Novel analytic tools for the study of porcine reproductive and respiratory syndrome virus (PRRSv) in endemic settings: lessons learned in the U.S

Deep Sequencing of Porcine Reproductive and Respiratory Syndrome Virus ORF7: A Promising Tool for Diagnostics and Epidemiologic Surveillance

Porcine reproductive and respiratory syndrome virus (PRRSV) is a major concern worldwide. Control of PRRSV is a challenging task due to various factors, including the viral diversity and variability. In this study, we evaluated an amplicon library preparation protocol targeting the ORF7 region of both PRRSV species, Betaarterivirus suid 1 and Betaarterivirus suid 2. We designed tailed primers for a two-step PCR procedure that generates ORF7-specific amplicon libraries suitable for use on Illumina sequencers. We tested the method with serum samples containing common laboratory strains and with pooled serum samples (n = 15) collected from different pig farms during 2019-2021 in Hungary. Testing spiked serum samples showed that the newly designed method is highly sensitive and detects the viral RNA even at low copy numbers (corresponding to approx. Ct 35). The ORF7 sequences were easily assembled even from clinical samples. Two different sequence variants were identified in five samples, and the Porcilis MLV vaccine strain was identified as the minor variant in four samples. An in-depth analysis of the deep sequencing results revealed numerous polymorphic sites along the ORF7 gene in a total of eight samples, and some sites (positions 12, 165, 219, 225, 315, 345, and 351) were found to be common in several clinical specimens. We conclude that amplicon deep sequencing of a highly conserved region of the PRRSV genome could support both laboratory diagnosis and epidemiologic surveillance of the disease.

Elimination of porcine reproductive and respiratory syndrome virus infection using an inactivated vaccine in combination with a roll-over method in a Hungarian large-scale pig herd

Background

Porcine reproductive and respiratory syndrome virus (PRRSV) causes severe economic losses worldwide and only four countries in Europe are free from PRRSV. Complete depopulation–repopulation is the safest and fastest, but also the most expensive method for eradicating PRRSV from a population. Another possible way to eliminate an endemic PRRSV infection is to replace the infected breeding stock by gilts reared isolated and protected from PRRSV on an infected farm. With this method it is possible to maintain continuous production on the farm. The authors report the first successful elimination of PRRSV in a Hungarian large-scale pig farm by using an inactivated vaccine and performing segregated rearing of the offspring.

Case presentation

The study was performed on a PRRSV infected farm (Farm A) with 1475 sows. The clinical signs of reproductive failure had been eliminated previously by using an inactivated vaccine (Progressis^®, Ceva). At the beginning of the elimination programme, gilts intended for breeding were vaccinated at 60 and 90–100 days of age. After that, gilts selected for breeding were vaccinated at 6 months of age, on the 60–70th day of pregnancy and at weaning.

Approximately 1200 piglets from vaccinated sows were transported at 7 weeks of age to a closed, empty farm (Farm B) after being tested negative for PRRSV by a polymerase chain reaction (PCR) method, and then were reared here until 14 weeks of age. At this age, all pigs were tested by PRRS ELISA. Seronegative gilts (n = 901) were subsequently transported from Farm B to a third, closed and empty farm (Farm C), and (having reached the breeding age) they were inseminated here after a second negative serological test (ELISA). At the same time, Farm A was depopulated, cleaned and disinfected. All pregnant gilts were transported from Farm C to Farm A after being re-tested negative for antibodies against PRRSV. Follow-up serology tests were performed after farrowing and results yielded only seronegative animals. Based on the subsequent negative test results, the herd was declared PRRSV free by the competent authority.

Conclusions

The presented farm was the first during the National PRRS Eradication Programme of Hungary to eradicate PRRSV successfully by vaccinating the sows with an inactivated vaccine and performing segregated rearing of the offspring. Production was almost continuous during the whole process of population replacement.

Influenza A virus vaccine research conducted in swine from 1990 to May 2018: A scoping review

BACKGROUND

Influenza A viruses of swine (IAV-S) are a global zoonotic and economic concern. Primary control is through vaccination yet a formal evidence map summarizing vaccine research conducted in pigs is not available.

