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Mortality during the post-weaning phase is a critical indicator of swine production system performance, influenced by a complex interaction of multiple factors of the epidemiological triad. This study leveraged retrospective data from 1723 groups of pigs marketed within a US swine production system to develop a Wean-Quality Score (WQS) using machine learning techniques. The study evaluated three machine learning models, Random Forest, Support Vector Machine, and Gradient Boosting Machine, to classify groups having high or low 60-day mortality, where high mortality groups represented 25 % of the groups among the study population with the highest mortality values (n=431; 60-day mortality=9.98 %), and the remaining 75 % of the groups were of low mortality (n=1292; 60-day mortality=2.75 %). The best-performing model, Random Forest (RF), outperformed the other ML models in terms of accuracy (0.90), sensitivity (0.84), and specificity (0.92) metrics, and was then selected for further analysis, which consisted of creating the WQS and ranking the most important factors for classifying groups as high or low mortality. The most important factors ranked through the RF model to classify groups with high mortality were pre-weaning mortality, weaning age, average parity of litters in sow farms, and PRRS status. Additionally, stocking conditions such as stocking density and time to fill the barn were important predictors of high mortality. The WQS was developed and correlated (r = 0.74) with the actual 60-day mortality of the groups, offering a valuable tool for assessing post-weaning survivability in swine production systems before weaning. This study highlights the potential of machine learning and comprehensive data utilization to improve the assessment and management of weaned pig quality in commercial swine production, which producers can utilize to identify and intervene in groups, according to the WQS., Competing Interests: Declaration of Competing Interest The authors declare no conflicts of interest., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Background: A Tonsil-Oral-Scrubbing (TOSc) method was developed to sample the sow's oropharyngeal and tonsillar area without snaring and has shown comparable porcine reproductive and respiratory syndrome virus (PRRSV) RNA detection rates with tonsil scraping in infected sows. This study investigated the effect of specific TOSc collection factors on the PRRSV RT-rtPCR results (detection rates and Ct values). Those factors include whether the sow was snared or not snared at TOSc collection ("snared" vs. "not snared"); whether the sow was laying down or standing at collection ("laying down" vs. "standing"); and type of collectors used for TOSc collection ("TOSc prototype" vs. "Spiral-headed AI catheter (SHAC)"). Volume of fluid was compared between "snared" and "not snared" groups, and collection time was compared between "laying down" and "standing" groups as well., Results: The effect for each factor was assessed in three independent studies following the same design: TOSc was collected twice from each studied sow, once with the baseline level for a factor ("not snared", or "standing", or "TOSc prototype"), and another time followed by the other level of the paired factor ("snared", "laying down", or "SHAC", correspondingly). Results showed that "not snared" TOSc had numerically higher PRRSV RNA detection rate (60.7% vs. 52.5%, p = 0.11), significantly lower median Ct values (31.9 vs. 32.3, p < 0.01), and significantly higher volume of fluid than "snared" samples (1.8 mL vs. 1.2 mL, p < 0.01); "laying down" TOSc samples did not differ statistically (60.7% vs. 60.7%) in the PRRSV RNA detection rate, obtained numerically lower median Ct values (30.9 vs. 31.3, p = 0.19), but took 40% less collection time compared to "standing" TOSc samples; samples collected using the "TOSc prototype" had numerically higher PRRSV RNA detection rate (91.7% vs. 88.3%, p = 0.27) and significantly lower median Ct values (32.8 vs. 34.5, p < 0.01) than that from "SHAC"., Conclusions: Under the conditions of this study best practices for TOSc collection aiming higher detection rate of PRRSV RNA while minimizing time for collection were suggested to be sampling TOSc without snaring, when sows are laying down, and using a prototype TOSc collector., (© 2024. The Author(s).)

