Variation in resistance to the porcine reproductive and respiratory syndrome virus (PRRSV) in Pietrain and Miniature pigs

Genetic background influences pig responses to porcine reproductive and respiratory syndrome virus

Porcine reproductive and respiratory syndrome virus (PRRSV) is a highly infectious and economically significant virus that causes respiratory and reproductive diseases in pigs. It results in reduced productivity and increased mortality in pigs, causing substantial economic losses in the industry. Understanding the factors affecting pig responses to PRRSV is crucial to develop effective control strategies. Genetic background has emerged as a significant determinant of susceptibility and resistance to PRRSV in pigs. This review provides an overview of the basic infection process of PRRSV in pigs, associated symptoms, underlying immune mechanisms, and roles of noncoding RNA and alternative splicing in PRRSV infection. Moreover, it emphasized breed-specific variations in these aspects that may have implications for individual treatment options.

The Connection between Immunocompetence and Reproduction in Wildlife

Reproduction rate is important for the survival of animal populations. During gravidity, a trade-off occurs between the individual well-being of gravid females and investment in offspring. Due to the high synthesis and energy requirements for the growing fetus, other physiological activities are downregulated in pregnant females. This causes changes in the composition of the reproductive microbiome and a decreased immune response to presented antigens and pathogens. As a result, the immunocompetence of gravid wild animals declines. In general, therefore, increased infection rates during pregnancy can be observed in all wildlife species studied. In the course of evolution, however, this has apparently evolved as a suitable strategy to ensure the survival of the population as a whole.

miRNA let-7 family regulated by NEAT1 and ARID3A/NF-κB inhibits PRRSV-2 replication in vitro and in vivo

Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically devastating diseases affecting the swine industry worldwide. To investigate the role of miRNAs in the infection and susceptibility of PRRS virus (PRRSV), twenty-four miRNA libraries were constructed and sequenced from PRRSV-infected and mock-infected Porcine alveolar macrophages (PAMs) of Meishan, Landrace, Pietrain and Qingping pigs at 9 hours post infection (hpi), 36 hpi, and 60 hpi. The let-7 family miRNAs were significantly differentially expressed between PRRSV-infected and mock-infected PAMs from 4 pig breeds. The let-7 family miRNAs could significantly inhibit PRRSV-2 replication by directly targeting the 3’UTR of the PRRSV-2 genome and porcine IL6, which plays an important role in PRRSV replication and lung injury. NEAT1 acts as a competing endogenous lncRNA (ceRNA) to upregulate IL6 by attaching let-7 in PAMs. EMSA and ChIP results confirmed that ARID3A could bind to the promoter region of pri-let-7a/let-7f/let-7d gene cluster and inhibit the expression of the let-7 family. Moreover, the NF-κB signaling pathway inhibits the expression of the let-7 family by affecting the nuclear import of ARID3A. The pEGFP-N1-let-7 significantly reduced viral infections and pathological changes in PRRSV-infected piglets. Taken together, NEAT1/ARID3A/let-7/IL6 play significant roles in PRRSV-2 infection and may be promising therapeutic targets for PRRS.

There are significant differences in susceptibility/resistance to PRRSV among different pig breeds. Especially the local pig breeds in China had strong resistance to PRRSV. However, due to the complexity of the interaction mechanism between pigs and PRRSV, the genetic mechanism leading to PRRSV susceptibility/resistance in different pig breeds is still unclear. MiRNAs play a vital regulatory role in immune response and development of PRRS. In this study, we found that the expression of miRNA let-7 family members were significantly different in PRRSV-infected/mock-infected PAMs from Pietrain, Qingping, Meishan, and Landrace pigs. Our findings illustrated that NEAT1/ARID3A/let-7/IL6 had a significant role in PRRSV-2 infection. What’s more, let-7 family could significantly reduce PRRSV infection and pathological changes in vitro and in vivo. This discovery provided a new idea for breeding PRRSV resistant pigs by revealing the molecular mechanism of PRRSV susceptibility in different pig breeds. Altogether, let-7 family have significant roles in PRRSV infection and may be promising therapeutic targets for PRRS.

[Opportunities and risks of the use of genetic resistances to infectious diseases in pigs - an overview]

Demands for health, performance and welfare in pigs, as well as the desire for consumer protection and reduced antibiotic use, require optimal measures in advance of disease development. This includes, in principle, the use of genetically more resistant lines and breeding animals, whose existence has been proven for a wide range of pathogen-host interactions. In addition, attempts are being made to identify the gene variants responsible for disease resistance in order to force the selection of suitable populations, also using modern biotechnical technics. The present work is intended to provide an overview of the research status achieved in this context and to highlight opportunities and risks for the future.The evaluation of the international literature shows that genetic disease resistance exist in many areas of swine diseases. However, polygenic inheritance, lack of animal models and the influence of environmental factors during evaluation render their implementation in practical breeding programs demanding. This is where modern molecular genetic methods, such as Gene Editing, come into play. Both approaches possess their pros and cons, which are discussed in this paper. The most important infectious diseases in pigs, including general diseases and epizootics, diseases of the respiratory and digestive tract and diseases of the immune system are taken into account.