OBJECTIVE

Ten characteristics of English language primary IAV-S vaccine research, conducted at the level of the pig or higher, were charted to identify research gaps, topics for systematic review, and coverage across different publication types.

DESIGN

Six online databases and grey literature were searched, without geographic, population, or study type restrictions, and abstracts screened independently and in duplicate for relevant research published between 1990 and May 2018. Full text data was charted by a single reviewer.

RESULTS

Over 11,000 unique citations were screened, identifying 376 for charting, including 175 proceedings from 60 conferences, and 170 journal articles from 51 journals. Reported outcomes were heterogeneous with measures of immunity (86%, n = 323) and virus detection (65%, n = 246) reported far more than production metrics (9%, n = 32). Study of transmissibility under conditions of natural exposure (n = 7), use of mathematical modelling (n = 11), and autogenous vaccine research reported in journals (n = 7), was limited.

CONCLUSIONS

Most research used challenge trials (n = 219) and may have poor field relevance or suitability for systematic review if the purpose is to inform clinical decisions. Literature on vaccinated breeding herds (n = 89) and weaned pigs (n = 136) is potentially sufficient for systematic review. Research under field conditions is limited, disproportionately reported in conference proceedings versus journal articles, and may be insufficient to support systematic review.

Animal Disease Surveillance in the 21st Century: Applications and Robustness of Phylodynamic Methods in Recent U.S. Human-Like H3 Swine Influenza Outbreaks

Emerging and endemic animal viral diseases continue to impose substantial impacts on animal and human health. Most current and past molecular surveillance studies of animal diseases investigated spatio-temporal and evolutionary dynamics of the viruses in a disjointed analytical framework, ignoring many uncertainties and made joint conclusions from both analytical approaches. Phylodynamic methods offer a uniquely integrated platform capable of inferring complex epidemiological and evolutionary processes from the phylogeny of viruses in populations using a single Bayesian statistical framework. In this study, we reviewed and outlined basic concepts and aspects of phylodynamic methods and attempted to summarize essential components of the methodology in one analytical pipeline to facilitate the proper use of the methods by animal health researchers. Also, we challenged the robustness of the posterior evolutionary parameters, inferred by the commonly used phylodynamic models, using hemagglutinin (HA) and polymerase basic 2 (PB2) segments of the currently circulating human-like H3 swine influenza (SI) viruses isolated in the United States and multiple priors. Subsequently, we compared similarities and differences between the posterior parameters inferred from sequence data using multiple phylodynamic models. Our suggested phylodynamic approach attempts to reduce the impact of its inherent limitations to offer less biased and biologically plausible inferences about the pathogen evolutionary characteristics to properly guide intervention activities. We also pinpointed requirements and challenges for integrating phylodynamic methods in routine animal disease surveillance activities.

Highly Efficient Generation of Pigs Harboring a Partial Deletion of the CD163 SRCR5 Domain, Which Are Fully Resistant to Porcine Reproductive and Respiratory Syndrome Virus 2 Infection

Porcine reproductive and respiratory syndrome virus (PRRSV) 1 and 2 differ in their recognition of CD163. Substitution of porcine CD163 SRCR5 domain with a human CD163-like SRCR8 confers resistance to PRRSV 1 but not PRRSV 2. The deletion of CD163 SRCR5 has been shown to confer resistance to PRRSV 1 in vivo and both PRRSV 1 and 2 in vitro. However, the anti-PRRSV 2 activity of modifying the CD163 SRCR5 domain has not yet been reported. Here, we describe the highly efficient generation of two pig breeds (Liang Guang Small Spotted and Large White pigs) lacking a short region of CD163 SRCR5, including the ligand-binding pocket. We generated a large number of gene-edited Large White pigs of the F0 generation for use in viral challenge studies. The results of this study show that these pigs are completely resistant to infection by species 2 PRRSV, JXA1, and MY strains. There were no clinical symptoms, pathological abnormalities, viremia, or anti-PRRSV antibodies in the CD163 SRCR5-edited pigs compared to wild-type controls after viral challenge. Porcine alveolar macrophages (PAMs) isolated from CD163 SRCR5-edited Large White pigs also displayed resistance to PRRSV in vitro. In addition, CD163 SRCR5-edited PAMs still exhibited a cytokine response to PRRSV infection, and no significant difference was observed in cytokine expression compared to wild-type PAMs. Taken together, these data suggest that CD163 SRCR5-edited pigs are resistant to PRRSV 2, providing a basis for the establishment of PRRSV-resistant pig lines for commercial application and further investigation of the essential region of SRCR5 involved in virus infection.

