Presentations | Interviews | Podcasts

Dr. Marcello Melini: Do all PRRS variants have the same level of infectiousness? (Sept 18, 2023, Leman Conference)

Dr. Mariana Kikuti: Time U.S. breeding herds remains PRRS naïve (Sept 17, Leman Conference)

[Portuguese] Dr. Mariana Kikuti: Vigilância ativa na suinocultura: Monitoramento regional de doenças em tempo real para prevenção de emergências (Sept 16, 2023, Leman Conference)

[Spanish] Dr. Marcello Melini: Cepas altamente virulentas y nuevas tendencias en el monitoreo de PRRS (Aug 9, 2023, Campus Porcino)

Dr. Mariana Kikuti: Reducing Losses, Maximizing Profits: Examining Sow Mortality (Jun 10, 2023,  The Swine Health Blackbelt podcast)

[Spanish] Dr. Cesar Corzo: Epidemiología y Herramientas de control: Síndrome Reproductivo y Respiratorio Porcino (PRRS) (May 1, 2023, MSD Salud Animal Latinoamérica)

Dr. Mariana Kikuti: PRRSV 1C variant - Will it stick around? (Jul 27, 2022, The Swine Health Blackbelt podcast)

 

Dr. Cesar Corzo: PRRS Management Workshop (Jul 15, 2022, Des Moines, IA)

Dr. Cesar Corzo: Understanding PRRS 1 4 4 (Oct 28, 2021, Pork checkoff webinar).

 

Dr. Dennis Makau: Post-epidemic dynamics of PEDV in the U.S:. Current trends and patterns (Sept 21, 2021, Leman Conference)

 

Dr. Mariana Kikuti: Characterization of the current PRRS Lineage 1C 1-4-4 Outbreak (Sept 20, 2021, Leman Conference)

 

Dr. Cesar Corzo: PRRS Occurrence in the U.S. Breeding Herd: An overview (Sept 20, 2021, Leman Conference)

 

Dr. Catalina Picasso-Risso: Overview of Porcine Deltacoronavirus Occurrence in the United States Breeding Herds (Sept 21, 2021, Leman Conference)

 

Dr. Cesar Corzo: How to have a successful disease control program? (Jan 11, 2021, Swine it)

 

Dr. Mariana Kikuti: Understanding PRRSV diversity at the pig and litter levels using whole-genome sequencing (Sept 21, 2020, Leman Conference)

 

Dr. Carles Vilalta: Comparison of Different Sampling Methodologies in Due-to-Wean Piglets and Litters (Sept 16, 2019, Leman Conference)

 

Dr. Juan Sanhueza: Investigation of gilts as a factor for delayed Time-to-Stability (Sept 16, 2019, Leman Conference)

 

Dr. Juan Sanhueza: PRRS Factors Related to Time-to-Stability and Summer Breaks (Sept 17, 2018, Leman Conference)

 

Dr. Carles Vilalta: Epidemiology of PRRS in the filtered sow farm population (Sept 17, 2018, Leman Conference)

Dr. Cesar Corzo: Brief update on MSHMP (Sept 17, 2018, Leman Conference)

 

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Publications

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2024: Porcine Deltacoronavirus Occurrence in the United States Breeding Herds since Its Emergence in 2014

Kikuti, M., Picasso-Risso, C., & Corzo, C. A. (2024). Porcine Deltacoronavirus Occurrence in the United States Breeding Herds since Its Emergence in 2014. Viruses, 16(3), 445. doi: https://doi.org/10.3390/v16030445

Abstract

PDCoV, an enveloped RNA virus, causes atrophic enteritis in neonatal piglets, leading to diarrhea, malabsorption, dehydration, and death. The study aims to fill the gap in the current epidemiological information about PDCoV in the U.S. pig population after its emergence in 2014. Data from the Morrison Swine Health Monitoring Project (MSHMP) between January 2015 and December 2023 were analyzed, representing approximately 60% of the U.S. breeding herd. Participating herds report weekly PDCoV health status. In total, 244 PDCoV outbreaks occurred in 186 sites from 22 production systems across 16 states. Case counts peaked during winter, and incidence ranged from 0.44% in 2017 to 4.28% in 2023. For sites that experienced more than one PDCoV outbreak during the study period, the interval between outbreaks was a median of 2.11 years. The South and Midwest regions reported the majority of cases. In 2017, a shift in the spatial distribution of cases from the Midwest to the South was observed. The findings underscore the importance of continued monitoring and strengthened control measures to mitigate the impact of PDCoV in U.S. breeding herds.

2024: Survival of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) in the Environment

Lugo Mesa V, Quinonez Munoz A, Sobhy NM, Corzo CA, Goyal SM. Survival of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) in the Environment. Vet Sci. 2024 Jan 5;11(1):22. doi: https://doi.org/10.3390/vetsci11010022. PMID: 38250928.

Simple Summary

This review summarizes the available information on the ex-vivo survival of the porcine reproductive and respiratory syndrome virus (PRRSV), the cause of porcine reproductive and respiratory syndrome in pigs. We highlight the possible role of different fomites and environmental sources in indirect transmission of this virus to susceptible hosts. The number of studies on this topic is limited but fomites (porous, non-porous, and liquid), insects, people, and pork meat have been studied, mostly under experimental conditions.
 
Abstract
 
Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically important diseases of swine, with losses due to poor reproductive performance and high piglet and growing pig mortality. Transmission of porcine reproductive and respiratory syndrome virus (PRRSV) may occur by both direct and indirect routes; the latter includes exposure to PRRSV-contaminated fomites, aerosols, and arthropod vectors. This review has collected available data on the ex-vivo environmental stability and persistence of PRRSV in an effort to highlight important sources of the virus and to determine the role of environmental conditions on the stability of the virus, especially temperature. The ex-vivo settings include fomites (solid, porous, and liquid fomites), insects, people, and pork meat, as well as the role of environmental conditions on the stability of the virus, especially temperature.

2024: Improvements in swine herd biosecurity reduce the incidence risk of porcine reproductive and respiratory syndrome virus in breeding herds in the Midwestern United States

Dee S, Brands L, Nerem J, Schelkopf A, Spronk G, Kikuti M, Corzo C, Havas K. Improvements in swine herd biosecurity reduce the incidence risk of porcine reproductive and respiratory syndrome virus in breeding herds in the Midwestern United States. J Am Vet Med Assoc. 2024 Jan 5:1-6. doi: https://doi.org/10.2460/javma.23.08.0437. Epub ahead of print. PMID: 38183764.

Abstract

Objective

Porcine reproductive and respiratory syndrome (PRRS) is a significant disease of swine. The purpose of this study was to determine whether application of a comprehensive, science-based approach to breeding herd biosecurity, known as next-generation biosecurity (NGB), could reduce PRRS incidence risk across a large commercial production company.

Animals

Pigs (381,404 sows across 76 breeding herds).

Methods

From 2009 to 2020, the annual incidence risk of PRRS in sow farms managed by the same company averaged 33%, ranging from 20% to 50%. To measure the effect of NGB on PRRS incidence risk, a retrospective cohort study was conducted from July 1, 2021, to June 30, 2023, across breeding herds managed by the same company. During the analysis, 2 groups of herds emerged: those that implemented protocols for all phases of NGB (NGB COMPLETE), and those that implemented all described protocols of biosecurity except for air filtration (NGB INCOMPLETE).

Results

During the 2-year assessment period, 56 breeding herds were classified as NGB COMPLETE, while 20 herds were NGB INCOMPLETE. The PRRS incidence risk in NGB COMPLETE herds was 8.9% as compared to 40.0% in NGB INCOMPLETE herds. From disease year 1 (July 1, 2021, to June 30, 2022) and disease year 2 (July 1, 2022, to June 30, 2023), system-wide PRRS incidence risk was 8.6% and 9.2%, respectively. The association between NGB status and PRRS incidence risk for the 2-year period was statistically significant at a P value of .006.

Clinical Relavence

Results of the present report provided evidence that improvements in biosecurity result in lower PRRS incidence risk under large-scale commercial swine production conditions.

