Discovery and characterization of a novel, highly divergent paramyxovirus in bearded seals, a new branch in North Atlantic virology

Introduction: Seals are important animals for Arctic and subarctic environments and a valuable resource for indigenous communities, but their virome remains poorly understood. During an effort to identify viruses circulating among North Atlantic seals, we discovered a new member of the Paramyxoviridae, a family including important RNA animal pathogens. This study aimed to characterize the novel virus and investigate its evolutionary relationships with other paramyxoviruses.

Methods: We conducted a metagenomic survey on paired tracheal and colon swabs collected from 59 seals — bearded (Erignathus barbatus, N=7), ringed (Pusa hispida, N=6), harp (Pagophilus groenlandicus, N=42), and harbour (Phoca vitulina, N=4) seals — from the northwest coast of Newfoundland, Canada. Virus-enriched nucleic acids isolated from each sample were subjected to reverse transcription and second-strand synthesis. Obtained dsDNA were pooled (N=9) according to species and location, and outsourced for Illumina sequencing. An in-house bioinformatics pipeline was used to identify viral contigs, and virus presence was confirmed by PCR and Sanger sequencing. Paramyxoviridae-wide phylogenetic analysis was performed with maximum likelihood methods on core protein concatenated alignments using a partition model.

Results: The complete genome of a novel paramyxovirus was identified in a pool from 7 bearded seals and confirmed to be present in one sample. We named the new virus bearded seal-associated paramyxovirus (BSAPV). The genome (15,989-nt) encoded five core paramyxoviral proteins — nucleoprotein, matrix, fusion, hemagglutinin-neuraminidase, and polymerase — and two proteins with no identifiable homologues. Phylogenetic analysis, including BSAPV and all 153 currently known paramyxoviral species, positioned BSAPV in a long-branched clade with Wenzhou pacific spadenose shark paramyxovirus (Scoliovirinae, Scoliodonvirus scoliodontis), its closest relative (pairwise identity of the L protein: 32.2%).

Conclusions: According to ICTV criteria, BSAPV is likely the first member of a novel paramyxoviral subfamily. This study expands our knowledge about marine paramyxoviruses, and future studies should investigate BSAPV ecology, spread, and host spectrum.