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Journal of General Virology header logo Journal of General Virology

Volume 104, Issue 12

A novel tamanavirus () of the European common frog () from the UK Open Access

Abstract

Flavivirids are small, enveloped, positive-sense RNA viruses from the family with genomes of ~9–13 kb. Metatranscriptomic analyses of metazoan organisms have revealed a diversity of flavivirus-like or flavivirid viral sequences in fish and marine invertebrate groups. However, no flavivirus-like virus has been identified in amphibians. To remedy this, we investigated the virome of the European common frog () in the UK, utilizing high-throughput sequencing at six catch locations. assembly revealed a coding-complete virus contig of a novel flavivirid ~11.2 kb in length. The virus encodes a single ORF of 3456 aa and 5′ and 3′ untranslated regions (UTRs) of 227 and 666 nt, respectively. We named this virus Rana tamanavirus (RaTV), as BLASTp analysis of the polyprotein showed the closest relationships to Tamana bat virus (TABV) and Cyclopterus lumpus virus from and , respectively. Phylogenetic analysis of the RaTV polyprotein compared to and Flavivirus-like members indicated that RaTV was sufficiently divergent and basal to the vertebrate Tamanavirus clade. In addition to the Mitcham strain, partial but divergent RaTV, sharing 95.64–97.39 % pairwise nucleotide identity, were also obtained from the Poole and Deal samples, indicating that RaTV is widespread in UK frog samples. Bioinformatic analyses of predicted secondary structures in the 3′UTR of RaTV showed the presence of an exoribonuclease-resistant RNA (xrRNA) structure standard in flaviviruses and TABV. To examine this biochemically, we conducted an Xrn1 digestion assay showing that RaTV probably forms a functional Xrn1-resistant xrRNA.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): amphibian viruses , Flaviviridae , flavivirus , metagenomics , Rana temporaria , sfRNA , structural RNA , tamanavirus and Xrn1
Funding
This study was supported by the:
  • National Health and Medical Research Council (AU) (Award APP2009707)
    • Principle Award Recipient: NataleeD. Newton
  • National Health and Medical Research Council (AU) (Award 2021272)
    • Principle Award Recipient: AndriiSlonchak
  • Australian Research Council (Award DP190103304)
    • Principle Award Recipient: AndriiSlonchak
  • Australian Research Council (Award DP190103304)
    • Principle Award Recipient: AlexanderA Khromykh
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2023-12-07
2025-01-19
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A novel tamanavirus (Flaviviridae) of the European common frog (Rana temporaria) from the UK
J. Gen. Virol. 104, 001927 (2023); https://doi.org/10.1099/jgv.0.001927
/content/journal/jgv/10.1099/jgv.0.001927
/content/journal/jgv/10.1099/jgv.0.001927
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