Depending on the taxonomy, these binomial names are followed by a so-called authority, i. The ICTV is currently evaluating whether a similar binomial species naming format should be mandated for virus species names because as of now, virus species naming is chaotic and thereby contributing to the continuous confusion between virus species and viruses Table 4. However, each virus species name is required to begin with a capitalized word and all other words are to be written in lower case except if they are proper nouns.
Taxon names that have been suggested or official proposed but not yet accepted by the ICTV should be indicated by quotation marks e. Virus names should not be italicized, and the individual words of a virus name should not be capitalized except if they are proper nouns Table 4. Virus names may be abbreviated Table 4. The names of groups of viruses belonging to taxa ranked higher than species, such as all members of a family, should be derived from the taxon name e.
The ICTV Virus Metadata Resource VMR is a developing resource in which virus names, virus name abbreviations, exemplar isolates, and GenBank accession numbers can be located in association with the taxa to which particular viruses are currently assigned.
Several steps are currently under discussion that, potentially, could bring virus taxonomy in harmony with other biological taxonomies. The acceptance of Negarnaviricota based on the analysis depicted in Fig. In addition, the viruses of several taxa, such as animal viruses of Herpesvirales and the prokaryotic viruses of Caudovirales , have long been considered as related and therefore should be joined at higher ranks.
Consequently, in , Koonin et al. The establishment of the realms was proposed to be justified based on the discovery of specific viral hallmark genes that can be used to evolutionary connect all their constituent viruses: 1 RdRps and RNA-directed DNA polymerases RdDps for most RNA viruses Riboviria ; 2 replication initiator proteins Reps of the His-hydrophobic-His HUH superfamily for all single-stranded DNA viruses; 3 vertical jelly-roll capsid proteins for many double-stranded DNA viruses; and 4 HKfold capsid proteins for viruses classified in Caudovirales and Herpesvirales.
If accepted by the ICTV, virus classification would finally begin to resemble the classification schemes of cellular organisms. Finally, procedural improvements might ensure improved communication of the ICTV with the virology community and thereby increased efficiency of the ICTV.
Such improvements may include automatic classification algorithms, fully online TaxoProp submissions and evaluation systems, harmonization of classification criteria across taxa, and faster ratification cycles. The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services or of the institution and company affiliated with the author.
National Center for Biotechnology Information , U. Encyclopedia of Virology. Published online Mar 1. Jens H. Guest Editor s : Dennis H. Bamford and Mark Zuckerman. Author information Copyright and License information Disclaimer. Copyright notice. Elsevier hereby grants permission to make all its COVIDrelated research that is available on the COVID resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source.
Abstract Virus taxonomy is the classification of viruses into categories called taxa and the development and implementation of a standardized nomenclature for taxa.
Glossary Classification The rational process of assigning viruses to taxa. Inclusion principle Viruses assigned to a lower taxon based on certain virus characteristics must also have the characteristics needed for classification into a higher-ranked taxon that includes the lower taxon. Monophyletic Belonging to a group of viruses that consists of all the descendants from a common ancestor. Nomenclature The often controversial assignment of names to taxa.
Polyphyletic Not being connected to a common ancestor. Polythetic Sharing many, but not all characteristics of a common core set of characteristics. Species Currently the lowest-ranked taxon in virus taxonomy.
Taxon A man-made category for viruses that share certain characteristics. Taxonomy Virus classification into taxa and taxon nomenclature. Virions Particles produced by some, but not all viruses, during the viral lifecycle for transfer of the viral genome from one host cell to another. History of Virus Taxonomy Early Taxonomic Developments — Virus taxonomy is a virology subspecialty that addresses the grouping classification of viruses physical entities into categories concepts called taxa and the development and implementation of a standardized system of naming nomenclature for taxa.
Baltimore Classification In , David Baltimore published a working classification of viruses that is still used today in parallel with official virus taxonomy. BCs were established based on the type of nucleic acid incorporated into virions, and thereby on the type of virus reproduction: 1. Current Virus Taxonomy —Present Influenced by the publication of the LHT system, the virology community clearly felt an urgent need for an official virus taxonomy. Open in a separate window. Taxonomic Process Contrary to common perception, the ICTV does not impose taxa on the virology community but instead evaluates, votes on, and administers submitted taxonomic proposals TaxoProps originating from the virology community.
Submitted TaxoProps undergo several steps of scrutiny: 1. Virus Classification Virus classification is the gathering of viruses into progressively more inclusive groups lower taxa included in higher-ranked taxa based on common genomic, phylogenetic, and phenotypic properties that, ideally, are proof of evolutionary relationships or descendance.