Effect of intervention practices to control the porcine epidemic diarrhea (PED) outbreak during the first epidemic year (2013-2014) on time to absence of clinical signs and the number of dead piglets per sow in Japan

Porcine epidemic diarrhea (PED) is an emerging and/or re-emerging disease of pigs in several countries, with high morbidity and mortality in suckling piglets. Farms affected with PED perform various intervention practices to control and/or eliminate the PED virus. The objectives of the present study were to assess the effect of biosecurity measures and intervention practices to control PED on time to absence of clinical signs (TAC) and number of dead suckling piglets during TAC. A questionnaire was administered to 120-PED affected farms located across Japan between 2013, when the first case was reported in Japan, and 2014. Farms were asked to provide information on farm characteristics and internal or external biosecurity measures during PED outbreak, as well as on intervention practices to control PED. The TAC was defined as the number of days from the date that clinical PED signs appeared to the date that clinical PED signs disappeared. The number of dead piglets per sow (DP/S) was calculated as the number of dead suckling piglets during TAC divided by the sow inventory. Regarding the effect of biosecurity measures during PED outbreak on TAC and DP/S, longer TAC was observed in Actinobacillus pleuropneumoniae-positive farms and farms outsourcing pig transport to the slaughterhouse (p <  0.05). In addition, farms with divided truck entrances had lower DP/S than those without divided entrances (p <  0.05).Regarding the effect of intervention practices to control PED on TAC and DP/S, farms that performed feedback at 2 weeks or later after PED outbreak had longer TAC and higher DP/S than other farms (p <  0.05). Farms that fixed the hours staff worked in farrowing barn had lower DP/S than the other farms (p <  0.05). In conclusion, variables associated with long TAC were Actinobacillus pleuropneumoniae -positive farms, farms outsourcing pig transport to the slaughterhouse, and farms performing feedback at 2 week or later after PED outbreak. Additionally, those associated with high DP/S were farms without divided entrances, farms without a fixed hours worked in the barn, and farms that performed feedback at 2 week or later after PED outbreak.

Evaluating an automated clustering approach in a perspective of ongoing surveillance of porcine reproductive and respiratory syndrome virus (PRRSV) field strains

Porcine reproductive and respiratory syndrome virus (PRRSV) has a major economic impact on the swine industry. The important genetic diversity needs to be considered for disease management. In this regard, information on the circulating endemic strains and their dispersal patterns through ongoing surveillance is beneficial. The objective of this project was to classify Quebec PRRSV ORF5 sequences in genetic clusters and evaluate stability of clustering results over a three-year period using an in-house automated clustering system. Phylogeny based on maximum likelihood (ML) was first inferred on 3661 sequences collected in 1998-2013 (Run 1). Then, sequences collected between January 2014 and September 2016 were sequentially added into 11 consecutive runs, each one covering a three-month period. For each run, detection of clusters, which were defined as groups of ≥15 sequences having a≥70% rapid bootstrap support (RBS) value, was automated in Python. Cluster stability was described for each cluster and run based on the number of sequences, RBS value, maximum pairwise distance and agreement in sequence assignment to a specific cluster. First and last run identified 29 and 33 clusters, respectively. In the last run, about 77% of the sequences were classified by the system. Most clusters were stable through time, with sequences attributed to one cluster in Run 1 staying in the same cluster for the 11 remaining runs. However, some initial groups were further subdivided into subgroups with time, which is important for monitoring since one specific wild-type cluster increased from 0% in 2007 to 45% of all sequences in 2016. This automated classification system will be integrated into ongoing surveillance activities, to facilitate communication and decision-making for stakeholders of the swine industry.

