Monday, June 12, 2017

PRRSV and HEV in UK Pigs at the Time of Slaughter

 2017 Jun 9;9(6). pii: E110. doi: 10.3390/v9060110.

UK Pigs at the Time of Slaughter: Investigation into the Correlation of Infection with PRRSV and HEV.

Author information

1
Animal and Plant Health Agency, Woodham Lane, New Haw, Surrey KT15 3NB, UK. jean-pierre.frossard@apha.gsi.gov.uk.
2
Animal and Plant Health Agency, Woodham Lane, New Haw, Surrey KT15 3NB, UK. Sylvia.Grierson@apha.gsi.gov.uk.
3
Animal and Plant Health Agency, Woodham Lane, New Haw, Surrey KT15 3NB, UK. tcheney87@hotmail.com.
4
Animal and Plant Health Agency, Woodham Lane, New Haw, Surrey KT15 3NB, UK. Falko.Steinbach@apha.gsi.gov.uk.
5
Animal and Plant Health Agency, Woodham Lane, New Haw, Surrey KT15 3NB, UK. Bhudipa.Choudhury@apha.gsi.gov.uk.
6
Surveillance Intelligence Unit, Animal and Plant Health Agency, Rougham Hill, Bury St Edmunds, Suffolk IP33 2RX, UK. Susanna.Williamson@apha.gsi.gov.uk.

Abstract

Hepatitis E virus (HEV) and porcine reproductive and respiratory syndrome virus (PRRSV) and are both globally prevalent in the pig population. While HEV does not cause clinical disease in pigs, its zoonotic potential has raised concerns in the food safety sector. PRRS has become endemic in the United Kingdom (UK) since its introduction in 1991, and continues to cause considerable economic losses to the swine industry. A better understanding of the current prevalence and diversity of PRRSV and HEV in the UK, and their potential association, is needed to assess risks and target control measures appropriately. This study used plasma, tonsil, and cecal content samples previously collected from pigs in 14 abattoirs in England and Northern Ireland to study the prevalence of several pathogens including PRRSV and HEV. The diversity of PRRSV strains detected in these samples was analyzed by sequencing open reading frame 5 (ORF5), revealing no substantial difference in PRRSV strains from these clinically unaffected pigs relative to those from clinical cases of disease in the UK. Despite the potential immuno-modulatory effect of PRRSV infection, previously demonstrated to affect Salmonellaand HEV shedding profiles, no significant association was found between positive PRRSV status and positive HEV status.

KEYWORDS: 

HEV; PRRSV; co-infections; evolution and molecular epidemiology; porcine viruses
PMID:
 
28598352
 
DOI:
 
10.3390/v9060110
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Friday, June 9, 2017

Modeling the spatio-temporal dynamics of PRRS cases at farm level using geographical distance and pig trade network matrices

 2017 Jun 7;13(1):163. doi: 10.1186/s12917-017-1076-6.

Modeling the spatio-temporal dynamics of porcine reproductive & respiratory syndrome cases at farm level using geographical distance and pig trade network matrices.

Author information

1
Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, 2108 Tupper Hall, one Shields Avenue, Davis, California, 95616, USA.
2
Boehringer-Ingelheim Vetmedica Inc, Saint Joseph, Missouri, USA.
3
Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, USA.
4
Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, 2108 Tupper Hall, one Shields Avenue, Davis, California, 95616, USA. beamartinezlopez@ucdavis.edu.

Abstract

BACKGROUND: 

Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically devastating infectious diseases for the swine industry. A better understanding of the disease dynamics and the transmission pathways under diverse epidemiological scenarios is a key for the successful PRRS control and elimination in endemic settings. In this paper we used a two step parameter-driven (PD) Bayesian approach to model the spatio-temporal dynamics of PRRS and predict the PRRS status on farm in subsequent time periods in an endemic setting in the US. For such purpose we used information from a production system with 124 pig sites that reported 237 PRRS cases from 2012 to 2015 and from which the pig trade network and geographical location of farms (i.e., distance was used as a proxy of airborne transmission) was available. We estimated five PD models with different weights namely: (i) geographical distance weight which contains the inverse distance between each pair of farms in kilometers, (ii) pig trade weight (PT ji ) which contains the absolute number of pig movements between each pair of farms, (iii) the product between the distance weight and the standardized relative pig trade weight, (iv) the product between the standardized distance weight and the standardized relative pig trade weight, and (v) the product of the distance weight and the pig trade weight.

RESULTS: 

The model that included the pig trade weight matrix provided the best fit to model the dynamics of PRRS cases on a 6-month basis from 2012 to 2015 and was able to predict PRRS outbreaks in the subsequent time period with an area under the ROC curve (AUC) of 0.88 and the accuracy of 85% (105/124).

CONCLUSION: 

The result of this study reinforces the importance of pig trade in PRRS transmission in the US. Methods and results of this study may be easily adapted to any production system to characterize the PRRS dynamics under diverse epidemic settings to more timely support decision-making.