Differentiating Taxa and Viruses In virus taxonomy, viruses and taxa need to be strictly differentiated. Nomenclature Virus Taxa In biological taxonomies, nomenclature is the process of assigning specific, ideally unique, names to organisms e. Virus taxon nomenclature is regulated by the rules of the ICVCN, which stipulate, for instance, that 1. Table 2 Rank-specific suffixes for virus taxon names. Table 3 Species names in non-virologic taxonomies. Thale cress Mycological Pleurotus ostreatus Jacq.
Table 4 Non-exhaustive list of currently used species naming formats in virus taxonomy. Future Developments Several steps are currently under discussion that, potentially, could bring virus taxonomy in harmony with other biological taxonomies. Acknowledgement The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services or of the institution and company affiliated with the author.
Further Reading Abudurexiti A. Taxonomy of the order Bunyavirales : Update Archives of Virology. Taxonomy of the order Mononegavirales : Update Expression of animal virus genomes. Bacteriological Reviews. Nomina ad infinitum. Chronica Botanica. Over een Contagium vivum fluidum als oorzaak van de Vlekziekte der Tabaksbladen. The nomenclature of plant viruses. Bunyavirus taxonomy: Limitations and misconceptions associated with the current ICTV criteria used for species demarcation.
The morphology and physiology of bacteriophages as revealed by the electron microscope. Journal of the Royal Microscopical Society. Classification of elongated plant viruses on the basis of particle morphology. Strengthening the interaction of the virology community with the international committee on taxonomy of viruses ICTV by linking virus names and their abbreviations to virus species.
Systematic Biology. Taxonomy: Get it right or leave it alone. A chemical basis for the classification of animal viruses. Improved clarity of meaning from the use of both formal species names and common vernacular virus names in virological literature. Virus taxonomy. Classification and nomenclature of viruses. Second report of the International Committee on Taxonomy of Viruses. Springer-Verlag; Archives of virology supplement. Classification and Nomenclature of Viruses. Fifth report of the International Committee on Taxonomy of Viruses.
Increasing the number of available ranks in virus taxonomy from five to ten and adopting the Baltimore classes as taxa at the basal rank. Contributions to characterization and classification of animal viruses. For example, the 24 bluetongue viruses are assigned to the species Bluetongue virus in the genus Orbivirus , family Reoviridae ; thus, 24 viruses assigned to a single species. Therefore sequences entered in GenBank must be associated with the name of a virus isolate.
The term virus isolate has no specific definition and can be applied to any virus, so long as that virus has existed for some time. Several terms are used by virologists to define a virus entity below the species level and are somewhat variable and confusing, but for virus sequences the term "virus isolate" seems the most appropriate, practical and useful [ 9 ]. The intent of GenBank is to collect sequences but the author, the person who enters the sequences in the database, is responsible for the accuracy of the sequences as well as for the validity of the associated information about the sequences, which includes the taxonomic information about the virus in question.
The primary taxonomic information pertains to an isolate of a previously recognized virus or of a newly recognized virus. Consequently, if the author errs in naming the virus or in its classification, the entry will be incorrect and might remain incorrect for a long period of time. GenBank has personnel qualified to review all entries and they effectively and immediately correct a large number of obvious mistakes. However, with regard to "new species", GenBank personnel do not have the means to determine whether this new taxon is justified and acceptable or not.
Obviously, this policy of GenBank cannot be changed from without, but it is certainly possible for GenBank to slightly modify the Entrez form in order to build in safety nets to avoid such situations in the future. The Entrez form of GenBank is a general form for all organisms, and one of the first questions asks the name of the organism. Whereas viruses are not organisms, this question immediately causes ambiguity because it is not clear whether the isolate name or the name of the species to which it belongs should be indicated, notwithstanding the fact that many investigators have not yet understood the difference between an isolate name, corresponding to a specific sequence of a virus, and the conceptual species name, to which a particular isolate has been assigned [ 10 , 8 ] see above.
The second drawback comes from the fact that the software dealing with Entrez and connected to the Taxonomy database of GenBank will by default assign any new virus name in the field "Organism" to a new "species" if it does not exist in the ICTV Master list, from which the current valid classification is derived.
This implies that most of the 3, "species" are in fact virus isolates only concrete entities , rather than species conceptual. The third problem arises from the fact that many virus species names and virus names are identical in the words that compose them, except that species names are written in italics and are not abbreviated, while virus names are not italicized and may be abbreviated [ 10 — 13 ]; unfortunately, databases can only use ASCII characters and cannot accept italics.