Resilience Effects of SGK1 and TAP1 DNA Markers during PRRSV Outbreaks in Reproductive Sows

The porcine reproductive and respiratory syndrome virus (PRRSV) is a major infectious stressor that causes serious health problems and productivity drops. Based on previous genome-wide analyses, we selected SGK1 and TAP1 as candidate genes for resilience, and genotyped three mutations, including a 3'UTR variant SGK1_rs338508371 and two synonymous variants TAP1_rs1109026889 and TAP1_rs80928141 in 305 Landrace × Large White sows. All polymorphisms affected the reproductive performance in the outbreak, but not during the endemic phase, thereby indicating a potential use of these markers for resilience. Moreover, some genotypes were associated with a stable performance across PRRSV phases. Thus, in the outbreak, the SGK1_rs338508371 AA sows had less piglets born alive (p < 0.0001) and more stillborns (p < 0.05) while other sows were able to keep their productivity. During the outbreak, TAP1_rs80928141 GG sows had less piglets born alive (p < 0.05) and both TAP1 polymorphisms influenced the number of mummies in an additive manner (p < 0.05). Remarkably, TAP1_rs80928141 AA sows had around one mummy more than GG sows (p < 0.01). Resilience to PRRSV could be improved by including the SGK1 and TAP1 markers in crossbreeding and/or selection schemes, as they contribute to maintaining a stable number of piglets born alive and lost, particularly mummies, despite the outbreak.

PBMCs transcriptome profiles identified breed-specific transcriptome signatures for PRRSV vaccination in German Landrace and Pietrain pigs

Porcine reproductive and respiratory syndrome (PRRS) is a devastating viral disease affecting the swine industry worldwide. Genetic variation in host immunity has been considered as one of the potential determinants to improve the immunocompetence, thereby resistance to PRRS. Therefore, the present study aimed to investigate the breed difference in innate immune response to PRRSV vaccination between German Landrace (DL) and Pietrain (Pi) pigs. We analyzed microarray-based transcriptome profiles of peripheral blood mononuclear cells (PBMCs) collected before (0 h) and 24 h after PRRSV vaccination from purebred DL and Pi pigs with three biological replicates. In total 4,269 transcripts were identified to be differentially expressed in PBMCs in at least any of four tested contrast pairs (i.e. DL-24h vs. DL-0h, Pi-24h vs. Pi-0h, DL-0h vs. Pi-0h and DL-24h vs. Pi-24h). The number of vaccine-induced differentially expressed genes (DEGs) was much higher (2,459) in DL pigs than that of Pi pigs (291). After 24 h of PRRSV vaccination, 1,046 genes were differentially expressed in PMBCs of DL pigs compared to that of Pi (DL-24h vs. Pi-24h), indicating the breed differences in vaccine responsiveness. The top biological pathways significantly affected by DEGs of both breeds were linked to immune response functions. The network enrichment analysis identified ADAM17, STAT1, MMS19, RPA2, BAD, UCHL5 and APC as potential regulatory genes for the functional network of PRRSV vaccine response specific for DL; while FOXO3, IRF2, ADRBK1, FHL3, PPP2CB and NCOA6 were found to be the most potential hubs of Pi specific transcriptome network. In conclusion, our data provided insights of breed-specific host transcriptome responses to PRRSV vaccination which might contribute in better understanding of PPRS resistance in pigs.

Identification of resilient sows in Porcine Reproductive and Respiratory Syndrome virus infected farms

The identification of resilient sows can improve reproductive performance in farms exposed to multiple challenges. A common challenge is the porcine reproductive and respiratory syndrome virus (PRRSV). A key issue to deal with disease resilience is to set up a feasible phenotyping strategy. Our aim was to develop a phenotyping criterion to discriminate susceptible from resilient sows in PRRSV-infected farms. A total of 517 Landrace x Large White gilts were classified as resilient (R) or susceptible (S) to PRRSV virus, following vaccination with MLV-PRRSV at 6-7 wk of age, in a PRRSV negative multiplication farm. Female piglets were phenotyped as R if their serum was negative to PRRSV at 7 and 21 d post-vaccination (DPV) or as S if their serum was positive at 7 and/or 21 DPV. Amongst them, 382 gilts were transferred to a PRRSV-positive production farm, where the number of piglets born alive (NBA), stillborn (NSB), mummified (NMU), lost (NLP=NSB+NMU) and total born (NTB = NBA+NLP) were recorded for almost three years. Data were collected during two periods according to the PRRSV farm health status, which were confirmed as either PRRSV-positive stable (endemic) or inestable (epidemic). Analyses were carried out under a Bayesian approach. The heritability for the resilience criterion was estimated using a threshold model. A linear (for NTB and NBA) and a binomial model (for NSB, NMU and NLP) on the resilience criterion by the farm health status were used to assess the difference between R and S sows. The heritability of the resilience criterion was 0.46 (SD 0.06). The probability of a piglet being lost was greater (≥0.97) in S than in R litters, regardless of whether the delivery occurred during a PRRSV outbreak (20.5% vs 17.0%) or not (15.8% vs 13.7%). The lower piglet mortality rate in R sows was due to NSB, in the endemic phase (13.0% vs 15.0% of NTB, with a posterior probability of 98% of S sows showing higher NSB than R sows), and to NMU, in the epidemic phase (4.0% vs 8.4% of NTB, with a posterior probability of >99% of S sows showing higher NMU than R sows). During a PRRSV outbreak, the S sows were twice as likely to give birth to a mummified piglet as compared to R sows. These findings provide evidence that the described phenotyping scheme has a potential use as a PRRSV resilience criterion.

How to prevent viremia rebound? Evidence from a PRRSv data-supported model of immune response

Background

Understanding what determines the between-host variability in infection dynamics is a key issue to better control the infection spread. In particular, pathogen clearance is desirable over rebounds for the health of the infected individual and its contact group. In this context, the Porcine Respiratory and Reproductive Syndrome virus (PRRSv) is of particular interest. Numerous studies have shown that pigs similarly infected with this highly ubiquitous virus elicit diverse response profiles. Whilst some manage to clear the virus within a few weeks, others experience prolonged infection with a rebound. Despite much speculation, the underlying mechanisms responsible for this undesirable rebound phenomenon remain unclear.