Aggregated diagnostic data collected over time from swine production systems is an important data source to investigate swine productivity and health, especially when combined with records concerning the pre-weaning and post-weaning phases of production. The combination of multiple data streams collected over the lifetime of the pigs is the essence of the whole-herd epidemiological investigation. This approach is particularly valuable for investigating the multifaceted and ever-changing factors contributing to wean-to-finish (W2F) swine mortality. The objective of this study was to use a retrospective dataset ("master table") containing information on 1,742 groups of pigs marketed over time to identify the major risk factors associated with W2F mortality. The master table was built by combining historical breed-to-market performance and health data with disease diagnostic records (Dx Codes) from marketed groups of growing pigs. After building the master table, univariate analyses were conducted to screen for risk factors to be included in the initial multivariable model. After a stepwise backward model selection approach, 5 variables and 2 interactions remained in the final model. Notably, the diagnosis variable significantly associated with W2F mortality was porcine reproductive and respiratory syndrome virus (PRRSV). Closeouts with clinical signs suggestive of Salmonella spp. or Escherichia coli infection were also associated with higher W2F mortality. Source sow farm factors that remained significantly associated with W2F mortality were the sow farm PRRS status, average weaning age, and the average pre-weaning mortality. After testing for the possible interactions in the final model, two interactions were significantly associated with wean-to-finish pig mortality: (1) sow farm PRRS status and a laboratory diagnosis of PRRSV and (2) average weaning age and a laboratory diagnosis of PRRS. Closeouts originating from PRRS epidemic or PRRS negative sow farms, when diagnosed with PRRS in the growing phase, had the highest W2F mortality rates. Likewise, PRRS diagnosis in the growing phase was an important factor in mortality, regardless of the average weaning age of the closeouts. Overall, this study demonstrated the utility of a whole-herd approach when analyzing diagnostic information along with breeding-to-market productivity and health information, to measure the major risk factors associated with W2F mortality in specified time frames and pig populations., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Magalhães, Zimmerman, Thomas, Moura, Trevisan, Schwartz, Burrough, Holtkamp, Wang, Rademacher, Silva and Linhares.)

The performance of five forecasting models was investigated for predicting nursery mortality using the master table built for 3242 groups of pigs (~13 million animals) and 42 variables, which concerned the pre-weaning phase of production and conditions at placement in growing sites. After training and testing each model's performance through cross-validation, the model with the best overall prediction results was the Support Vector Machine model in terms of Root Mean Squared Error (RMSE = 0.406), Mean Absolute Error (MAE = 0.284), and Coefficient of Determination (R 2 = 0.731). Subsequently, the forecasting performance of the SVM model was tested on a new dataset containing 72 new groups, simulating ongoing and near real-time forecasting analysis. Despite a decrease in R 2 values on the new dataset (R 2 = 0.554), the model demonstrated high accuracy (77.78%) for predicting groups with high (>5%) or low (<5%) nursery mortality. This study demonstrated the capability of forecasting models to predict the nursery mortality of commercial groups of pigs using pre-weaning information and stocking condition variables collected post-placement in nursery sites.

Background: The Hungarian national eradication program of PRRS was successfully completed between 2014 and 2022. There were doubts about the efficiency of the eradication program in Hungary from the beginning to the tune that it might only be carried out efficiently through depopulation-repopulation of the infected herds, which is a very costly procedure. In our study, we investigated the impact of the depopulation-repopulation procedure, which played a prominent role in the PRRS eradication program on the productivity of the Hungarian swine sector-namely, on the number of slaughter pigs per sow per year and the total live slaughter weight per sow per year., Material and Methods: Since 2014, we monitored the evolution of the PRRS eradication through the depopulation-repopulation approach on the large-scale breeding herds in Hungary. Most producers replaced their herds with animals that were free of PRRS and other infectious diseases (mycoplasmosis, actinobacillosis, swine dysentery, atrophic rhinitis, etc.). On this basis, we evaluated the change in the number of slaughter pigs per sow per year as a consequence of depopulation-repopulation of the herds being carried out. In the statistical analysis linear regression was used., Conclusions: The results of our study demonstrate that the PRRS eradication program with the herd depopulation-repopulation approach led to a considerable improvement of the productivity of Hungarian pig farming. This result also demonstrates that, independent of the PRRS eradication, it is still necessary to consider investments into the individual production units to increase efficiency, and to carry out herd depopulation-repopulation in cases where the current genetics limits improvements in productivity.

Background: Ileitis is a wasting disease of pigs. Clinical symptoms are diarrhea in growing pigs, wasting and reduced performance. Ileitis is ubiquitous in pig producing countries all around the world. It is estimated that the economic losses caused by the disease are USD 4.65 per fattening pig, and American pig farmers lose USD 56.1 million annually. It has become necessary to develop a slaughterhouse ileitis monitoring method that is simple, feasible to perform at modern slaughter lines, leads to immediate results and is cost effective. The practical experiences of applying the method are presented below., Methods: Our studies were performed on pig herds and slaughterhouses in Central European countries (Hungary, Romania, Poland, Croatia, and Slovakia). Experiences were evaluated based on visual and palpation. The results of our investigations were evaluated by a scoring method. Authors made histological and immunohistochemical examinations of investigated ileums. The hypothetic economic losses due to the disease in each farm were determined by estimating the loss of profit according to Holtkamp's presentation in 2019., Results: The essentials of the method we have developed are: it can be performed during slaughterhouse processing, it does not interfere with or make it impossible to carry out normal technological processes, and the results of the procedure are correlated with the results of other laboratory diagnostic tests for ileitis (histology, immunohistochemistry, herd serology, fecal PCR). It is noteworthy that the results of the method can be used to immediately estimate the impact of Lawsonia intracellularis infection on the performance of the herd from which the slaughter animals come., Conclusion: Using the results of the slaughtered pigs' visual and tactile examination at the slaughterhouse, the magnitude of the loss caused by Lawsonia intracellularis infection can be estimated quickly and accurately, and the return on investment of the strategy to be applied can be accurately planned., Competing Interests: I.M., P.M., H.,S., S.v.B. are employed by MSD Animal Health, which have a commercial interest in selling pharmaceutical products for pigs. The employment did not inflict any bias regarding the study, which has been conducted as part of the first author&rsquo;s enrolment as independent researcher. Other authors declare no conflict of interest.

