Zvonimir Poljak

Epidemiological investigations in regard to porcine reproductive and respiratory syndrome (PRRS) in Quebec, Canada. Part 2: Prevalence and risk factors in breeding sites

Porcine reproductive and respiratory syndrome virus (PRRSV) is a major threat for swine industry and understanding factors involved in its epidemiology is undoubtedly essential for disease control. As a part of a larger project, a cross-sectional study was performed on breeding sites in a moderate density area of swine production in Quebec to estimate the prevalence of PRRSV infected sites and to evaluate if characteristics of sites and biosecurity practices, either as specific measures or as a global score, were associated with PRRSV status. A questionnaire and diagnostic procedures were performed on 54 breeding sites between September 2006 and August 2008. A biosecurity score that had been previously computed using two-step clustering procedure was used, classifying breeding sites into two biosecurity patterns (high vs. low) according to 21 specific biosecurity measures. The apparent prevalence of PRRSV infected sites was 74.0% (95% CI, 60.3-85.0). Univariable and multivariable logistic regression models with robust standard errors adjusting for potential clustering of sites due to same ownership were computed. In a first multivariable model evaluating characteristics of sites and specific biosecurity variables, four main effects were significantly associated (P<0.05) with PRRSV positive status: large pig inventory (OR: 10.7), proximity to closest pig site (OR: 7.3), absence of shower (OR: 8.7) and free access to the main entrance of the site by the rendering truck (OR: 7.0). In a second multivariable model including a global biosecurity score as a surrogate for a specific pattern of biosecurity measures, this score was not retained in the final model. The adjusted population attributable fractions were 16% for the proximity to closest pig site variable, 27% for the absence of shower variable, and 10% for the free access to main entrance of the site by the rendering truck. These two latter biosecurity measures, manageable directly on the site, should be prioritized and be part of any intervention strategy designed for PRRSV control.

Epidemiological investigations in regard to porcine reproductive and respiratory syndrome (PRRS) in Quebec, Canada. Part 1: biosecurity practices and their geographical distribution in two areas of different swine density.

Porcine reproductive and respiratory syndrome virus (PRRSV) is a considerable threat to the swine industry and implementing biosecurity measures is essential for the control of its transmission. The aims of this study were: (1) to describe biosecurity practices in production sites located in a moderate density (MD) and a high density (HD) pig area according to production type; (2) to group sites in different patterns according to their biosecurity practices; and (3) to determine the geographical distribution of sites according to biosecurity patterns. Biosecurity practices were selected based on PRRS epidemiology. A questionnaire was completed on 125 breeding sites (MD=54; HD=71) and 120 growing (HD) sites, between 2005 and 2008. Depending on area and production type, the frequency of biosecurity practices used ranged from 0 to 2% for barrier at site entrance, 0 to 19% for use of shower, 25 to 35% for washing truck between loads of pigs, 51 to 57% for absence of rendering or rendering without access to the site, and 26 to 51% for absence of gilt purchase or purchase with quarantine. Better practices pertaining to entrance protocol (i.e. no-entry sign, shower, ≥24 h downtime) were reported more frequently on breeding sites in the MD than the HD area (P<0.05). In the HD area, growing sites had in general a lower level of biosecurity than breeding sites. Using a two-step clustering procedure performed separately for breeding and growing sites, two different patterns were obtained for each production type, which corresponded to a high and low level of biosecurity. For breeding sites, a higher biosecurity level was observed at sites located away from other pig sites, set at more than 300 m from the public road, having higher sow inventory, or being part of an integrated production (P<0.05). Spatial clusters of sites for each biosecurity pattern were detected. This study identified some shortcomings regarding biosecurity that should be addressed before implementing any PRRSV regional control. Vicinity of sites with different biosecurity levels also suggests difficulties in planning priorities of intervention based on geographical distribution of sites.

Bayesian analysis of risk factors for infection with a genotype of porcine reproductive and respiratory syndrome virus in Ontario swine herds using monitoring data.