Results

We aimed at identifying immune mechanisms that can reproduce and explain the rebound patterns observed in PRRSv infection using a mathematical modelling approach of the within-host dynamics. As diverse mechanisms were found to influence PRRSv infection, we established a model that details the major mechanisms and their regulations at the between-cell scale. We developed an ABC-like optimisation method to fit our model to an extensive set of experimental data, consisting of non-rebounder and rebounder viremia profiles. We compared, between both profiles, the estimated parameter values, the resulting immune dynamics and the efficacies of the underlying immune mechanisms. Exploring the influence of these mechanisms, we showed that rebound was promoted by high apoptosis, high cell infection and low cytolysis by Cytotoxic T Lymphocytes, while increasing neutralisation was very efficient to prevent rebounds.

Conclusions

Our paper provides an original model of the immune response and an appropriate systematic fitting method, whose interest extends beyond PRRS infection. It gives the first mechanistic explanation for emergence of rebounds during PRRSv infection. Moreover, results suggest that vaccines or genetic selection promoting strong neutralising and cytolytic responses, ideally associated with low apoptotic activity and cell permissiveness, would prevent rebound.

Electronic supplementary material

The online version of this article (10.1186/s12918-018-0666-7) contains supplementary material, which is available to authorized users.

Fecal Microbiota Transplantation Is Associated With Reduced Morbidity and Mortality in Porcine Circovirus Associated Disease

Porcine circovirus associated disease (PCVAD) is a term used to describe the multi-factorial disease syndromes caused by porcine circovirus type 2 (PCV-2), which can be reproduced in an experimental setting through the co-infection of pigs with PCV-2 and porcine reproductive and respiratory syndrome virus (PRRSV). The resulting PCVAD-affected pigs represent a subpopulation within the co-infected group. In co-infection studies, the presence of increased microbiome diversity is linked to a reduction in clinical signs. In this study, fecal microbiota transplantation (FMT) was investigated as a means to prevent PCVAD in pigs co-infected with PRRSV and PCV-2d. The sources of the FMT material were high-parity sows with a documented history of high health status and robust litter characteristics. The analysis of the donated FMT material showed the absence of common pathogens along with the presence of diverse microbial phyla and families. One group of pigs (n = 10) was administered the FMT while a control group (n = 10) was administered a sterile mock-transplant. Over the 42-day post-infection period, the FMT group showed fewer PCVAD-affected pigs, as evidenced by a significant reduction in morbidity and mortality in transplanted pigs, along with increased antibody levels. Overall, this study provides evidence that FMT decreases the severity of clinical signs following co-infection with PRRSV and PCV-2 by reducing the prevalence of PCVAD.

The Importance of Endophenotypes to Evaluate the Relationship between Genotype and External Phenotype

With the exception of a few Mendelian traits, almost all phenotypes (traits) in livestock science are quantitative or complex traits regulated by the expression of many genes. For most of the complex traits, differential expression of genes, rather than genomic variation in the gene coding sequences, is associated with the genotype of a trait. The expression profiles of the animal's transcriptome, proteome and metabolome represent endophenotypes that influence/regulate the externally-observed phenotype. These expression profiles are generated by interactions between the animal's genome and its environment that range from the cellular, up to the husbandry environment. Thus, understanding complex traits requires knowledge about not only genomic variation, but also environmental effects that affect genome expression. Gene products act together in physiological pathways and interaction networks (of pathways). Due to the lack of annotation of the functional genome and ontologies of genes, our knowledge about the various biological systems that contribute to the development of external phenotypes is sparse. Furthermore, interaction with the animals' microbiome, especially in the gut, greatly influences the external phenotype. We conclude that a detailed understanding of complex traits requires not only understanding of variation in the genome, but also its expression at all functional levels.

Genetic resistance - an alternative for controlling PRRS?

PRRS is one of the most challenging diseases for world-wide pig production. Attempts for a sustainable control of this scourge by vaccination have not yet fully satisfied. With an increasing knowledge and methodology in disease resistance, a new world-wide endeavour has been started to support the combat of animal diseases, based on the existence of valuable gene variants with regard to any host-pathogen interaction. Several groups have produced a wealth of evidence for natural variability in resistance/susceptibility to PRRS in our commercial breeding lines. However, up to now, exploiting existing variation has failed because of the difficulty to detect the carriers of favourable and unfavourable alleles, especially with regard to such complex polygenic traits like resistance to PRRS. New hope comes from new genomic tools like next generation sequencing which have become extremely fast and low priced. Thus, research is booming world-wide and the jigsaw puzzle is filling up – slowly but steadily. On the other hand, knowledge from virological and biomedical basic research has opened the way for an “intervening way”, i.e. the modification of identified key genes that occupy key positions in PRRS pathogenesis, like CD163. CD163 was identified as the striking receptor in PRRSV entry and its knockout from the genome by gene editing has led to the production of pigs that were completely resistant to PRRSV – a milestone in modern pig breeding. However, at this early step, concerns remain about the acceptance of societies for gene edited products and regulation still awaits upgrading to the new technology. Further questions arise with regard to upcoming patents from an ethical and legal point of view. Eventually, the importance of CD163 for homeostasis, defence and immunity demands for more insight before its complete or partial silencing can be answered. Whatever path will be followed, even a partial abolishment of PRRSV replication will lead to a significant improvement of the disastrous herd situation, with a significant impact on welfare, performance, antimicrobial consumption and consumer protection. Genetics will be part of a future solution.