2023: Porcine Reproductive and Respiratory Syndrome (PRRSV2) Viral Diversity within a Farrow-to-Wean Farm Cohort Study

Kikuti, M.; Vilalta, C.; Sanhueza, J.; Pamornchainavakul, N.; Kevill, J.; Yang, M.; Paploski, I.A.D.; Lenskaia, T.; Odogwu, N.M.; Kiehne, R.; VanderWaal, K.; Schroeder, D. and Corzo, C., Porcine Reproductive and Respiratory Syndrome (PRRSV2) Viral Diversity within a Farrow-to-Wean Farm Cohort Study. Viruses 2023, 15, 1837. https://doi.org/10.3390/v15091837

Abstract

Describing PRRSV whole-genome viral diversity data over time within the host and within-farm is crucial for a better understanding of viral evolution and its implications. A cohort study was conducted at one naïve farrow-to-wean farm reporting a PRRSV outbreak. All piglets 3–5 days of age (DOA) born to mass-exposed sows through live virus inoculation with the recently introduced wild-type virus two weeks prior were sampled and followed up at 17–19 DOA. Samples from 127 piglets were individually tested for PRRSV by RT-PCR and 100 sequences were generated using Oxford Nanopore Technologies chemistry. Female piglets had significantly higher median Ct values than males (15.5 vs. 13.7, Kruskal–Wallis p < 0.001) at 3–5 DOA. A 52.8% mortality between sampling points was found, and the odds of dying by 17–19 DOA decreased with every one unit increase in Ct values at 3–5 DOA (OR = 0.76, 95% CI 0.61–0.94, p = 0.01). Although the within-pig percent nucleotide identity was overall high (99.7%) between 3–5 DOA and 17–19 DOA samples, ORFs 4 and 5a showed much lower identities (97.26% and 98.53%, respectively). When looking solely at ORF5, 62% of the sequences were identical to the 3–5 DOA consensus. Ten and eight regions showed increased nucleotide and amino acid genetic diversity, respectively, all found throughout ORFs 2a/2b, 4, 5a/5, 6, and 7.

2023: Estimating the effectiveness of control actions on African swine fever transmission in commercial swine populations in the United States

Sykes, A.L., Galvis, J.A., O’Hara, K.C., Corzo, C. and Machado, G., 2023. Estimating the effectiveness of control actions on African swine fever transmission in commercial swine populations in the United States. Preventive Veterinary Medicine, p.105962. https://doi.org/10.1016/j.prevetmed.2023.105962

Abstract

Given the proximity of African swine fever (ASF) to the U.S., there is an urgent need to better understand the possible dissemination pathways of the virus within the U.S. swine industry and to evaluate mitigation strategies. Here, we extended PigSpread, a farm-level spatially-explicit stochastic compartmental transmission model incorporating six transmission routes including between-farm swine movements, vehicle movements, and local spread, to model the dissemination of ASF. We then examined the effectiveness of control actions similar to the ASF national response plan. The average number of secondary infections during the first 60 days of the outbreak was 49 finisher farms, 17 nursery farms, 5 sow farms, and less than one farm in other production types. The between-farm movements of swine were the predominant route of ASF transmission with an average contribution of 71.1%, while local spread and movement of vehicles were less critical with average contributions of 14.6% and 14.4%. We demonstrated that the combination of quarantine, depopulation, movement restrictions, contact tracing, and enhanced surveillance, was the most effective mitigation strategy, resulting in an average reduction of 79.0% of secondary cases by day 140 of the outbreak. Implementing these control actions led to a median of 495,619 depopulated animals, 357,789 diagnostic tests, and 54,522 movement permits. Our results suggest that the successful elimination of an ASF outbreak is likely to require the deployment of all control actions listed in the ASF national response plan for more than 140 days, as well as estimating the resources needed for depopulation, testing, and movement permits under these controls.

2023: Mapping the Dynamics of Contemporary PRRSV-2 Evolution and Its Emergence and Spreading Hotspots in the U.S. Using Phylogeography

Pamornchainavakul, N., Paploski, I.A., Makau, D.N., Kikuti, M., Rovira, A., Lycett, S., Corzo, C.A. and VanderWaal, K., 2023. Mapping the Dynamics of Contemporary PRRSV-2 Evolution and Its Emergence and Spreading Hotspots in the US Using Phylogeography. Pathogens, 12(5), p.740. https://doi.org/10.3390/pathogens12050740

Abstract

The repeated emergence of new genetic variants of PRRSV-2, the virus that causes porcine reproductive and respiratory syndrome (PRRS), reflects its rapid evolution and the failure of previous control efforts. Understanding spatiotemporal heterogeneity in variant emergence and spread is critical for future outbreak prevention. Here, we investigate how the pace of evolution varies across time and space, identify the origins of sub-lineage emergence, and map the patterns of the inter-regional spread of PRRSV-2 Lineage 1 (L1)—the current dominant lineage in the U.S. We performed comparative phylogeographic analyses on subsets of 19,395 viral ORF5 sequences collected across the U.S. and Canada between 1991 and 2021. The discrete trait analysis of multiple spatiotemporally stratified sampled sets (n = 500 each) was used to infer the ancestral geographic region and dispersion of each sub-lineage. The robustness of the results was compared to that of other modeling methods and subsampling strategies. Generally, the spatial spread and population dynamics varied across sub-lineages, time, and space. The Upper Midwest was a main spreading hotspot for multiple sub-lineages, e.g., L1C and L1F, though one of the most recent emergence events (L1A(2)) spread outwards from the east. An understanding of historical patterns of emergence and spread can be used to strategize disease control and the containment of emerging variants.

2023: Disentangling transport movement patterns of trucks either transporting pigs or while empty within a swine production system before and during the COVID-19 epidemic

Picasso-Risso, C., Vilalta, C., Sanhueza, J.M., Kikuti, M., Schwartz, M. and Corzo, C.A., 2023. Disentangling transport movement patterns of trucks either transporting pigs or while empty within a swine production system before and during the COVID-19 epidemic. Frontiers in Veterinary Science, 10, p.1201644. https://doi.org/10.3389/fvets.2023.1201644

Abstract

Transport of pigs between sites occurs frequently as part of genetic improvement and age segregation. However, a lack of transport biosecurity could have catastrophic implications if not managed properly as disease spread would be imminent. However, there is a lack of a comprehensive study of vehicle movement trends within swine systems in the Midwest. In this study, we aimed to describe and characterize vehicle movement patterns within one large Midwest swine system representative of modern pig production to understand movement trends and proxies for biosecurity compliance and identify potential risky behaviors that may result in a higher risk for infectious disease spread. Geolocation tracking devices recorded vehicle movements of a subset of trucks and trailers from a production system every 5 min and every time tracks entered a landmark between January 2019 and December 2020, before and during the COVID-19 pandemic. We described 6,213 transport records from 12 vehicles controlled by the company. In total, 114 predefined landmarks were included during the study period, representing 5 categories of farms and truck wash facilities. The results showed that trucks completed the majority (76.4%, 2,111/2,762) of the recorded movements. The seasonal distribution of incoming movements was similar across years (P > 0.05), while the 2019 winter and summer seasons showed higher incoming movements to sow farms than any other season, year, or production type (P < 0.05). More than half of the in-movements recorded occurred within the triad of sow farms, wean-to-market stage, and truck wash facilities. Overall, time spent at each landmark was 9.08% higher in 2020 than in 2019, without seasonal highlights, but with a notably higher time spent at truck wash facilities than any other type of landmark. Network analyses showed high connectivity among farms with identifiable clusters in the network. Furthermore, we observed a decrease in connectivity in 2020 compared with 2019, as indicated by the majority of network parameter values. Further network analysis will be needed to understand its impact on disease spread and control. However, the description and quantification of movement trends reported in this study provide findings that might be the basis for targeting infectious disease surveillance and control.

