Comparison of host genetic factors influencing pig response to infection with two North American isolates of porcine reproductive and respiratory syndrome virus

The WUR0000125 PRRS resilience SNP had no apparent effect on pigs' infectivity and susceptibility in a novel transmission trial

BACKGROUND

Porcine reproductive and respiratory syndrome (PRRS) remains one of the most important infectious diseases for the pig industry. A novel small-scale transmission experiment was designed to assess whether the WUR0000125 (WUR for Wageningen University and Research) PRRS resilience single nucleotide polymorphism (SNP) confers lower susceptibility and infectivity to pigs under natural porcine reproductive and respiratory syndrome virus (PRRSV-2) transmission.

METHODS

Commercial full- and half-sib piglets (n = 164) were assigned as either Inoculation, Shedder, or Contact pigs. Pigs were grouped according to their relatedness structure and WUR genotype, with R- and R+ referring to pigs with zero and one copy of the dominant WUR resilience allele, respectively. Barcoding of the PRRSV-2 strain (SD09-200) was applied to track pig genotype-specific transmission. Blood and nasal swab samples were collected and concentrations of PRRSV-2 were determined by quantitative (q)-PCR and cell culture and expressed in units of median tissue culture infectious dose (TCID₅₀). The Log₁₀TCID₅₀ at each sampling event, derived infection status, and area under the curve (AUC) were response variables in linear and generalized linear mixed models to infer WUR genotype differences in Contact pig susceptibility and Shedder pig infectivity.

RESULTS

All Shedder and Contact pigs, except one, became infected through natural transmission. There was no significant (p > 0.05) effect of Contact pig genotype on any virus measures that would indicate WUR genotype differences in susceptibility. Contact pigs tended to have higher serum AUC (p = 0.017) and log₁₀TCID₅₀ (p = 0.034) when infected by an R+ shedder, potentially due to more infectious R+ shedders at the early stages of the transmission trial. However, no significant Shedder genotype effect was found in serum (p = 0.274) or nasal secretion (p = 0.951) that would indicate genotype differences in infectivity.

CONCLUSIONS

The novel design demonstrated that it is possible to estimate genotype effects on Shedder pig infectivity and Contact pig susceptibility that are not confounded by family effects. The study, however, provided no supportive evidence that genetic selection on WUR genotype would affect PRRSV-2 transmission. The results of this study need to be independently validated in a larger trial using different PRRSV strains before dismissing the effects of the WUR marker or the previously detected GBP5 gene on PRRSV transmission.

Role of genetic factors in different swine breeds exhibiting varying levels of resistance/susceptibility to PRRSV

Porcine reproductive and respiratory syndrome (PRRS), caused by the PRRS virus (PRRSV), is an economically significant contagious disease. Traditional approaches based on vaccines or medicines were challenging to control PRRSV due to the diversity of viruses. Different breeds of pigs infected with PRRSV have been reported to have different immune responses. However, due to the complexity of interaction mechanism between host and PRRSV, the genetic mechanism leading to PRRSV susceptibility/resistance in various pig breeds is still unclear. Herein, the role of host genetic components in PRRSV susceptibility is systematically described, and the molecular mechanisms by which host genetic factors such as SNPs, cytokines, receptor molecules, intestinal flora, and non-coding RNAs regulate PRRSV susceptibility/resistance. Therefore, improving the resistance to disease of individual animals through disease-resistance breeding technology is of profound significance for uplifting the sustainable and healthy development of the pig industry.

Genome wide association study of thyroid hormone levels following challenge with porcine reproductive and respiratory syndrome virus

Introduction: Porcine reproductive and respiratory syndrome virus (PRRSV) causes respiratory disease in piglets and reproductive disease in sows. Piglet and fetal serum thyroid hormone (i.e., T3 and T4) levels decrease rapidly in response to Porcine reproductive and respiratory syndrome virus infection. However, the genetic control of T3 and T4 levels during infection is not completely understood. Our objective was to estimate genetic parameters and identify quantitative trait loci (QTL) for absolute T3 and/or T4 levels of piglets and fetuses challenged with Porcine reproductive and respiratory syndrome virus. Methods: Sera from 5-week-old pigs (N = 1792) at 11 days post inoculation (DPI) with Porcine reproductive and respiratory syndrome virus were assayed for T3 levels (piglet_T3). Sera from fetuses (N = 1,267) at 12 or 21 days post maternal inoculation (DPMI) with Porcine reproductive and respiratory syndrome virus of sows (N = 145) in late gestation were assayed for T3 (fetal_T3) and T4 (fetal_T4) levels. Animals were genotyped using 60 K Illumina or 650 K Affymetrix single nucleotide polymorphism (SNP) panels. Heritabilities, phenotypic correlations, and genetic correlations were estimated using ASREML; genome wide association studies were performed for each trait separately using Julia for Whole-genome Analysis Software (JWAS). Results: All three traits were low to moderately heritable (10%-16%). Phenotypic and genetic correlations of piglet_T3 levels with weight gain (0-42 DPI) were 0.26 ± 0.03 and 0.67 ± 0.14, respectively. Nine significant quantitative trait loci were identified for piglet_T3, on Sus scrofa chromosomes (SSC) 3, 4, 5, 6, 7, 14, 15, and 17, and collectively explaining 30% of the genetic variation (GV), with the largest quantitative trait loci identified on SSC5, explaining 15% of the genetic variation. Three significant quantitative trait loci were identified for fetal_T3 on SSC1 and SSC4, which collectively explained 10% of the genetic variation. Five significant quantitative trait loci were identified for fetal_T4 on SSC1, 6, 10, 13, and 15, which collectively explained 14% of the genetic variation. Several putative immune-related candidate genes were identified, including CD247, IRF8, and MAPK8. Discussion: Thyroid hormone levels following Porcine reproductive and respiratory syndrome virus infection were heritable and had positive genetic correlations with growth rate. Multiple quantitative trait loci with moderate effects were identified for T3 and T4 levels during challenge with Porcine reproductive and respiratory syndrome virus and candidate genes were identified, including several immune-related genes. These results advance our understanding of growth effects of both piglet and fetal response to Porcine reproductive and respiratory syndrome virus infection, revealing factors associated with genomic control of host resilience.