Porcine reproductive and respiratory syndrome virus (PRRSV) causes a significant economic impact on swine production. It has been demonstrated that PRRS modified-live virus (MLV) vaccination of pigs, with one full dose, significantly reduces clinical consequences of wild-type PRRSV infection compared to non-vaccinates. However, there is limited information about the effect that two doses of PRRSV MLV vaccine have on the performance of growing pigs, compared to vaccination with a single dose. This study was conducted with the objectives to compare (a) the wild-type PRRSV detection in oral fluids over time, (b) key closeout productivity indicators, and (c) economic performance between lots of growing pigs vaccinated with two doses of Ingelvac PRRS® MLV vaccine and lots vaccinated with a single dose of the same vaccine. This randomized field trial included 15 lots of growing pigs from PRRSV positive-unstable sow farms and 66 lots from PRRSV positive-stable sow farms, according to the American association of swine veterinarians' terminology. All pig lots received the first vaccination either around processing or weaning age. Lots allocated in the two doses group received the second vaccination three to four weeks after the first vaccination. The pig lots were monitored for PRRSV detection over time. Six oral fluids samples were collected in three weeks intervals and were tested for wild-type PRRSV-2 RNA by RT-qPCR and open reading frame 5 (ORF)- 5 sequencing. Regression models were used to compare wild-type PRRSV detection dynamics on oral fluids samples and to compare key closeout performance indicators between one dose group and two doses group. Additionally, a benefit-cost ratio analysis compared economic performance between one dose group and two doses group. The proportion of wild-type PRRSV detection on oral fluids samples and the log counts of viral RNA per ml of oral fluids from the two doses group was lower than the one dose group on lots originated from PRRSV positive-stable sow farms, with a risk ratio of 1.24 and a rate ratio of 1.17, respectively. The two doses group had a significantly lower mortality rate than the one dose group, with a rate ratio of 1.21. The effect size increased on lots originated from PRRSV positive-unstable sow farms, and on lots with higher frequency and diversity of wild-type PRRSV detection during the growth phase. No differences in growth performance were detected between two doses group and one dose group. The second MLV vaccination dose had a benefit-cost ratio of 1.83. For lots originated from PRRSV positive-unstable farms, the benefit-cost ratio was 4.45, and for lots originated from PRRSV positive-stable farms, the benefit-cost ratio was 0.45. Under study conditions, vaccinating growing pig lots with two doses of PRRS MLV vaccine was a useful strategy to immunize growing pigs against PRRSV, lowering the wild-type PRRSV detection, lowering mortality rate, and increasing profitability, compared to lots of growing pigs that received a single dose of the same vaccine., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Effective biosecurity practices in swine production are key in preventing the introduction and dissemination of infectious pathogens. Ideally, on-farm biosecurity practices should be chosen by their impact on bio-containment and bio-exclusion; however, quantitative supporting evidence is often unavailable. Therefore, the development of methodologies capable of quantifying and ranking biosecurity practices according to their efficacy in reducing disease risk has the potential to facilitate better-informed choices of biosecurity practices. Using survey data on biosecurity practices, farm demographics, and previous outbreaks from 139 herds, a set of machine learning algorithms were trained to classify farms by porcine reproductive and respiratory syndrome virus status, depending on their biosecurity practices and farm demographics, to produce a predicted outbreak risk. A novel interpretable machine learning toolkit, MrIML-biosecurity, was developed to benchmark farms and production systems by predicted risk and quantify the impact of biosecurity practices on disease risk at individual farms. By quantifying the variable impact on predicted risk, 50% of 42 variables were associated with fomite spread while 31% were associated with local transmission. Results from machine learning interpretations identified similar results, finding substantial contribution to predicted outbreak risk from biosecurity practices relating to the turnover and number of employees, the surrounding density of swine premises and pigs, the sharing of haul trailers, distance from the public road and farm production type. In addition, the development of individualized biosecurity assessments provides the opportunity to better guide biosecurity implementation on a case-by-case basis. Finally, the flexibility of the MrIML-biosecurity toolkit gives it the potential to be applied to wider areas of biosecurity benchmarking, to address biosecurity weaknesses in other livestock systems and industry-relevant diseases., (© 2021 Wiley-VCH GmbH.)