Field evaluation of two commercial RT-rtPCR assays for porcine reproductive and respiratory syndrome virus detection using sera from ill and healthy pigs, China

Porcine reproductive and respiratory syndrome virus (PRRSV) is a highly contagious respiratory virus causing severe morbidity in pigs worldwide. Control strategies for PRRSV often rely on detecting PRRSV, culling or isolating sick pigs, disinfecting pig barns, vaccination, and monitoring for virus spread. Given the high economic impact of PRRSV on pig farms, there is a great need for rapid and reliable PRRSV detection assays. We compared the performance of 2 commercial reverse-transcription real-time PCR (RT-rtPCR) assays, the VetMAX PRRSV NA and EU reagents (ABI assay) and the PRRSV general RT-rtPCR kit (Anheal assay), for the molecular detection of PRRSV in sera collected from pigs in China. Between June and September 2015, sera were collected from 219 healthy and 104 suspected PRRSV-infected pigs on 4 farms in China. Employing blinding, the 2 assays were run by 2 laboratories (Guangzhou Animal Health Inspection Institute [GAHII] and Sun Yat-sen University [SYSU] laboratories) and compared. Although both assays detected PRRSV with 100% specificity at both laboratories, the sensitivity (95% vs. 78% at GAHII; 94% vs. 72% at SYSU Laboratory) and the reproducibility (kappa value 0.933 vs. 0.931) were slightly better for the ABI assay compared to the Anheal assay.

Surveillance of porcine reproductive and respiratory syndrome virus in the United States using risk mapping and species distribution modeling

Porcine reproductive and respiratory syndrome virus (PRRSv) outbreaks cause significant financial losses to the U.S. swine industry, where the pathogen is endemic. Seasonal increases in the number of outbreaks are typically observed using PRRSv epidemic curves. However, the nature and extent to which demographic and environmental factors influence the risk for PRRSv outbreaks in the country remains unclear. The objective of this study was to develop risk maps for PRRSv outbreaks across the United States (U.S.) and compare ecological dynamics of the disease in five of the most important swine production regions of the country. This study integrates spatial information regarding PRRSv surveillance with relevant demographic and environmental factors collected between 2009 and 2016. We used presence-only Maximum Entropy (Maxent), a species distribution modeling approach, to model the spatial risk of PRRSv in swine populations. Data fitted the selected model relatively well when the modeling approach was conducted by region (training and testing AUCs<0.75). All of the Maxent models selected identified high-risk areas, with probabilities greater than 0.5. The relative contribution of pig density to PRRSv risk was highest in pig-densely populated areas (Minnesota, Iowa and North Carolina), whereas climate and land cover were important in areas with relatively low pig densities (Illinois, Indiana, South Dakota, Nebraska, Kansas, Oklahoma, Colorado, and Texas). Although many previous studies associated the risk of PRRSv with high pig density and climatic factors, the study here quantifies, for the first time in the peer-reviewed literature, the spatial variation and relative contribution of these factors across different swine production regions in the U.S. The results will help in the design and implement of early detection, prevention, and control strategies for one of the most devastating diseases affecting the swine industry in the U.S.