Integrated time-series transcriptomic and metabolomic analyses reveal different inflammatory and adaptive immune responses contributing to host resistance to PRRSV

Porcine reproductive and respiratory syndrome virus (PRRSV) is a highly contagious disease that affects the global pig industry. To understand mechanisms of susceptibility/resistance to PRRSV, this study profiled the time-serial white blood cells transcriptomic and serum metabolomic responses to PRRSV in piglets from a crossbred population of PRRSV-resistant Tongcheng pigs and PRRSV-susceptible Large White pigs. Gene set enrichment analysis (GSEA) illustrated that PRRSV infection up-regulated the expression levels of marker genes of dendritic cells, monocytes and neutrophils and inflammatory response, but down-regulated T cells, B cells and NK cells markers. CIBERSORT analysis confirmed the higher T cells proportion in resistant pigs during PRRSV infection. Resistant pigs showed a significantly higher level of T cell activation and lower expression levels of monocyte surface signatures post infection than susceptible pigs, corresponding to more severe suppression of T cell immunity and inflammatory response in susceptible pigs. Differentially expressed genes between resistant/susceptible pigs during the course of infection were significantly enriched in oxidative stress, innate immunity and humoral immunity, cell cycle, biotic stimulated cellular response, wounding response and behavior related pathways. Fourteen of these genes were distributed in 5 different QTL regions associated with PRRSV-related traits. Chemokine CXCL10 levels post PRRSV infection were differentially expressed between resistant pigs and susceptible pigs and can be a promising marker for susceptibility/resistance to PRRSV. Furthermore, the metabolomics dataset indicated differences in amino acid pathways and lipid metabolism between pre-infection/post-infection and resistant/susceptible pigs. The majority of metabolites levels were also down-regulated after PRRSV infection and were significantly positively correlated to the expression levels of marker genes in adaptive immune response. The integration of transcriptome and metabolome revealed concerted molecular events triggered by the infection, notably involving inflammatory response, adaptive immunity and G protein-coupled receptor downstream signaling. This study has increased our knowledge of the immune response differences induced by PRRSV infection and susceptibility differences at the transcriptomic and metabolomic levels, providing the basis for the PRRSV resistance mechanism and effective PRRS control.

Thyroid hormone suppression in feeder pigs following polymicrobial or porcine reproductive and respiratory syndrome virus-2 challenge

Thyroid hormones are powerful regulators of growth, development, and basal metabolic rate and can be dysregulated under conditions of severe stress or illness. To understand the role of these hormones in porcine disease response, serum samples were obtained from three batches of nursery-aged pigs (n = 208) exposed to a natural polymicrobial disease challenge with an array of bacterial and viral pathogens. Levels of total thyroxin (T4) and triiodothyronine (T3) assessed in sera by radioimmunoassay, decreased significantly by 14 days post-exposure (DPE). Levels of T3 partially rebounded by 48 DPE, while T4 levels remain depressed. Post-exposure T3 and T4 levels were positively correlated with acute and long-term average daily gain (ADG). Cross-sectional sampling of animals maintained at the high health source farms, showed no equivalent change in either hormone when managed under standard industrial conditions. To further elucidate the effect of porcine reproductive and respiratory syndrome virus (PRRSV)-infection on thyroid hormone levels, archived sera over 42 days post inoculation (DPI) from nursery pigs (N = 190) challenged with one of two PRRSV2 strains by the PRRS Host Genetics Consortium were similarly assessed, with animals selected in a two-by-two design, to investigate biological extremes in ADG and viral load (VL). All animals showed a similar decrease in both thyroid hormones reaching a minimum at 7 DPI and returning to near pre-challenge levels by 42 DPI. Post-challenge T3 and T4 levels were significantly greater in high ADG groups, with no significant association with VL or strain. The results of this study demonstrate porcine susceptibility to thyroid disruption in response to disease challenge and demonstrate a relationship between this response and growth performance.

Associations of natural variation in the CD163 and other candidate genes on host response of nursery pigs to porcine reproductive and respiratory syndrome virus infection

Pigs with complete resistance to porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) have been produced by genetically knocking out the CD163 gene that encodes a receptor of the PRRSV for entry into macrophages. The objectives of this study were to evaluate associations of naturally occurring single nucleotide polymorphisms (SNPs) in the CD163 gene and in three other candidate genes (CD169, RGS16, and TRAF1) with host response to PRRSV-only infection and to PRRS vaccination and PRRSV/porcine circovirus 2b (PCV2b) coinfection. SNPs in the CD163 gene were not included on SNP genotyping panels that were used for previous genome-wide association analyses of these data. An additional objective was to identify the potential genetic interaction of variants at these four candidate genes with a mutation in the GBP5 gene that was previously identified to be associated with host response to PRRSV infection. Finally, the association of SNPs with expression level of the nearby gene was tested. Several SNPs in the CD163, CD169, and RGS16 genes were significantly associated with host response under PRRSV-only and/or PRRSV/PCV2b coinfection. The effects of all SNPs that were significant in the PRRSV-only infection trials depend on genetic background. The effects of some SNPs in the CD163, CD169, and RGS16 genes depend on genotype at the putative causative mutation in the GBP5 gene, which indicates a potential biological interaction of these genes with GBP5. In addition, genome-wide association results for the PRRSV-only infection trials revealed that SNPs located in the CDK5RAP2 or MEGF9 genes, near the TRAF1 gene, had suggestive effects on PRRS viral load, which indicates that these SNPs might contribute to PRRSV neuropathogenesis. In conclusion, natural genetic variants in the CD163, CD169, and RGS16 genes are associated with resistance to PRRSV and/or PCV2b infection and appear to interact with the resistance quantitative trait locus in the GBP5 gene. The identified SNPs can be used to select for increased natural resistance to PRRSV and/or PRRSV-PCV2b coinfection.

