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

Hinds, Joseph; Apaa, Ternenge; Parry, Rhys H.; Withers, Amy J.; MacKenzie, Laura; Staley, Ceri; Morrison, Joshua; Bennett, Malcolm; Bremner-Harrison, Samantha; Chadwick, Elizabeth A.; Hailer, Frank; Harrison, Stephen W.R.; Lambin, Xavier; Loose, Mathew; Mathews, Fiona; Tarlinton, Rachael; Blanchard, Adam

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, 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-Valérien swine virus and marmot norovirus HT16, showing 39.5 and 38.8 % protein identity with ORF1 and 43.3 and 42.9 % for VP1. Stoat valovirus is borderline for meeting the ICTV criteria for a new genus, demonstrating 60 % divergence in ORF1 compared to the other valovirus’, however it clusters basally within the Valovirus genus, supporting leaving it included in this genus.

Citation

Hinds, J., Apaa, T., Parry, R. H., Withers, A. J., MacKenzie, L., Staley, C., Morrison, J., Bennett, M., Bremner-Harrison, S., Chadwick, E. A., Hailer, F., Harrison, S. W., Lambin, X., Loose, M., Mathews, F., Tarlinton, R., & Blanchard, A. (2024). Multiple novel caliciviruses identified from stoats (Mustela erminea) in the United Kingdom. Access Microbiology, 6(7), Article 000813.v4. https://doi.org/10.1099/acmi.0.000813.v4

• Journal Article Type: Article
• Acceptance Date: Jul 1, 2024
• Online Publication Date: Jul 9, 2024
• Publication Date: 2024-07
• Deposit Date: Jul 11, 2024
• Publicly Available Date: Jul 11, 2024
• Journal: Access Microbiology
• Electronic ISSN: 2516-8290
• Publisher: Microbiology Society
• Peer Reviewed: Peer Reviewed
• Volume: 6
• Issue: 7
• Article Number: 000813.v4
• DOI: https://doi.org/10.1099/acmi.0.000813.v4
• Keywords: calicivirus , metagenomics , Mustela erminea , mustelid , stoat , valovirus and vesivirus
• Public URL: https://nottingham-repository.worktribe.com/output/37153541
• Publisher URL: https://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.0.000813.v4