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 12 publications

(9 citation statements)

References 79 publications

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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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“…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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“…Similarly, the data mining of over 10 9 meta-transcriptomic contigs from diverse ecosystems has revealed several divergent clades of RNA bacteriophage 10 , while recent meta-transcriptomic studies have led to a remarkable 5-fold expansion in the diversity of viroid-like circular RNAs 11 . Despite such progress in uncovering RNA virus diversity through ecological sampling and sequencing, it is probable that more divergent groups of RNA viruses remain to be discovered 9,12 . This is in part because the BLAST-based sequence similarity searching approaches used to discover new RNA virus sequences have limitations in detecting highly divergent RdRPs 13 , while profile alignment-based approaches (i.e., HMM) necessarily entail a high false positive rate when detecting more divergent RNA virus sequences 14,15 .…”

Section: Introductionmentioning

confidence: 99%

Using artificial intelligence to document the hidden RNA virosphere

Hou

Fang

et al. 2023

Preprint

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RNA viruses are diverse components of global ecosystems. The metagenomic identification of RNA viruses is currently limited to those with sequence similarity to known viruses, such that highly divergent viruses that comprise the "dark matter" of the virosphere remain challenging to detect. We developed a deep learning algorithm - LucaProt - to search for highly divergent RNA-dependent RNA polymerase (RdRP) sequences in 10,487 global meta-transcriptomes. LucaProt integrates both sequence and structural information to accurately and efficiently detect RdRP sequences. With this approach we identified 180,571 RNA viral species and 180 superclades (viral phyla/classes). This is the broadest diversity of RNA viruses described to date, including many viruses undetectable using BLAST or HMM approaches. The newly identified RNA viruses were present in diverse ecological niches, including the air, hot springs and hydrothermal vents, and both virus diversity and abundance varied substantially among ecological types. We also identified the longest RNA virus genome (nido-like) observed so far, at 47,250 nucleotides, and expanded the diversity of RNA bacteriophage to more than ten phyla/classes. This study marks the beginning of a new era of virus discovery, with the potential to redefine our understanding of the global virosphere and reshape our understanding of virus evolutionary history.

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The RNA virosphere: How big and diverse is it?

Cited by 12 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 RNA viruses from the Atlantic Ocean: Ecogenomics, biogeography, and total virioplankton mass contribution from surface to the deep ocean

Using artificial intelligence to document the hidden RNA virosphere

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