Epidemiological investigations of the introduction of porcine reproductive and respiratory syndrome virus in Chile, 2013-2015

Porcine reproductive and respiratory syndrome (PRRS) is endemic in most pork producing countries. In Chile, eradication of PRRS virus (PRRSV) was successfully achieved in 2009 as a result of the combined efforts of producers and the animal health authorities. In October 2013, after several years without detecting PRRSV under surveillance activities, suspected cases were confirmed on a commercial swine farm. Here, we describe the PRRS epidemic in Chile between October 2013 and April 2015, and we studied the origins and spread of PRRSV throughout the country using official surveillance data and Bayesian phylogenetic analysis. Our results indicate that the outbreaks were caused by a PRRSV closely related to viruses present in swine farms in North America, and different from the strain that circulated in the country before 2009. Using divergence time estimation analysis, we found that the 2013–2015 PRRSV may have been circulating in Chile for at least one month before the first detection. A single strain of PRRSV spread into a limited number of commercial and backyard swine farms. New infections in commercial systems have not been reported since October 2014, and eradication is underway by clearing the disease from the few commercial and backyard farms that remain positive. This is one of the few documented experiences of PRRSV introduction into a disease-free country.

Novel approaches for Spatial and Molecular Surveillance of Porcine Reproductive and Respiratory Syndrome Virus (PRRSv) in the United States

The US swine industry has been impaired over the last 25 years by the far-reaching financial losses caused by the porcine reproductive and respiratory syndrome (PRRS). Here, we explored the relations between the spatial risk of PRRS outbreaks and its phylodynamic history in the U.S during 1998–2016 using ORF5 sequences collected from swine farms in the Midwest region. We used maximum entropy and Bayesian phylodynamic models to generate risk maps for PRRS outbreaks and reconstructed the evolutionary history of three selected phylogenetic clades (A, B and C). High-risk areas for PRRS were best-predicted by pig density and climate seasonality and included Minnesota, Iowa and South Dakota. Phylodynamic models demonstrated that the geographical spread of the three clades followed a heterogeneous spatial diffusion process. Furthermore, PRRS viruses were characterized by typical seasonality in their population size. However, endemic strains were characterized by a substantially slower population growth and evolutionary rates, as well as smaller spatial dispersal rates when compared to emerging strains. We demonstrated the prospects of combining inferences derived from two unique analytical methods to inform decisions related to risk-based interventions of an important pathogen affecting one of the largest food animal industries in the world.

Land altitude, slope, and coverage as risk factors for Porcine Reproductive and Respiratory Syndrome (PRRS) outbreaks in the United States

Porcine reproductive and respiratory syndrome (PRRS) is, arguably, the most impactful disease on the North American swine industry. The Swine Health Monitoring Project (SHMP) is a national volunteer initiative aimed at monitoring incidence and, ultimately, supporting swine disease control, including PRRS. Data collected through the SHMP currently represents approximately 42% of the sow population of the United States. The objective of the study here was to investigate the association between geographical factors (including land elevation, and land coverage) and PRRS incidence as recorded in the SHMP. Weekly PRRS status data from sites participating in the SHMP from 2009 to 2016 (n = 706) was assessed. Number of PRRS outbreaks, years of participation in the SHMP, and site location were collected from the SHMP database. Environmental features hypothesized to influence PRRS risk included land coverage (cultivated areas, shrubs and trees), land altitude (in meters above sea level) and land slope (in degrees compared to surrounding areas). Other risk factors considered included region, production system to which the site belonged, herd size, and swine density in the area in which the site was located. Land-related variables and pig density were captured in raster format from a number of sources and extracted to points (farm locations). A mixed-effects Poisson regression model was built; and dependence among sites that belonged to a given production system was accounted for using a random effect at the system level. The annual mean and median number of outbreaks per farm was 1.38 (SD: 1.6), and 1 (IQR: 2.0), respectively. The maximum annual number of outbreaks per farm was 9, and approximately 40% of the farms did not report any outbreak. Results from the final multivariable model suggested that increments of swine density and herd size increased the risk for PRRS outbreaks (P < 0.01). Even though altitude (meters above sea level) was not significant in the final model, farms located in terrains with a slope of 9% or higher had lower rates of PRRS outbreaks compared to farms located in terrains with slopes lower than 2% (P < 0.01). Finally, being located in an area of shrubs/ herbaceous cover and trees lowered the incidence rate of PRRS outbreaks compared to being located in cultivated/ managed areas (P < 0.05). In conclusion, highly inclined terrains were associated with fewer PRRS outbreaks in US sow farms, as was the presence of shrubs and trees when compared to cultivated/ managed areas. Influence of terrain characteristics on spread of airborne diseases, such as PRRS, may help to predicting disease risk, and effective planning of measures intended to mitigate and prevent risk of infection.

