Phylogenetic Diversity and Geographic Distribution of Atlantic Salmon Calicivirus in Major Salmon Farming Regions

Salovirus is a genus within the family Caliciviridae, which contains a single member species, Salovirus nordlandense, also known as Atlantic salmon calicivirus (ASCV). While previous work has shown that ASCV can replicate in fish cell lines and establish systemic infection in vivo, its exact role in disease remains unclear and very little is known about its geographic distribution and evolution among Atlantic salmon. To expand the phylogenetic range of ASCV and better understand its potential role in disease, we screened publicly available transcriptomes for ASCV-like sequences. Notably, we detected ASCV in sequencing projects of Atlantic salmon (Salmo salar) (n = 40) and wild common whitefish (Coregonus lavaretus) (n = 1), across Chile, Scotland and Norway. Our phylogenetic analysis identified two viral species, which we provisionally name Salovirus nordlandense 1 and 2, each containing distinct genotypes. Both viral species were found in all three countries, with no clear geographic pattern, indicating that saloviruses have spread through the Atlantic salmon trade. It was notable that 88% of these transcriptomes were generated for the study of other pathogens, including infectious salmon anaemia virus, piscine myocarditis virus and Piscirickettsia salmonis, suggesting that saloviruses might be frequently associated with co-infections. Overall, this study indicates that viruses, like ASCV, can silently spread through aquacultural practices, potentially contributing to a variety of fish diseases.