2023: Time farms stay naïve for Porcine Reproductive and Respiratory Syndrome

Kikuti, M., Picasso-Risso, C., Melini, C.M. and Corzo, C.A., 2023. Time Farms Stay Naïve for Porcine Reproductive and Respiratory Syndrome. Animals, 13(2), p.310. https://doi.org/10.3390/ani13020310

Simple Summary

Porcine Reproductive and Respiratory Syndrome (PRRS) is one of the main infectious diseases affecting swine herds in the U.S. Control and elimination are facing challenges, including the absence of a vaccine that confers sterilizing immunity. Elimination through herd closure can also be a long, uncertain, and costly process, with herds often taking around 41 weeks to start consistently weaning virus-free piglets after an outbreak is detected. Thus, producers and practitioners may hesitate in pursuing elimination if there is a perception that the herd will soon face another PRRS outbreak, opting instead to maintain some level of immunity in the herd indefinitely. Of all the breeding herds monitored over 12 years, only about 1/6 eliminated PRRS from their herds and remained, on average, PRRS-free for two years. After eliminating PRRS, the average percentage of new outbreaks per year was 23%, similar to the national average of 20–25% (regardless of the previous PRRS status). Additional factors might contribute to the decision to pursue elimination, and further studies are warranted.

Abstract

Background: Hesitation on eliminating Porcine Reproductive and Respiratory Syndrome virus (PRRSV) from breeding herds exists since it is difficult to predict how long the herd will remain virus-free. We aimed to estimate the time that breeding herds remained virus-free (naïve) after PRRSV elimination was achieved. Methods: Production systems voluntarily shared their breeding herds’ health status weekly between July 2009 and October 2021. PRRSV incidence rate and the total number of days a breeding herd remained virus-free were estimated. Results: A total of 221 (17%) herds reached the naïve status 273 times. The median time sites remained in this status was approximately two years. The overall PRRS incidence rate after sites achieved a naïve status was 23.43 PRRS outbreaks per 100 farm years. Conclusion: Estimates obtained here provide insights on how frequently and for how long sites remain naïve, which contribute to informing management practices for PRRS control.

2023: Assessing the role of sow parity on PRRSv detection by RT-qPCR through weekly processing fluids monitoring in breeding herds

Sanhueza, J.M., Schwartz, M., Corzo, C.A., Kikuti, M., Yeske, P., Leuwerke, B., Schelkopf, A., Williams, T., Feuerbach, S., Johnson, C. and Toohill, E., 2023. Assessing the role of sow parity on PRRSv detection by RT-qPCR through weekly processing fluids monitoring in breeding herds. Preventive Veterinary Medicine, 213, p.105854. https://doi.org/10.1016/j.prevetmed.2023.105854

Highlights

•Processing fluids were used to monitor the breeding herd PRRS status.

•PRRS virus maintenance in breeding herds was not affected by the sow parity.

•An aggregated sample of 15 litters correlated with individual litter results.

•At least nine weeks of negative results were possible before a positive result.

 

Abstract

The use of processing fluids to monitor the breeding herd’s porcine reproductive and respiratory syndrome (PRRS) status has gained industry acceptance. However, little is known about PRRS virus RT-qPCR detection dynamics in processing fluids and factors that may contribute to maintain PRRS virus in the herd after an outbreak. This study aimed to describe weekly RT-qPCR processing fluid results in breeding herds after an outbreak and to evaluate the proportion of RT-qPCR positive results among parity groups. Processing tissues of 15 first parity (P1), 15 second parity (P2), and 15 third parity or higher (P3+) litters (parity groups) were collected weekly for between 19 and 46 weeks in nine breeding herds. Processing fluids were aggregated, and RT-qPCR tested by parity group weekly. Additionally, a subset of 743 processing fluid samples of litters that formed 50 parity groups, as previously described, were RT-qPCR tested individually at the litter level. The agreement between RT-qPCR results of processing fluid samples of parity groups (15 litters) and results based on individual litter testing was assessed using overall percent of agreement, Kappa statistic, and McNemar test. The association between RT-qPCR results and the parity group was evaluated using a generalized estimating equations model, after accounting for the effects of sampling week, breeding herd PRRS control strategy (i.e., open to replacements v/s closed) and herd. An autoregressive correlation structure was used to account for the repeated samplings within a herd in time. The overall agreement was 98 %, and Kappa statistic 0.955 (McNemar p = 1.0). Sensitivity of parity group processing fluid samples was estimated at 100 % (95 % CI 89–100 %), while specificity was estimated at 94 % (95 % CI 71–100 %). Although P1 aggregated litters had on average a higher proportion of RT-qPCR positive results from outbreak week 25 onwards, the proportion was not significantly different to the one observed for P2 and P3+ aggregated litters (p > 0.13). Additionally, herds that interrupted gilt entry had lower odds of PRRS RT-qPCR positivity than herds that continued entering gilts (OR = 0.35, 95 % CI 0.16–0.78). PRRS virus persistence in processing fluids was not affected by the sow parity effect in most of the breeding herds studied. No evidence of disagreement between RT-qPCR results of an aggregated sample of 15 litters and those of individual litters was observed. This level of litter aggregation testing strategy may be of particular use at the last stages of an elimination program under low PRRS virus prevalence.

2022: Sow mortality in a pig production system in the midwestern USA: Reasons for removal and factors associated with increased mortality

Kikuti, M., Preis, G.M., Deen, J., Pinilla, J.C. and Corzo, C.A., 2022. Sow mortality in a pig production system in the midwestern USA: Reasons for removal and factors associated with increased mortality. Veterinary Record, p.e2539. https://doi.org/10.1002/vetr.2539

Background

Sow mortality has become a growing concern in the pig production industry over the past decade. Therefore, we aimed to describe sow mortality and associated factors in a production system in the midwestern USA.

Methods

Mortality records from 2009 to 2018 for four farrow-to-wean farms were described. Environmental, farm- and individual-level factors associated with weekly mortality and individual risk of dying throughout a sow's lifetime were assessed.

Results

Deaths occurred at a median of 116 days from last service, or 26 days postpartum. The median parity upon death was two. Overall, the main reasons for death were locomotion (27%) and reproduction (24%). A higher weekly number of deaths was associated with spring (incidence rate ratio [IRR] 1.27, compared to winter). Sows had a higher mortality when they were exposed to at least one porcine reproductive and respiratory syndrome (PRRS) outbreak during their lifetime (IRR 1.55) and when housed in groups (pens) during gestation (IRR 1.32). Conversely, they had  a lower mortality when housed in filtered farms (IRR 0.76), accounting for an interaction term between parity at removal and PRRS outbreak exposure.

Limitations

Issues with data completion and information accuracy were present, and prospective data collection throughout sows’ lifetimes is still needed.

Conclusion

Efforts to reduce infectious diseases within the herd and manage environmental stressors should help reduce mortality.

2022: Porcine reproductive and respiratory syndrome prevalence and processing fluids use for diagnosis in United States breeding herds

Kikuti, M., Vilalta, C., Sanhueza, J., Melini, C.M. and Corzo, C.A., 2022. Porcine reproductive and respiratory syndrome prevalence and processing fluids use for diagnosis in United States breeding herds. Frontiers in Veterinary Science, 9. 10.3389/fvets.2022.953918

Introduction

Processing fluids have been recently adopted by the U.S. swine industry as a breeding herd PRRS monitoring tool due to their increased representativeness of animals within the herd. Here, we use the Morrison Swine Health Monitoring Project (MSHMP) database, representative of ~50% of the U.S. swine breeding herd, to describe processing fluids submissions for PRRS diagnosis and their relation to PRRS prevalence and time to stability over time between 2009 and 2020.

Methods

An ecological time series Poisson regression modeling the number of status 1 farms and weekly percentage of processing fluids submissions for PRRS diagnosis was done. Time to stability was calculated for sites that detected a PRRS outbreak within the study period and modeled through a proportional hazards mixed effect survival model using production system as a random-effect factor and epiweek as a panel variable.

Results

Processing fluids diagnosis submissions increased starting in 2017. The difference between each year's highest and lowest weekly prevalence averaged 10.9% between 2009 and 2017, whereas it averaged 5.0% in 2018–2020 period. Each year's lowest weekly prevalence ranged from 11.3 to 19.5% in 2009–2017 and from 22.4 to 29.2% in 2018–2020. We also detected an increasing proportion of breeding sites that did not reach stability within 1 year of reporting an outbreak (chi-square for trend p < 0.0001). The total time to stability was not associated with the region of the country in which the site was located, the site’s air filtration status, its PRRS status before the outbreak, or the different statuses a site achieved to be classified as stable, when accounting for the production system in the multivariate model. However, a higher proportion of system-wide processing fluids use was associated with increased time to stability.