It is particularly unfortunate that we are in this situation and that different names have not been created for virus species, but this is a reality that cannot be changed, at least in the short term, and consequently we need to find a way to finesse these problems and still adhere to acceptable virus nomenclature. It seems that the only possibility is to redesign software to show taxonomy as it should be shown, and to restore the difference between the two names, if not by italics at least by some equivalent means.
The fourth problem also is associated with the ASCII code and that is the impossibility of using Greek letters, which are incorporated in many phage names. For this, one solution might be to have ICTV change these names slightly by spelling out the Greek letters, c.
Because of lower costs and more efficient technology, sequencing is increasing exponentially. Known viral sequences already are in the hundreds of thousands and it is conceivable that millions more will become available in the coming years. The number of virus taxa and isolates also increases exponentially and is therefore linearly related to sequencing activities, as shown in Figure 1.
It is therefore critical to have all data stored and named properly and with taxonomic updates in real time. Linear correlation between the number of virus sequences recorded at GenBank between and and the number of virus taxa and virus isolates.
Not all virologists determining sequences are fully aware of or interested in virus taxonomy. These people are the primary source of information and they consequently are the primary sources of data entry errors. Left adrift, they will not make efforts to solve these particular sorts of problems, so other solutions should be put in place to remedy the problem.
Insisting that they follow taxonomic rules seems incompatible with the general "author" principle of GenBank, but it is possible to "invite" them to enter the proper information directly on the Entrez form. The organization structure of ICTV, the generally accepted leader in viral taxonomy, can be conceived of as pyramidal [ 7 ]. Each SG comprises from three to 15 experts selected for their expertise in recognized and new viruses and new sequences of viruses in each family; obviously this is an increasingly difficult task, given the rapid increase in available data.
These 82 SGs present taxonomic proposals from the level of species to the level of order, the proposals are reviewed by the Executive Committee EC of the ICTV and, 18 months later, through a posting on ICTVnet and two rounds of discussions, are then ratified or not and voted upon or not by the ICTV membership at large.
This system, although well organized and in full compliance with the international code for virus taxonomy and nomenclature [ 14 ], is neither adapted to a large number of new isolates and species nor to a quick acceptance, so that changes are envisioned. In addition, by statute, the ICTV does not have the mandate to deal with virus isolates, which are not taxa.
This is a fundamental problem because no organization is responsible for certifying isolate names or for determining to which virus species they belong. However, ICTV, for historical reasons, lists a large number of unclassified virus isolates and SG members are the most knowledgeable people to deal with such an issue. Obviously, this should be considered by ICTV in order to solve this issue of unassigned viruses erroneously purported to be "species" and found in various databases.
It is not the responsibility of the authors to decide whether their new virus isolates belong to an existing or a new species, not the responsibility of GenBank to police authors and organize virus taxonomy and nomenclature, and not the responsibility of ICTV to deal with non-taxonomic issues, such as isolate names, but it is our communal responsibility to work together to make the system functional; and it certainly is feasible.
Here we call for collaboration of all parties to establish a generally satisfactory system for virus taxonomy and nomenclature of virus isolates, sequence data, and all other virological data. Obtaining solutions will necessitate the collaboration of all those involved in producing, collecting and classifying viruses.
Placing the 3, unassigned "species" which likely are simply "viruses" registered at GenBank will require manual classification by the ICTV SG members. Most of these "species" are probably isolates of recognized species and are in the GenBank database by default as new "species" because, whether they have been named or not, they have not been entered in the GenBank forms. Some of these GenBank "species", however, may actually be new species that have not yet been submitted to ICTV and, if so, they should be proposed through the normal channels of the Taxonomic Proposals TaxoProps for evaluation and official ratification before they can be recognized as new species.
As a remedy to the general problem of virus classification, we suggest a two-tier plan. This would help avoid spelling errors or the creation of incorrect new names by authors. In the case of an unaccepted or provisional virus name, the default should be "unassigned virus in the genus, or in the family, or in the order or in the virus kingdom". This information also would be stored in a proposed new database called TaxoProp Management System TPMS , with a pending status to be resolved promptly see below.
The second tier of the remedy would be to establish the TPMS database to handle all new TaxoProps containing information originating from an SG member, from any individual virologist or directly from GenBank. Resolving the mechanics of the system is only a partial solution and more details are needed in order for this to be functional in real time. ICTV has established a sophisticated and democratic system to receive, review, discuss, re-discuss and finally approve taxonomic proposals, whether they concern a new species or a new order [ 15 ].