Porcine reproductive and respiratory syndrome (PRRS) has a worldwide distribution. This economically important endemic disease causes reproductive failure in breeding stock and respiratory tract illness in young pigs. In Ontario restricted fragment length polymorphism (RFLP) 1-18-4 has been determined as one of the most common virus genotypes. Individual-level models (ILMs) for infectious diseases, fitted in a Bayesian MCMC framework, have been used to describe both the spatial and temporal spread of diseases. They are an intuitive and flexible class of models that can take into account population heterogeneity via various individual-level covariates. The objective of this study is to identify relative importance of risk factors for the spread of the genotype 1-18-4 from monitoring data in southern Ontario using ILMs. Specifically, we explore networks through which resources are obtained or delivered, as well as the ownership structure of herds, and identify factors that may be contributing to high risk of infection. A population of 316 herds which experienced their PRRS outbreaks between September 2004 and August 2007 are included in the analyses, in which 194 (61%) are sow herds. During the study period, 45 herds (27 sow herds) experienced their first outbreak due to RFLP 1-18-4. Our results show that the three relatively most important factors for the spread of 1-18-4 genotype in Ontario swine herds were sharing the same herd ownership, gilt source and market trucks. All other networks had relatively smaller impact on spread of this PRRSV genotype. Spatial proximity could not be identified as important contributor to spread. Our findings also suggest that gilt acclimation should be practiced whenever possible and appropriate to reduce the risk for the herd and for others as it is already widely implemented and recommended in the North American swine industry.

Spatial and temporal patterns of porcine reproductive and respiratory syndrome virus (PRRSV) genotypes in Ontario, Canada, 2004–2007

BackgroundThe spread of PRRSV among pig herds has been investigated experimentally, but few observational studies have investigated this subject. Because PRRSV is endemic and live modified vaccines are used in Ontario, the spatial and temporal distributions of 6 PRRSV genotypes were investigated in the province during the period from 2004–2007. The purpose was to find evidence of spread of PRRSV genotypes and determine if spread could be attributed to supplier or ownership connections between herds. Sequence information from PRRSV ORF5 and related source-herd demographic information were obtained from diagnostic submissions to the Animal Health Laboratory, University of Guelph.ResultsA spatial cluster that could not be attributed to supplier or ownership connections among herds in the cluster was detected for RFLP type 1-3-4. Because of genetic dissimilarity among members of the cluster, it was considered to be a result of past spread of the RFLP type. A spatio-temporal cluster detected for RFLP type 1-18-4 was attributed to a shared gilt supplier among the herds in the cluster. Significant spatio-temporal patterns detected for RFLP type 2-5-2, which is considered to be a vaccine-type virus were most likely due to grouping of herds in an ownership that used the corresponding vaccine. Clustering within herd-ownership was a risk factor for presence of five of the six genotypes investigated in the present study.ConclusionsAlthough the literature indicates that PRRSV can spread via aerosol between pig herds, the present study found no strong evidence of this occurring in Ontario. The evidence pointed toward transmission of PRRSV occurring in this population by common sources of animals or similarity of herd ownership, which is a proxy measure for other connections between herds. It is also apparent that the recognition and testing of these connections between herds is a necessary part of interpreting spatio-temporal patterns of PRRSV genotypes.

Correlation among genetic, Euclidean, temporal, and herd ownership distances of porcine reproductive and respiratory syndrome virus strains in Quebec, Canada

