animals), production system (intensive), food production system (milk), type of activity (professional), participation in livestock competitions (yes), replacement young ewe bought (yes), and natural feeding management (yes). This knowledge empowers the implementation of effective preventive measures. Overall, biosecurity measures should be promoted and implemented with the main aim of reducing viral transmission and reducing the prevalence of this disease. We recognise that government authorities should promote and audit voluntary control and eradication programs in small ruminant flocks in the region studied.

A large-scale study on the seroprevalence of small ruminant lentiviral infection in the Polish goat population

A large-scale study was carried out in a Polish goat population in 2014-2022 to determine the herd-level (between-herd) and within-herd seroprevalence of small ruminant lentivirus (SRLV) infection. A total of 8354 adult goats (aged >1 year) from 165 herds located in various regions of Poland were serologically tested using a commercial ELISA. One hundred twenty eight herds were randomly selected while 37 were enrolled based on convenience non-random sampling. At least 1 seropositive result was obtained in 103 / 165 herds. For all these herds the probability that they were truly positive (herd-level positive predictive value) was calculated. It was ≥ 90% in 91 seropositive herds and 73% to < 90% in 12 herds in which only 1-4 goats were seropositive (22 goats in total). The seropositive goats in the latter herds were retested using a different commercial ELISA and 14 goats (9 males and 5 females) from 9 herds were confirmed to be seropositive (serial testing). The true herd-level seroprevalence was estimated at 61% (95% confidence interval [CI 95%]: 53%-68%). It differed significantly between herd size classes (p = 0.003): the highest prevalences were found in the medium (51 - 100 adult goats) and large herds (>100 adult goats) - 72% (CI 95%: 56-84%) and 86% (CI 95%: 67%-95%), respectively, while prevalences in very small (≤ 20 adult goats) and small herds (21 - 50 adult goats) were 46% (CI 95%: 34%-59%) and 57% (CI 95%: 43%-70%), respectively. The true herd-level seroprevalence differed significantly also between geographical regions of Poland (p = 0.003), with the highest values in the north-western and the lowest in the southern region of the country. The true within-herd seroprevalence estimated using a Bayesian approach ranged from 0.7% to 100% with the median (IQR) of 42% (17%-84%), and did not vary significantly between herd size classes (p = 0.393) or geographical regions of Poland (p = 0.570). Concluding, SRLV infection is widespread in the Polish goat population, the north-western region of Poland is most extensively infected, and herds counting > 50 adult goats are more often infected.

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.

Single Nucleotide Polymorphisms in Genes Encoding Toll-Like Receptors 7 and 8 and Their Association with Proviral Load of SRLVs in Goats of Polish Carpathian Breed

Toll-like receptors (TLRs) 7 and 8 are important in single-stranded viral RNA recognition, so genetic variation of these genes may play a role in SRLVs infection and disease progression. Present study aimed to identify SNPs in genes encoding TLR7 and TLR8 in goats of Carpathian breed and analyze their association with the SRLVs provirus concentration as index of disease progression. A total of 14 SNPs were detected, 6 SNPs in the TLR7 gene locus and 8 SNPs in the TLR8 gene. Nine of the 14 identified polymorphisms, 4 in the TLR7 gene and 5 in TLR8 gene, were significantly associated with the SRLVs proviral concentration. These SNPs were located in 3'UTR, 5'UTR and intron sequences as well as in the coding sequences, but they led to silent changes. Homozygous genotypes of three TLR7 SNPs (synonymous variant 1:50703293, 3'UTR variant 1:50701297 and 5'UTR variant 1:50718645) were observed in goats with lower provirus copy number as well as in seronegative animals. The results obtained in this study suggest that SNPs of TLR7/TLR8 genes may induce differential innate immune response towards SRLVs affecting proviral concentration and thereby disease pathogenesis and progression. These findings support a role for genetic variations of TLR7 and TLR8 in SRLVs infection and warrants further studies on the effect of TLR7/TLR8 polymorphisms on SRLVs infection in different populations.

Bayesian Estimation of the True Seroprevalence and Risk Factor Analysis of Bovine Leukemia Virus Infection in Pakistan

Simple Summary

The enzootic bovine leucosis is the most common and economically important viral disease of cattle, caused by bovine leukemia virus (BLV). In cattle, infection with BLV leads to decreased milk production and premature culling and also impairs the immune system predisposing animals to other infections and increasing severity of disease. The aim of this study was to estimate the true seropositivity to BLV at the farm and within-farm levels in Pakistan, using a latent class analysis. In addition, some factors influencing BLV seropositivity were analyzed. We tested 1380 dairy cattle from 451 herds and 92 water buffalo. Analysis at the within-herd and herd levels showed 3.8% of cattle and 1.4% of herds were truly seropositive. All 92 serum samples from water buffalo were negative. The study demonstrated strong association between BLV seroprevalence and herd size but not with common housing of cattle representing indigenous breeds with exotic breed or their crossbred and also common housing of cattle and water buffalo.

Abstract

The objective of this study was to determine the true seroprevalence of bovine leukemia virus (BLV) infection in dairy cattle from Pakistan at the animal and herd-level. We tested 1380 dairy cattle from 451 herds and 92 water buffalo. The sera were tested by ELISA and the results were analyzed using Bayesian inference. The median posterior estimate of the herd level true BLV prevalence was 1.4%, with a 95% credible interval (CI) 0.7–3.1, whereas the median posterior estimate of the within-farm true seroprevalence was 3.8% with a 95% CI 2.8–4.8. All 92 sera collected from water buffalo were negative. Several risk factors potentially associated with seropositivity to BLV infections in Pakistan were analyzed using logistic regression model based on calculation of an odds ratio (OR). The study showed an association between seropositivity and medium herd (≥50) size (OR = 23.57, 95% CI: 3.01–103.48). Common housing of indigenous cattle with exotic-breed cattle (OR = 0.67, 95% CI: 06–2.35) or housing indigenous or their crossbred cattle with exotic-breed cattle (OR = 0.95, 95% CI: 0.14–3.01) had no effect on the BLV seroprevalence. Similarly, common housing of cattle and water buffalo was not risk factor for increased BLV seropositivity (OR = 27.10, 95% CI: 0.63–119.34).

Worldwide Prevalence of Small Ruminant Lentiviruses in Sheep: A Systematic Review and Meta-Analysis

Small Ruminant Lentiviruses (SRLV) are highly prevalent retroviruses with significant genetic diversity and antigenic heterogeneity that cause a progressive wasting disease of sheep called Maedi-visna. This work provides a systematic review and meta-analysis of the last 40 years (1981-2020) of scientific publications on SRLV individual and flock prevalence. Fifty-eight publications and 314 studies were included. Most articles used a single diagnostic test to estimate prevalence (77.6%), whereas articles using three or more tests were scarce (6.9%). Serological tests are more frequently used than direct methods and ELISA has progressively replaced AGID over the last decades. SRLV infection in sheep is widespread across the world, with Europe showing the highest individual prevalence (40.9%) and being the geographical area in which most studies have been performed. Africa, Asia, and North America show values between 16.7% to 21.8% at the individual level. South and Central America show the lowest individual SRLV prevalence (1.7%). There was a strong positive correlation between individual and flock prevalence (ρ = 0.728; p ≤ 0.001). Despite the global importance of small ruminants, the coverage of knowledge on SRLV prevalence is patchy and inconsistent. There is a lack of a gold standard method and a defined sampling strategy among countries and continents.

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.

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.

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.