Swine wean-to-finish (W2F) mortality is a multifactorial, dynamic process and a key performance indicator of commercial swine production. Although swine producers typically capture the relevant data, analysis of W2F mortality risk factors is often hindered by the fact that, even if data is available, they are typically in different formats, non-uniform, and dispersed among multiple unconnected databases. In this study, an automated framework was created to link multiple data streams to specific cohorts of market animals, including sow farm productivity parameters, sow farm and growing pig health factors, facilities, management factors, and closeout data from a Midwestern USA production system. The final dataset (master-table) contained breeding-to-market data for 1,316 cohorts of pigs marketed between July 2018 and June 2019. Following integration into a master-table, continuous explanatory variables were categorized into quartiles averages, and the W2F mortality was log-transformed, reporting geometric mean mortality of 8.69 % for the study population. Further, univariate analyses were performed to identify individual variables associated with W2F mortality (p < 0.10) for further inclusion in a multivariable model, where model selection was applied. The final multivariable model consisted of 13 risk factors and accounted for 68.2 % (R 2 ) of the variability of the W2F mortality, demonstrating that sow farm health and performance are closely linked to downstream W2F mortality. Higher sow farm productivity was associated with lower subsequent W2F mortality and, conversely, lower sow farm productivity with higher W2F mortality e.g., groups weaned in the highest quartiles for pre-weaning mortality and abortion rate had 13.5 %, and 12.5 %, respectively, which was statistically lower than the lowest quartiles for the same variables (10.5 %, and 10.6 %). Moreover, better sow farm health status was also associated with lower subsequent W2F mortality. A significant difference was detected in W2F mortality between epidemic versus negative groups for porcine reproductive and respiratory syndrome virus (15.4 % vs 8.7 %), and Mycoplasma hyopneumoniae epidemic versus negative groups (13.7 % vs 9.9 %). Overall, this study demonstrated the application of a whole-herd analysis by aggregating information of the pre-weaning phase with the post-weaning phase (breeding-to-market) to identify and measure the major risk factors of W2F mortality., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Porcine reproductive and respiratory syndrome virus (PRRSV) became pandemic in the 1980's and today remains one of the most significant pathogens of the global swine industry. At the herd level, control of PRRSV is complicated by its extreme genetic diversity and its ability to persist in pigs, despite an active immune response. Ultimately, PRRSV control or elimination requires the coordination and active cooperation of producers and veterinarians at the regional level. Early voluntary PRRSV regional control programs focused on routine diagnostic testing and voluntary data-sharing regarding the PRRSV status of participants' herds, but no pre-defined action plans or decision trees were developed to secure project successes (or recover from failures). Given that control of PRRSV is paramount to producer profitability, we propose a coordinated approach for detecting, controlling, and ultimately eliminating wild-type PRRSV from herds participating in regional projects. Fundamental to project success is real-time, multi-platform communication of all data, information, and events that concern the regional project and project participants. New to this approach is the concept of agreed-upon action plans to be implemented by project participants in response to specific events or situations. The simultaneous and coordinated implementation of these strategies allows for early detection of wild-type PRRSV virus introductions and rapid intervention based on agreed-upon response plans. An example is given of a project in progress in the Midwest USA., Competing Interests: DC and DG are employed by Carthage Veterinary Service, Ltd. LG is employed by TriOak Foods Inc. RP is employed by Boehringer Ingelheim Animal Health USA Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Magalhães, Zimmerman, Holtkamp, Classen, Groth, Glowzenski, Philips, Silva and Linhares.)

Because contaminated livestock trailers are a significant risk for transmitting viruses between herds, various methods of washing, disinfecting, and thermo-assisted drying and decontamination (TADD) have been evaluated for their effectiveness in inactivating porcine reproductive and respiratory syndrome virus (PRRSV) on contaminated surfaces. Information on when to expect negative qRT-PCR results after adequate trailer sanitation is lacking. The objective of this study was to evaluate whether there are conditions associated with washing-disinfectant-TADD procedures that will consistently produce a negative qRT-PCR result for the purpose of monitoring compliance with trailer sanitation and decontamination protocols for PRRSV on metal surfaces. 144 diamond plate aluminum coupons were spiked with PRRSV or phosphate-buffered saline (PBS) and treated with a designated disinfectant protocol. Disinfectants evaluated included multiple accelerated® hydrogen peroxide (AHP) disinfectants and a quaternary ammonium and glutaraldehyde combination disinfectant. Disinfectant was applied for 5 or 60 minutes of contact time at either 20 °C or -10 °C in a matrix of feces or PBS. All coupons were heated until the surface temperature of the coupon reached 71 °C and then held for 10 minutes to simulate TADD under field conditions. Post-treatment swabs for all treatment groups, except negative control groups, were positive by PRRSV qRT-PCR. Under the conditions evaluated in this study, consistently negative qRT-PCR results after treatments were not found. Therefore, for the purpose of monitoring compliance with trailer sanitation and decontamination protocols for PRRSV, alternatives to qRT-PCR should be explored., (Copyright © 2021 Elsevier B.V. All rights reserved.)