Comparison of the immune competence of Turopolje, German Landrace × Turopolje, and German Landrace × Pietrain pigs after PRRSV vaccination

The competences of the immune systems of the ancient pig breed Turopolje (T×T), German Landrace × Turopolje (L×T) and 'modern' pig breed German Landrace × Pietrain (L×P) were compared in this study. All pigs were immunized with a modified live vaccine against 'Porcine Reproductive and Respiratory Syndrome' (PRRS) virus (Ingelvac PRRS MLV(®)) to simulate an infection. Antibody production against PRRS MLV was evaluated in serum. Elimination of the viral infectious fragments during the experimental period was monitored in serum, leukocytes and tonsils by RT-qPCR. Furthermore relevant immune marker genes were quantified either on gene expression level using RT-qPCR [toll like receptor (TLR) 7, TLR8, TRAF6, CD163, SIGLEC1, CD4, CD8, CD14, CD19, tumor necrosis factor alpha (TNFα), interleukin (IL) 1, IL2, IL6, IL12], and on protein level using ELISA [interleukin (IL)-1, IL-2, IL-6, and IL-12]. The three breeds showed individual inactivation efficiencies as a reaction to the PRRS MLV vaccination. T×T eliminated the virus in serum within 16 days, followed by L×T (28 days) and L×P (36 days). The antibody titers against PRRS MLV of L×T and L×P were significantly higher compared to T×T (p<0.05). The gene expression data and protein analysis of interleukins revealed that T×T reacted with a type 1 immune response. In contrast, the two other breeds (L×T and L×P) showed a type 2 immune response, which resulted in the higher synthesis of B-cells and an increased concentration of specific anti-PRRS MLV antibodies.

Microbiome associations in pigs with the best and worst clinical outcomes following co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2)

On a world-wide basis, co-infections involving porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) are common and contribute to a range of polymicrobial disease syndromes in swine. Both viruses compromise host defenses, resulting in increased susceptibility to infections by primary and secondary pathogens that can affect growth performance as well as increased morbidity and mortality. An experimental population of 95 pigs was co-infected with PRRSV and PCV2. At 70days post-infection (dpi), 20 representative pigs were selected as having the best or worst clinical outcome based on average daily gain (ADG) and the presence of clinical disease. Worst clinical outcome pigs had prolonged and greater levels of viremia as measured by qPCR. Serum, lung and fecal samples collected at 70 dpi were analyzed using a comprehensive DNA microarray technology, the Lawrence Livermore Microbial Detection Array, to detect over 8000 microbes. Bacterial species, such as Bacillus cereus, were detected at a higher rate in the serum of worst performing pigs. At the level of the fecal microbiome, the overall microbial diversity was lower in the worst clinical outcome group. The results reinforce the importance of pathogen load in determining clinical outcome and suggest an important role of microbial diversity as a contributing factor in disease.

ORF5 of porcine reproductive and respiratory syndrome virus (PRRSV) is a target of diversifying selection as infection progresses from acute infection to virus rebound

Genetic variation in both structural and nonstructural genes is a key factor in the capacity of porcine reproductive and respiratory syndrome virus (PRRSV) to evade host defenses and maintain within animals, farms and metapopulations. However, the exact mechanisms by which genetic variation contribute to immune evasion remain unclear. In a study to understand the role of host genetics in disease resistance, a population of pigs were experimentally infected with a type 2 PRRSV isolate. Four pigs that showed virus rebound at 42days post-infection (dpi) were analyzed by 454 sequencing to characterize the rebound quasispecies. Deep sequencing of variable regions in nsp1, nsp2, ORF3 and ORF5 showed the largest number of nucleotide substitutions at day 28 compared to days 4 and 42 post-infection. Differences were also found in genetic variations when comparing tonsil versus serum. The results of dN/dS ratios showed that the same regions evolved under negative selection. However, eight amino acid sites were identified as possessing significant levels of positive selection, including A27V and N32S substitutions in the GP5 ectodomain region. These changes may alter GP5 peptide signal sequence processing and N-glycosylation, respectively. The results indicate that the greatest genetic diversity occurs during the transition between acute and rebound stages of infection, and the introduction of mutations that may result in a gain of fitness provides a potential mechanism for persistence.

Investigation on host susceptibility of Tibetan pig to infection of porcine reproductive and respiratory syndrome virus through viral challenge study

Previous reports showed that infection of porcine reproductive and respiratory syndrome virus (PRRSV) stimulated a variable host response and pig susceptibility to PRRSV was largely dependent on its genetic composition. In the present study, host susceptibility of Tibetan pig to PRRSV was compared with other two pig breeds, ZangMei black and Large White, by challenge of them with highly pathogenic PRRSV (HP-PRRSV). In the first challenge test, each eight piglets of the three breeds were inoculated with HP-PRRSV and clinical symptoms, viremia and animal mortality were examined up to 28 days post inoculation (DPI). In the secondary pathological study, each twelve piglets of the three breeds were challenged and three pigs of each breed were sacrificed on 4, 7, and 14 DPI for examination of gross damage and lung microscopic lesions. The results showed that no typical clinical signs such as cough, diarrhea and high fever were observed in challenged Tibetan pigs, which however all occurred in Large White accompanied with ∼40% mortality (3/8). In addition, a significant low and short viremia was detected specifically in Tibetan pigs. Based on histopathological analysis of lung sections, a mild to moderate interstitial pneumonia in Tibetan pigs and a much severe pneumonia in Large White were identified on 7-14 DPI. In summary, the study demonstrated that three genetically different pig breeds exhibited a differential host susceptibility to HP-PRRSV and Tibetan pig was much less susceptible to the virus in the three tested pig breeds.

