The <scp>RNA</scp> virosphere: How big and diverse is it?

Domínguez-Huerta, Guillermo; Wainaina, James; Culley, Alexander I.; Kuhn, Jens H.; Sullivan, Matthew B.

doi:10.1111/1462-2920.16312

Cited by 11 publications

(9 citation statements)

References 79 publications

(112 reference statements)

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“…In the last few years, virus taxonomy has changed from a specialist niche to an interdisciplinary field that encompasses virology, bioinformatics, evolutionary biology and, occasionally, philosophical considerations on the meaning of taxonomy, particularly when inferring deeper, less compelling, evolutionary relationships [6,[28][29][30][31][32][33] or the nature of virus species and the associated principles of categorization [34][35][36]. This change of scope has largely been due to the introduction of highthroughput sequencing technology [37,38], recognition of the true diversity of the virosphere [8,[39][40][41] and progress in computational phylogenetics [42][43][44]. The next decade of virus taxonomy will be very challenging and requires a continuing effort to unravel the genetic make-up and evolution of virus genomes, as these are shaped by biological and ecological mechanisms.…”

Section: Discussionmentioning

confidence: 99%

Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV)

Siddell

Smith

Adriaenssens

et al. 2023

Journal of General Virology

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The taxonomy of viruses is developed and overseen by the International Committee on Taxonomy of Viruses (ICTV), which scrutinizes, approves and ratifies taxonomic proposals, and maintains a list of virus taxa with approved names (https://ictv.global). The ICTV has approximately 180 members who vote by simple majority. Taxon-specific Study Groups established by the ICTV have a combined membership of over 600 scientists from the wider virology community; they provide comprehensive expertise across the range of known viruses and are major contributors to the creation and evaluation of taxonomic proposals. Proposals can be submitted by anyone and will be considered by the ICTV irrespective of Study Group support. Thus, virus taxonomy is developed from within the virology community and realized by a democratic decision-making process. The ICTV upholds the distinction between a virus or replicating genetic element as a physical entity and the taxon category to which it is assigned. This is reflected by the nomenclature of the virus species taxon, which is now mandated by the ICTV to be in a binomial format (genus + species epithet) and is typographically distinct from the names of viruses. Classification of viruses below the rank of species (such as, genotypes or strains) is not within the remit of the ICTV. This article, authored by the ICTV Executive Committee, explains the principles of virus taxonomy and the organization, function, processes and resources of the ICTV, with the aim of encouraging greater understanding and interaction among the wider virology community.

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Section: Discussionmentioning

confidence: 99%

Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV)

Siddell

Smith

Adriaenssens

et al. 2023

Journal of General Virology

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“…To address this phenomenon, diverse strategies have emerged, culminating in a comprehensive proposal for establishing a megataxonomy of the virus world (Koonin et al, 2020). However, despite extensive efforts to characterize the viral component of the biosphere, it is evident that only a minuscule fraction, likely encompassing less than one percent of the entire virosphere, has been comprehensively characterized to date (Geoghegan and Holmes, 2017; Dominguez-Huerta et al, 2023). Consequently, our understanding of the vast global virome remains limited, with its remarkable diversity and its interactions with various host organisms (Dolja et al, 2020; Edgar et al, 2022; Koonin et al, 2022; Mifsud et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Novel tri-segmented rhabdoviruses: A data mining expedition unveils the cryptic diversity of cytorhabdoviruses