Discussion

Altogether, the temporal concurrence of processing fluids used for PRRS virus monitoring suggests that the adoption of this sampling strategy may help explain the changes observed in PRRS status 1 prevalence since 2018, although further studies are still needed.

2022: Growing pig incidence rate, control and prevention of porcine epidemic diarrhea virus in a large pig production system in the United States

Kikuti, M., Drebes, D., Robbins, R., Dufresne, L., Sanhueza, J.M. and Corzo, C.A., 2022. Growing pig incidence rate, control and prevention of porcine epidemic diarrhea virus in a large pig production system in the United States. Porcine Health Management, 8(1), pp.1-7. doi.org/10.1186/s40813-022-00268-9

Background

In 2013, PEDV was introduced in the United States (U.S.) and rapidly spread across the country. Here we describe the occurrence of PEDV in the growing pig herd of one large U.S. production system through an active surveillance set in place between October 2019 and November 2020 designed to assess disease status upon placement into the growing pig site, before shipping to the slaughter plant and when diarrhea events were present at the site. We also assessed the impact of preventive procedures implemented in PEDV incidence that comprised site-specific equipment segregation and biosecurity changes regarding personnel movement between sites.

Results

36.50% (100/274) of the sites had at least one PEDV introduction event before preventive procedures were implemented, yielding an incidence rate of 2.41 per 100 farm-weeks. Most (63/100) of them occurred in sites where animals were placed negative and PEDV was detected in clinical samples in a median of 8 weeks post placement. After preventive procedures were implemented, the overall PEDV incidence rate dropped to 0.37 per 100 farm-weeks (84.65% reduction, p < 0.001).

Conclusion

These results highlight the importance of systematic surveillance to identify the burden of diseases, areas of improvement in prevention and control, and to allow the measurement of the impact of policy/protocol changes.

2022: Investigation of the distance to slaughterhouses and weather parameters in the occurrence of porcine reproductive and respiratory syndrome outbreaks in U.S. swine breeding herds

Moeller, J., Mount, J., Geary, E., Campler, M.R., Corzo, C.A., Morrison, R.B. and Arruda, A.G., 2022. Investigation of the distance to slaughterhouses and weather parameters in the occurrence of porcine reproductive and respiratory syndrome outbreaks in US swine breeding herds. The Canadian Veterinary Journal= La Revue Veterinaire Canadienne, 63(5), pp.528-534.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9009730/

Abstract

Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically important diseases affecting the swine industry. The main objective of this study was to assess whether sow farm distance to slaughterhouses and meteorological variables were associated with PRRS outbreaks. This case-control study paired 104 sow farms with or without a reported PRRS outbreak (N = 208) during the same period. Data on the distance to the closest slaughterhouse, swine density, presence of an air filtration system, or a neighboring farm, and weather conditions were collected, and a multivariable conditional logistic regression model was created to investigate the association between variables of interest and the occurrence of a PRRS outbreak.

Swine density, presence of an air filtration system, presence of a neighboring farm, and PRRS herd-level status before the outbreak were associated with the occurrence of PRRS outbreaks. Farms in areas with higher swine density and nearby swine farms had increased odds of reporting an outbreak compared to farms in low swine density areas and farms having no neighbors. Under the conditions of this study, none of the meteorological variables or the distance to the closest slaughterhouse were associated with occurrence of PRRS outbreaks.

2022: Measuring How Recombination Re-shapes the Evolutionary History of PRRSV-2: A Genome-Based Phylodynamic Analysis of the Emergence of a Novel PRRSV-2 Variant

Pamornchainavakul, N., Kikuti, M., Paploski, I.A., Makau, D.N., Rovira, A., Corzo, C.A. and VanderWaal, K., 2022. Measuring How Recombination Re-shapes the Evolutionary History of PRRSV-2: A Genome-Based Phylodynamic Analysis of the Emergence of a Novel PRRSV-2 Variant. Frontiers in veterinary science, 9. doi.org/10.3389/fvets.2022.846904

Abstract

While the widespread and endemic circulation of porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) causes persistent economic losses to the U.S. swine industry, unusual increases of severe cases associated with the emergence of new genetic variants are a major source of concern for pork producers. Between 2020 and 2021, such an event occurred across pig production sites in the Midwestern U.S. The emerging viral clade is referred to as the novel sub-lineage 1C (L1C) 1-4-4 variant. This genetic classification is based on the open reading frame 5 (ORF5) gene. However, although whole genome sequence (WGS) suggested that this variant represented the emergence of a new strain, the true evolutionary history of this variant remains unclear. To better elucidate the variant's evolutionary history, we conducted a recombination detection analysis, time-scaled phylogenetic estimation, and discrete trait analysis on a set of L1C-1-4-4 WGSs (n = 19) alongside other publicly published WGSs (n = 232) collected over a 26-year period (1995–2021). Results from various methodologies consistently suggest that the novel L1C variant was a descendant of a recombinant ancestor characterized by recombination at the ORF1a gene between two segments that would be otherwise classified as L1C and L1A in the ORF5 gene. Based on analysis of different WGS fragments, the L1C-1-4-4 variant descended from an ancestor that existed around late 2018 to early 2019, with relatively high substitution rates in the proximal ORF1a as well as ORF5 regions. Two viruses from 2018 were found to be the closest relatives to the 2020-21 outbreak strain but had different recombination profiles, suggesting that these viruses were not direct ancestors. We also assessed the overall frequency of putative recombination amongst ORF5 and other parts of the genome and found that recombination events which leave detectable numbers of descendants are not common. However, the rapid spread and high virulence of the L1C-1-4-4 recombinant variant demonstrates that inter-sub-lineage recombination occasionally found amongst the U.S. PRRSV-2 might be an evolutionary mechanisms that contributed to this emergence. More generally, recombination amongst PRRSV-2 accelerates genetic change and increases the chance of the emergence of high fitness variants.

2021: Phylogenetically Distinct Near-Complete Genome Sequences of Porcine Reproductive and Respiratory Syndrome Virus Type 2 Variants from Four Distinct Disease Outbreaks at U.S. Swine Farms over the Past 6 Years

Schroeder, D.C., Odogwu, N.M., Kevill, J., Yang, M., Krishna, V.D., Kikuti, M., Pamornchainavakul, N., Vilalta, C., Sanhueza, J., Corzo, C.A. and Rovira, A., 2021. Phylogenetically distinct near-complete genome sequences of porcine reproductive and respiratory syndrome virus type 2 variants from four distinct disease outbreaks at US swine farms over the past 6 years. Microbiology Resource Announcements, 10(33), pp.e00260-21. https://doi.org/10.1128/MRA.00260-21

Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV) continues to mutate, causing disruptive PRRS outbreaks in farms that lead to reproductive failure and respiratory disease-associated mortality. We present four new PRRSV type 2 variants in the United States belonging to four distinct orf5 sublineages within lineage 1.

2021: Emergence of a new Lineage 1C variant of Porcine Reproductive and Respiratory Syndrome Virus 2 in the United States

Kikuti, M., Paploski, I.A., Pamornchainavakul, N., Picasso-Risso, C., Schwartz, M., Yeske, P., Leuwerke, B., Bruner, L., Murray, D., Roggow, B.D. and Thomas, P., 2021. Emergence of a new lineage 1C variant of porcine reproductive and respiratory syndrome virus 2 in the United States. Frontiers in Veterinary Science, p.1223. doi.org/10.3389/fvets.2021.752938

Abstract

We report an ongoing regional outbreak of an emerging porcine reproductive and respiratory syndrome virus (PRRSV2) variant within Lineage 1C affecting 154 breeding and grow-finishing sites in the Midwestern U.S. Transmission seemed to have occurred in two waves, with the first peak of weekly cases occurring between October and December 2020 and the second starting in April 2021. Most of cases occurred within a 120 km radius. Both orf5 and whole genome sequencing results suggest that this represents the emergence of a new variant within Lineage 1C distinct from what has been previously circulating. A case-control study was conducted with 50 cases (sites affected with the newly emerged variant) and 58 controls (sites affected with other PRRSV variants) between October and December 2020. Sites that had a market vehicle that was not exclusive to the production system had 0.04 times the odds of being a case than a control. A spatial cluster (81.42 km radius) with 1.68 times higher the number of cases than controls was found. The average finishing mortality within the first 4 weeks after detection was higher amongst cases (4.50%) than controls (0.01%). The transmission of a highly similar virus between different farms carrying on trough spring rises concerns for the next high transmission season of PRRS.