Genetic and phenotypic parameters for Aleutian disease tests and their correlations with pelt quality, reproductive performance, packed-cell volume, and harvest length in mink

Aleutian disease (AD), caused by the Aleutian mink disease virus (AMDV), is a major health concern that results in global economic losses to the mink industry. The unsatisfactory outcome of the culling strategy, immunoprophylaxis, and medical treatment in controlling AD have urged mink farmers to select AD resilient mink based on several detection tests, including enzyme-linked immunosorbent assay (ELISA), counterimmunoelectrophoresis (CIEP), and iodine agglutination test (IAT). However, the genetic analysis of these AD tests and their correlations with pelt quality, reproductive performance, packed-cell volume (PCV), and harvest length (HL) have not been investigated. In this study, data on 5,824 mink were used to estimate the genetic and phenotypic parameters of four AD tests, including two systems of ELISA, CIEP, and IAT, and their genetic and phenotypic correlations with two pelt quality, five female reproductive performance, PCV, and HL traits. Significances (P < 0.05) of fixed effects (sex, year, dam age, and color type), covariates (age at harvest and blood sampling), and random effects (additive genetic, permanent environmental, and maternal effects) were determined under univariate models using ASReml 4.1 software. The genetic and phenotypic parameters for all traits were estimated under bivariate models using ASReml 4.1 software. Estimated heritabilities (±SE) were 0.39 ± 0.06, 0.61 ± 0.07, 0.11 ± 0.07, and 0.26 ± 0.05 for AMDV antigen-based ELISA (ELISA-G), AMDV capsid protein-based ELISA, CIEP, and IAT, respectively. The ELISA-G also showed a moderate repeatability (0.58 ± 0.04) and had significant negative genetic correlations (±SE) with reproductive performance traits (from -0.41 ± 0.16 to -0.49 ± 0.12), PCV (-0.53 ± 0.09), and HL (-0.45 ± 0.16). These results indicated that ELISA-G had the potential to be applied as an indicator trait for genetic selection of AD resilient mink in AD endemic ranches and therefore help mink farmers to reduce the adverse effects caused by AD.

Using PRRSV-Resilient Sows Improve Performance in Endemic Infected Farms with Recurrent Outbreaks

Simple Summary

Porcine reproductive and respiratory syndrome (PRRS) is a viral disease responsible for huge economic losses to the pig industry. The selection of PRRSV resilient sows has been proposed as a strategy to control this disease. A simulation model was developed to test the differences in reproductive performance and economic outcome of resilient or susceptible sows under farm PRRSV endemic conditions with or without recurrent PRRSV outbreaks. The data from phenotyped sows came from a PRRSV-positive farm with 1500 sows that suffered a PRRSV outbreak that lasted 24 weeks within three years. The reproductive parameters were generally better for resilient than for susceptible sows in PRRSV-positive farms suffering recurrent PRRSV outbreaks. Consequently, the piglet production cost was lower for resilient than for susceptible sows in any condition but showed only significant differences in PRRSV endemic farms suffering recurrent outbreaks. Finally, the annual gross margin by sow is significantly better for resilient than for susceptible sows under endemic conditions with or without recurrent outbreaks. Thus, the selection of PRRSV resilient sows is always a profitable approach for producers supporting the control of this disease.

Abstract

The selection of porcine reproductive and respiratory syndrome (PRRS) resilient sows has been proposed as a strategy to control this disease. A discrete event-based simulation model was developed to mimic the outcome of farms with resilient or susceptible sows suffering recurrent PRRSV outbreaks. Records of both phenotypes were registered in a PRRSV-positive farm of 1500 sows during three years. The information was split in the whole period of observation to include a PRRSV outbreak that lasted 24 weeks (endemic/epidemic or En/Ep) or only the endemic phase (En). Twenty simulations were modeled for each farm: Resilient/En, Resilient/En_Ep, Susceptible/En, and Susceptible/En_Ep during twelve years and analyzed for the productive performance and economic outcome, using reference values. The reproductive parameters were generally better for resilient than for susceptible sows in the PRRSV En/Ep scenario, and the contrary was observed in the endemic case. The piglet production cost was always lower for resilient than for susceptible sows but showed only significant differences in the PRRSV En/Ep scenario. Finally, the annual gross margin by sow is significantly better for resilient than for susceptible sows for the PRRSV endemic (12%) and endemic/epidemic scenarios (17%). Thus, the selection of PRRSV resilient sows is a profitable approach for producers to improve disease control.

Gene expression in tonsils in swine following infection with porcine reproductive and respiratory syndrome virus

Background

Porcine reproductive and respiratory syndrome (PRRS) is a threat to pig production worldwide. Our objective was to understand mechanisms of persistence of PRRS virus (PRRSV) in tonsil. Transcriptome data from tonsil samples collected at 42 days post infection (dpi) were generated by RNA-seq and NanoString on 51 pigs that were selected to contrast the two PRRSV isolates used, NVSL and KS06, high and low tonsil viral level at 42 dpi, and the favorable and unfavorable genotypes at a genetic marker (WUR) for the putative PRRSV resistance gene GBP5.

Results

The number of differentially expressed genes (DEGs) differed markedly between models with and without accounting for cell-type enrichments (CE) in the samples that were predicted from the RNA-seq data. This indicates that differences in cell composition in tissues that consist of multiple cell types, such as tonsil, can have a large impact on observed differences in gene expression. Based on both the NanoString and the RNA-seq data, KS06-infected pigs showed greater activation, or less inhibition, of immune response in tonsils at 42 dpi than NVSL-infected pigs, with and without accounting for CE. This suggests that the NVSL virus may be better than the KS06 virus at evading host immune response and persists in tonsils by weakening, or preventing, host immune responses. Pigs with high viral levels showed larger CE of immune cells than low viral level pigs, potentially to trigger stronger immune responses. Presence of high tonsil virus was associated with a stronger immune response, especially innate immune response through interferon signaling, but these differences were not significant when accounting for CE. Genotype at WUR was associated with different effects on immune response in tonsils of pigs during the persistence stage, depending on viral isolate and tonsil viral level.

Conclusions

Results of this study provide insights into the effects of PRRSV isolate, tonsil viral level, and WUR genotype on host immune response and into potential mechanisms of PRRSV persistence in tonsils that could be targeted to improve strategies to reduce viral rebreaks. Finally, to understand transcriptome responses in tissues that consist of multiple cell types, it is important to consider differences in cell composition.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-021-02785-1.

Selection for Favorable Health Traits: A Potential Approach to Cope with Diseases in Farm Animals

Disease is a global problem for animal farming industries causing tremendous economic losses (>USD 220 billion over the last decade) and serious animal welfare issues. The limitations and deficiencies of current non-selection disease control methods (e.g., vaccination, treatment, eradication strategy, genome editing, and probiotics) make it difficult to effectively, economically, and permanently eliminate the adverse influences of disease in the farm animals. These limitations and deficiencies drive animal breeders to be more concerned and committed to dealing with health problems in farm animals by selecting animals with favorable health traits. Both genetic selection and genomic selection contribute to improving the health of farm animals by selecting certain health traits (e.g., disease tolerance, disease resistance, and immune response), although both of them face some challenges. The objective of this review was to comprehensively review the potential of selecting health traits in coping with issues caused by diseases in farm animals. Within this review, we highlighted that selecting health traits can be applied as a method of disease control to help animal agriculture industries to cope with the adverse influences caused by diseases in farm animals. Certainly, the genetic/genomic selection solution cannot solve all the disease problems in farm animals. Therefore, management, vaccination, culling, medical treatment, and other measures must accompany selection solution to reduce the adverse impact of farm animal diseases on profitability and animal welfare.

