50 years of the International Committee on Taxonomy of Viruses: progress and prospects

Adams, Michael J.; Lefkowitz, Elliot J.; King, Andrew M. Q.; Harrach, Balázs; Harrison, Robert L.; Knowles, Nick J.; Kropinski, Andrew M.; Krupovìč, Mart; Kuhn, Jens H.; Mushegian, Arcady; Nibert, Max L.; Sabanadzovic, Sead; Sanfaçon, Hélène; Siddell, Stuart G.; Simmonds, Peter; Varsani, Arvind; Zerbini, F. Murilo; Orton, Richard; Smith, Donald B.; Gorbalenya, Alexander E.; Davison, Andrew J.

doi:10.1007/s00705-016-3215-y

Cited by 83 publications

(64 citation statements)

References 21 publications

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“…The ICTV is committed to the incorporation of viruses known only by their genome sequence into the current taxonomy [3, 25]. This is a logical step if the ITCV taxonomy is to remain relevant as a guide to viral diversity; viral sequences reconstructed from HTS data represent viruses as much as those whose phenotypic properties are known (at least in part).…”

Section: Discussionmentioning

confidence: 99%

Virus classification – where do you draw the line?

Simmonds

Aiewsakun

2018

Arch Virol

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High-throughput sequencing (HTS) and its use in recovering and assembling novel virus sequences from environmental, human clinical, veterinary and plant samples has unearthed a vast new catalogue of viruses. Their classification, known by their sequences alone, sets a major challenge to traditional virus taxonomy, especially at the family and species levels, which have been historically based largely on descriptive taxon definitions. These typically entail some knowledge of their phenotypic properties, including replication strategies, virion structure and clinical and epidemiological features, such as host range, geographical distribution and disease outcomes. Little to no information on these attributes is available, however, for viruses identified in metagenomic datasets. If such viruses are to be included in virus taxonomy, their assignments will have to be guided largely or entirely by metrics of genetic relatedness. The immediate problem here is that the International Committee on Taxonomy of Viruses (ICTV), an organisation that authorises the taxonomic classification of viruses, provides little or no guidance on how similar or how divergent viruses must be in order to be considered members of new species or new families. We have recently developed a method for scoring genomic (dis)similarity between viruses (Genome Relationships Applied to Virus Taxonomy – GRAViTy) among the eukaryotic and prokaryotic viruses currently classified by the ICTV. At the family and genus levels, we found large-scale consistency between genetic relationships and their taxonomic assignments for eukaryotic viruses of all genome configurations and genome sizes. Family assignments of prokaryotic viruses have, however, been made at a quite different genetic level, and groupings currently classified as sub-families are a much better match to the eukaryotic virus family level. These findings support the ongoing reorganisation of bacteriophage taxonomy by the ICTV Phage Study Group. A rapid and objective means to explore metagenomic viral diversity and make evidence-based assignments for such viruses at each taxonomic layer is essential. Analysis of sequences by GRAViTy provides evidence that family (and genus) assignments of currently classified viruses are largely underpinned by genomic relatedness, and these features could serve as a guide towards an evidence-based classification of metagenomic viruses in the future.

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Section: Discussionmentioning

confidence: 99%

Virus classification – where do you draw the line?

Simmonds

Aiewsakun

2018

Arch Virol

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“…This question is answered in best practice by evaluating the degree of relatedness of the candidate virus to previously identified viruses infecting the same host or established monophyletic groups of viruses, often known as genotypes or clades, which may or may not include viruses of different hosts. This is formally addressed in the framework of the official classification of virus taxonomy and is overseen and coordinated by the ICTV 4 . Viruses are clustered in taxa in a hierarchical scheme of ranks in which the species represents the lowest and most populous rank containing the least diverged groups (taxa) of viruses (Box 2).…”

Section: Classifying and Naming Viruses And Virus Speciesmentioning

confidence: 99%

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

Gorbalenya¹,

Baker²,

Baric³

et al. 2020

Nat Microbiol

6,121

3,085

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The present outbreak of a coronavirus-associated acute respiratory disease called coronavirus disease 19 (COVID-19) is the third documented spillover of an animal coronavirus to humans in only two decades that has resulted in a major epidemic. The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the classification of viruses and taxon nomenclature of the family Coronaviridae, has assessed the placement of the human pathogen, tentatively named 2019-nCoV, within the Coronaviridae. Based on phylogeny, taxonomy and established practice, the CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome corona- viruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus, and designates it as SARS-CoV-2. In order to facilitate communication, the CSG proposes to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date. While the full spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined, the independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying viruses at the species level to complement research focused on individual pathogenic viruses of immediatesignificance. This will improve our understanding of virus-host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.

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“…The ICTV database contains the complete taxonomy for every release since the taxonomy was first produced in 1971 (Table 2) (6,8). Each of these releases can be accessed using the taxonomy browser by following the appropriate link on the release history web page (http://ictv.global/ taxonomyReleases.asp).…”

Section: Historical Taxonomy Releasesmentioning

confidence: 99%

“…The taxonomic classification of viruses and naming of virus taxa is the responsibility of the International Committee on Taxonomy of Viruses (ICTV) (6). The ICTV is charged with the task of developing, refining, and maintaining a universal virus taxonomy by the Virology Division of the International Union of Microbiological Societies (7).…”

Section: Introductionmentioning

confidence: 99%

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Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

Lefkowitz

Dempsey

Hendrickson

et al. 2017

Nucleic Acids Research

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891

683

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The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy.

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50 years of the International Committee on Taxonomy of Viruses: progress and prospects

Cited by 83 publications

References 21 publications

Virus classification – where do you draw the line?

Virus classification – where do you draw the line?

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

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