2021: Porcine reproductive and respiratory syndrome virus 2 (PRRSV-2) genetic diversity and occurrence of wild type and vaccine-like strains in the United States swine industry

Kikuti, M., Sanhueza, J., Vilalta, C., Paploski, I.A.D., VanderWaal, K. and Corzo, C.A., 2021. Porcine reproductive and respiratory syndrome virus 2 (PRRSV-2) genetic diversity and occurrence of wild type and vaccine-like strains in the United States swine industry. PloS one, 16(11), p.e0259531. doi.org/10.1371/journal.pone.0259531

Abstract

Porcine reproductive and respiratory syndrome virus genotype 2 (PRRSV-2) genetic diversity in the U.S. was assessed using a database comprising 10 years’ worth of sequence data obtained from swine production systems routine monitoring and outbreak investigations. A total of 26,831 ORF5 PRRSV-2 sequences from 34 production systems were included in this analysis. Within group mean genetic distance (i.e. mean proportion of nucleotide differences within ORF5) per year according to herd type was calculated for all PRRSV-2 sequences. The percent nucleotide difference between each sequence and the ORF5 sequences from four commercially available PRRSV-2 vaccines (Ingelvac PRRS MLV, Ingelvac PRRS ATP, Fostera PRRS, and Prevacent PRRS) within the same lineage over time was used to classify sequences in wild-type or vaccine-like. The mean ORF5 genetic distance fluctuated from 0.09 to 0.13, being generally smaller in years in which there was a relative higher frequency of dominant lineage. Vaccine-like sequences comprised about one fourth of sequences obtained through routine monitoring of PRRS. We found that lineage 5 sequences were mostly Ingelvac PRRS MLV-like. Lineage 8 sequences up to 2011 were 62.9% Ingelvac PRRS ATP-like while the remaining were wild-type viruses. From 2012 onwards, 51.9% of lineage 8 sequences were Ingelvac PRRS ATP-like, 45.0% were Fostera PRRS-like, and only 3.2% were wild-type. For lineage 1 sequences, 0.1% and 1.7% of the sequences were Prevacent PRRS-like in 2009–2018 and 2019, respectively. These results suggest that repeated introductions of vaccine-like viruses through use of modified live vaccines might decrease within-lineage viral diversity as vaccine-like strains become more prevalent. Overall, this compilation of private data from routine monitoring provides valuable information on PRRSV viral diversity.

2021: Integrating animal movements with phylogeography to model the spread of PRRSV in the USA

Makau, D.N., Alkhamis, M.A., Paploski, I.A.D., Corzo, C.A., Lycett, S. and VanderWaal, K., 2021. Integrating animal movements with phylogeography to model the spread of PRRSV in the USA. Virus Evolution, 7(2), p.veab060. https://doi.org/10.1093/ve/veab060

Abstract

Viral sequence data coupled with phylodynamic models have become instrumental in investigating the outbreaks of human and animal diseases, and the incorporation of the hypothesized drivers of pathogen spread can enhance the interpretation from phylodynamic inference. Integrating animal movement data with phylodynamics allows us to quantify the extent to which the spatial diffusion of a pathogen is influenced by animal movements and contrast the relative importance of different types of movements in shaping pathogen distribution. We combine animal movement, spatial, and environmental data in a Bayesian phylodynamic framework to explain the spatial diffusion and evolutionary trends of a rapidly spreading sub-lineage (denoted L1A) of porcine reproductive and respiratory syndrome virus (PRRSV) Type 2 from 2014 to 2017. PRRSV is the most important endemic pathogen affecting pigs in the USA, and this particular virulent sub-lineage emerged in 2014 and continues to be the dominant lineage in the US swine industry to date. Data included 984 open reading frame 5 (ORF5) PRRSV L1A sequences obtained from two production systems in a swine-dense production region (∼85,000 mi2) in the USA between 2014 and 2017. The study area was divided into sectors for which model covariates were summarized, and animal movement data between each sector were summarized by age class (wean: 3–4 weeks; feeder: 8–25 weeks; breeding: ≥21 weeks). We implemented a discrete-space phylogeographic generalized linear model using Bayesian evolutionary analysis by sampling trees (BEAST) to infer factors associated with variability in between-sector diffusion rates of PRRSV L1A. We found that between-sector spread was enhanced by the movement of feeder pigs, spatial adjacency of sectors, and farm density in the destination sector. The PRRSV L1A strain was introduced in the study area in early 2013, and genetic diversity and effective population size peaked in 2015 before fluctuating seasonally (peaking during the summer months). Our study underscores the importance of animal movements and shows, for the first time, that the movement of feeder pigs (8–25 weeks old) shaped the spatial patterns of PRRSV spread much more strongly than the movements of other age classes of pigs. The inclusion of movement data into phylodynamic models as done in this analysis may enhance our ability to identify crucial pathways of disease spread that can be targeted to mitigate the spatial spread of infectious human and animal pathogens.

2021: Forecasting viral disease outbreaks at the farm-level for commercial sow farms in the U.S.

Paploski, I.A.D., Bhojwani, R.K., Sanhueza, J.M., Corzo, C.A. and VanderWaal, K., 2021. Forecasting viral disease outbreaks at the farm-level for commercial sow farms in the US. Preventive Veterinary Medicine,196, p.105449. https://doi.org/10.1016/j.prevetmed.2021.105449 

Abstract

Porcine epidemic diarrhea virus (PEDv) was introduced to the U.S. in 2013 and is now considered to be endemic. Like many endemic diseases, it is challenging for producers to estimate and respond to spatial and temporal variation in risk. Utilizing a regional spatio-temporal dataset containing weekly PEDv infection status for ∼15 % of the U.S. sow herd, we present a machine learning platform developed to forecast the probability of PEDv infection in sow farms in the U.S. Participating stakeholders (swine production companies) in a swine-dense region of the U.S. shared weekly information on a) PEDv status of farms and b) animal movements for the past week and scheduled movements for the upcoming week. Environmental (average temperature, humidity, among others) and land use characteristics (hog density, proportion of area with different land uses) in a 5 km radius around each farm were summarized. Using the Extreme Gradient Boosting (XGBoost) machine learning model with Synthetic Minority Over-sampling Technique (SMOTE), we developed a near real-time tool that generates weekly PEDv predictions (pertaining to two-weeks in advance) to farms of participating stakeholders. Based on retrospective data collected between 2014 and 2017, the sensitivity, specificity, positive and negative predictive values of our model were 19.9, 99.9, 70.5 and 99.4 %, respectively. Overall accuracy was 99.3 %, although this metric is heavily biased by imbalance in the data (less than 0.7 % of farms had an outbreak each week). This platform has been used to deliver weekly real-time forecasts since December 2019. The forecast platform has a built-in feature to re-train the predictive model in order to remain as relevant as possible to current epidemiological situations, or to expand to a different disease. These dynamic forecasts, which account for recent animal movements, present disease distribution, and environmental factors, will promote data-informed and targeted disease management and prevention within the U.S. swine industry.