Quantifying Individual Response to PRRSV Using Dynamic Indicators of Resilience Based on Activity

Pigs are faced with various perturbations throughout their lives, some of which are induced by management practices, others by natural causes. Resilience is described as the ability to recover from or cope with a perturbation. Using these data, activity patterns of an individual, as well as deviations from these patterns, can potentially be used to quantify resilience. Dynamic indicators of resilience (DIORs) may measure resilience on a different dimension by calculating variation, autocorrelation and skewness of activity from the absolute activity data. The aim of this study was to investigate the potential of using DIORs of activity, such as average, root mean square error (RMSE), autocorrelation or skewness as indicators of resilience to infection with the Porcine Reproductive and Respiratory Syndrome Virus (PRRSV). For this study, individual activity was obtained from 232 pigs equipped with ear tag accelerometers and inoculated with PRRSV between seven and 9 weeks of age. Clinical scores were assigned to each individual at 13 days post-challenge and used to distinguish between a resilient and non-resilient group. Mortality post-challenge was also recorded. Average, RMSE, autocorrelation and skewness of activity were calculated for the pre- and post-challenge phases, as well as the change in activity level pre- vs. post-challenge (i.e., delta). DIORs pre-challenge were expected to predict resilience to PRRSV in the absence of PRRSV infection, whereas DIORs post-challenge and delta were expected to reflect the effect of the PRRSV challenge. None of the pre-challenge DIORs predicted morbidity or mortality post-challenge. However, a higher RMSE in the 3 days post-challenge and larger change in level and RMSE of activity from pre- to post-challenge tended to increase the probability of clinical signs at day 13 post-infection (poor resilience). A higher skewness post-challenge (tendency) and a larger change in skewness from pre- to post-challenge increased the probability of mortality. A decrease in skewness post-challenge lowered the risk of mortality. The post-challenge DIOR autocorrelation was neither linked to morbidity nor to mortality. In conclusion, results from this study showed that post-challenge DIORs of activity can be used to quantify resilience to PRRSV challenge.

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.

Genetic relationships of antibody response, viremia level, and weight gain in pigs experimentally infected with porcine reproductive and respiratory syndrome virus1

Genetic and antigenic variability between Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) isolates has encumbered vaccine development. Here, the genetic basis of PRRSV antibody response was assessed using data from experimental infection trials of commercial crossbred weaner pigs across with one of two distinct PRRSV isolates, NVSL-97-7895 (~750 pigs) and KS-2006-72109 (~450 pigs). Objectives were to estimate the genetic parameters of antibody response, measured as the sample to positive ratio (S:P) of PRRSV N-protein specific IgG in serum at 42 d post infection (dpi); assess the relationship of S:P at 42 dpi with serum viremia and growth under infection; and identify genomic regions associated with S:P at 42 dpi. Estimates of heritability of S:P at 42 dpi for NVSL and KS06 were 0.31 ± 0.09 and 0.40 ± 0.10 and appeared to be under similar genetic control (genetic correlation 0.73 ± 0.39). Estimates of genetic correlations of S:P were generally weak with viral load (NVSL: -0.20 ± 0.18; KS06: -0.69 ± 0.20), measured as area under the curve of log10 serum viremia from 0 to 21 dpi, and with weight gain (WG) from 0 to 42 dpi (NVSL: -0.38 ± 0.19; KS06: -0.08 ± 0.25). However, genetic correlations of S:P at 42 dpi with daily serum viremia and with 3-d WG revealed dynamic relationships, with S:P at 42 dpi having the strongest negative genetic correlations with daily viremia when IgG production starts (10-20 dpi), and negative genetic correlations with WG early after infection but positive later on. This suggests that animals that placed more emphasis on immune response early in infection reaped benefits of that later in infection by more effectively clearing the virus. The WUR10000125 SNP on SSC4, previously associated with response to PRRSV, did not have a significant effect on S:P at 42 dpi (P > 0.05) but genotype-specific genetic correlations of S:P with daily viremia and 3-d WG suggested that the lower WG of pigs with the unfavorable AA WUR10000125 genotype may be due to their utilization of a more energetically costly host response compared to pigs with the favorable genotype. Genome-wide association studies identified three SNPs in the Major Histocompatibility Complex associated with S:P that explained ~10 (NVSL) and 45% (KS06) of the genetic variance but were not associated with viremia or WG. In conclusion, antibody response to PRRSV infection is a possible biomarker for improved host response to PRRSV infection.

Effect of polymorphisms in porcine guanylate-binding proteins on host resistance to PRRSV infection in experimentally challenged pigs

Guanylate-binding proteins (GBP1 and GBP5) are known to be important for host resistance against porcine reproductive and respiratory syndrome virus (PRRSV) infection. In this study, the effects of polymorphisms in GBP1 (GBP1E2 and WUR) and GBP5 on host immune responses against PRRSV were investigated to elucidate the mechanisms governing increased resistance to this disease. Seventy-one pigs [pre-genotyped based on three SNP markers (GBP1E2, WUR, and GBP5)] were assigned to homozygous (n = 36) and heterozygous (n = 35) groups and challenged with the JA142 PRRSV strain. Another group of nineteen pigs was kept separately as a negative control group. Serum and peripheral blood mononuclear cells (PBMCs) were collected at 0, 3, 7, 14, 21 and 28 days post-challenge (dpc). Viremia and weight gain were measured in all pigs at each time point, and a flow cytometry analysis of PBMCs was performed to evaluate T cell activation. In addition, 15 pigs (5 pigs per homozygous, heterozygous and negative groups) were sacrificed at 3, 14 and 28 dpc, and the local T cell responses were evaluated in the lungs, bronchoalveolar lavage cells (BALc), lymph nodes and tonsils. The heterozygous pigs showed lower viral loads in the serum and lungs and higher weight gains than the homozygous pigs based on the area under the curve calculation. Consistently, compared with the homozygous pigs, the heterozygous pigs exhibited significantly higher levels of IFN-α in the serum, proliferation of various T cells (γδT, Th1, and Th17) in PBMCs and tissues, and cytotoxic T cells in the lungs and BALc. These results indicate that the higher resistance in the pigs heterozygous for the GBP1E2, WUR and GBP5 markers could be mediated by increased antiviral cytokine (IFN-α) production and T cell activation.

