Development, Evaluation, and Clinical Application of PRRSV-2 Vaccine-like Real-Time RT-PCR Assays

In this study, we developed and validated (1) singleplex real-time RT-PCR assays for specific detection of five PRRSV-2 MLV vaccine viruses (Ingelvac MLV, Ingelvac ATP, Fostera, Prime Pac, and Prevacent) and (2) a four-plex real-time RT-PCR assay (IngelvacMLV/Fostera/Prevacent/XIPC) including the internal positive control XIPC for detecting and distinguishing the three most commonly used vaccines in the USA (Prevacent, Ingelvac MLV, and Fostera). The singleplex and 4-plex vaccine-like PCRs and the reference PCR (VetMAXTM PRRSV NA&EU, Thermo Fisher Scientific, Waltham, MA, USA) did not cross-react with non-PRRSV swine viral and bacterial pathogens. The limits of detection of vaccine-like PCRs ranged from 25 to 50 genomic copies/reactions. The vaccine-like PCRs all had excellent intra-assay and inter-assay repeatability. Based on the testing of 531 clinical samples and in comparison to the reference PCR, the diagnostic sensitivity, specificity, and agreement were in the respective range of 94.67-100%, 100%, and 97.78-100% for singleplex PCRs and 94.94-100%, 100%, and 97.78-100% for the 4-plex PCR, with a CT cutoff of 37. In addition, 45 PRRSV-2 isolates representing different genetic lineages/sublineages were tested with the vaccine-like PCRs and the results were verified with sequencing. In summary, the vaccine-like PCRs specifically detect the respective vaccine-like viruses with comparable performances to the reference PCR, and the 4-plex PCR allows to simultaneously detect and differentiate the three most commonly used vaccine viruses in the same sample. PRRSV-2 vaccine-like PCRs provide an additional tool for detecting and characterizing PRRSV-2.

In Vivo and In Vitro Characterization of the Recently Emergent PRRSV 1-4-4 L1C Variant (L1C.5) in Comparison with Other PRRSV-2 Lineage 1 Isolates

The recently emerged PRRSV 1-4-4 L1C variant (L1C.5) was in vivo and in vitro characterized in this study in comparison with three other contemporary 1-4-4 isolates (L1C.1, L1A, and L1H) and one 1-7-4 L1A isolate. Seventy-two 3-week-old PRRSV-naive pigs were divided into six groups with twelve pigs/group. Forty-eight pigs (eight/group) were for inoculation, and 24 pigs (four/group) served as contact pigs. Pigs in pen A of each room were inoculated with the corresponding virus or negative media. At two days post inoculation (DPI), contact pigs were added to pen B adjacent to pen A in each room. Pigs were necropsied at 10 and 28 DPI. Compared to other virus-inoculated groups, the L1C.5-inoculated pigs exhibited more severe anorexia and lethargy, higher mortality, a higher fraction of pigs with fever (>40 °C), higher average temperature at several DPIs, and higher viremia levels at 2 DPI. A higher percentage of the contact pigs in the L1C.5 group became viremic at two days post contact, implying the higher transmissibility of this virus strain. It was also found that some PRRSV isolates caused brain infection in inoculation pigs and/or contact pigs. The complete genome sequences and growth characteristics in ZMAC cells of five PRRSV-2 isolates were further compared. Collectively, this study confirms that the PRRSV 1-4-4 L1C variant (L1C.5) is highly virulent with potential higher transmissibility, but the genetic determinants of virulence remain to be elucidated.

A comparison of three sampling approaches for detecting PRRSV in suckling piglets