2021: Assessing the litter level agreement of RT-PCR results for porcine reproductive and respiratory syndrome virus in testicles, tails and udder wipes diagnostic samples relative to serum from piglets

Vilalta, C., Sanhueza, J.M., Schwartz, M., Kikuti, M., Torremorell, M. and Corzo, C.A., 2021. Assessing the litter level agreement of RT-PCR results for porcine reproductive and respiratory syndrome virus in testicles, tails and udder wipes diagnostic samples relative to serum from piglets. Preventive veterinary medicine, 186, p.105211. doi.org/10.1016/j.prevetmed.2020.105211

Abstract

Porcine reproductive and respiratory syndrome (PRRS) is currently the most detrimental disease in the U.S swine industry. Clinical signs of PRRS virus (PRRSv) infection in breeding herds include reproductive failure with abortions, stillbirths, premature farrowings and increased pre-weaning mortality. Serum from due-to-wean piglets is considered the most suitable specimen to monitor PRRSv infection and stability in breeding herds. However, processing fluids (PF - the serosanguinous exudate resultant of the collection of tails and testicles during processing) are a new specimen proposed to monitor piglets at processing (3–5 days of age) and udder wipes (UW) of lactating sows is yet another specimen to monitor infection status of suckling piglets indirectly. Here, we assessed which specimen type (e.g. sera, testicles, tails or UW) should be used to accurately establish the PRRSv status of a litter. Twenty-four litters were conveniently selected on a farm at 10 weeks post PRRSv outbreak. Blood samples, tails and testicles from every piglet in a litter, and an udder skin wipe from the sow were collected at processing (3–5 days). Individual litter testicles and tails as well as the udder wipe were placed each in a reclosable bag to prevent cross-contamination. Sensitivity (Se), specificity (Sp), negative predictive value (NPV), positive predictive value (PPV) and global agreement at the litter level were calculated using the sera results of the litter as the gold standard. The optimum cycle threshold (Ct) value to classify a sample as negative was ≥35 for serum and ≥36 for the aggregated samples (testicles, tails, and UW) based on the ROC curve analysis. Using those thresholds, the fluid collected from the testicles showed the best overall performance (Se = 92 % [62–100]; Sp = 82 % [48–98], NPV = 90 % [55–100], PPV = 85 % [55–98], global agreement = 87 %) compared to tail fluid and UW. Sensitivity of the tail fluid was 62 % (32–86) and the UW was 23 % (5–54), both of which yielded a 100 % specificity and PPV. This study provides information on the contribution of each of the tissues collected at processing on the detection of PRRSv, which becomes relevant in countries were castration and/or tail docking is banned.

2021: Phylogenetic Structure and Sequential Dominance of Sub-Lineages of PRRSV Type-2 Lineage 1 in the United States

Paploski, I.A., Pamornchainavakul, N., Makau, D.N., Rovira, A., Corzo, C.A., Schroeder, D.C., Cheeran, M.C., Doeschl-Wilson, A., Kao, R.R., Lycett, S. and VanderWaal, K., 2021. Phylogenetic structure and sequential dominance of sub-lineages of PRRSV type-2 lineage 1 in the United States. Vaccines, 9(6), p.608. https://doi.org/10.3390/vaccines9060608

Abstract

The genetic diversity and frequent emergence of novel genetic variants of porcine reproductive and respiratory syndrome virus type-2 (PRRSV) hinders control efforts, yet drivers of macro-evolutionary patterns of PRRSV remain poorly documented. Utilizing a comprehensive database of >20,000 orf5 sequences, our objective was to classify variants according to the phylogenetic structure of PRRSV co-circulating in the U.S., quantify evolutionary dynamics of sub-lineage emergence, and describe potential antigenic differences among sub-lineages. We subdivided the most prevalent lineage (Lineage 1, accounting for approximately 60% of available sequences) into eight sub-lineages. Bayesian coalescent SkyGrid models were used to estimate each sub-lineage’s effective population size over time. We show that a new sub-lineage emerged every 1 to 4 years and that the time between emergence and peak population size was 4.5 years on average (range: 2–8 years). A pattern of sequential dominance of different sub-lineages was identified, with a new dominant sub-lineage replacing its predecessor approximately every 3 years. Consensus amino acid sequences for each sub-lineage differed in key GP5 sites related to host immunity, suggesting that sub-lineage turnover may be linked to immune-mediated competition. This has important implications for understanding drivers of genetic diversity and emergence of new PRRSV variants in the U.S.

2021: Dynamic network connectivity influences the spread of a sub-lineage of porcine reproductive and respiratory syndrome virus

Makau, D.N., Paploski, I.A., Corzo, C.A. and VanderWaal, K., 2022. Dynamic network connectivity influences the spread of a sub‐lineage of porcine reproductive and respiratory syndrome virus. Transboundary and Emerging Diseases, 69(2), pp.524-537. https://doi.org/10.1111/tbed.14016

Abstract

Swine production in the United States is characterized by dynamic farm contacts through animal movements; such movements shape the risk of disease occurrence on farms. Pig movements have been linked to the spread of a virulent porcine reproductive and respiratory syndrome virus (PRRSV), RFLP type 1-7-4, herein denoted as phylogenetic sub-lineage 1A [L1A]. This study aimed to quantify the contribution of pig movements to the risk of L1A occurrence on farms in the United States. Farms were defined as L1A-positive in a given 6-month period if at least one L1A sequence was recovered from the farm. Temporal network autocorrelation modelling was performed using data on animal movements and 1,761 PRRSV ORF5 sequences linked to 494 farms from a dense pig production area in the United States between 2014 and 2017. A farm's current and past exposure to L1A and other PRRSV variants was assessed through its primary and secondary contacts in the animal movement network. Primary and secondary contacts with an L1A-positive farm increased the likelihood of L1A occurrence on a farm by 19% (p = .04) and 23% (p = .03), respectively. While the risk posed by primary contacts with PRRS-positive farms is unsurprising, the observation that secondary contacts also increase the likelihood of infection is novel. Risk of L1A occurrence on a farm also increased by 3.0% (p = .01) for every additional outgoing shipment, possibly due to biosecurity breaches during loading and transporting pigs from the farm. Finally, use of vaccines or field virus inoculation on sow farms one year prior reduced the risk of L1A occurrence in downstream farms by 36% (p = .04), suggesting that control measures that reduce viral circulation and enhance immunological protection in sow farms have a carry-over effect on L1A occurrence in downstream farms. Therefore, coordinated disease management interventions between farms connected via animal movements may be more effective than individual farm-based interventions.

2020: Spatial relative risk and factors associated with porcine reproductive and respiratory syndrome outbreaks in United States breeding herds

Sanhueza, J.M., Stevenson, M.A., Vilalta, C., Kikuti, M. and Corzo, C.A., 2020. Spatial relative risk and factors associated with porcine reproductive and respiratory syndrome outbreaks in United States breeding herds. Preventive veterinary medicine, 183, p.105128. doi.org/10.1016/j.prevetmed.2020.105128

Abstract

Details of incident cases of porcine reproductive and respiratory syndrome (PRRS) in United States breeding herds were obtained from the Morrison’s Swine Health Monitoring Project. Herds were classified as cases if they reported an outbreak in a given season of the year and non-cases if they reported it in a season other than the case season or if they did not report a PRRS outbreak in any season. The geographic distribution of cases and non-cases was compared in each season of the year. The density of farms that had a PRRS outbreak during summer was higher in Southern Minnesota and Northwest-central Iowa compared to the density of the underlying population of non-case farms. This does not mean that PRRS outbreaks are more frequent during summer in absolute terms, but that there was a geographical clustering of herds breaking during summer in this area. Similar findings were observed in autumn. In addition, the density of farms reporting spring outbreaks was higher in the Southeast of the United States compared to that of the underlying population of non-case farms. A similar geographical clustering of PRRS outbreaks was observed during winter in the Southeast of the United States. Multivariable analyses, adjusting for the effect of known confounders, showed that the incidence rate of PRRS was significantly lower during winter and autumn during the porcine epidemic diarrhea (PED) epidemic years (2013−2014), compared to PRRS incidence rates observed during the winter and autumn of PED pre-epidemic years (2009−2012). After 2014, an increase in the incidence rate of PRRS was observed during winter and spring but not during autumn or summer. Pig dense areas were associated with a higher incidence rate throughout the year. However, this association tended to be stronger during the summer. Additionally, herds with ≥2500 sows had an increased incidence rate during all seasons except spring compared to those with <2500 sows. PRRS incidence was lower in year-round air-filtered herds compared to non-filtered herds throughout the year. We showed that not only the spatial risk of PRRS varies regionally according to the season of the year, but also that the effect of swine density, herd size and air filtering on PRRS incidence may also vary according to the season of the year. Further studies should investigate regional and seasonal drivers of disease. Breeding herds should maintain high biosecurity standards throughout the year.