Genetic Markers Associated with Field PRRSV-Induced Abortion Rates

In gilts and sows, the more severe clinical manifestation of porcine reproductive and respiratory syndrome virus (PRRSV) occurs in late gestation and can result in up to a 40% abortion incidence. Despite the known genetic component in resilience to PRRSV, there is scarce information regarding the abortive outcome of this disease. We tested the relationship between eight molecular markers (six from published studies and two identified in the present study in the HDAC6 gene) and the probability of abortion during a PRRSV outbreak, using data from two commercial Landrace x Large White sow farms with an incidence of abortion of 35% and 17%. From the markers tested, USP18_-1533G>A did not segregate in these populations, and CD163_c.3534C>T and HDAC6_g.2360C>T did not affect the abortion rate. In contrast, the minor allele of two markers in SSC4 (WUR1000125 in GBP1 and rs340943904 in GBP5), which lower viremia in growing pigs, and the major alleles of CD163_rs1107556229 and HDAC6_rs325981825 were associated with a lower probability of abortion during PRRSV outbreaks. The more striking result was for the MX1 gene, where the odds ratio of aborting versus not aborting was nine times lower in the sows homozygous for a 275-bp insertion than in the other genotypes. Interactions between markers were not relevant. All together, we bring here the first evidence that mutations in the host genome can predispose or protect from complete reproductive failure in sows infected with PRRSV.

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.

Identification of factors associated with virus level in tonsils of pigs experimentally infected with porcine reproductive and respiratory syndrome virus

Porcine reproductive and respiratory syndrome (PRRS) is one of the most important global swine diseases from both an economic and animal welfare standpoint. PRRS has plagued the US swine industry for over 25 yr, and containment of PRRS virus (PRRSV) has been unsuccessful to date. The primary phase of PRRS, tracked by serum viremia, typically clears between 21 and 42 d postinfection (dpi) but tonsils are a main site of PRRSV persistence and PRRSV can be detected in tonsils in excess of 150 dpi. Measuring tonsil virus (TV) levels at late stages of infection (6 to 7 wk postinfection) can be used to assess tonsil persistence, as levels of virus in tonsil at this time likely influence how long the virus will remain in the tissue. TV levels were measured on pigs experimentally infected with either the NVSL-97-7895 (NVSL; n = 524) or KS-2006-72109 (KS06; n = 328) PRRSV type 2 isolates across five trials. The objectives of this study were to (i) estimate the heritability of TV levels at 35 or 42 dpi; (ii) identify factors the affect TV level, including serum viremia; (iii) identify genomic regions associated with TV level; and (iv) compare results for the two PRRSV isolates. TV level was lowly heritable for both isolates (NVSL: 0.05 ± 0.06; KS06: 0.11 ± 0.10). Level of TV was phenotypically associated with traits related to viral clearance from serum: pigs with low TV levels had an earlier and faster rate of maximal serum viral clearance, lower total serum viral load, and lower viremia level at 35 or 42 dpi. Although no genomic regions with major effects on TV level were identified, several showed some association (>0.1% of total genetic variance in the NVSL-infected dataset, the KS06-infected dataset, and the combined dataset). These regions contained the genes CCL1, CCL2, CCL8, HS3ST3B1, GALNT10, TCF7, C1QA/B/C, HPSE, G0S2, and CD34, which are involved in viral infiltration or replication, immune cell migration, and viral clearance from tissue. Results were similar between the two PRRSV isolates. In conclusion, selection for viral clearance traits in serum may reduce PRRSV persistence in the tonsil across PRRSV isolates. However, genetic correlations need to be estimated to determine whether this will be successful.

Establishment of Systems to Enable Isolation of Porcine Monoclonal Antibodies Broadly Neutralizing the Porcine Reproductive and Respiratory Syndrome Virus

The rapid evolution of porcine reproductive and respiratory syndrome viruses (PRRSV) poses a major challenge to effective disease control since available vaccines show variable efficacy against divergent strains. Knowledge of the antigenic targets of virus-neutralizing antibodies that confer protection against heterologous PRRSV strains would be a catalyst for the development of next-generation vaccines. Key to discovering these epitopes is the isolation of neutralizing monoclonal antibodies (mAbs) from immune pigs. To address this need, we sought to establish systems to enable the isolation of PRRSV neutralizing porcine mAbs. We experimentally produced a cohort of immune pigs by sequential challenge infection with four heterologous PRRSV strains spanning PRRSV-1 subtypes and PRRSV species. Whilst priming with PRRSV-1 subtype 1 did not confer full protection against a subsequent infection with a PRRSV-1 subtype 3 strain, animals were protected against a subsequent PRRSV-2 infection. The infection protocol resulted in high serum neutralizing antibody titers against PRRSV-1 Olot/91 and significant neutralization of heterologous PRRSV-1/-2 strains. Enriched memory B cells isolated at the termination of the study were genetically programmed by transduction with a retroviral vector expressing the Bcl-6 transcription factor and the anti-apoptotic Bcl-xL protein, a technology we demonstrated efficiently converts porcine memory B cells into proliferating antibody-secreting cells. Pools of transduced memory B cells were cultured and supernatants containing PRRSV-specific antibodies identified by flow cytometric staining of infected MARC-145 cells and in vitro neutralization of PRRSV-1. Collectively, these data suggest that this experimental system may be further exploited to produce a panel of PRRSV-specific mAbs, which will contribute both to our understanding of the antibody response to PRRSV and allow epitopes to be resolved that may ultimately guide the design of immunogens to induce cross-protective immunity.

