Study of Porcine Reproductive and Respiratory Syndrome Virus Subpopulations in a Swine Production Chain Using Oxford Nanopore Sequencing

PRRS continues to represent one of the major health and economic challenges for the Italian pig farming industry. Among the least understood, yet potentially most critical aspects for infection control, is the frequency of co-infections caused by different viral strains within the same farm. The simultaneous presence of multiple variants could, in fact, reflect critical issues in internal biosecurity—favoring viral persistence and spread—or indicate repeated introductions from the outside, suggesting gaps in external biosecurity. This project aims to investigate these dynamics within a large Italian production chain through the amplification of the genomic region spanning from ORF5 to ORF7, followed by third-generation Oxford Nanopore sequencing. The resulting sequences will be compared with those available in major international databases, with the goal of determining whether the observed epidemiological structure stems primarily from the internal circulation of multiple strains or from continuous external introductions. The findings will contribute to the development of more targeted and effective strategies for PRRS control.