2020: Contrasting animal movement and spatial connectivity networks in shaping transmission pathways of a genetically diverse virus

VanderWaal, K., Paploski, I.A., Makau, D.N. and Corzo, C.A., 2020. Contrasting animal movement and spatial connectivity networks in shaping transmission pathways of a genetically diverse virus. Preventive veterinary medicine, 178, p.104977. https://doi.org/10.1016/j.prevetmed.2020.104977

Abstract

Analyses of livestock movement networks has become key to understanding an industry’s vulnerability to infectious disease spread and for identifying farms that play disproportionate roles in pathogen dissemination. In addition to animal movements, many pathogens can spread between farms via mechanisms mediated by spatial proximity. Heterogeneities in contact patterns based on spatial proximity are less commonly considered in network studies, and studies that jointly consider spatial connectivity and animal movement are rare. The objective of this study was to determine the extent to which movement versus spatial proximity networks determine the distribution of an economically important endemic virus, porcine reproductive and respiratory syndrome virus (PRRSV), within a swine-dense region of the U.S. PRRSV can be classified into numerous phylogenetic lineages. Such data can be used to better resolve between-farm infection chains and elucidate types of contact most associated with transmission. Here, we construct movement and spatial proximity networks; farms within the networks were classified as cases if a given PRRSV lineage had been recovered at least once in a year for each of three years analyzed. We evaluated six lineages and sub-lineages across three years, and evaluated the epidemiological relevance of each network by applying network k-tests to statistically evaluate whether the pattern of case occurrence within the network was consistent with transmission via network linkages. Our results indicated that animal movements, not local area spread, play a dominant role in shaping transmission pathways, though there were differences amongst lineages. The median number of case farms inter-linked via animal movements was approximately 4.1x higher than random expectations (range: 1.7–13.7; p < 0.05, network k-test), whereas this measure was only 2.7x higher than random expectations for farms linked via spatial proximity (range: 1.3–5.4; p < 0.05, network k-test). For spatial proximity networks, contact based on proximities of <5 km appeared to have greater epidemiological relevance than longer distances, likely related to diminishing probabilities of local area spread at greater distances. However, the greater overall levels of connectivity of the spatial network compared to the movement network highlights the vulnerability of pig populations to widespread transmission via this route. By combining genetic data with network analysis, this research advances our understanding of dynamics of between-farm spread of PRRSV, helps establish the relative importance of transmission via animal movements versus local area spread, and highlights the potential for targeted control strategies based upon heterogeneities in network connectivity.

2019: Temporal dynamics of co-circulating lineages of Porcine Reproductive and Respiratory Syndrome virus

Paploski, I.A.D., Corzo, C., Rovira, A., Murtaugh, M.P., Sanhueza, J.M., Vilalta, C., Schroeder, D.C. and VanderWaal, K., 2019. Temporal dynamics of co-circulating lineages of porcine reproductive and respiratory syndrome virus. Frontiers in Microbiology, 10, p.2486. https://doi.org/10.3389/fmicb.2019.02486

Abstract

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is the most important endemic pathogen in the U.S. swine industry. Despite control efforts involving improved biosecurity and different vaccination protocols, the virus continues to circulate and evolve. One of the foremost challenges in its control is high levels of genetic and antigenic diversity. Here, we quantify the co-circulation, emergence and sequential turnover of multiple PRRSV lineages in a single swine-producing region in the United States over a span of 9 years (2009–2017). By classifying over 4,000 PRRSV sequences (open-reading frame 5) into phylogenetic lineages and sub-lineages, we document the ongoing diversification and temporal dynamics of the PRRSV population, including the rapid emergence of a novel sub-lineage that appeared to be absent globally pre-2008. In addition, lineage 9 was the most prevalent lineage from 2009 to 2010, but its occurrence fell to 0.5% of all sequences identified per year after 2014, coinciding with the emergence or re-emergence of lineage 1 as the dominant lineage. The sequential dominance of different lineages, as well as three different sub-lineages within lineage 1, is consistent with the immune-mediated selection hypothesis for the sequential turnover in the dominant lineage. As host populations build immunity through natural infection or vaccination toward the most common variant, this dominant (sub-) lineage may be replaced by an emerging variant to which the population is more susceptible. An analysis of patterns of non-synonymous and synonymous mutations revealed evidence of positive selection on immunologically important regions of the genome, further supporting the potential that immune-mediated selection shapes the evolutionary and epidemiological dynamics for this virus. This has important implications for patterns of emergence and re-emergence of genetic variants of PRRSV that have negative impacts on the swine industry. Constant surveillance on PRRSV occurrence is crucial to a better understanding of the epidemiological and evolutionary dynamics of co-circulating viral lineages. Further studies utilizing whole genome sequencing and exploring the extent of cross-immunity between heterologous PRRS viruses could shed further light on PRRSV immunological response and aid in developing strategies that might be able to diminish disease impact.