The effect of a porcine reproductive and respiratory syndrome outbreak on genetic parameters and reaction norms for reproductive performance in pigs1

The objective of this study was to estimate genetic parameters of antibody response and reproductive traits after exposure to porcine reproductive and respiratory syndrome virus. Blood samples were taken approximately 60 d after the outbreak. Antibody levels were quantified as the sample-to-positive ratio (S/P ratio) using a fluorescent microsphere assay. Reproductive traits included total number born (TNB), number born alive (NBA), number stillborn (NSB), number mummified (NBM), and number born dead (NBD). Mortality traits were log transformed for genetic analyses. Data were split into prior, during, and after the disease outbreak phases using visual appraisal of the estimates of farm-year-week effects for each reproductive trait. For NBA, data from all phases were combined into a reaction norm analysis with regression on estimates of farm-year-week effects for NBA. Heritability for S/P ratio was estimated at 0.17 ± 0.05. Heritability estimates for reproduction traits were all low and were lower during the outbreak for NBA but greater for mortality traits. TNB was not greatly affected during the outbreak, as many sows that farrowed during the outbreak were mated prior to the outbreak. Heritability for TNB decreased from 0.13 (prior) to 0.08 (after). Genetic correlation estimates between prior to and during the outbreak were high for TNB (0.86 ± 0.23) and NBA (0.98 ± 0.38) but lower for mortality traits: 0.65 ± 0.43, -0.42 ± 0.55, and 0.29 ± 1.39 for LNSB, LNBM, and LNBD, respectively. TNB prior to and after the outbreak had a lower genetic correlation (0.32 ± 0.33). In general, genetic correlation estimates of S/P ratio with reproductive performance during the outbreak were below 0.20 in absolute value, except for LNSB (-0.73 ± 0.29). Based on the reaction norm model, estimates of genetic correlations between the intercept and slope terms ranged from 0.24 ± 0.50 to 0.54 ± 0.35 depending on the parameterization used, indicating that selection for the intercept may result in indirect selection for steeper slopes, and thus, less resilient animals. In general, estimates of genetic correlations between farm-year-week effect classes based on the reaction norm model resembled estimates of genetic correlations from the multivariate analysis. Overall, compared to previous studies, antibody S/P ratios showed a lower heritability (0.17 ± 0.05) and low genetic correlations with reproductive performance during a porcine reproductive and respiratory syndrome outbreak, except for the LNSB.

Key Gaps in the Knowledge of the Porcine Respiratory Reproductive Syndrome Virus (PRRSV)

The porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important swine diseases in the world. It is causing an enormous economic burden due to reproductive failure in sows and a complex respiratory syndrome in pigs of all ages, with mortality varying from 2 to 100% in the most extreme cases of emergent highly pathogenic strains. PRRSV displays complex interactions with the immune system and a high mutation rate, making the development, and implementation of control strategies a major challenge. In this review, the biology of the virus will be addressed focusing on newly discovered functions of non-structural proteins and novel dissemination mechanisms. Secondly, the role of different cell types and viral proteins will be reviewed in natural and vaccine-induced immune response together with the role of different immune evasion mechanisms focusing on those gaps of knowledge that are critical to generate more efficacious vaccines. Finally, novel strategies for antigen discovery and vaccine development will be discussed, in particular the use of exosomes (extracellular vesicles of endocytic origin). As nanocarriers of lipids, proteins and nucleic acids, exosomes have potential effects on cell activation, modulation of immune responses and antigen presentation. Thus, representing a novel vaccination approach against this devastating disease.

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.

Diversity across major and candidate genes in European local pig breeds

The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krškopolje (Krškopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and an uneven admixture of the breeds studied. The results are in agreement with available knowledge regarding breed history and management, although largest panels of neutral markers should be employed to get a deeper understanding of the population's structure and relationships.

Harnessing longitudinal information to identify genetic variation in tolerance of pigs to Porcine Reproductive and Respiratory Syndrome virus infection

BACKGROUND

High resistance (the ability of the host to reduce pathogen load) and tolerance (the ability to maintain high performance at a given pathogen load) are two desirable host traits for producing animals that are resilient to infections. For Porcine Reproductive and Respiratory Syndrome (PRRS), one of the most devastating swine diseases worldwide, studies have identified substantial genetic variation in resistance of pigs, but evidence for genetic variation in tolerance has so far been inconclusive. Resistance and tolerance are usually considered as static traits. In this study, we used longitudinal viremia measurements of PRRS virus infected pigs to define discrete stages of infection based on viremia profile characteristics. These were used to investigate host genetic effects on viral load (VL) and growth at different stages of infection, to quantify genetic variation in tolerance at these stages and throughout the entire 42-day observation period, and to assess whether the single nucleotide polymorphism (SNP) WUR10000125 (WUR) with known large effects on resistance confers significant differences in tolerance.

RESULTS

Genetic correlations between resistance and growth changed considerably over time. Individuals that expressed high genetic resistance early in infection tended to grow slower during that time-period, but were more likely to experience lower VL and recovery in growth by the later stage. The WUR genotype was most strongly associated with VL at early- to mid-stages of infection, and with growth at mid- to late-stages of infection. Both, single-stage and repeated measurements random regression models identified significant genetic variation in tolerance. The WUR SNP was significantly associated only with the overall tolerance slope fitted through all stages of infection, with the genetically more resistant AB pigs for the WUR SNP being also more tolerant to PRRS.

CONCLUSIONS

The results suggest that genetic selection for improved tolerance of pigs to PRRS is possible in principle, but may be feasible only with genomic selection, requiring intense recording schemes that involve repeated measurements to reliably estimate genetic effects. In the absence of such records, consideration of the WUR genotype in current selection schemes appears to be a promising strategy to improve simultaneously resistance and tolerance of growing pigs to PRRS.

Genetic Analysis of a Commercial Egg Laying Line Challenged With Newcastle Disease Virus

In low income countries, chickens play a vital role in daily life. They provide a critical source of protein through egg production and meat. Newcastle disease, caused by avian paramyxovirus type 1, has been ranked as the most devastating disease for scavenging chickens in Africa and Asia. High mortality among flocks infected with velogenic strains leads to a devastating loss of dietary protein and buying power for rural households. Improving the genetic resistance of chickens to Newcastle Disease virus (NDV), in addition to vaccination, is a practical target for improvement of poultry production in low income countries. Because response to NDV has a component of genetic control, it can be influenced through selective breeding. Adding genomic information to a breeding program can increase the amount of genetic progress per generation. In this study, we challenged a commercial egg-laying line with a lentogenic strain of NDV, measured phenotypic responses, collected genotypes, and associated genotypes with phenotypes. Collected phenotypes included viral load at 2 and 6 days post-infection (dpi), antibody levels pre-challenge and 10 dpi, and growth rates pre- and post-challenge. Six suggestive QTL associated with response to NDV and/or growth were identified, including novel and known QTL confirming previously reported associations with related traits. Additionally, previous RNA-seq analysis provided support for several of the genes located in or near the identified QTL. Considering the trend of negative genetic correlation between antibody and Newcastle Disease tolerance (growth under disease) and estimates of moderate to high heritability, we provide evidence that these NDV response traits can be influenced through selective breeding. Producing chickens that perform favorably in challenging environments will ultimately increase the supply of quality protein for human consumption.