This system is very sophisticated in principle but is too complex and takes too long to be compatible with modern virology work. It would therefore be possible to computerize the verification of the names in order to "bypass" ICTV EC scrutiny and only then obtain approval of the ICTV membership by electronic voting.
This in turn would considerably reduce the turn-around time: essentially, as soon as a name would be proposed by an ICTV SG, it would be automatically verified and accepted if all the rules were followed. In order to have taxonomic consistency, it is absolutely essential that we strengthen the relationships between ICTV and GenBank.
This could be done with an electronic link between TPMS and GenBank, supplemented with improved and regular personal relations. For example, GenBank has appointed virus experts for a number of families of viruses.
This, in turn, would provide a more active role for the SG members and would activate the overall system of virus taxonomy. Due to the rapid increase in the number of TaxoProps and the increasing difficulty in manually handling several thousand taxonomic names, it is planned by ICTV to create a database to handle all ICTV taxa, from inception to acceptance, and from species to order Fig.
The goal of the TPMS database is to electronically handle all the virus taxa at large including virus isolates , i. A consensus statement published by meeting participants recommended that viruses detected solely by metagenomic sequencing contain sufficient information in their genomic sequence to support their classification and naming 30 , The ICTV concurred with that recommendation.
Therefore, the ICTV is now accepting proposals for new virus taxa supported solely by metagenomic sequence information.
This policy should ensure that the official ICTV virus taxonomy will be much more reflective of the true diversity of existing viruses.
But at the same time, this will require that the systems in place for characterizing virus diversity, proposing new virus taxa, storing these taxa in the ICTV database, and browsing and searching for these taxa from the ICTV web pages, be streamlined and made capable of handling the many thousands of new taxa that will need to be created. The ICTV may also need to modify its policies and procedures for naming of virus species and expand the available taxonomic ranks needed to classify these viruses, to handle the large number of new, diverse viruses discovered using metagenomic sequencing methods.
In the past, the ICTV has continually modified and modernized its approach to virus taxonomy through, for example, moving to sequence-based characters as the primary source of information needed for classification 30 ; developing and utilizing automated computational methods to facilitate the grouping of viruses into taxa existing and new based on a comparison of their genomic sequences 10 , 32 — 35 ; operating more efficiently and shortening the time taken to approve proposals for new taxa; and now, basing taxonomic decisions solely on the information contained in genomic sequences It is only through this process of continued evaluation of the current state of virus discovery and research, responding to new data and new understanding by updating policies and procedures, that the ICTV will be able to remain current and continue to be relevant to the scientific community.
We would like to acknowledge the assistance and support of the entire ICTV Executive Committee, and the extensive work of the ICTV Study Group chairs and members, for their work preparing and reviewing taxonomy proposals, and in preparing the Online 10th Report chapters. Supplementary Data are available at NAR online. National Center for Biotechnology Information , U. Journal List Nucleic Acids Res v. Nucleic Acids Res. Published online Oct Author information Article notes Copyright and License information Disclaimer.
Corresponding author. To whom correspondence should be addressed. This article has been cited by other articles in PMC. The ICTV database of virus taxonomy Every year, virologists submit proposals to the ICTV recommending the creation of new taxa as well as renaming, moving, or abolishing existing taxa.
Table 1. Database Records for the Species Measles morbillivirus. Open in a separate window. Figure 1. Figure 2. Figure 3. Table 2. Taxonomy Release History. Figure 4. Supplementary Material Supplementary Data Click here for additional data file. Conflict of interest statement. None declared. King A. Polaszek A. A universal register for animal names. Lapage S. International code of nomenclature of bacteria, and Statutes of the International Committee on Systematic Bacteriology, and Statutes of the Bacteriology and Applied Microbiology Section of the International Union of Microbiological Societies: bacteriological code.
C: American Society for Microbiology. Carolus Linnaeus Systema naturae, General Assembly. Ride W. London: International Trust for Zoological Nomenclature. Adams M.
Schleifer K. Tracking the changes in virus taxonomy. International Committee on Nomenclature of Viruses. Wildy P. Simmonds P. Methods for virus classification and the challenge of incorporating metagenomic sequence data. Knipe D. Fields Virology. Buchen-Osmond C. Baltimore D. Expression of animal virus genomes. Lefkowitz E. Taxonomy and Classification of Viruses. Manual of Clinical Microbiology. C: ASM Press.
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