There has been a tremendous increase in recent years of population-based diagnostic monitoring and surveillance strategies in swine populations. One example is the use of processing fluids (PF) to screen breeding herds for porcine reproductive and respiratory syndrome virus (PRRSV) activity. An important question from practitioners using such methods is on how intensively can the sample be pooled. More specifically, processing fluids of how many litters can be pooled into a single sample for diagnostic testing to preserve a high probability of PRRSV RNA detection at low prevalence situations? The objective of this study was to model the effect of pooling PF samples on the probability of PRRSV RNA detection. For this study, a PRRSV-positive PF field sample with a RT-rtPCR quantification cycle (Cq) value of 28 was selected to represent a litter of 11 pigs with a single viremic piglet. PF samples from a PRRSV-naïve herd were used to perform 6 replications of 8 two-fold serial dilutions of the PRRSV-positive sample, thus modeling the pooling effect (dilution). Each two-fold dilution represented an increase in the number of PRRS-negative pigs in the sample by a factor of 2. Samples were tested for PRRSV RNA by RT-rtPCR and the data was analyzed using linear and probit regression models. There was an average increment of 1.37 points in Ct for each two-fold dilution. The estimated probability of testing positive on RT-rtPCR was 43 %, 80 %, and 95 % when there was a single PRRSv-positive piglet among 784, 492, and 323 PRRSv-negative piglets contributing to the sample respectively. Results from this study support the practice of collecting and aggregating PF samples from multiple litters for PRRSV RNA testing., (Copyright © 2021 Elsevier B.V. All rights reserved.)

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., (Copyright © 2021 Elsevier B.V. All rights reserved.)

PRRS is a viral disease characterized by increasing reproduction losses in breeding herds and worsening performance of growing pigs, which leads to a considerable economic impact. A better understanding of the differences in the infection patterns of the virus in growing pig batches would help to develop cost-effective surveillance methods and disease control and elimination programs. Therefore, field studies documenting growing pig productivity according to the patterns of wild-type-PRRSV (wt-PRRSV) detection in the field are needed. This study was conducted with the objectives to (1) characterize patterns of wt-PRRSV-1 and wt-PRRSV-2 RNA detection over time in modified-live virus (MLV)-vaccinated batches of growing pigs raised in pig-dense regions of the USA; (2) compare wean-to-finish mortality among batches of growing pigs characterized with the different patterns of wt-PRRSV-1 and wt-PRRSV-2 detection; and (3) compare wean-to-finish mortality among batches of growing pigs characterized with the different patterns of wt-PRRSV-2 detection and vaccinated with two different doses of PRRS MLV vaccine. Eighty-one batches of growing pigs were originated from PRRSV positive-stable and unstable sow farms and vaccinated with two different doses of PRRS MLV vaccine. All batches were monitored for wt-PRRSV by testing six oral fluids every three weeks from weaning to marketing. Diagnostics were conducted to detect wt-PRRSV-1 and wt-PRRSV-2 by RT-qPCR testing and ORF-5 region sequencing. K-means clustering analysis was applied to identify batches sharing similar patterns of wt-PRRSV detection over time. Regression analyses were used to compare mortality among batches of growing pigs characterized with different patterns of wt-PRRSV detection over time. Thirty-eight percent of batches were detected with wt-PRRSV-1 during the growth phase, with three different patterns of detection. Detection of wt-PRRSV-1 was not associated with significant increase on mortality. Ninety-one percent of batches were detected with wt-PRRSV-2 during the growth phase, with four different patterns of detection. Batches originated from PRRSV positive-unstable farms had highest mortality rate (p < 0.0001) and were characterized as Unstable wt-PRRSV-2 detection pattern. Batches characterized with Early wt-PRRSV-2 detection pattern had higher mortality than batches characterized by Mid, Late and No wt-PRRSV-2 detection during the growth phase (p < 0.0001). Batches with Mid wt-PRRSV-2 detection had higher mortality than batches characterized with Late wt-PRRSV-2 detection (p < 0.0124). Mortality rate of batches characterized with Unstable and Early wt-PRRSV-2 detection patterns was lower when pigs were vaccinated with two doses of PRRS MLV vaccine, compared to batches that received only one dose. Results presented in this study suggested that early wt-PRRSV exposure on pig populations was associated with higher wean-to-finish mortality. Additionally, results suggested that vaccination with two PRRS MLV doses was associated with lower mortality rate, when growing pig populations had early wt-PRRSV exposure., (Copyright © 2021 Elsevier B.V. All rights reserved.)