Genomic prediction of piglet response to infection with one of two porcine reproductive and respiratory syndrome virus isolates

Background

Genomic prediction of the pig’s response to the porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) would be a useful tool in the swine industry. This study investigated the accuracy of genomic prediction based on porcine SNP60 Beadchip data using training and validation datasets from populations with different genetic backgrounds that were challenged with different PRRSV isolates.

Results

Genomic prediction accuracy averaged 0.34 for viral load (VL) and 0.23 for weight gain (WG) following experimental PRRSV challenge, which demonstrates that genomic selection could be used to improve response to PRRSV infection. Training on WG data during infection with a less virulent PRRSV, KS06, resulted in poor accuracy of prediction for WG during infection with a more virulent PRRSV, NVSL. Inclusion of single nucleotide polymorphisms (SNPs) that are in linkage disequilibrium with a major quantitative trait locus (QTL) on chromosome 4 was vital for accurate prediction of VL. Overall, SNPs that were significantly associated with either trait in single SNP genome-wide association analysis were unable to predict the phenotypes with an accuracy as high as that obtained by using all genotyped SNPs across the genome. Inclusion of data from close relatives into the training population increased whole genome prediction accuracy by 33% for VL and by 37% for WG but did not affect the accuracy of prediction when using only SNPs in the major QTL region.

Conclusions

Results show that genomic prediction of response to PRRSV infection is moderately accurate and, when using all SNPs on the porcine SNP60 Beadchip, is not very sensitive to differences in virulence of the PRRSV in training and validation populations. Including close relatives in the training population increased prediction accuracy when using the whole genome or SNPs other than those near a major QTL.

Genomic regions associated with host response to porcine reproductive and respiratory syndrome vaccination and co-infection in nursery pigs

BACKGROUND

The WUR1000125 (WUR) single nucleotide polymorphism (SNP) can be used as a genetic marker for host response to porcine reproductive and respiratory syndrome (PRRS), PRRS vaccination, and co-infection with porcine circovirus type 2b (PCV2b). Objectives of this study were to identify genomic regions other than WUR associated with host response to PRRS vaccination and PRRSV/PCV2b co-infection and regions with a different effect on host response to co-infection, depending on previous vaccination for PRRS.

METHODS

Commercial crossbred nursery pigs were pre-selected for WUR genotype (n = 171 AA and 198 AB pigs) where B is the dominant and favorable allele. Half of the pigs were vaccinated for PRRS and 4 weeks later, all pigs were co-infected with PRRS virus and PCV2b. Average daily gain (ADG) and viral load (VL) were quantified post vaccination (Post Vx) and post co-infection (Post Co-X). Single-SNP genome-wide association analyses were then conducted to identify genomic regions associated with response to vaccination and co-infection.

RESULTS

Multiple SNPs near the major histocompatibility complex were significantly associated with PCV2b VL (-log ₁₀ P ≥ 5.5), regardless of prior vaccination for PRRS. Several SNPs were also significantly associated with ADG Post Vx and Post Co-X. SNPs with a different effect on ADG, depending on prior vaccination for PRRS, were identified Post Vx (-log ₁₀ P = 5.6) and Post Co-X (-log ₁₀ P = 5.5). No SNPs were significantly associated with vaccination VL (-log₁₀ P ≤ 4.7) or PRRS VL (-log₁₀ P ≤ 4.3). Genes near SNPs associated with vaccination VL, PRRS VL, and PCV2b VL were enriched (P ≤ 0.01) for immune-related pathways and genes near SNPs associated with ADG were enriched for metabolism pathways (P ≤ 0.04). SNPs associated with vaccination VL, PRRS VL, and PCV2b VL showed overrepresentation of health QTL identified in previous studies and SNPs associated with ADG Post Vx of Non-Vx pigs showed overrepresentation of growth QTL.

CONCLUSIONS

Multiple genomic regions were associated with PCV2b VL and ADG Post Vx and Post Co-X. Different SNPs were associated with ADG, depending on previous vaccination for PRRS. Results of functional annotation analyses and novel approaches of using previously-reported QTL support the identified regions.

Effect of a major quantitative trait locus for porcine reproductive and respiratory syndrome (PRRS) resistance on response to coinfection with PRRS virus and porcine circovirus type 2b (PCV2b) in commercial pigs, with or without prior vaccination for PRRS

A major QTL for host response to porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) infection was identified in a previous study. Single nucleotide polymorphism WUR10000125 (WUR), which is in complete linkage disequilibrium with the putative causative mutation, can be used as a tag SNP for the QTL. However, the effect of WUR following PRRS vaccination and/or coinfection with other pathogens is not known. Therefore, objectives of this study were to estimate the effect of WUR on host response following PRRS vaccination and coinfection of PRRSV with porcine circovirus type 2b (PCV2b), to estimate genetic parameters for host response to vaccination and coinfection, and to estimate the effect of previously identified candidate SNP under PRRSV-only or PCV2b-only infection on host response to coinfection. Data from 2 trials, comprising a total of 396 commercial crossbred nursery pigs from a single genetic source, were used for all analyses. Pigs were preselected based on WUR genotype: approximately half AA and half AB, where B is the favorable and dominant allele. At weaning, pigs were shipped to Kansas State University, where half of the pigs were vaccinated with a PRRS modified live virus vaccine. Four weeks later, all pigs were coinfected with field strains of PRRSV and PCV2b and followed for 42 d. Body weight and serum viremia measurements were collected following vaccination and coinfection to calculate ADG and viral load (VL), respectively. Average heritability estimates for PRRS VL, PCV2b VL, and ADG were 0.29, 0.09, and 0.40, respectively. After vaccination, AB pigs had lower vaccination VL ( = 0.03) and faster gain ( = 0.004) than AA pigs, as expected. After coinfection, AB pigs had lower PRRSV VL ( < 0.001) but did not significantly differ from AA pigs in growth rate ( = 0.86). For PCV2b VL, suggestive evidence of an interaction between vaccination and WUR genotype ( = 0.11) was detected, where AB pigs had significantly lower PCV2b VL when vaccinated ( = 0.007) but not when they were not vaccinated ( = 0.87). In addition to WUR, several PRRS-associated SNP and a PCV2b-associated SNP had significant effects on host response to coinfection. In conclusion, marker-assisted selection based on WUR genotype alone, or along with other candidate SNP for PRRSV and PCV2b infection, is a promising strategy to select for improved host response to not just PRRS but also coinfection of PRRSV with PCV2b and perhaps other pathogens.