Determining whether porcine reproductive and respiratory syndrome virus (PRRSV) is circulating within a breeding herd is a longstanding surveillance challenge. Most commonly, piglets in farrowing rooms are sampled to infer the PRRSV status of the sow herd, with sample size based on the expectation of hypergeometric distribution and piglet selection based on simple random sampling (SRS), i.e., randomly selecting individuals from a population in a manner that all individuals have equal chance of being selected. Conceptually straightforward, the assumptions upon which it is based (homogeneous population and independence of individuals) rarely hold in modern swine facilities. Alternative approaches for sample selection include two-stage stratified sampling (2SS), i.e., randomly selecting litters (first stratum) and randomly selecting piglets (second stratum) within selected litters, and risk-based sampling (RBS), i.e., selecting litters with a higher risk of having viremic piglets, and randomly selecting pigs within those litters. The objectives of this study were to 1) characterize the pattern of distribution of PRRSV-viremic piglets in farrowing rooms and 2) compare the efficiency of SRS, 2SS, and RBS for the detection of PRRSV-viremic piglets. In 12 sow farms, serum samples were collected from all 4510 piglets in 422 litters housed in 23 farrowing rooms and tested for PRRSV RNA. At the population level, the distribution of PRRSV-viremic pigs was analyzed for population homogeneity and spatial clustering. At the litter level, litter size and sow parity were evaluated as risk factors. A non-homogeneous distribution of PRRSV-viremic piglets was observed in nearly all farrowing rooms (15/16), and spatial clustering detected on 11 occasions (11/16). Simulated sampling based on farrowing room data determined that 2SS required 1-to-25 fewer samples than SRS to detect ≥ 1 viremic piglet in 13 of 16 rooms and the same number of samples in 3 rooms. RBS required 1-to-7 fewer samples than 2SS to detect ≥ 1 viremic piglet in 7 of 16 rooms, the same number of samples in 6 rooms, and 1 more sample in 3 rooms. Notably, SRS was less efficient than either 2SS or RBS in detecting PRRSV-viremic piglets in farrowing rooms, regardless of the confidence level. It may be concluded that the core assumptions upon which most current surveillance methods are based do not hold in modern farrowing room facilities. Simulation-based sample size tables for SRS and 2SS are provided.

Finding PRRSV in sow herds: Family oral fluids vs. serum samples from due-to-wean pigs

The aim of this study was to compare the detection of porcine reproductive and respiratory syndrome virus (PRRSV) in due-to-wean litters in commercial swine breeding herds using family oral fluids (FOF) vs. individual piglet serum samples. FOF and piglet serum samples were collected in 199 due-to-wean litters on six farms containing 2177 piglets. All samples were individually tested for PRRSV RNA by RT-rtPCR. A litter was considered PRRSV-positive when PRRSV RNA was detected in ≥ 1 piglet serum sample or the FOF sample. Mixed effect logistic regression with farm as a random effect was used 1) to evaluate the probability of obtaining a PRRSV RNA positive FOF as a function of the proportion of viremic piglets in a litter and 2) the effect of litter size and parity on the probability that a litter would test PRRSV RNA positive in FOF. A Bayesian prevalence estimation under misclassification (BayesPEM) analysis was used to calculate the PRRSV prevalence and 95 % credible interval given the condition that all samples (FOF and serum) tested negative. In total, 34 of 199 litters (17.1 %) contained ≥ 1 viremic piglet(s), and 28 of 199 litters (14.1 %) were FOF positive. When all piglet serum samples within a litter tested negative, 1 of 165 FOF (0.6 %) tested PRRSV RNA positive. The probability of a PCR-positive FOF sample from litters with 10 %, 20 %, 30 %, 40 %, and 50 % within-litter PRRSV prevalence was 3.5 %, 35.1 %, 88.8 %, 99.2 %, and >99.9 %, respectively. The odds of a PCR-positive FOF in a first parity litter were 3.36 times (95 % CI: 2.10-5.38) that of a parity ≥ 2 litter. The odds of a positive FOF result in a litter with ≤ 11 piglets were 9.90 times (95 % CI: 4.62-21.22) that of a litter with > 11 piglets. FOF was shown to be an efficacious sample type for PRRSV detection in farrowing rooms. A risk-based approach for litter selection combined with FOF collection can be used to improve on-farm PRRSV detection with a limited sample size, compared to sampling multiple individual pigs. Finally, the BayesPEM analysis showed that PRRSV may still be present in breeding herds when all samples (serum and FOF) test PRRSV RNA negative, i.e., negative surveillance results should be interpreted with caution.

