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

Abstract

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), 15.0 km (0.04-45.7) and 218 days (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 5 km.ConclusionsThis study suggests that transmission of PRRSV is likely to occur between sites belonging to the same owner or through area spread within a 5 km distance. Both should be considered in the perspective of prevention.

Association Between PRRSV ORF5 Genetic Distance and Differences in Space, Time, Ownership and Animal Sources Among Commercial Pig Herds

“…Although the magnitude and significance of the correlation coefficients do not change, it is important to account for the effect of ownership, given the association between ownership and genetic distance and the spatial aggregation of herds within the same ownership. This finding is similar to what was detected in a study from Québec (Lambert et al., ). First, in the Québec study, the correlation between sequence distance and spatial separation was not significant when continuous distance measures were considered.…”

“…The Mantel test was used to test the Spearman rank correlation between geographic distance, temporal distance and sequence distance using the vegan package (version 1.15, http://cran.r-project.org/web/packages/vegan/index.html) in R (version 2.09). The partial Mantel test makes it possible to test correlation between two variables while adjusting for a third variable that may be correlated with both main variables (Goldberg et al., ; Mondaca‐Fernandez et al., ; Lambert et al., ). The partial Mantel statistic was used to test correlation between geographic, temporal and sequences distances; sequentially including each of these variables as the ‘adjusting’ variable.…”

“…These previous investigations did not measure the effect of ownership, and their authors limited their analysis to testing for correlation using the Mantel test. A more recent study in a region of Québec detected significant correlation between spatial proximity and genetic similarity before and after adjusting for herd ownership again using the Mantel test and the partial Mantel test (Lambert et al., ), but only after continuous measures of distance had been reclassified to binary measures of proximal and distant.…”

Lessons learned and knowledge gaps about the epidemiology and control of porcine reproductive and respiratory syndrome virus in North America

“…Some studies relied on serologic evidence of PRRSV circulation in various herd types. Some investigators have relied on descriptive statistics, 41,140 contingency tables, 40 Cox proportional hazard models, 73,142 generalized additive models and methods to detect spatial and space-time clustering and clusters commonly used in spatial epidemiology, 141 statistical models of individual-level infectious disease transmission, 35 results of the Mantel correlation test, 39,[143][144][145] and linear regression based on a permutation approach. 40,[143][144][145] The analytic approach has also differed among studies.…”

“…Investigators of epidemiological studies 40,77 identified area spread and argued that aerosol transmission played a critical role in transmission. 141 Few studies have been conducted to investigate membership in important networks such as ownership, 35,41,141,144,145 sources of animals and semen, 35,77,140,141 or transportation or service providers. Furthermore, several authors reported the possibility of area spread for some discrete genotypes, although such spread was not identified as the dominant mechanism of spread 41,141 or could be explained in some cases because of common sources of animals.…”