A major gene for host response to porcine reproductive and respiratory syndrome is not unfavorably associated with overall performance under nonchallenging conditions in commercial pig lines

A QTL for host response to porcine reproductive and respiratory syndrome (PRRS) was identified in a previous study. The SNP WUR10000125 (WUR) is used as a tag SNP for this QTL. The favorable (B) allele at this SNP is in low frequency in commercial populations, possibly because this allele is unfavorably associated with an important trait under nonchallenging conditions and, therefore, may have been selected against. Therefore, objectives of this study were to estimate the effect of WUR on traits under selection in commercial lines under nonchallenging conditions and to estimate the effect of WUR genotype of parents on performance of crossbred progeny in a commercial-like environment. Data were collected on 4 purebred lines: a Landrace dam line (D1), a Large White dam line (D2), a synthetic sire line (S1), and a Pietrain sire line (S2). Traits analyzed included total number born, number stillborn, farrowing survival, lactation survival, litter mortality, daily feed intake (DFI), backfat, average test daily gain (TGR), average lifetime daily gain (LGR), and Topigs Norsvin selection index (TSI) value, indicative of overall economic value. Deregressed EBV were calculated for each trait (except TSI) and analyzed within line. In the S1 line, AB and BB pigs had significantly lower TGR (P = 0.002) and LGR (P = 0.001) than AA pigs but also lower DFI (P = 0.004). Conversely, AB and BB pigs had significantly higher DFI (P < 0.001) and AB pigs had significantly higher TGR (P = 0.03) than AA pigs in the S2 line. The effect of WUR on TSI was not significant for any line (P ≥ 0.15). Analyses of phenotypic records collected on crossbred progeny of S1 sires and D1 × D2 F₁ females showed no significant effect of parent WUR genotype on DFI, backfat, TGR, or LGR (P ≥ 0.07). In conclusion, the effect of WUR was nonsignificant for most traits but the magnitude and direction of the effect differed by trait and by line. The favorable allele for host response to PRRS was associated with greater DFI and a tendency for greater TGR in the S2 line, but the opposite direction of effect was detected for the S1 line. Regardless of the effect on individual traits, no significant effect of WUR on TSI was detected for any line. Therefore, selecting for the B allele is expected to result in progeny with increased resistance to PRRS without compromising overall economic value under normal, nonchallenging conditions.

Use of multi-trait and random regression models to identify genetic variation in tolerance to porcine reproductive and respiratory syndrome virus

BACKGROUND

A host can adopt two response strategies to infection: resistance (reduce pathogen load) and tolerance (minimize impact of infection on performance). Both strategies may be under genetic control and could thus be targeted for genetic improvement. Although there is evidence that supports a genetic basis for resistance to porcine reproductive and respiratory syndrome (PRRS), it is not known whether pigs also differ genetically in tolerance. We determined to what extent pigs that have been shown to vary genetically in resistance to PRRS also exhibit genetic variation in tolerance. Multi-trait linear mixed models and random regression sire models were fitted to PRRS Host Genetics Consortium data from 1320 weaned pigs (offspring of 54 sires) that were experimentally infected with a virulent strain of PRRS virus to obtain genetic parameter estimates for resistance and tolerance. Resistance was defined as the inverse of within-host viral load (VL) from 0 to 21 (VL21) or 0 to 42 (VL42) days post-infection and tolerance as the slope of the reaction-norm of average daily gain (ADG21, ADG42) on VL21 or VL42.

RESULTS

Multi-trait analysis of ADG associated with either low or high VL was not indicative of genetic variation in tolerance. Similarly, random regression models for ADG21 and ADG42 with a tolerance slope fitted for each sire did not result in a better fit to the data than a model without genetic variation in tolerance. However, the distribution of data around average VL suggested possible confounding between level and slope estimates of the regression lines. Augmenting the data with simulated growth rates of non-infected half-sibs (ADG0) helped resolve this statistical confounding and indicated that genetic variation in tolerance to PRRS may exist if genetic correlations between ADG0 and ADG21 or ADG42 are low to moderate.

CONCLUSIONS

Evidence for genetic variation in tolerance of pigs to PRRS was weak when based on data from infected piglets only. However, simulations indicated that genetic variance in tolerance may exist and could be detected if comparable data on uninfected relatives were available. In conclusion, of the two defense strategies, genetics of tolerance is more difficult to elucidate than genetics of resistance.

Genomewide association of piglet responses to infection with one of two porcine reproductive and respiratory syndrome virus isolates

Porcine reproductive and respiratory syndrome (PRRS) is a devastating disease in the swine industry. Identification of host genetic factors that enable selection for improved performance during PRRS virus (PRRSV) infection would reduce the impact of this disease on animal welfare and production efficiency. We conducted genomewide association study (GWAS) analyses of data from 13 trials of approximately 200 commercial crossbred nursery-age piglets that were experimentally infected with 1 of 2 type 2 isolates of PRRSV (NVSL 97-7985 [NVSL] and KS2006-72109 [KS06]). Phenotypes analyzed were viral load (VL) in blood during the first 21 d after infection (dpi) and weight gain (WG) from 0 to 42 dpi. We accounted for the previously identified QTL in the region on SSC4 in our models to increase power to identify additional regions. Many regions identified by single-SNP analyses were not identified using Bayes-B, but both analyses identified the same regions on SSC3 and SSC5 to be associated with VL in the KS06 trials and on SSC6 in the NVSL trials ( < 5 × 10); for WG, regions on SSC5 and SSC17 were associated in the NVSL trials ( < 3 × 10). No regions were identified with either method for WG in the KS06 trials. Except for the region on SSC4, which was associated with VL for both isolates (but only with WG for NVSL), identified regions did not overlap between the 2 PRRSV isolate data sets, despite high estimates of the genetic correlation between isolates for traits based on these data. We also identified genomic regions whose associations with VL or WG interacted with either PRRSV isolate or with genotype at the SSC4 QTL. Gene ontology (GO) annotation terms for genes located near moderately associated SNP ( < 0.003) were enriched for multiple immunologically (VL) and metabolism- (WG) related GO terms. The biological relevance of these regions suggests that, although it may increase the number of false positives, the use of single-SNP analyses and a relaxed threshold also increased the identification of true positives. In conclusion, although only the SSC4 QTL was associated with response to both PRRSV isolates, genes near associated SNP were enriched for the same GO terms across PRRSV isolates, suggesting that host responses to these 2 isolates are affected by the actions of many genes that function together in similar biological processes.