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. 2022 Sep;69(5):e2175-e2184.
doi: 10.1111/tbed.14556. Epub 2022 Apr 22.

Phylodynamic and phylogeographic reconstruction of porcine reproductive and respiratory syndrome virus (PRRSV) in Europe: Patterns and determinants

Giovanni Franzo  1 , Giulia Faustini  1 , Matteo Legnardi  1 , Mattia Cecchinato  1 , Michele Drigo  1 , Claudia Maria Tucciarone  1
Affiliations

Phylodynamic and phylogeographic reconstruction of porcine reproductive and respiratory syndrome virus (PRRSV) in Europe: Patterns and determinants

Giovanni Franzo et al. Transbound Emerg Dis. 2022 Sep.

Abstract

Porcine reproductive and respiratory syndrome (PRRS) is among the most devastating diseases affecting the pig industry. Despite vaccines having been available for decades, the remarkable genetic variability of this virus, leading to poor cross-protection, has limited their efficacy, and other measures must be adopted to effectively control the viral circulation. Some recent studies have investigated the factors involved in viral spreading and persistence, at least at the local level. However, despite the topic's relevance, no statistically grounded evidence is currently available evaluating the variables more involved in porcine reproductive and respiratory syndrome virus (PRRSV) epidemiological success at a broader scale, such as the European scale. In the present study, an extensive phylodynamic and phylogeographic analysis was performed on more than 1000 ORF5 sequences to investigate the history, dynamics and spreading patterns of PRRSV within European borders. Moreover, several potential predictors, representative of swine population features and trade, human population, economy and geographic characteristics, were evaluated through a specifically designed generalized linear model (GLM) to assess their weight on viral migration rate between countries over time. Although pig stock density, mean PRRSV strain genetic diversity, investments in agriculture (including a likely role of vaccination) and farmer education were involved to a certain extent, the major determinant was proven to be by far the live pig trade. Providing a robust depiction of PRRSV European molecular epidemiology patterns and determinants, the present study could contribute to a more rational allocation of limited resources based on an effective prioritization of control measures.

Keywords: Europe; GLM; ORF5; PRRSV; control; phylodynamics; phylogeography.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

FIGURE 1
FIGURE 1
Plot reporting the mean relative genetic diversity (effective population size × generation time; Ne × t) of the European porcine reproductive and respiratory syndrome virus (PRRSV) population over time. This measure can be considered a proxy for the variation in PRRSV population size over time. The results of the five independent runs (obtained by randomly subsampling the whole sequence datasets) have been color‐coded. 95HPD has been reported as a shaded area
FIGURE 2
FIGURE 2
Phylogeographic reconstruction of porcine reproductive and respiratory syndrome virus (PRRSV) migration among European countries over time. Each picture represents a different decade. The edges connecting the countries have been color‐coded from black to red based on the estimated age
FIGURE 3
FIGURE 3
Well‐supported migration paths (i.e., Bayesian factor [BF]>10) among countries, estimated in the five independent BEAST runs, are depicted as edges whose colour is proportional to the posterior probability of the inferred link. The location of each country has been matched with its centroid
FIGURE 4
FIGURE 4
Density plot of the number of transition events (expressed as log10) among countries, aggregated by macro area. The value is indicative of the movement intensity of strains from one region to the other. The average value is shown by a dashed line
FIGURE 5
FIGURE 5
Area chart reporting the percentage of estimated lineages present in the European countries (colour‐coded) over time. The width of each band is proportional to the estimated number of porcine reproductive and respiratory syndrome virus (PRRSV) lineages present in a country in a particular period
See this image and copyright information in PMC

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