Evolutionary dynamics of PRRS virus in Italian Pig farms: a retrospective study

Porcine Reproductive and Respiratory Syndrome (PRRS) causes huge economic losses to pig farms worldwide. Currently available vaccines do not always offer complete protection, due to the extreme variability of the virus. Therefore, good farming practices must be improved to prevent the disease from spreading across the pig production system. In this study, we inferred the dynamics of PRRSV population in Italy by applying bayesian methods on our ORF7 sequence dataset collected during a 15-years period. Random subsets from the overall dataset were built to reduce analysis runtime. Calculated evolutionary rate was consistent between subsets and with other findings on PRRSV and other RNA viruses (4-7 × 10^{- 3} substitution/site/year) while Time to the Most Recent Common Ancestor was less consistent (from 1980 to 1990). Despite this, in all population dynamic reconstructions, a massive increase in size calculated in early 2000s lasting until around 2010 was inferred. This spike is followed by very heterogeneous dynamics with some differences between subsets, probably due to the random sampling. Geographical origin was inferred in Emilia-Romagna region despite Lombardy being the region with the highest number of farmed animals and farm size. These findings reflect the choices regarding farm management and biosecurity taken in the last two decades, and not strictly related to PRRS. Phylogeny and phylogeography are powerful tools to better understand microorganisms population dynamics and make appropriate choices for disease control.