BackgroundPorcine reproductive and respiratory syndrome (PRRS) is a viral disease that has a major economic impact for the swine industry. Its control is mostly directed towards preventing its spread which requires a better understanding of the mechanisms of transmission of the virus between herds. The objectives of this study were to describe the genetic diversity and to assess the correlation among genetic, Euclidean and temporal distances and ownership to better understand pathways of transmission.ResultsA cross-sectional study was conducted on sites located in a high density area of swine production in Quebec. Geographical coordinates (longitude/latitude), date of submission and ownership were obtained for each site. ORF5 sequencing was attempted on PRRSV positive sites. Proportion of pairwise combinations of strains having ≥98% genetic homology were analysed according to Euclidean distances and ownership. Correlations between genetic, Euclidean and temporal distances and ownership were assessed using Mantel tests on continuous and binary matrices. Sensitivity of the correlations between genetic and Euclidean as well as temporal distances was evaluated for different Euclidean and temporal distance thresholds. An ORF5 sequence was identified for 132 of the 176 (75%) PRRSV positive sites; 122 were wild-type strains. The mean (min-max) genetic, Euclidean and temporal pairwise distances were 11.6% (0–18.7), 15.0u2009km (0.04-45.7) and 218u2009days (0–852), respectively. Significant positive correlations were observed between genetic and ownership, genetic and Euclidean and between genetic and temporal binary distances. The relationship between genetic and ownership suggests either common sources of animals or semen, employees, technical services or vehicles, whereas that between genetic and Euclidean binary distances is compatible with area spread of the virus. The latter correlation was observed only up to 5u2009km.ConclusionsThis study suggests that transmission of PRRSV is likely to occur between sites belonging to the same owner or through area spread within a 5u2009km distance. Both should be considered in the perspective of prevention.

Genetic Characterization of H1N1 and H1N2 Influenza A Viruses Circulating in Ontario Pigs in 2012

The objective of this study was to characterize H1N1 and H1N2 influenza A virus isolates detected during outbreaks of respiratory disease in pig herds in Ontario (Canada) in 2012. Six influenza viruses were included in analysis using full genome sequencing based on the 454 platform. In five H1N1 isolates, all eight segments were genetically related to 2009 pandemic virus (A(H1N1)pdm09). One H1N2 isolate had hemagglutinin (HA), polymerase A (PA) and non-structural (NS) genes closely related to A(H1N1)pdm09, and neuraminidase (NA), matrix (M), polymerase B1 (PB1), polymerase B2 (PB2), and nucleoprotein (NP) genes originating from a triple-reassortant H3N2 virus (tr H3N2). The HA gene of five Ontario H1 isolates exhibited high identity of 99% with the human A(H1N1)pdm09 [A/Mexico/InDRE4487/09] from Mexico, while one Ontario H1N1 isolate had only 96.9% identity with this Mexican virus. Each of the five Ontario H1N1 viruses had between one and four amino acid (aa) changes within five antigenic sites, while one Ontario H1N2 virus had two aa changes within two antigenic sites. Such aa changes in antigenic sites could have an effect on antibody recognition and ultimately have implications for immunization practices. According to aa sequence analysis of the M2 protein, Ontario H1N1 and H1N2 viruses can be expected to offer resistance to adamantane derivatives, but not to neuraminidase inhibitors.

Clustering of and Risk Factors for the Porcine High Fever Disease in a Region of Vietnam

Porcine high fever disease (PHFD) emerged in 2006 in China and spread to Vietnam. Little work has been carried out to investigate PHFD risk factors and space-time dynamics. To fill this gap, we investigated probable cases of PHFD at household level as the outcome. A study area, approximately 100 sq. km, was selected from a province of southern Vietnam that had reported the outbreak of PHFD in 2008. A survey was conducted in the study area to collect information about swine health problems during 2008. The questionnaire included three sections: general information, clinical signs of disease in pigs and production factors believed to be risk factors. Cases were defined at the household level and included interpretation of clinical signs in series. Logistic regression with a random intercept at the hamlet level was used to assess risk factors for PHFD at the household level. Spatial clustering was investigated using the D-function and a Cuzick-Edwards test. Spatial clusters were evaluated using a spatial relative risk surface and the spatial scan statistic using a Bernoulli model. Space-time clustering was explored using a space-time K-function and Knoxs test. Space-time clusters were evaluated using a space-time permutation model in SaTScan. Of 955 households with questionnaire data, 33.4% were classified as cases. The statistical significance of space and space-time clustering differed between methods employed. The risk factors associated with occurrence of cases were higher numbers of sows and finishing pigs (log 2 transformed), receiving pigs from an external source and the interaction between using water green crop (WGC) as pig feed and owning ducks with or without direct contact with pigs. The interaction between the presence of ducks and feeding WGC to pigs suggested the involvement of pathogens that might be present in water (environment) and could further replicate in or on ducks.