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%)., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Investments in biosecurity practices are made by producers to reduce the likelihood of introducing pathogens such as porcine reproductive and respiratory syndrome virus (PRRSv). The assessment of biosecurity practices in breeding herds is usually done through surveys. The objective of this study was to evaluate the use of machine-learning (ML) algorithms to identify key biosecurity practices and factors associated with breeding herds self-reporting (yes or no) a PRRS outbreak in the past 5 years. In addition, we explored the use of the positive predictive value (PPV) of these models as an indicator of risk for PRRSv introduction by comparing PPV and the frequency of PRRS outbreaks reported by the herds in the last 5 years. Data from a case control study that assessed biosecurity practices and factors using a survey in 84 breeding herds in U.S. from 14 production systems were used. Two methods were developed, method A identified 20 variables and accurately classified farms that had reported a PRRS outbreak in the previous 5 years 76% of the time. Method B identified six variables which 5 of these had already been selected by model A, although model B outperformed the former model with an accuracy of 80%. Selected variables were related to the frequency of risk events in the farm, swine density around the farm, farm characteristics, and operational connections to other farms. The PPVs for methods A and B were highly correlated to the frequency of PRRSv outbreaks reported by the farms in the last 5 years (Pearson r = 0.71 and 0.77, respectively). Our proposed methodology has the potential to facilitate producer's and veterinarian's decisions while enhancing biosecurity, benchmarking key biosecurity practices and factors, identifying sites at relatively higher risk of PRRSv introduction to better manage the risk of pathogen introduction., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Background: To mitigate production impact of porcine reproductive and respiratory syndrome (PRRS) virus outbreaks, it has been common to preventively vaccinate swine breeding herds using PRRS modified live virus (MLV) vaccine. However, attenuated PRRS virus (PRRSv) may result negative impact on farm productivity. The objective of this study was to measure the immediate impact of PRRS type 2 MLV vaccine on breeding herd performance under field conditions. Eight PRRS-stable farms routinely mass vaccinating females with commercial PRRS MLV vaccines were enrolled on study. Vaccination dates were collected and weekly changes in abortions, neonatal losses, pre-weaning mortality, pigs weaned per sow, and wean-to-first-service interval were assessed for up to 6 weeks after each vaccination. A 6-week period prior to each vaccination was established as baseline. Statistical process control (SPC) analysis was conducted to detect significant productivity decreases after MLV interventions, on each farm, and a mixed regression model was used, at the aggregated data level, to assess the productivity change 6 weeks after PRRS MLV vaccinations, compared to baseline., Results: Out of 65 herd-MLV vaccinations, SPC analysis detected increase on abortions 4 times (6.1%), on neonatal losses 7 times (10.7%), on pre-weaning mortality 2 times (3%), on wean-to-first-service interval 2 times (3%), and no change in total pigs weaned. On aggregated data analysis, there was no significant change in abortion rate, neonatal losses, number of pigs weaned per sow, and wean-to-first-service interval. However, there was an increase of 0.26% of pre-weaning mortality 2 weeks after vaccination compared to the baseline., Conclusions: Under study conditions, individual PRRS-stable sow farms had experienced transient, and numerically small changes in productivity following PRRS type 2 MLV vaccination. There was a small increase of pre-weaning mortality 2 weeks after vaccination, but no evidence of significant production impact at aggregated data analysis for abortion rate, neonatal losses, pigs weaned per sow and wean-to-first-service interval., Competing Interests: Competing interestsThe authors declare that they have no competing interests.

Modern commercial pig production is a complex process that requires successful producers to understand and resolve factors associated with perturbations in production. One important perturbation is inventory loss due to mortality. In this study, data on 60 lots of approximately 2000 weaned pigs (n = 115,213) from one commercial production system were collected through the wean-to-finish (WTF) cycle with the objective of establishing patterns of mortality, estimating differences in profit/loss among patterns of mortality, and identifying production practices associated with mortality patterns. Information provided by the production system included the number of pigs in each lot at the time of placement (beginning inventory), weaning weight, barn dimensions, number of dead pigs (NDP) daily, capacity placed (proportion pigs actually placed versus what had been planned to be placed) and average weight sold. Analysis of NDP revealed three mortality patterns (clusters I, II, III) composed of 6, 40, and 14 lots, respectively, that differed in the temporal onset and/or level of mortality. Average daily gain (ADG) and feed conversion ratio (FCR) were calculated by growth phase for each cluster. An economic model showed profit differences among clusters due to poor biological performance by clusters I and III in the late finishing phase. Cluster II (n = 40) had fewer dead pigs and the highest profit compared to clusters I (n = 6) and III (n = 14). Area per pig (stocking density) was the only factor associated with the differences in mortality patterns. Routine monitoring and the analysis of mortality patterns for associations with production and management factors can help swine producers improve biological performance and improve profit.