Expression profiling of the GBP1 gene as a candidate gene for porcine reproductive and respiratory syndrome resistance

A genomic region in pig chromosome 4 has been previously associated with higher viraemia levels and lower weight gain following porcine reproduction and respiratory syndrome virus (PRRSV) infection. The region includes the marker WUR1000125, a G>A polymorphism next to a putative polyadenylation site in the 3'-untranslated region (3'-UTR) of the guanylate-binding protein 1, interferon-induced (GBP1) gene. The protein encoded by GBP1 is a negative regulator of T-cell responses. We show here that GBP1 expression is lower in liver and tonsils of pigs carrying the WUR1000125-G allele due to differential allele expression (allele A expression is 1.9-fold higher than for allele G). We also show that the GBP1 gene has two active polyadenylation signals 421 bp apart and that polyadenylation usage is dependent on the WUR1000125 genotype. The distal site is the most prevalently used in all samples, but the presence of the A allele favours the generation of shorter transcripts from the proximal site. This is confirmed by a differential allele expression study in AG genotype liver and tonsil samples. The interaction between WUR1000125 and other mutations identified in the 5'- and 3'-UTR regions of this gene needs to be studied. In conclusion, our study indicates that the WUR1000125 mutation is associated with changes in the expression of the negative T-cell regulator GBP1 gene. However, the chromosome 4 locus for PRRSV viraemia levels and weight gain contains a cluster of four other GBP genes that remain to be studied as candidate genes for this QTL.

Virological and serological characterization of vaccinated and non-vaccinated piglet subpopulations coming from vaccinated and non-vaccinated sows

The present study describes the virological and serological profiles of PCV2 vaccinated (V) and non-vaccinated (NV) piglet subpopulations coming from V and NV sows in a PCV2 subclinically infected farm. Four hundred seventy-six piglets born from V or NV sows were further subdivided in a total of four groups: NV sows-NV pigs (NV-NV), NV sows-V pigs (NV-V); V sows-NV pigs (V-NV) and V sows-V pigs (V-V). Seventy-five pigs were randomly selected at the beginning of the trial from each group and they were bled at 4, 8, 12, 16, 21 and 25 weeks of age. All animals included in the trial were weighed at 4 and 25 weeks of age and their average daily weight gain (ADWG) was calculated. Serum samples obtained at different time points were used to assess PCV2 infection (viremia) and the level of antibodies by means of immunoperoxidase monolayer assay (IPMA) against this pathogen. IPMA titers (classified in high, medium or low) and PCR results (positive or negative) were analyzed using a multiple correspondence and K-means cluster analysis. According to these tests, animals included in the study were classified into the following four clusters: (1) 93 piglets that were viremic mainly from 12 to 25 weeks of age and with PCV2 antibody titers increasing over time; (2) 75 piglets with late PCV2 infection and seroconversion (later than 16 weeks of age); (3) 26 piglets with high but decreasing PCV2 antibody titers and low percentages of PCV2 PCR positive serum samples; and (4) 105 piglets with medium and high IPMA titers throughout the trial and sporadic PCR positive samples. The defined subpopulations of piglets were observed in all experimental groups (NV-NV, NV-V, V-NV and V-V) although in variable percentages. Thus, animals from clusters 1 and 2 belonged mainly to the NV-NV and V-NV groups and animals from clusters 3 and 4 were distributed mainly into the NV-V and V-V groups. Finally, the ADWG of pigs belonging to clusters 3 and 4 was significantly higher (p=0.02) than that of pigs belonging to clusters 1 and 2. Within each cluster, no statistically significant differences were found in ADWG between treatment groups.

Difference in microRNA expression and editing profile of lung tissues from different pig breeds related to immune responses to HP-PRRSV

Porcine reproductive and respiratory syndrome (PRRS) is one of the most devastating diseases for the pig industry. Our goal was to identify microRNAs involved in the host immune response to PRRS. We generated microRNA expression profiles of lung tissues from Tongcheng or Landrace pigs infected with a highly pathogenic PRRS virus (PRRSV) at 3, 5, 7 dpi (day post infection) and control individuals from these two breeds. Our data showed that 278 known and 294 novel microRNAs were expressed in these combined microRNA transcriptomes. Compared with control individuals, almost half of the known microRNAs (116 in Tongcheng and 153 in Landrace) showed significantly differential expression (DEmiRNAs) at least once. The numbers of down-regulated DEmiRNAs were larger than the corresponding number of up-regulated DEmiRNAs in both breeds. Interestingly, miR-2320-5p, which was predicted to bind to conserved sequences of the PRRSV genome, was down-regulated significantly at 3 dpi after PRRSV infection in both breeds. In addition, PRRSV infection induced a significant increase of microRNA editing level in both breeds. Our results provide novel insight into the role of microRNA in response to PRRSV infection in vivo, which will aid the research for developing novel therapies against PRRSV.