Bejerman,

Dietzgen,

Debat

2023

Preprint

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Cytorhabdoviruses (genusCytorhabdovirus, familyRhabdoviridae) are plant-infecting viruses with enveloped, bacilliform virions. Established members of the genusCytorhabdovirushave unsegmented single-stranded negative-sense RNA genomes (ca. 10-16 kb) which encode four to ten proteins. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and genomic characterization of 93 novel viruses with genetic and evolutionary cues of cytorhabdoviruses. Strikingly, five unprecedented cytorhabdoviruses with tri-segmented genomes were also identified. This finding represents the first tri-segmented viruses in the familyRhabdoviridae. Interestingly, the nucleocapsid and polymerase were the only typical rhabdoviral proteins encoded by those tri-segmented viruses, whereas in three of them, a protein similar to the emaravirus (familyFimoviridae) silencing suppressor was found, while the other predicted proteins had no matches in any sequence databases. Genetic distance and evolutionary insights suggest that all these novel viruses may represent members of novel species. Phylogenetic analyses, of both novel and previously classified plant rhabdoviruses, provide compelling support for the division of the genusCytorhabdovirusinto three distinct genera. This proposed reclassification not only enhances our understanding of the evolutionary dynamics within this group of plant rhabdoviruses but also illuminates the remarkable genomic diversity they encompass. This study not only represents a significant expansion of genomics of cytorhabdoviruses that will enable future research on the evolutionary peculiarity of this genus, but also shows the plasticity in the rhabdovirus genome organization with the discovery of tri-segmented members with a unique evolutionary trajectory.

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“…Furthermore, the study of RNA viruses presents both culture‐dependent and ‐independent methodological limitations due to the difficulty of isolating viruses and hosts in addition to the relatively smaller genome size and higher taxonomic diversity that complicate the metagenomic surveys (Liao et al, 2022). These reasons explain why the study of RNA viruses has remained relatively unexplored by the scientific community until recent years (Callanan et al, 2020; Dominguez‐Huerta et al, 2023; Zayed et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

“…Over the course of the last decade, metagenomic studies have brought to light that RNA viruses are widespread and diverse, particularly the ssRNA viruses (Dominguez‐Huerta et al, 2023). In certain marine environments, these viruses have been found to be as abundant as DNA viruses (Culley et al, 2006; Culley & Steward, 2007).…”

Section: Introductionmentioning

confidence: 99%

Novel RNA viruses from the Atlantic Ocean: Ecogenomics, biogeography, and total virioplankton mass contribution from surface to the deep ocean

Vila‐Nistal,

Maestre‐Carballa,

Martinez‐Hernández

et al. 2023

Environmental Microbiology

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Marine viruses play a major role in the energy and nutrient cycle and affect the evolution of their hosts. Despite their importance, there is still little knowledge about RNA viruses. Here, we have explored the Atlantic Ocean, from surface to deep (4.296 m), and used viromics and quantitative methods to unveil the genomics, biogeography, and the mass contribution of RNA viruses to the total viroplankton. A total of 2481 putative RNA viral contigs (>500 bp) and 107 larger bona fide RNA viral genomes (>2.5 kb) were identified; 88 of them representing novel viruses belonging mostly to two clades: Yangshan assemblage (sister clade to the class Alsuviricetes) and Nodaviridae. These viruses were highly endemic and locally abundant, with little or no presence in other oceans since only ≈15% of them were found in at least one of the Tara sampling metatranscriptomes. Quantitative data indicated that the abundance of RNA viruses in the surface and deep chlorophyll maximum zone was within ≈106 VLP/mL representing a potential contribution of 5.2%–24.4% to the total viroplankton community (DNA and RNA viruses), with DNA viruses being the predominant members (≈107 VLP/mL). However, for the deep sample, the observed trend was the opposite, although as further discussed, several biases should be considered. Together these results contribute to our understanding of the diversity, abundance, and distribution of RNA viruses in the oceans and provide a basis for further investigation into their ecological roles and biogeography.

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The RNA virosphere: How big and diverse is it?

Cited by 11 publications

References 79 publications

Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV)

Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV)

Novel tri-segmented rhabdoviruses: A data mining expedition unveils the cryptic diversity of cytorhabdoviruses

Novel RNA viruses from the Atlantic Ocean: Ecogenomics, biogeography, and total virioplankton mass contribution from surface to the deep ocean

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