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., (© The Author(s) 2018. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Biosecurity is defined as the set of practices carried out to prevent the introduction and spread of infectious agents in a herd. These practices are essential in swine production, especially for highly infectious agents such as porcine reproductive and respiratory syndrome virus (PRRSv). Even with years of research and experience over the last three decades, PRRSv is still causing productivity losses and is the major health problem affecting the global swine industry. Despite knowledge of the various ways in which the virus can be transmitted from one herd to another (e.g. animals, semen, truck, air, and people), determining the most frequent ways in which the virus is transmitted in the field is difficult. A systematic approach to assess vulnerabilities at a herd level related to PRRSv transmission could help producers prioritize biosecurity practices to reduce or avoid the occurrence of outbreaks. The aim of this study was to develop a biosecurity vulnerability score that represents the relative vulnerability of swine breeding herds to the introduction of PRRSv. To create the biosecurity vulnerability score (outcome), a multi-criteria decision analysis methodology was used to rank and quantify biosecurity practices based on expert opinion. To validate the biosecurity vulnerability score, a survey of biosecurity practices and PRRS outbreak histories in 125 breed-to-wean herds in the U.S. swine industry was used. Data on the frequency of PRRS outbreaks was used to test the hypothesis that biosecurity vulnerability scores were different between farms that have a low incidence of PRRS outbreaks, compared to farms that have a high incidence. In the two databases used, the scores consistently showed that farms with higher scores have a higher frequency of PRRS outbreaks. In the first validation, farms that had never had an outbreak investigation before had a significant (p < 0.02) lower score (0.29; 0.21-0.37) when compared to farms that had 2 or more outbreaks (0.43; 0.39-0.46). In the second, the farms of the control group also had significant (p < 0.004) lower scores (0.30; 0.27-0.33) compared to the case group (0.35; 0.33-0.38). Also, the results suggest that events related to swine movements, transmission by air and water, and people movements should be prioritized. The biosecurity vulnerability scores may be useful to assess vulnerabilities on biosecurity protocols in order to reduce the frequency of PRRS outbreaks and may help producers and veterinarians prioritize investments in improving biosecurity practices over time., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Veterinary diagnostic laboratories (VDLs) play a significant role in the prevention and mitigation of endemic animal diseases and serve an important role in surveillance of, and the response to, outbreaks of transboundary and emerging animal diseases. They also allow for business continuity in livestock operations and help improve human health. Despite these critical societal roles, there is no academic literature on the economic impact of VDLs. We present a case study on the economic impact of the Iowa State University Veterinary Diagnostic Laboratory (ISUVDL). We use economic contribution analysis coupled with a stakeholder survey to estimate the impact. Results suggest that the ISUVDL is responsible for $2,162.46 million in direct output, $2,832.45 million in total output, $1,158.19 million in total value added, and $31.79 million in state taxes in normal years. In an animal health emergency this increases to $8,446.21 million in direct output, $11,063.06 million in total output, $4,523.70 million in total value added, and $124.15 million in state taxes. The ISUVDL receives $4 million annually as a direct state government appropriation for operating purposes. The $31.79 million in state taxes in normal years and the $124.15 million in state taxes in an animal health emergency equates to a 795% and 3104% return on investment, respectively. Estimates of the economic impact of the ISUVDL provide information to scientists, administrators, and policymakers regarding the efficacy and return on investment of VDLs., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Porcine epidemic diarrhea virus (PEDV) spread rapidly across the United States in part due to contaminated livestock trailers. The objective of this study was to test a peroxygen-based disinfectant for the ability to inactivate PEDV on aluminum surfaces at 4 °C or -10 °C. Forty 3-week-old individually housed barrows were used as a bioassay to determine the infectivity of PEDV after treatment with either a 1:100 or 1:600 dilution of a peroxygen-based disinfectant with 10 or 30 min of contact time. One coupon matched to one pig was the experimental unit. Coupons in the positive control and disinfectant treatment groups were contaminated with 2 mL of feces spiked with PEDV. A negative control group was contaminated with PEDV-negative feces. Following treatment, the feces and disinfectant remaining in the coupons was collected and administered to pigs intragastrically. Rectal swabs were collected from pigs 3 and 7 days post-inoculation (DPI) and tested for PEDV by RT-qPCR. Samples from all coupons, except the negative control, were positive by RT-qPCR for PEDV before and after treatment. All rectal swabs from the pigs in the negative control and the seven disinfectant treatment groups were RT-qPCR negative for PEDV on 3 and 7 DPI. All pigs in the positive control at 4 °C and 3 of 4 pigs in the positive control conducted at -10 °C were RT-qPCR positive for PEDV on 3 and 7 DPI. Both the 1:100 and 1:600 dilutions of peroxygen-based disinfectant successfully inactivated PEDV under the conditions of this study., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Background: Since its emergence in 2013, porcine epidemic diarrhea virus (PEDV) spread rapidly throughout the country due, in part, to contaminated livestock trailers. The objective of this study was to test the efficacy of an accelerated hydrogen peroxide (AHP) disinfectant for inactivating PEDV in swine feces on metal surfaces under freezing conditions. One 15.24 X 15.24 X 2.54 cm aluminum coupon, contaminated with swine feces, and randomly matched to one pig was the experimental unit. Eight treatment groups representing two AHP concentrations (1:16 and 1:32) in a 10% propylene glycol solution, two contact times in a -10 °C freezer (40 min and 60 min), and two levels of fecal contamination (5 mL and 10 mL) in addition to negative and positive control groups were evaluated. Forty 3-week-old pigs, intragastrically inoculated with the contents of the coupons after treatment, were used as a bioassay to determine the infectivity of PEDV after treatment. Infectivity was determined by detection of virus with a nucleocapsid (N) gene-based quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR) on rectal swabs collected from the inoculated pigs on days three and seven post-inoculation., Results: All post-treatment swabs from the negative control coupons were negative for PEDV via RT-qPCR. All post-treatment swabs collected from coupons in the AHP disinfectant treatment groups and the positive control group were positive for PEDV via RT-qPCR. For the bioassay, no rectal swabs from pigs in the negative control (0 of 4) or the AHP disinfectant treatment groups (0 of 32) were positive for PEDV. Rectal swabs from all pigs within the positive control group (4 of 4) were positive for PEDV by RT-qPCR., Conclusions: Under the conditions of this study, 1:16 and 1:32 dilutions of the AHP disinfectant successfully inactivated PEDV in swine feces on metal surfaces when applied at -10 °C with 40 or 60 min of contact time. This study also suggests that a positive RT-qPCR result for PEDV on an environmental sample should be expected when the AHP disinfectant is applied under freezing conditions, but does not necessarily indicate that an infectious dose of PEDV remains after disinfection.