Estimation of Time-Dependent Reproduction Numbers for Porcine Reproductive and Respiratory Syndrome across Different Regions and Production Systems of the US

Porcine reproductive and respiratory syndrome (PRRS) is, arguably, the most impactful disease for the North American swine industry, due to its known considerable economic losses. The Swine Health Monitoring Project (SHMP) monitors and reports weekly new PRRS cases in 766 sow herds across the US. The time-dependent reproduction number (TD-R) is a measure of a pathogen's transmissibility. It may serve to capture and report PRRS virus (PRRSV) spread at the regional and system levels. The primary objective of the study here was to estimate the TD-R values for PRRSV using regional and system-level PRRS data, and to contrast it with commonly used metrics of disease, such as incidence estimates and space-time clusters. The second objective was to test whether the estimated TD-Rs were homogenous across four US regions. Retrospective monthly incidence data (2009-2016) were available from the SHMP. The dataset was divided into four regions based on location of participants, and demographic and environmental features, namely, South East (North Carolina), Upper Midwest East (UME, Minnesota/Iowa), Upper Midwest West (Nebraska/South Dakota), and South (Oklahoma panhandle). Generation time distributions were fit to incidence data for each region, and used to calculate the TD-Rs. The Kruskal-Wallis test was used to determine whether the median TD-Rs differed across the four areas. Furthermore, we used a space-time permutation model to assess spatial-temporal patterns for the four regions. Results showed TD-Rs were right skewed with median values close to "1" across all regions, confirming that PRRS has an overall endemic nature. Variation in the TD-R patterns was noted across regions and production systems. Statistically significant periods of PRRSV spread (TD-R > 1) were identified for all regions except UME. A minimum of three space-time clusters were detected for all regions considering the time period examined herein; and their overlap with "spreader events" identified by the TD-R method varied according to region. TD-Rs may help to measure PRRS spread to understand, in quantitative terms, disease spread, and, ultimately, support the design, implementation, and monitoring of interventions aimed at mitigating the impact of PRRSV spread in the US.

Using Machine Learning to Predict Swine Movements within a Regional Program to Improve Control of Infectious Diseases in the US

Between-farm animal movement is one of the most important factors influencing the spread of infectious diseases in food animals, including in the US swine industry. Understanding the structural network of contacts in a food animal industry is prerequisite to planning for efficient production strategies and for effective disease control measures. Unfortunately, data regarding between-farm animal movements in the US are not systematically collected and thus, such information is often unavailable. In this paper, we develop a procedure to replicate the structure of a network, making use of partial data available, and subsequently use the model developed to predict animal movements among sites in 34 Minnesota counties. First, we summarized two networks of swine producing facilities in Minnesota, then we used a machine learning technique referred to as random forest, an ensemble of independent classification trees, to estimate the probability of pig movements between farms and/or markets sites located in two counties in Minnesota. The model was calibrated and tested by comparing predicted data and observed data in those two counties for which data were available. Finally, the model was used to predict animal movements in sites located across 34 Minnesota counties. Variables that were important in predicting pig movements included between-site distance, ownership, and production type of the sending and receiving farms and/or markets. Using a weighted-kernel approach to describe spatial variation in the centrality measures of the predicted network, we showed that the south-central region of the study area exhibited high aggregation of predicted pig movements. Our results show an overlap with the distribution of outbreaks of porcine reproductive and respiratory syndrome, which is believed to be transmitted, at least in part, though animal movements. While the correspondence of movements and disease is not a causal test, it suggests that the predicted network may approximate actual movements. Accordingly, the predictions provided here might help to design and implement control strategies in the region. Additionally, the methodology here may be used to estimate contact networks for other livestock systems when only incomplete information regarding animal movements is available.