Isolation, associated pathology and genomic characterization of cetacean picornavirus, a novel picornavirus species from a beluga whale (Delphinapterus leucas) and a harbor porpoise (Phocoena phocoena) from Alaska

We report the isolation in the beluga (Delphinapterus leucas) kidney cell line (BWK) the genome of two new isolates of a novel cetacean picornavirus species, Senecavirus cetus, in dead stranded cetaceans from Alaska. Cetacean Picornavirus 1 (CPV1) isolates were from a harbor porpoise stranded in 2017, and a beluga, stranded in 2019. Infected BWK cells from both isolates displaying extensive cytopathic effects were processed for transmission electron microscopy, revealing identical non-envelope virus particles in the cytoplasm with morphology and size consistent with other picornaviruses. Whole-genome sequencing of CPV1, strain beluga whale/NMFS2021287/USA/2019 from a dead beluga whale found at Campbell Creek, Turnagain Arm, Alaska, USA, and strain Harbor porpoise/NMFS2017026/USA/2017 isolated from a harbor porpoise found dead on St. Paul Island, showed a genome-wide nucleotide identity of 98.8% with a genome size of 7455bp. Comparison with other picornavirus genomes showed the cetacean picornavirus is most similar to Senecavirus A (SVA), the sole species in the genus Senecavirus, family Picornaviridae, with a 54.5% genome-wide pairwise nucleotide identity. Sequence divergence between the new species and SVA was 40.5% and 44.5% nucleotide identity for the 3Dpol and P1 proteins, respectively. SVA has been silently circulating in swine production facilities in the USA since the late 1980s. More recently, SVA caused sporadic vesicular disease in swine in Canada and the USA. Phylogenetic and genetic analyses supported CPV1 as a member of the Senecavirus genus and provided the first evidence of Senecavirus-like picornavirus infecting marine mammals. These discoveries provide important information on the evolutionary relationships and taxonomy of Senecaviruses and increase our understanding of the genomic characteristics of cetacean picornaviruses. Our findings also highlight the importance of studies of viruses found in the marine environment and expand the known host range of Senecaviruses.