Molecular characterization of H3N2 influenza A viruses isolated from Ontario swine in 2011 and 2012

BackgroundData about molecular diversity of commonly circulating type A influenza viruses in Ontario swine are scarce. Yet, this information is essential for surveillance of animal and public health, vaccine updates, and for understanding virus evolution and its large-scale spread.MethodsThe study population consisted of 21 swine herds with clinical problems due to respiratory disease. Nasal swabs from individual pigs were collected and tested by virus isolation in MDCK cells and by rtRT-PCR. All eight segments of 10 H3N2 viruses were sequenced using high-throughput sequencing and molecularly characterized.ResultsWithin-herd prevalence ranged between 2 and 100%. Structurally, Ontario H3N2 viruses could be classified into three different groups. Group 1 was the most similar to the original trH3N2 virus from 2005. Group 2 was the most similar to the Ontario turkey H3N2 isolates with PB1 and NS genes originating from trH3N2 virus and M, PB2, PA and NP genes originating from the A(H1N1)pdm09 virus. All Group 3 internal genes were genetically related to A(H1N1)pdm09. Analysis of antigenic sites of HA1 showed that Group 1 had 8 aa changes within 4 antigenic sites, A(1), B(3), C(2) and E(2). The Group 2 viruses had 8 aa changes within 3 antigenic sites A(3), B(3) and C(2), while Group 3 viruses had 4 aa changes within 3 antigenic sites, B(1), D(1) and E(2), when compared to the cluster IV H3N2 virus [A/swine/Ontario/33853/2005/(H3N2)].ConclusionsThe characterization of the Ontario H3N2 viruses clearly indicates reassortment of gene segments between the North American swine trH3N2 from cluster IV and the A(H1N1)pdm09 virus.

Network, cluster and risk factor analyses for porcine reproductive and respiratory syndrome using data from swine sites participating in a disease control program.

The objectives of this study were to describe networks of Ontario swine sites and their service providers (including trucking, feed, semen, gilt and boar companies); to categorize swine sites into clusters based on site-level centrality measures, and to investigate risk factors for porcine reproductive and respiratory syndrome (PRRS) using information gathered from the above-mentioned analyses. All 816 sites included in the current study were enrolled in the PRRS area regional control and elimination projects in Ontario. Demographics, biosecurity and network data were collected using a standardized questionnaire and PRRS status was determined on the basis of available diagnostic tests and assessment by site veterinarians. Two-mode networks were transformed into one-mode dichotomized networks. Cluster and risk factor analyses were conducted separately for breeding and growing pig sites. In addition to the clusters obtained from cluster analyses, other explanatory variables of interest included: production type, type of animal flow, use of a shower facility, and number of neighboring swine sites within 3km. Unadjusted univariable analyses were followed by two types of adjusted models (adjusted for production systems): a generalizing estimation equation model (GEE) and a generalized linear mixed model (GLMM). Results showed that the gilt network was the most fragmented network, followed by the boar and truck networks. Considering all networks simultaneously, approximately 94% of all swine sites were indirectly connected. Unadjusted risk factor analyses showed significant associations between almost all predictors of interest and PRRS positivity, but these disappeared once production system was taken into consideration. Finally, the vast majority of the variation on PRRS status was explained by production system according to GLMM, which shows the highly correlated nature of the data, and raises the point that interventions at this level could potentially have high impact in PRRS status change and/or maintenance.

An economic evaluation of intervention strategies for Porcine Epidemic Diarrhea (PED)

The economic losses of Porcine Epidemic Diarrhea (PED) and the net benefits of strategies to control the virus are calculated for individual farrow-to-finish herds. A production simulation model that estimates the number of pigs by population cohorts on a weekly basis for a farrow-to-finish farm depending on production parameters is simulated under normal operating conditions and then with an outbreak of PED. The estimated annual costs of a PED outbreak with the closure of the breeding herd as the only intervention is approximately