Immune Control of PRRS: Lessons to be Learned and Possible Ways Forward

Porcine reproductive and respiratory syndrome (PRRS) is an elusive model of host/virus relationship in which disease is determined by virus pathogenicity, pig breed susceptibility and phenotype, microbial infectious pressure, and environmental conditions. The disease can be controlled by farm management programs, which can be supported by vaccination or conditioning of animals to circulating PRRS virus (PRRSV) strains. Yet, PRRS still represents a cause of heavy losses for the pig industry worldwide. Immunological control strategies are often compounded by poor and late development of adaptive immunity in both vaccinated and infected animals. Also, there is evidence that results of field trials can be worse than those of experimental studies in isolation facilities. Neutralizing antibody (NA) was shown to prevent PRRSV infection. Instead, the role of NA and adaptive immunity on the whole in virus clearance after established PRRSV infections is still contentious. Pigs eventually eliminate PRRSV infection, which may be correlated with an “educated,” innate immune response, which may also develop following vaccination. In addition to vaccination, an immunomodulation strategy for PRRS can be reasonably advocated in pig “problem” farms, where a substantial control of disease prevalence and disease-related losses is badly needed. This is not at odds with vaccination, which should be preferably restricted to PRRSV-free animals bound for PRRSV-infected farm units. Oral, low-dose, interferon-α treatments proved effective on farm for the control of respiratory and reproductive disease outbreaks, whereas the results were less clear in isolation facilities. Having in mind the crucial interaction between PRRSV and bacterial lipopolysaccharides for occurrence of respiratory disease, the strong control actions of low-dose type I interferons on the inflammatory response observed in vitro and in vivo probably underlie the rapid clinical responses observed in field trials.

Identification of a single nucleotide promoter polymorphism regulating the transcription of ubiquitin specific protease 18 gene related to the resistance to porcine reproductive and respiratory syndrome virus infection

Porcine reproductive and respiratory syndrome (PRRS), characterized by reproductive failure in sows and respiratory disease and mortality in piglets, is a major infectious disease that causes great economic loss throughout the world. Previous studies revealed that the overexpression of porcine ubiquitin specific protease 18 (USP18) gene inhibits PRRSV replication in vitro. The objective of this study is to compare the promoter activity of USP18 in Chinese indigenous Dapulian (DPL) pigs and Duroc×Landrace×Yorkshire (DLY) commercial pigs and screen single nucleotide polymorphism (SNP) affecting porcine USP18 transcription. We found that the promoter activity was significantly higher in DPL pigs than DLY commercial pigs (p<0.05), deletion of the promoter from -1790 to -1314bp decreased the transcriptional activity by roughly 60% (p<0.05) and a SNP G-1533A in this region increased the mRNA expression both prior to and post PRRSV infection in MARC-145 cells. Population genetics analysis showed that allele A was only detected in Chinese pig breeds which are generally resistant to PRRSV. These results suggest that the SNP G-1533A polymorphism in the promoter region of porcine USP18 gene is a potential DNA marker for the resistance to PRRSV.

Integrative model of the immune response to a pulmonary macrophage infection: what determines the infection duration?

The immune mechanisms which determine the infection duration induced by pathogens targeting pulmonary macrophages are poorly known. To explore the impact of such pathogens, it is indispensable to integrate the various immune mechanisms and to take into account the variability in pathogen virulence and host susceptibility. In this context, mathematical models complement experimentation and are powerful tools to represent and explore the complex mechanisms involved in the infection and immune dynamics. We developed an original mathematical model in which we detailed the interactions between the macrophages and the pathogen, the orientation of the adaptive response and the cytokine regulations. We applied our model to the Porcine Respiratory and Reproductive Syndrome virus (PRRSv), a major concern for the swine industry. We extracted value ranges for the model parameters from modelling and experimental studies on respiratory pathogens. We identified the most influential parameters through a sensitivity analysis. We defined a parameter set, the reference scenario, resulting in a realistic and representative immune response to PRRSv infection. We then defined scenarios corresponding to graduated levels of strain virulence and host susceptibility around the reference scenario. We observed that high levels of antiviral cytokines and a dominant cellular response were associated with either short, the usual assumption, or long infection durations, depending on the immune mechanisms involved. To identify these mechanisms, we need to combine the levels of antiviral cytokines, including , and . The latter is a good indicator of the infected macrophage level, both combined provide the adaptive response orientation. Available PRRSv vaccines lack efficiency. By integrating the main interactions between the complex immune mechanisms, this modelling framework could be used to help designing more efficient vaccination strategies.

Breed-specific transcriptome response of spleen from six to eight week old piglet after infection with Streptococcus suis type 2

Different pig breeds have shown differential susceptibility to the pathogen infection; however, molecular mechanisms of the infection susceptibility are not fully understood. Streptococcus suis type 2 (SS2) is an important zoonotic pathogen. To identify the genes responsible for infection susceptibility, pigs from two different breeds (Enshi black and Landrace) were inoculated with SS2 and their spleen transcriptome profiles were investigated in the present study. The differentially expressed genes (DEGs) were analyzed from infected versus control pigs in each breed, and then compared between both pig breeds. Enshi black pig showed more DEGs than Landrace (830 vs. 611) and most of these were due to down-regulated genes (543 vs. 387). However some DEGs were uniquely expressed in one breed, some were expressed in opposite direction in both breeds. A number of candidate genes and pathways are identified which might be involved in susceptibility to SS2, for example, MMP9 and Resistin were only significantly expressed in Landrace. NPG3 and PMAP23 were up-regulated in Landrace whereas down-regulated in Enshi black. LENG8 in control Landrace have inherently higher expression than control Enshi black. IGKV6 is down-regulated in Landrace but up-regulated in Enshi black. Overall, the transcriptome profiles are consistent with the clinical signs, i.e. the Enshi black is more susceptible to SS2 infection than Landrace. This is the first study to identify differential gene expression between indigenous and modern commercial pigs after in vivo SS2 infection using RNA-seq. The significant DEGs in splenic profiles between two pig breeds suggested considerable involvement of genetic background in susceptibility to the SS2 infection in pigs.

