Multiple novel Caliciviruses identified from stoats (Mustela erminea) in the United Kingdom

Abstract

The Caliciviridae family, comprising positive-sense RNA viruses, is characterised by its non-enveloped, small virions, broad host range, and notable tendency for host switching. These viruses are primarily associated with gastroenteric disease, though they can lead to haemorrhagic or respiratory infections. Our study employed a metagenomics analysis of faecal samples from Stoats (Mustela erminea), identifying two novel Calicivirus species, tentatively named Stoat vesivirus and Stoat valovirus. Stoat vesivirus was identified in three samples (ST008, ST006, ST004), exhibiting a genome wide nucleotide identity of approximately 92%. The complete coding sequences of these samples were 8471 (ST004) and 8322 (ST006) nucleotides in length, respectively. Each comprised three open reading frames (ORF), closely resembling the Vesivirus mink calicivirus (China/2/2016), with 70-72% similarity in ORF1, 61-62% in ORF2 and 71% in ORF3. Phylogenetic analysis robustly supported Stoat vesivirus as belonging within the Vesivirus genus. The second Calivicirus (Stoat valovirus), detected solely in sample ST008, was 6527 nucleotides in length and with complete coding sequences present. It shared highest similarity with St-Valerien swine virus and Marmot norovirus HT16, showing 39.5% and 38.8% protein identity with ORF1 and 43.3% and 42.9% for VP1. Phylogenetic analysis suggested that while Stoat valovirus is borderline for new genus demarcation criteria, with greater than 60% divergence at ORF1, it clusters basally within the Valovirus genus, supporting its inclusion in this genus.