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

Olendraitė, Ingrida; Brown, Katherine A.; Firth, Andrew E.

doi:10.1101/2022.10.18.512700

Cited by 12 publications

(18 citation statements)

References 137 publications

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“…2022 ; Edgar et al. 2022 ; Mifsud et al 2022 ; Olendraite, Brown, and Firth 2022 ). To understand the host range of flavivirid sequences throughout the Metazoa and hence more accurately determine the age of the Flaviviridae , we used the Serratus RNA-dependent RNA polymerase (RdRp) search ( https://www.serratus.io/explorer/rdrp ) to mine the Sequence Read Archive (SRA) database for novel flavivirid sequences.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians

et al. 2022

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The flavivirids (family Flaviviridae) are a group of positive-sense RNA viruses that include well-documented agents of human disease. Despite their importance and ubiquity, the time-scale of flavivirid evolution is uncertain. An ancient origin, spanning millions of years, is supported by their presence in both vertebrates and invertebrates and by the identification of a flavivirus-derived endogenous viral element in the peach blossom jellyfish genome (Craspedacusta Sowerby, phylum Cnidaria), implying that the flaviviruses arose early in the evolution of the Metazoa. To date, however, no exogenous flavivirid sequences have been identified in these hosts. To help resolve the antiquity of the Flaviviridae, we mined publicly available transcriptome data across the Metazoa. From this, we expanded the diversity within the family through the identification of 32 novel viral sequences and extended the host range of the pestiviruses to include amphibians, reptiles, and ray-finned fish. Through cophylogenetic analysis we found cross-species transmission to be the predominate macroevolutionary event across the non-vectored flavivirid genera (median, 68%), including a cross-species transmission event between bats and rodents, although long-term virus-host co-divergence was still a regular occurrence (median, 23%). Notably, we discovered flavivirus-like sequences in basal metazoan species, including the first associated with Cnidaria. This sequence formed a basal lineage to the genus Flavivirus and was closer to arthropod and crustacean flaviviruses than those in the tamanavirus group that include a variety of invertebrate and vertebrate viruses. Combined, these data attest an ancient origin of the flaviviruses, likely close to the emergence of the metazoans 750–800 million years ago.

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Section: Introductionmentioning

confidence: 99%

Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians

et al. 2022

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“…So, what is a hantavirid? For now, the answer has become rather unsatisfactory: Hantavirids form a distinct clade of animal-infecting cluster 1 bunyavirals that are closely related to viruses assigned to families Arenaviridae , Cruliviridae , Fimoviridae , Phasmaviridae , Peribunyaviridae , and Tospoviridae [ 116 ]. Their evolutionary history is unclear and will likely not be resolved until targeted studies increase confidence in the overall spectrum of hantavirid hosts.…”

Section: Discussion and Future Directionsmentioning

confidence: 99%

A Brief History of Bunyaviral Family Hantaviridae

Kuhn

Schmaljohn

2023

Diseases

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The discovery of Hantaan virus as an etiologic agent of hemorrhagic fever with renal syndrome in South Korea in 1978 led to identification of related pathogenic and nonpathogenic rodent-borne viruses in Asia and Europe. Their global distribution was recognized in 1993 after connecting newly discovered relatives of these viruses to hantavirus pulmonary syndrome in the Americas. The 1971 description of the shrew-infecting Hantaan-virus-like Thottapalayam virus was long considered an anomaly. Today, this virus and many others that infect eulipotyphlans, bats, fish, rodents, and reptiles are classified among several genera in the continuously expanding family Hantaviridae.

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“…RNA virus HMM profiles were constructed and distributed by vFams [49], RVDB-prot [50], efam [51], and VirSorter2 [52]; in particular, RVDB-prot has been updated frequently and has high potential applicability. NeoRdRp [53], RdRp-scan [54], and Olendraite et al [55] also provide HMM-based databases; however, they target only the RdRp domain as the hallmark of nonretroviral RNA viruses (i.e., Orthornavirae). Palmscan with PALMdb also targets RdRp domains utilizing position-specific scoring matrix approaches [56].…”

Section: Development Of Computational Methodsmentioning

confidence: 99%

Current trends inRNAvirus detection through metatranscriptome sequencing data

et al. 2023

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With advances in sequencing technology, metatranscriptome sequencing from a variety of environmental and biological sources has revealed the existence of various previously unknown RNA viruses. This review presents recent major RNA virome studies sampled from invertebrate and vertebrate species as well as aquatic environments. In particular, we focus on severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) and related RNA virus identification through metatranscriptome sequencing analyses. Recently developed bioinformatics software and databases for RNA virus identification are introduced. A relationship between newly identified RNA viruses and endogenous viral elements in host genomes is also discussed.

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

Cited by 12 publications

References 137 publications

Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians

Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians

A Brief History of Bunyaviral Family Hantaviridae

Current trends inRNAvirus detection through metatranscriptome sequencing data

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