Genome-wide gene expression profiles in lung tissues of pig breeds differing in resistance to porcine reproductive and respiratory syndrome virus

Porcine reproductive and respiratory syndrome (PRRS) caused by PRRS virus (PRRSV) is an infectious disease characterized by severe reproductive deficiency in pregnant sows, typical respiratory symptoms in piglets, and high mortality rate of piglets. In this study, we employed an Affymetrix microarray chip to compare the gene expression profiles of lung tissue samples from Dapulian (DPL) pigs (a Chinese indigenous pig breed) and Duroc×Landrace×Yorkshire (DLY) pigs after infection with PRRSV. During infection with PRRSV, the DLY pigs exhibited a range of clinical features that typify the disease, whereas the DPL pigs showed only mild signs of the disease. Overall, the DPL group had a lower percentage of CD4⁺ cells and lower CD4⁺/CD8⁺ratios than the DLY group (p<0.05). For both IL-10 and TNF-α, the DLY pigs had significantly higher levels than the DPL pigs (p<0.01). The DLY pigs have lower serum IFN-γ levels than the DPL pigs (p<0.01). The serum IgG levels increased slightly from 0 dpi to 7 dpi, and peaked at 14 dpi (p<0.0001). Microarray data analysis revealed 16 differentially expressed (DE) genes in the lung tissue samples from the DLY and DPL pigs (q≤5%), of which LOC100516029 and LOC100523005 were up-regulated in the PRRSV-infected DPL pigs, while the other 14 genes were down-regulated in the PRRSV-infected DPL pigs compared with the PRRSV-infected DLY pigs. The mRNA expression levels of 10 out of the 16 DE genes were validated by real-time quantitative RT-PCR and their fold change was consistent with the result of microarray data analysis. We further analyzed the mRNA expression level of 8 differentially expressed genes between the DPL and DLY pigs for both uninfected and infected groups, and found that TF and USP18 genes were important in underlying porcine resistance or susceptibility to PRRSV.

Quantitative analysis of porcine reproductive and respiratory syndrome (PRRS) viremia profiles from experimental infection: a statistical modelling approach

Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically significant viral diseases facing the global swine industry. Viremia profiles of PRRS virus challenged pigs reflect the severity and progression of infection within the host and provide crucial information for subsequent control measures. In this study we analyse the largest longitudinal PRRS viremia dataset from an in-vivo experiment. The primary objective was to provide a suitable mathematical description of all viremia profiles with biologically meaningful parameters for quantitative analysis of profile characteristics. The Wood's function, a gamma-type function, and a biphasic extended Wood's function were fit to the individual profiles using Bayesian inference with a likelihood framework. Using maximum likelihood inference and numerous fit criteria, we established that the broad spectrum of viremia trends could be adequately represented by either uni- or biphasic Wood's functions. Three viremic categories emerged: cleared (uni-modal and below detection within 42 days post infection(dpi)), persistent (transient experimental persistence over 42 dpi) and rebound (biphasic within 42 dpi). The convenient biological interpretation of the model parameters estimates, allowed us not only to quantify inter-host variation, but also to establish common viremia curve characteristics and their predictability. Statistical analysis of the profile characteristics revealed that persistent profiles were distinguishable already within the first 21 dpi, whereas it is not possible to predict the onset of viremia rebound. Analysis of the neutralizing antibody(nAb) data indicated that there was a ubiquitous strong response to the homologous PRRSV challenge, but high variability in the range of cross-protection of the nAbs. Persistent pigs were found to have a significantly higher nAb cross-protectivity than pigs that either cleared viremia or experienced rebound within 42 dpi. Our study provides novel insights into the nature and degree of variation of hosts' responses to infection as well as new informative traits for subsequent genomic and modelling studies.

Fresh Pork and Porcine Reproductive and Respiratory Syndrome Virus: Factors Related to the Risk of Disease Transmission

Porcine reproductive and respiratory syndrome virus (PRRS) is a highly infectious virus. Experimentally, the disease can be induced in naïve pigs by the oral, intranasal and intramuscular routes. Depending on the virulence of the strain of the virus and the age of the pig, peak viremia can occur within 7 days of infection, and live virus can be isolated from blood or lymph nodes for several months post-infection. Young pigs tend to develop higher titres of viremia than older pigs infected by the same route and dose with the same strain of virus. Porcine reproductive and respiratory syndrome virus survives in pork harvested from infected pigs for extended periods at temperatures of -20 or -70°C. In experimentally infected pigs, survival of PRRS virus in muscle held at 4°C has been demonstrated for at least 7 days, and infectivity of the virus in these samples was confirmed by bioassay. The optimal pH range for the survival of PRRS virus is thought to be 6.0 to 7.5. The elevated pH of non-meat tissues (generally one pH unit higher) is likely to favour extended survival of PRRS virus in pig carcasses from which all superficial and deep lymph nodes have not been removed. It is likely that exsanguinated carcasses held at 4°C retain sufficient blood or lymph tissue to contain infective doses of PRRS virus. Porcine reproductive and respiratory syndrome virus is rapidly inactivated by heat, providing a predictable method to ensure that pork tissues are free of viable virus and feeding of cooked swill or garbage should not constitute a risk to pigs. While the probability of viable PRRS virus being present in a pig carcass may be low, the risk is not zero. The importation of raw pork into countries where PRRS is not endemic represents a hazard with potentially severe economic consequences.