KEYWORDS: 

Bayesian approach; Decision making; Disease dynamics; Parameter-driven model; Risk assessment; Risk-based surveillance
PMID:
 
28592317
 
DOI:
 
10.1186/s12917-017-1076-6

Tuesday, May 30, 2017

Oral fluids versus blood sampling for PRRSv serology

 2017 May;204:25-34. doi: 10.1016/j.vetmic.2017.04.001. Epub 2017 Apr 4.

Oral fluid versus blood sampling in group-housed sows and finishing pigs: Feasibility and performance of antibody detection for porcine reproductive and respiratory syndrome virus (PRRSV).

Author information

1
Agence Nationale de Sécurité Sanitaire (ANSES), Unité Epidémiologie et Bien-Etre du Porc, B.P. 53, 22440 Ploufragan, France; Université Bretagne-Loire, France. Electronic address: christelle.fablet@anses.fr.
2
Agence Nationale de Sécurité Sanitaire (ANSES), Unité Virologie Immunologie Porcines, B.P. 53, 22440 Ploufragan, France; Union des Groupements de Producteurs de Viande de Bretagne (UGPVB), 104 rue Eugène Pottier, CS 26553, 35065 Rennes, France; Université Bretagne-Loire, France.
3
Agence Nationale de Sécurité Sanitaire (ANSES), Unité Epidémiologie et Bien-Etre du Porc, B.P. 53, 22440 Ploufragan, France; Université Bretagne-Loire, France.
4
Agence Nationale de Sécurité Sanitaire (ANSES), Unité Virologie Immunologie Porcines, B.P. 53, 22440 Ploufragan, France; Université Bretagne-Loire, France.

Abstract

The feasibility of using individual and pen-based oral fluid samples to detect PRRSV antibodies in growing-finishing pigs and group-housed sows was investigated. The diagnostic performances of a commercial oral fluid ELISA (OF-ELISA) and a serum ELISA (SER-ELISA) performed on individual or pooled samples from 5 or 10 pigs and sows was evaluated. The performance of the OF-ELISA was also assessed for pen-based oral fluids. Eight hundred and thirty-four pigs and 1598 sows from 42 PRRSV-infected and 3 PRRSV-negative herds were oral fluid sampled and bled. PRRSV antibodies were detected by an OF-ELISA performed at individual, pool (5 or 10 samples) and pen levels. Serum samples were tested by a SER-ELISA at individual and pool levels. The sensitivity and specificity of ELISAs for individual samples were assessed by Bayesian analysis. The relative diagnostic performance for the pools was calculated by taking individual samples as the gold standard. SER-ELISA and individual OF-ELISA results were used as references for estimating OF-ELISA performance for pen-based samples. Individual oral fluid collection was feasible in all kinds of pigs, whereas pen-based samples were unsuccessful in 40% of the group-housed sow pens. High levels of sensitivity comparable to those of the SER-ELISA were found for the OF-ELISA when performed on individual, 5-sample pool or pen-based samples from pigs or sows. The OF-ELISA lacked specificity for individual samples from sows. Pooling 5 individual oral fluid samples or using pen-based samples increased test specificity.

KEYWORDS: 

Diagnostic performance; ELISA; Oral fluid; PRRSV antibody; Serum
PMID:
 
28532802
 
DOI:
 
10.1016/j.vetmic.2017.04.001

Tuesday, April 18, 2017

Geographical factors for PRRS outbreaks

 2017 Apr 17;12(4):e0172638. doi: 10.1371/journal.pone.0172638. eCollection 2017.

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


Abstract

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.
PMID:
 
28414720
 
DOI:
 
10.1371/journal.pone.0172638

Wednesday, April 5, 2017

Unraveling the contact patterns and network structure of pig shipments in the US and its association with PRRSV outbreaks.

 2017 Mar 1;138:113-123. doi: 10.1016/j.prevetmed.2017.02.001. Epub 2017 Feb 2.

Unraveling the contact patterns and network structure of pig shipments in the United States and its association with porcine reproductive and respiratory syndrome virus (PRRSVoutbreaks.

Author information

1
Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA. Electronic address: pvmlee@ucdavis.edu.
2
Boehringer - Ingelheim Vetmedica, Inc., St. Joseph, MO, USA.
3
Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
4
Center for Animal Disease Modeling and Surveillance (CADMS), Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA.

Abstract

The analysis of the pork value chain is becoming key to understanding the risk of infectious disease dissemination in the swine industry. In this study, we used social network analysis to characterize the swine shipment network structure and properties in a typical multisite swine production system in the US. We also aimed to evaluate the association between network properties and porcine respiratory and reproductive syndrome virus (PRRSV) transmission between production sites. We analyzed the 109,868 swine shipments transporting over 93 million swine between more than 500 production sites from 2012 to 2014. A total of 248 PRRSV positive occurrences were reported from 79 production sites during those 3 years. The temporal dynamics of swine shipments was evaluated by computing network properties in one-month and three-month networks. The association of PRRS occurrence in sow farms with centrality properties from one-month and three-month networks was assessed by using the multilevel logistic regression. All monthly networks showed a scale-free network topology with positive degree assortativity. The regression model revealed that out-degree centrality had a negative association with PRRS occurrence in sow farms in both one-month and three-month networks [OR=0.79 (95% CI, 0.63-0.99) in one-month network and 0.56 (95% CI, 0.36, 0.88) in three-month network] and in-closeness centrality model was positively associated with PRRS occurrence in sow farms in the three-month network [OR=2.45 (95% CI, 1.14-5.26)]. We also describe how the occurrence of porcine epidemic diarrheac (PED) outbreaks severely affected the network structure as well as the PRRS occurrence reports and its association with centrality measures in sow farms. The structure of the swine shipment network and the connectivity between production sites influenced on the PRRSV transmission. The use of network topology and characteristics combining with spatial analysis based on fine scale geographical location of production sites will be useful to inform the design of more cost-efficient, risk-based surveillance and control measures for PRRSV as well as other diseases in the US swine industry.

