Analysis of ORF5 sequences of Porcine Reproductive and Respiratory Syndrome virus (PRRSV) circulating within swine farms in Costa Rica

BACKGROUND: Worldwide, Porcine Reproductive and Respiratory Syndrome (PRRS) is among the diseases that cause the highest economic impact in modern pig production. PRRS was first detected in Costa Rica in 1996 and has since then severely affected the local swine industry. Studies of the molecular characterization of circulating strains, correlation with clinical records, and associations with pathogens associated with Porcine Respiratory Disease Complex (PRDC) have not been done in Costa Rica. RESULTS: Sequencing and phylogenetic analysis of ORF5 proved that PRRSV-2 was the only species detected in all locations analyzed. These sequences were grouped into three clusters. When comparing samples from San Jose, Alejuela, and Puntarenas to historical isolates of the previously described lineages (1 to 9), it has been shown that these were closely related to each other and belonged to Lineage 5, along with the samples from Heredia. Intriguingly, samples from Cartago clustered in a separate clade, phylogenetically related to Lineage 1. Epitope analysis conducted on the GP5 sequence of field isolates from Costa Rica revealed seven peptides with at least 80% amino acid sequence identity with previously described and experimentally validated immunogenic regions. Previously described epitopes A, B, and C, were detected in the Santa Barbara-Heredia isolate. CONCLUSIONS: Our data suggest that the virus has three distinct origins or introductions to the country. Future studies will elucidate how recently introduced vaccines will shape the evolutionary change of circulating field strains. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12917-021-02925-7.