Control of porcine reproductive and respiratory syndrome (PRRS) through genetic improvements in disease resistance and tolerance

Infections caused by porcine reproductive and respiratory syndrome virus (PRRSV) have a severe economic impact on pig production in North America, Europe, and Asia. The emergence and eventual predominance of PRRS in the 1990s are the likely result of changes in the pork industry initiated in the late 1970s, which allowed the virus to occupy a unique niche within a modern commercial production system. PRRSV infection is responsible for severe clinical disease, but can maintain a life-long subclinical infection, as well as participate in several polymicrobial syndromes. Current vaccines lessen clinical signs, but are of limited use for disease control and elimination. The relatively poor protective immunity following vaccination is a function of the virus's capacity to generate a large degree of genetic diversity, combined with several strategies to evade innate and adaptive immune responses. In 2007, the PRRS Host Genetics consortium (PHGC) was established to explore the role of host genetics as an avenue for PRRS control. The PHGC model for PRRS incorporates the experimental infection of large numbers of growing pigs and has created the opportunity to study experimental PRRSV infection at the population level. The results show that pigs can be placed into distinct phenotypic groups, including pigs that show resistance (i.e., low virus load) or pigs that exhibit “tolerance” to infection. Tolerance was illustrated by pigs that gain weight normally in the face of a relatively high virus load. Genome-wide association analysis has identified a region on chromosome 4 (SSC4) correlated with resistance; i.e., lower cumulative virus load within the first 42 days of infection. The genomic region is near a family of genes involved in innate immunity. The region is also associated with higher weight gain in challenged pigs, suggesting that pigs with the resistance alleles don't seem to simultaneously experience reduction in growth, i.e., that resistance and tolerance are not antagonistically related. These results create the opportunity to develop breeding programs that will produce pigs with increased resistance to PRRS and simultaneously high growth rate. The identification of genomic markers involved in actual tolerance will likely prove more difficult, primarily because tolerance is difficult to quantify and because tolerance mechanism are still poorly understood. Another avenue of study includes the identification of genomic markers related to improved response following vaccination.

Using SNP array data to test for host genetic and breed effects on Porcine Reproductive and Respiratory Syndrome Viremia

Background

The effect of breed on Porcine Reproductive and Respiratory Syndrome Viremia (PRRSV) was tested using data collected in 17 Italian commercial pig farms and 1096 genotypes obtained by the PorcineSNP60 BeadChip. A binomial logistic model was used to investigate the relationship between breed-clusters and PRRSV susceptibility. Breed-clusters were defined using the matrix of genomic kinship between all pairs of piglets.

Results

Only the contemporary group effect, defined as all piglets reared in the same herd, in the same year and whose samples were collected in the same season, was significant. Sex, age and breed-cluster showed no statistically significant effect on PRRS viremia, although the Landrace and Cross breed-clusters showed the lowest Odds-Ratio

Conclusions

The model failed to detect a significant breed-cluster effect, highlighting the impact of environment and management on PRRS viremia incidence. Incomplete exposure over the observed period may have masked possible breed differences.

Probing genetic control of swine responses to PRRSV infection: current progress of the PRRS host genetics consortium

Background

Understanding the role of host genetics in resistance to porcine reproductive and respiratory syndrome virus (PRRSV) infection, and the effects of PRRS on pig health and related growth, are goals of the PRRS Host Genetics Consortium (PHGC).

Methods

The project uses a nursery pig model to assess pig resistance/susceptibility to primary PRRSV infection. To date, 6 groups of 200 crossbred pigs from high health farms were donated by commercial sources. After acclimation, the pigs were infected with PRRSV in a biosecure facility and followed for 42 days post infection (dpi). Blood samples were collected at 0, 4, 7, 10, 14, 21, 28, 35 and 42 dpi for serum and whole blood RNA gene expression analyses; weekly weights were recorded for growth traits. All data have been entered into the PHGC relational database. Genomic DNAs from all PHGC1-6 pigs were prepared and genotyped with the Porcine SNP60 SNPchip.

Results

Results have affirmed that all challenged pigs become PRRSV infected with peak viremia being observed between 4-21 dpi. Multivariate statistical analyses of viral load and weight data have identified PHGC pigs in different virus/weight categories. Sera are now being compared for factors involved in recovery from infection, including speed of response and levels of immune cytokines. Genome-wide association studies (GWAS) are underway to identify genes and chromosomal locations that identify PRRS resistant/susceptible pigs and pigs able to maintain growth while infected with PRRSV.

Conclusions

Overall, the PHGC project will enable researchers to discover and verify important genotypes and phenotypes that predict resistance/susceptibility to PRRSV infection. The availability of PHGC samples provides a unique opportunity to continue to develop deeper phenotypes on every PRRSV infected pig.

Genetic control of host resistance to porcine reproductive and respiratory syndrome virus (PRRSV) infection

This manuscript focuses on the advances made using genomic approaches to identify biomarkers that define genes and pathways that are correlated with swine resistance to infection with porcine reproductive and respiratory syndrome virus (PRRSV), the most economically important swine viral pathogen worldwide. International efforts are underway to assess resistance and susceptibility to infectious pathogens using tools such as gene arrays, single nucleotide polymorphisms (SNPs) chips, genome-wide association studies (GWAS), proteomics, and advanced bioinformatics. These studies should identify new candidate genes and biological pathways associated with host PRRS resistance and alternate viral disease processes and mechanisms; they may unveil biomarkers that account for genetic control of PRRS or, alternately, that reveal new targets for therapeutics or vaccines. Previous genomic approaches have expanded our understanding of quantitative trait loci (QTL) controlling traits of economic importance in pig production, e.g., feed efficiency, meat production, leanness; only recently have these included health traits and disease resistance. Genomic studies should have substantial impact for the pig industry since it is now possible to include the use of biomarkers for basic health traits alongside broader set of markers utilized for selection of pigs for improved performance and reproductive traits, as well as pork quality. Additionally these studies may reveal alternate PRRS control mechanisms that can be exploited for novel drugs, biotherapeutics and vaccine designs.