Visualization and application of disease diagnosis codes for population health management using porcine diseases as a model

Accurate and timely results of diagnostic investigations and laboratory testing guide clinical interventions for the continuous improvement of animal health and welfare. Infectious diseases can severely limit the health, welfare, and productivity of populations of animals. Livestock veterinarians submit thousands of samples daily to veterinary diagnostic laboratories (VDLs) for disease diagnosis, pathogen monitoring, and surveillance. Individual diagnostic laboratory reports are immediately useful; however, aggregated historical laboratory data are increasingly valued by clinicians and decision-makers to identify changes in the health status of various animal populations over time and geographical space. The value of this historical information is enhanced by visualization of trends of agent detection, disease diagnosis, or both, which helps focus time and resources on the most significant pathogens and fosters more effective communication between livestock producers, veterinarians, and VDL professionals. Advances in data visualization tools allow quick, efficient, and often real-time scanning and analysis of databases to inform, guide, and modify animal health intervention algorithms. Value is derived at the farm, production system, or regional level. Visualization tools allow client-specific analyses, benchmarking, formulation of research questions, and monitoring the effects of disease management and precision farming practices. We present here the approach taken to visualize trends of disease occurrence using porcine disease diagnostic code data for the period 2010 to 2019. Our semi-automatic standardized creation of a visualization platform allowed the transformation of diagnostic report data into aggregated information to visualize and monitor disease diagnosis.

Collecting oral fluid samples from due-to-wean litters

Oral fluids are a common diagnostic sample in group-housed nursery, grow-finish, and adult swine. Although oral fluids from due-to-wean litters could be a valuable tool in monitoring pathogens and predicting the health status of pig populations post-weaning, it is generally not done because of inconsistent success in sample collection. The objective of this study was to determine the optimum procedure for collecting oral fluid samples from due-to-wean litters. Successful collection of oral fluids from due-to-wean litters using "Litter Oral Fluid" (LOF) or "Family Oral Fluid" (FOF) sampling techniques were compared in 4 phases involving 920 attempts to collect oral fluids. Phase 1 testing showed that prior exposure to a rope improved the success rates of both LOF (33.4%) and FOF (16.4%) techniques. Phase 2 determined that longer access to the rope (4 h vs 30 min) did not improve the success rate for either LOF or FOF. Phase 3 evaluated the effect of attractants and found that one (Baby Pig Restart®) improved the success rate when used with the FOF technique. Phase 4 compared the success rates of "optimized LOF" (litters previously trained) vs "optimized FOF" (litter previously trained and rope treated with Baby Pig Restart®) vs standard FOF. No difference was found between the FOF-based techniques, but both were superior to the "optimized LOF" technique. Thus, FOF-based procedures provided a significantly higher probability of collecting oral fluids from due-to-wean litters (mean success rate 84.9%, range 70% to 92%) when compared to LOF-based methods (mean success rate 24.1%, range 16.5% to 32.2%).

Assessment of abattoir based monitoring of PRRSV using oral fluids

Various porcine reproductive and respiratory syndrome virus (PRRSV) regional elimination projects have been implemented in the U.S., but none have yet succeeded. In part, this reflects the need for efficient methods to monitor over time the progress of PRRSV status of participating herds. This study assessed the feasibility of monitoring PRRSV using oral fluids collected at the abattoir. A total of 36 pig lots were included in the study. On-farm oral fluid (n = 10) and serum (n = 10) collected within two days of shipment to the abattoir were used to establish the reference PRRSV status of the population. Oral fluids (n = 3 per lot) were successfully collected from 32 lots (89%) at the lairage. Three veterinary diagnostic laboratories (VDLs) tested the sera (VDL1 and VDL3: n = 316, VDL2: n = 315) and oral fluids (VDL1 and VDL3: n = 319, VDL2: n = 320) for PRRSV antibodies (ELISA) and RNA (rRT-PCR). Environmental samples (n = 64, 32 before and 32 after pigs were placed in lairage) were tested for PRRSV RNA at one VDL. All oral fluids (farm and abattoir) tested positive for PRRSV antibody at all VDLs. PRRSV positivity frequency on serum ranged from 92.4% to 94.6% among VDLs, with an overall agreement of 97.6%. RNA was detected on 1.3% to 1.9%, 8.1% to 17.7%, and 8.3% to 17.7% of sera, on-farm and abattoir oral fluids, respectively. Between-VDLs rRT-PCR agreement on sera and oral fluids (farm and abattoir) ranged from 97.8% to 99.0%, and 79.0% to 81.2%, respectively. Between-locations agreement of oral fluids varied from 31.3% to 50% depending on the VDL. This study reported the application of swine oral fluids collected at the abattoir for monitoring PRRSV, and describes the between-VDL agreement for PRRS testing of serum and oral fluid field samples.