Meta-Transcriptomic Identification of Divergent Amnoonviridae in Fish

Turnbull, Olivia M. H.; Ortiz-Báez, Ayda Susana; Eden, John‐Sebastian; Shī, Mǎng; Williamson, Jane E.; Gaston, Troy F.; Zhang, Yongzhen; Holmes, Edward C.; Geoghegan, Jemma L.

doi:10.3390/v12111254

Cited by 22 publications

(16 citation statements)

References 19 publications

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“…Note that the tree of orthomyxo-like viruses ( fig. 7 ) does not extend to other Articulavirales clades such as the Amnoonviridae ( Turnbull et al 2020 ) and the unclassified gecko-derived Lauta virus ( Ortiz-Baez et al 2020 ), and the PB1 encoded by GFBM010604515.1 is more closely related to Orthomyxoviridae PB1 proteins than the PB1 proteins of these other virus groups.…”

Section: Resultsmentioning

confidence: 99%

Identification of RNA Virus–Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets

Olendraitė

Brown

Firth

2023

Molecular Biology and Evolution

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RNA viruses are abundant, highly diverse, and infect all or most eukaryotic organisms. However, only a tiny fraction of the number and diversity of RNA virus species have been catalogued. To cost effectively expand the diversity of known RNA virus sequences we mined publicly available transcriptomic datasets. We developed 77 family-level Hidden Markov Model profiles for the viral RNA dependent RNA polymerase – the only universal “hall-mark” gene of RNA viruses. By using these to search the NCBI Transcriptome Shotgun Assembly database, we identified 5,867 contigs encoding RNA virus RdRps or fragments thereof and analysed their diversity, taxonomic classification, phylogeny and host associations. Our study expands the known diversity of RNA viruses, and the 77 curated RdRp pHMMs provide a useful resource for the virus discovery community.

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Section: Resultsmentioning

confidence: 99%

Identification of RNA Virus–Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets

Olendraitė

Brown

Firth

2023

Molecular Biology and Evolution

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“…22.7% a.a. identity, 60% coverage in a TBLASTN comparison with influenza B virus PB1) and did not cluster within established genera (Figure 9). Note that the tree of orthomyxo-like viruses (Figure 9) does not extend to other Articulavirales clades such as the Amnoonviridae (Turnbull et al, 2020) and the unclassified gecko-derived Lauta virus (Ortiz-Baez et al, 2020), and the PB1 encoded by GFBM010604515.1 is more closely related to Orthomyxoviridae PB1 proteins than the PB1 proteins of these other virus groups.…”

Section: Resultsmentioning

confidence: 99%

Identification of RNA virus-derived RdRp sequences in publicly available transcriptomic datasets

Olendraitė

Brown

Firth

2022

Preprint

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RNA viruses are abundant, highly diverse, and infect all or most eukaryotic organisms. However, only a tiny fraction of the number and diversity of RNA virus species have been catalogued. To cost effectively expand the diversity of known RNA virus sequences we mined publicly available transcriptomic datasets. We developed 77 family-level Hidden Markov Model profiles for the viral RNA dependent RNA polymerase - the only universal "hall-mark" gene of RNA viruses. By using these to search the NCBI Transcriptome Shotgun Assembly database, we identified 5,867 contigs encoding RNA virus RdRps or fragments thereof and analysed their diversity, taxonomic classification, phylogeny and host associations. Our study expands the known diversity of RNA viruses, and the 77 curated RdRp pHMMs provide a useful resource for the virus discovery community.

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“…Aquatic animals serve as hosts for both families. The Amnoonviridae is a family of primarily fish-infecting viruses 18 , and two species have been found in amphibians 19,20 . Tilapia lake virus, a genus within this family, has important implications for the global aquaculture industry because it is associated with severe disease in tilapia 21 .…”

Section: Introductionmentioning

confidence: 99%

Evidence for an aquatic origin of influenza virus and the orderArticulavirales

Parry

Mifsud

et al. 2023

Preprint

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The emergence of novel disease-causing viruses in mammals is part of the long evolutionary history of viruses. Tracing these evolutionary histories contextualises virus spill over events and may help to elucidate how and why they occur. We used a combination of total RNA sequencing and transcriptome data mining to extend the diversity and evolutionary history of the order Articulavirales, which includes the influenza viruses. From this, we identified the first instance of Articulavirales in the Cnidaria (including corals), constituting a novel and divergent family that we tentatively named the Cnidenomoviridae. This may be the basal group within the Articulavirales. We also extended the known evolutionary history of the influenza virus lineage by identifying a highly divergent, sturgeon-associated influenza virus. This suggests that fish were among the first hosts of influenza viruses. Finally, we substantially expanded the known diversity of quaranjaviruses and proposed that this genus be reclassified as a family (the Quaranjaviridae). We find evidence that vertebrate infecting Quaranjaviridae may have initially evolved in crustaceans before spilling into terrestrial Chelicerata (i.e., ticks). Together, our findings indicate that the Articulavirales has evolved over at least 600 million years, first emerging in aquatic animals. Importantly, the evolution of this order was not shaped by strict virus-host codivergence, but rather by multiple aquatic-terrestrial transitions and substantial host jumps, some of which are still observable today.

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Meta-Transcriptomic Identification of Divergent Amnoonviridae in Fish

Cited by 22 publications

References 19 publications

Identification of RNA Virus–Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets

Identification of RNA Virus–Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets

Identification of RNA virus-derived RdRp sequences in publicly available transcriptomic datasets

Evidence for an aquatic origin of influenza virus and the orderArticulavirales

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