Piscine orthoreovirus 3a detected from farmed coho salmon with jaundice syndrome displays positive selection and polymorphisms in S1 and M2 viral segment

Piscine orthoreovirus (PRV) is associated with heart and skeletal muscle inflammation (HSMI) and circulatory disorders in salmonid species. In Chile, PRV affects the coho salmon industry most, as this virus correlates with both HSMI disease and jaundice syndrome. However, the causality of the latter has not been proven. In this study, we characterize nucleotide codifying and amino acid sequences of the PRV-3 detected in coho salmon with clinical signs and macroscopic evidence of jaundice syndrome in the seawater phase. The results support the diversification of the PRV-3 into two variants, PRV-3a and PRV-3b. The PRV-3a has been predominantly detected in coho salmon in the last five years. In addition, the new molecular sequences are characterized by polymorphisms exclusive to Chile in the σ3, p13 proteins encoded by the S1 segment and the μ1 protein encoded by the M2 segment. Additionally, we detected positive selection within the nucleotide sequence corresponding to the σ3 outer capsid protein. So far, PRV-3a has not been reported in other hosts in Chile, such as Atlantic salmon or rainbow trout. These findings highlight the diversification of PRV-3 in Chile and demonstrate a strong host-pathogen relationship which warrants further research to establish a link between PRV and jaundice syndrome in coho salmon.