Poster presentations

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  • Pamornchainavakul, N.; Makau, D.N.; Paploski, I.A. D.; Corzo, C.A.; VanderWaal, K. Unveiling invisible farm-to-farm -2 transmission links and routes through transmission tree and network analysis. Evolutionary Applications, v. 1, p. 1, 2023.
  • M. Kikuti, C.M. Melini, X. Yue, I.A.D. Paploski, N. Pamornchainavakul, J. P. Baker, D. Makau, K. VanderWaal, C.A. Corzo. Monitoring of porcine reproductive and respiratory syndrome virus variant emergence. 2023 NAPRRS/NC229: International Conference of Swine Viral Diseases. Chicago, IL. 2023.
  • M. Kikuti, C.M. Melini, X. Yue, M. Culhane, C.A. Corzo. Opening the pools: What is behind tongue tips sampling and other welfare-friendly postmortem samples for accurately detecting PRRSV? 2023 NAPRRS/NC229: International Conference of Swine Viral Diseases. Chicago, IL. 2023.
  • Claudio Marcello Melini, Mariana Kikuti, Montserrat Torremorell, Kimberly VanderWaal, Stephanie Rossow, Cesar A. Corzo. Evaluation of infectiousness of three porcine reproductive and respiratory syndrome virus (PRRSV) variants. 2023 NAPRRS/NC229: International Conference of Swine Viral Diseases. Chicago, IL. 2023.
  • Xiaomei Yue, Mariana Kikuti, Marcello Melini, Emily Geary, Paulo Fioravante, Cesar Corzo. An early warning tool for PRRS virus occurrence in the U.S. swine breeding herds. 2023 NAPRRS/NC229: International Conference of Swine Viral Diseases. Chicago, IL. 2023.
  • N. Pamornchainavakul, M. Kikuti, I.A.D. Paploski, C.A. Corzo, and K.VanderWaal. Predicting PRRSV-2 Variant Emergence: Insights from a Decade of Genomic Analysis. 2023 NAPRRS/NC229: International Conference of Swine Viral Diseases. Chicago, IL. 2023.
  • Igor A. D. Paploski, Gabriela Kiesel, Dennis N. Makau, Nakarin Pamornchainavakul, Julia P. Baker, Mariana Kikuti, Cesar A. Corzo, Kimberly VanderWaal. Weathering the storm: extreme weather events and their association with PED and PRRS occurrence. 2023 NAPRRS/NC229: International Conference of Swine Viral Diseases. Chicago, IL. 2023.
  • Scott Dee. Case study: The impact of Next Generation Biosecurity on preventing PRRSV infections in breeding herds from a large-scale commercial swine production system in the US. 2023 NAPRRS/NC229: International Conference of Swine Viral Diseases. Chicago, IL. 2023.
  • Joaquín Álvarez-Norambuena; Mariana Kikuti; Albert Rovira; Cesar A. Corzo. Evaluation of sanger sequencing detection of PRRS virus in in-vitro co-infections. 54th American Association of Swine Veterinarians Meeting. Aurora, CO. 2023.
  • M. Kikuti, C.M. Mellini, S. Rossow, A. Rovira, C.A Corzo. Progression of the newly emerged PRRSv L1C 144 variant in breeding herds. 54th American Association of Swine Veterinarians Meeting. Aurora, CO. 2023.
  • Claudio Marcello Melini, Mariana Kikuti, Montse Torremorell, Laura Bruner, Chase Stahl, Brian Roggow, Paul Yeske, Brad Leuwerke, Matt Allerson, Katie O’Brien,  Mark Schwartz, Cesar A. Corzo. Addressing biocontainment through environmental contamination assessment in farms housing PRRS 1-4-4 Lineage 1C positive pigs. 54th American Association of Swine Veterinarians Meeting. Aurora, CO. 2023.
  • Claudio Marcello Melini, Mariana Kikuti, Montserrat Torremorell; Kimberly VanderWaal, Stephanie Rossow, Jerry Torrison, Cesar A. Corzo. Evaluation of infectiousness and virulence of the newly emergent and virulent Minnesota PRRS virus variant. 54th American Association of Swine Veterinarians Meeting. Aurora, CO. 2023.
  • Kikuti, M., Vilalta, C., Sanhueza, J., Melini, C.M., Corzo, C.A. Porcine reproduction and respiratory syndrome prevalence and processing fluids use for diagnosis in United States breeding herds. The American Association of Extension Veterinarians Symposium. 2022.
  • Kikuti, M., Vilalta, C., Sanhueza, J., Melini, C.M., Corzo, C.A. Relación entre la prevalencia del Síndrome Reproductivo y Respiratorio Porcino y el uso de fluidos de procesamiento para diagnóstico en granjas de cría de los Estados Unidos. Conferencia Porcina Allen D. Leman en Español. 2022.
  • Kikuti, M., Preis, G.M., Deen, J., Pinilla, J.C., Corzo, C.A. Sow mortality: Removal reasons and factors associated with increased mortality. Leman, 2022.
  • Álvarez-Norambuena, J.; Kikuti, M.; Rovira, A.; Corzo, C.A. Experimental in-vitro evaluation of PRRSv modified-live vaccine and wild-type virus sequenced detection in co-infections. Leman, 2022.
  • Pamornchainavakul, N., Makau, D.N., Paploski, I.A.D., Kikuti, M., Lycett, S., Corzo C.A., VanderWaal, K. Early indicators of the emergence potential of PRRSV-2 variants based on phylogenetic structure, Leman, 2022.
  • Kikuti, M., Vilalta, C., Sanhueza, J.M., Paploski, I.A.D., VanderWaal, K. Corzo, C. Occurrence of wild type and vaccine-like porcine reproductive and respiratory syndrome virus 2 (PRRSV-2) strains in the United States. 53rd American Association of Swine Veterinarians Meeting. Indianapolis, IN. 2022.
  • Kikuti, M., Pamornchainavakul, N., Paploski, I.A.D., Rossow, S., Rovira, A., VanderWaal, K., Corzo, C.A. Newly emerged PRRSv Lineage 1C RFLP 144 variant in breeding herds. 26th International Pig Veterinary Society Congress - IPVS2022. Rio de Janeiro, Brazil. 2022.
  • Paploski, I.A.D.; Pamornchainavakul, N.; Makau, D.; Rovira, A.; Corzo, C.; Kikuti, M.; Schroeder, D.; Cheeran, M; Doeschl-Wilson, A.; Kao, R.; Lycett, S.; VanderWaal, K. N-glycosylation patterns of epidemic PRRSV2PRRSV-2 sub-lineages in the U.S. 26th International Pig Veterinary Society Congress - IPVS2022. Rio de Janeiro, Brazil. 2022.
  • Picasso‐Risso, C., Kikuti, M., Corzo, C.A. Porcine Deltacoronavirus occurrence in the United States breeding herds. 26th International Pig Veterinary Society Congress - IPVS2022. Rio de Janeiro, Brazil. 2022.
  • Makau, D., VanderWaal, K, Kikuti, M., Picasso‐Risso, C.; Geary, E., Corzo, C.A. Current trends and patterns of PEDV in the United States. 26th International Pig Veterinary Society Congress - IPVS2022. Rio de Janeiro, Brazil. 2022.
  • Kikuti, M., Sanhueza, J., Vilalta, C., Paploski, I.A.D., VanderWaal, K., Corzo, C.A.. Porcine reproductive and respiratory syndrome virus 2 (PRRSV-2) genetic diversity and occurrence of wild type and vaccine-like strains in the United States swine industry. 16th International Symposium of Veterinary Epidemiology and Economics. Halifax, Canada, 2022.
  • Kikuti, M., Sanhueza, J., Vilalta, C., Paploski, I.A.D., VanderWaal, K., Corzo, C.A.. Porcine reproductive and respiratory syndrome virus 2 (PRRSV-2) genetic diversity and occurrence of wild type and vaccine-like strains in the United States swine industry. North American PRRS Symposium. Chicago, IL. 2021.
  • Kikuti, M., Paploski, I.A.D., Pamornchainavakul, N., Picasso-Risso, C., A Rovira, VanderWaal, K., Corzo, C.A.. Newly emerged Lineage 1C porcine reproductive and respiratory syndrome virus (PRRSV2) variant. North American PRRS Symposium. Chicago, IL. 2021.
  • Kikuti, M., Paploski I., Pamornchainavakul, N., Picasso-Risso C., Schwartz M., Yeske P., Leuwerke B., Bruner L., Murray D., Roggow B., Thomas P., Feldmann L., Allerson M., Hensch M., Bauman T., Sexton B., Rovira A., VanderWaal K., Corzo, C.A. Emergence of a new lineage 1c variant of porcine reproductive and respiratory syndrome virus 2 in the United States. Epidemics8 - 8th International Conference on Infectious Disease Dynamics. 2021.
  • Kikuti, M., Sanhueza J., Vilalta C., Paploski I., VanderWaal K., Corzo, C.A. Porcine reproductive and respiratory syndrome virus 2 (PRRSV-2) genetic diversity and occurrence of wild type and vaccine-like strains in the United States swine industry. Epidemics8 - 8th International Conference on Infectious Disease Dynamics. 2021.
  • Vilalta, C., Sanhueza, J., Kikuti, M., Picasso-Risso C., Corzo, C.A. Evaluation of the relationship between manure pumping and reporting an outbreak in US breeding herds. Leman Conference. Saint Paul, MN. 2021.
  • Kikuti, M., Vilalta, C., Sanhueza, J., Pamornchainavakul, N., Kevill, J.L., Paploski, I.A.D., Kienhe, R., VanderWaal, K., Schroeder, D., Corzo, C.A.. PRRS viral diversity in piglets born during an outbreak. 2021 AASV Annual Meeting. 2021.
  • Montoya Lopez, J.; Kikuti, M.; Vilalta, C.; Sanhueza, J.; Corzo, C.A. PRRSv farm prevalence in near-to-market-pigs in the United States. 2021 AASV Annual Meeting. 2021.
  • Montoya Lopez, J.; Vilalta, C.; Sanhueza, J.; Corzo, C.A. Prevalence of PRRSv, PEDv, PDCoV and TGEv in pig farm manure pits. 2021 AASV Annual Meeting. 2021.
  • Montoya Lopez, J.; Kikuti, M.; Vilalta, C.; Sanhueza, J.; Corzo, C.A. PRRSv prevalence in near-to-market-pigs in the United States. Leman Conference. Saint Paul, MN. 2020.
  • Kikuti, M., Sanhueza, J., Vilalta, C., Corzo, C.A. Molecular characterization of type 2 porcine reproductive and respiratory syndrome virus (PRRSv) in the United States. International Pig Veterinary Society Congress IPVS 2020. Rio de Janeiro, Brazil. 2020.
  • Sanhueza, J.M.; Corzo C.A.; Kikuti, M.; Vilalta, C.. Investigation of gilts as a factor for delayed time-to-stability. 2020 AASV Annual Meeting. Atlanta, GA. 2020.
  • Kiktui,M., Vilalta, C., Sanhueza, J., Kienhe, R., VanderWaal, K., Schroeder, D., Corzo, C.A. Viremia and mortality in piglets born to sows during a PRRSV outbreak. 2020 AASV Annual Meeting. Atlanta, GA. 2020.
  • Kikuti, M., Sanhueza, J., Vilalta, C., VanderWaal, K., Corzo, C.A. Spatio-temporal dynamics of porcine reproductive and respiratory syndrome virus (PRRSv) in the United States. 2020 AASV Annual Meeting. Atlanta, GA. 2020.

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