KEYWORDS: 

Infectious disease; PED; PRRS; Pork value chain; Social network analysis; Swine
PMID:
 
28237226
 
DOI:
 
10.1016/j.prevetmed.2017.02.001

Monday, April 3, 2017

Quasispecies evolution of PRRSv early during in vivo infection

 2017 Mar 30. doi: 10.1007/s00705-017-3342-0. [Epub ahead of print]

Quasispecies evolution of the prototypical genotype 1 porcine reproductive and respiratory syndrome virus early during in vivo infection is rapid and tissue specific.

Author information

1
PAPRSB Institute of Health Sciences, Universiti Brunei Darussalam, Bandar Seri Begawan, Brunei.
2
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
3
Northwest A&F University, Xianyang, China.
4
Animal and Plant Health Agency, Preston, UK.
5
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK. tahar.aitali@roslin.ed.ac.uk.

Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV) is a major infectious threat to the pig industry worldwide. Increasing evidence suggests that microevolution within a quasispecies population can give rise to high sequence heterogeneity in PRRSV; potentially impacting the pathogenicity of the virus. Here, we report on micro-evolutionary events taking place within the viral quasispecies population in lung and lymph node 3 days post infection (dpi) following experimental in vivo infection with the prototypical Lelystad PRRSV (LV). Sequence analysis revealed 16 high frequency single nucleotide variants (SNV) or differences from the reference LV genome which are assumed to be representative of the consensus inoculum genome. Additionally, 49 other low frequency SNVs were also found in the inoculum population. At 3 dpi, a total of 9 and 10 SNVs of varying frequencies could already be detected in the LV population infecting the lung and lymph nodes, respectively. Interestingly, of these, three and four novel SNVs emerged independently in the two respective tissues when compared to the inoculum. The remaining variants, though already present at lower frequencies in the inoculum, were positively selected and their frequency increased within the quasispecies population. Hence, we were able to determine directly from tissues infected with PRRSV the repertoire of genetic variants within the viral quasispecies population. Our data also suggest that microevolution of these variants is rapid and some may be tissue-specific.
PMID:
 
28361286
 
DOI:
 
10.1007/s00705-017-3342-0

Tuesday, March 14, 2017

(!) Sampling guidelines for oral fluids-based surveys of group-housed animals

 2017 Feb 17. pii: S0378-1135(16)30527-2. doi: 10.1016/j.vetmic.2017.02.004. [Epub ahead of print]

Sampling guidelines for oral fluid-based surveys of group-housed animals.

Author information

1
Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA. Electronic address: mrotolo@iastate.edu.
2
Department of Statistics, College of Liberal Arts and Sciences, Iowa State University, Ames, IA, USA.
3
Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA; Department of Statistics, College of Liberal Arts and Sciences, Iowa State University, Ames, IA, USA.
4
Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
5
Smithfield Foods, Algona, IA, USA.

Abstract

Formulas and software for calculating sample size for surveys based on individual animal samples are readily available. However, sample size formulas are not available for oral fluids and other aggregate samples that are increasingly used in production settings. Therefore, the objective of this study was to develop sampling guidelines for oral fluid-based porcine reproductive and respiratory syndrome virus (PRRSV) surveys in commercial swine farms. Oral fluid samples were collected in 9 weekly samplings from all pens in 3 barns on one production site beginning shortly after placement of weaned pigs. Samples (n=972) were tested by real-time reverse-transcription PCR (RT-rtPCR) and the binary results analyzed using a piecewise exponential survival model for interval-censored, time-to-event data with misclassification. Thereafter, simulation studies were used to study the barn-level probability of PRRSV detection as a function of sample size, sample allocation (simple random sampling vs fixed spatial sampling), assay diagnostic sensitivity and specificity, and pen-level prevalence. These studies provided estimates of the probability of detection by sample size and within-barn prevalence. Detection using fixed spatial sampling was as good as, or better than, simple random sampling. Sampling multiple barns on a site increased the probability of detection with the number of barns sampled. These results are relevant to PRRSV control or elimination projects at the herd, regional, or national levels, but the results are also broadly applicable to contagious pathogens of swine for which oral fluid tests of equivalent performance are available.

KEYWORDS: 

Modeling; Monitoring; Oral fluid; PRRSV; Probability of detection; Sample size; Sampling; Surveillance
PMID:
 
28284415
 
DOI:
 
10.1016/j.vetmic.2017.02.004