In May of 2013, porcine epidemic diarrhea virus (PEDV) was detected in swine for the first time in North America. It spread rapidly, in part due to contaminated livestock trailers. The objective of this study was to test the efficacy of an accelerated hydrogen peroxide disinfectant for inactivating PEDV in the presence of feces on metal surfaces, such as those found in livestock trailers. Three-week-old barrows were inoculated intragastrically with 5 mL of PEDV-negative feces for the negative control, 5 mL of untreated PEDV-positive feces for the positive control, and 5 mL or 10 mL of PEDV-positive feces that was subjected to treatment with a 1:16 or 1:32 concentrations of accelerated hydrogen peroxide disinfectant for a contact time of 30 min at 20°C. These pigs served as a bioassay to determine the infectivity of virus following treatment. Rectal swabs collected from the inoculated pigs on days 3 and 7 post-inoculation were tested by using PEDV-specific real-time reverse transcription polymerase chain reaction and the proportion of pigs in each group that became infected with PEDV was assessed. None of the pigs used for the bioassay in the 4 treatment groups and the negative control group became infected with PEDV, which was significantly different from the positive control group ( P < 0.05) in which all pigs were infected. The results suggest that the application of the accelerated hydrogen peroxide under these conditions was sufficient to inactivate the virus in feces found on metal surfaces.

Epidemiological investigations were conducted on a case series of six Senecavirus A (SVA)-affected breeding herds in the United States to determine potential routes of introduction and enhance the swine industry's knowledge of SVA's clinical presentation and spread. Each SVA-affected herd was evaluated using a standard form to ensure that all relevant data were collected. The form was used to guide a detailed discussion about the clinical presentation of SVA and risk events that occurred in the 4 weeks prior to the first observation of clinical signs with the herd veterinarian and farm personnel. Each event was then subjectively assigned a risk level of low, medium or high likelihood for SVA introduction by the investigation team. The clinical presentation of SVA varied by case. All SVA-affected herds (six of six) reported increases in pre-weaning mortality and sow anorexia. Vesicular lesions were observed in four of six herds, and mild-to-moderate neonatal diarrhoea was observed in three of six herds. No gross anatomic or histologic lesions were observed in neonatal pigs that tested positive for SVA via PCR. Multiple potential routes of introduction were identified. Events subjectively rated as high risk for SVA introduction were on-farm employee entry (six of six), carcass disposal (four of six), cull sow removal (three of six) and breeding replacement entry (two of six). Non-swine domestic animals, rodents, other visitors, repairs outside swine barns, feed delivery, weaned pig removal and semen entry were assigned a high risk level in one of six herds. Cases occurred in breeding herds of all sizes with variable biosecurity in both swine dense and swine sparse areas., (© 2016 Blackwell Verlag GmbH.)