Novel viruses discovered in the transcriptomes of agnathan fish

Mercer, Lewis K.; Harding, Emma F.; Yan, Grace J. H.; White, Peter A.

doi:10.1111/jfd.13602

Cited by 8 publications

(3 citation statements)

References 31 publications

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“…Next‐generation sequencing technology has revolutionized the era of modern microbiology by identifying novel viruses without prior knowledge of the nucleotide sequences present in the clinical samples (Bassi et al, 2022). Transcriptomic and metagenomic raw data deposited in public depositories such as the Sequence Read Archive (SRA) database (https://www.ncbi.nlm.nih.gov/sra) of the National Center for Biotechnology Information (NCBI) have been reanalysed by researchers in order to expand the current knowledge of viruses across different kingdoms (Edgar et al, 2022; Mifsud et al, 2022), including fish species (Mercer et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Discovery of two novel tilapia lake virus‐like virus isolates in the transcriptomic data of guppy fish (Poecilia reticulata)

2023

Journal of Fish Diseases

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Section: Introductionmentioning

confidence: 99%

Discovery of two novel tilapia lake virus‐like virus isolates in the transcriptomic data of guppy fish (Poecilia reticulata)

2023

Journal of Fish Diseases

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“…The discovery of DNA viruses primarily relies on either tissue DNA sequencing or PCR-based approaches. Many new viruses have been discovered this way [ 27 – 29 ], however a novel approach is to utilise transcriptomic data to discover DNA viruses through bioinformatic approaches [ 15 , 30 – 32 ].…”

Section: Discussionmentioning

confidence: 99%

“…Raw sequencing reads ( n = 235) encompassing a wide diversity of reptile and amphibian species ( n = 122) were assembled into transcriptomes for each dataset prior to viral discovery, as previously described [ 15 ]. Briefly, publicly available RNA sequencing datasets were obtained from the National Centre of Biotechnology Institute (NCBI) Sequence Read Archive (SRA).…”

Section: Methodsmentioning

confidence: 99%

Revealing the uncharacterised diversity of amphibian and reptile viruses

Harding

Russo²,

Yan³

et al. 2022

ISME Communications

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Amphibians and non-avian reptiles represent a significant proportion of terrestrial vertebrates, however knowledge of their viruses is not proportional to their abundance. Many amphibians and reptiles have strict habitual environments and localised populations and are vulnerable to viral outbreaks and potential elimination as a result. We sought to identify viruses that were hidden in amphibian and reptile metatranscriptomic data by screening 235 RNA-sequencing datasets from a 122 species covering 25 countries. We identified 26 novel viruses and eight previously characterised viruses from fifteen different viral families. Twenty-five viruses had RNA genomes with identity to Arteriviridae, Tobaniviridae, Hantaviridae, Rhabdoviridae, Astroviridae, Arenaviridae, Hepeviridae, Picornaviridae, Orthomyxoviridae, Reoviridae, Flaviviridae and Caliciviridae. In addition to RNA viruses, we also screened datasets for DNA viral transcripts, which are commonly excluded from transcriptomic analysis. We identified ten DNA viruses with identity to Papillomaviridae, Parvoviridae, Circoviridae and Adomaviridae. With the addition of these viruses, we expand the global amphibian and reptile virome and identify new potentially pathogenic viruses that could challenge populations. We speculate that amphibian viruses often have simpler genomes than those in amniotes, as in the case of the Secondpapillomavirinae and Orthomyxoviridae viruses identified in this study. In addition, we find evidence of inter-family recombination in RNA viruses, and we also identify new members of the recombinant Adomaviridae family. Overall, we provide insights into the uncharacterised diversity of amphibian and reptile viruses with the aim of improving population management, treatment and conservation into the future.

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Caliciviruses of fish

Mikalsen,

Evensen

2024

Aquaculture Virology

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Novel viruses discovered in the transcriptomes of agnathan fish

Cited by 8 publications

References 31 publications

Discovery of two novel tilapia lake virus‐like virus isolates in the transcriptomic data of guppy fish (Poecilia reticulata)

Discovery of two novel tilapia lake virus‐like virus isolates in the transcriptomic data of guppy fish (Poecilia reticulata)

Revealing the uncharacterised diversity of amphibian and reptile viruses

Caliciviruses of fish

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