Elliot J. LefkowitzpersName, Donald M. DempseypersName, R. Curtis HendricksonpersName, Richard OrtonpersName, Stuart G. SiddellpersName, Donald B. SmithpersName (2018date). “Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV).”
Object of study — A CONTROLLED VOCABULARYterm WITH A PUBLISHED CONSTITUTION - the virus taxonomyterm, its governing committee, its two rulebooks, its annual proposal-to-ratification cycle, and a database that records every change back to 1971date
Research question — how the universal virus taxonomyterm is developed, approved, recorded and made available
Contribution — a description of the ICTVterm taxonomyterm database and web site, its schema, its change vocabulary and its complete taxon history
phenomenon · claim-type · cross-domain-transfer · mechanism · claim-relation · replication-status · limitation — grounded in the full text| phenomenon | a scientific vocabulary that changes every year by vote, whose changes are typed and stored rather than left to be reconstructed from the literature — “The tables store a controlled vocabulary used for specific fields where the possible data values remain fairly constant. These include taxonomy level (currently species, genus, subfamily, family, and order), possible taxonomic changes from the previous release (new, split, move, merge, rename, and abolish), and virus genome type (e.g. dsDNA, ssDNA, dsRNA, ssRNA(+), ssRNA(–), etc.) that forms part of the annotation available for the member viruses of each species.” | |
| claim-type | method — “The tables store a controlled vocabulary used for specific fields where the possible data values remain fairly constant. These include taxonomy level (currently species, genus, subfamily, family, and order), possible taxonomic changes from the previous release (new, split, move, merge, rename, and abolish), and virus genome type (e.g. dsDNA, ssDNA, dsRNA, ssRNA(+), ssRNA(–), etc.) that forms part of the annotation available for the member viruses of each species.” | |
| method — evidence | — “Every year, virologists submit proposals to the ICTV recommending the creation of new taxa as well as renaming, moving, or abolishing existing taxa. These proposals are submitted to the appropriate study group which then evaluates and modifies the proposal as necessary, in consultation with the original author. Once a year, the ICTV Executive Committee (EC) meets, discusses all submitted proposals, and will either accept a proposal, send it back for modification, or reject it. Then the set of accepted proposals are sent to the ICTV membership for ratification. Once ratified, the newly approved taxonomy is entered in the ICTV taxonomic database.” | |
| object of study — evidence | — “Every year, virologists submit proposals to the ICTV recommending the creation of new taxa as well as renaming, moving, or abolishing existing taxa. These proposals are submitted to the appropriate study group which then evaluates and modifies the proposal as necessary, in consultation with the original author. Once a year, the ICTV Executive Committee (EC) meets, discusses all submitted proposals, and will either accept a proposal, send it back for modification, or reject it. Then the set of accepted proposals are sent to the ICTV membership for ratification. Once ratified, the newly approved taxonomy is entered in the ICTV taxonomic database.” | |
| research question — evidence | — “Unlike for other groups of biological organisms, the ICTV charge extends not only to developing the guidelines for naming of taxa, but to establishing guidelines for taxonomic classification of viruses, and approving the proposed taxonomy and names before they become official.” | |
| contribution — evidence | — “Each record in the taxonomy table stores data on a single taxon including its name, numerical id, parent taxon, release number and date, most recent taxonomic change, filename of the proposal establishing the taxon, and a pointer to its previous record if a change has occurred in taxon data (such as moving a species to another genus). With this information, a complete history of every taxon can be reconstructed from the database.” | |
| mechanism | A CONTROLLED VOCABULARY OF CHANGES TO A CONTROLLED VOCABULARY, IN A DATABASE COLUMN: `possible taxonomic changes from the previous release (new, split, move, merge, rename, and abolish)`. SIX OPERATIONS. This project has been reconstructing that list by hand from macdonald2015, welsh2024, larson2015 and leask2012; virology has had it as an enumerated field since the taxonomy's first release — “The tables store a controlled vocabulary used for specific fields where the possible data values remain fairly constant. These include taxonomy level (currently species, genus, subfamily, family, and order), possible taxonomic changes from the previous release (new, split, move, merge, rename, and abolish), and virus genome type (e.g. dsDNA, ssDNA, dsRNA, ssRNA(+), ssRNA(–), etc.) that forms part of the annotation available for the member viruses of each species.” | mechanisms[0] |
| mechanism | AND THE HISTORY IS RECONSTRUCTABLE BY DESIGN: each record stores `release number and date, most recent taxonomic change, filename of the proposal establishing the taxon, and a pointer to its previous record if a change has occurred ... With this information, a complete history of every taxon can be reconstructed from the database`. The proposal that made the change is named in the row — “Each record in the taxonomy table stores data on a single taxon including its name, numerical id, parent taxon, release number and date, most recent taxonomic change, filename of the proposal establishing the taxon, and a pointer to its previous record if a change has occurred in taxon data (such as moving a species to another genus). With this information, a complete history of every taxon can be reconstructed from the database.” | mechanisms[1] |
| mechanism | THE GOVERNANCE IS A PUBLISHED PROCEDURE: `Every year, virologists SUBMIT PROPOSALS ... recommending the creation of new taxa as well as renaming, moving, or abolishing existing taxa ... the ICTV Executive Committee meets, discusses all submitted proposals, and will either ACCEPT a proposal, SEND IT BACK for modification, or REJECT it. Then the set of accepted proposals are sent to the ICTV membership FOR RATIFICATION` — “Every year, virologists submit proposals to the ICTV recommending the creation of new taxa as well as renaming, moving, or abolishing existing taxa. These proposals are submitted to the appropriate study group which then evaluates and modifies the proposal as necessary, in consultation with the original author. Once a year, the ICTV Executive Committee (EC) meets, discusses all submitted proposals, and will either accept a proposal, send it back for modification, or reject it. Then the set of accepted proposals are sent to the ICTV membership for ratification. Once ratified, the newly approved taxonomy is entered in the ICTV taxonomic database.” | mechanisms[2] |
| mechanism | and virology is unusual in giving one body BOTH powers: `Unlike for other groups of biological organisms, the ICTV charge extends not only to developing the guidelines for naming of taxa, but to establishing guidelines for taxonomic classification of viruses, and approving the proposed taxonomy and names before they become official`. Zoology and bacteriology separate the naming rules from the classification decision; virology does not — “Unlike for other groups of biological organisms, the ICTV charge extends not only to developing the guidelines for naming of taxa, but to establishing guidelines for taxonomic classification of viruses, and approving the proposed taxonomy and names before they become official.” | mechanisms[3] |
| extends | Linnaean taxonomy, named in the paper as the origin of the principles, applied to entities that are not organisms — “The process used to study any new biological entity begins by classifying it in relation to other known biological organisms, and then giving it a name ( 1 – 3 ). This process of classification and naming comprises the discipline of taxonomy, and has been an integral part of biological research since at least the 18th Century when Carl Linnaeus defined the principles of modern taxonomy” | claim_relations[0] |
| supports | the position that a scientific vocabulary needs a governing body, a written code and a versioned record - the ICTV has all three and the paper describes each — “The rules governing the ICTV and its operations are defined by the ICTV Statutes ( http://ictv.global/statutes.asp ), while the rules for creating and naming virus taxa are provided in the International Code of Virus Classification and Nomenclature” | claim_relations[1] |
| sense | `taxonomic change` - AN ENUMERATED TYPE WITH SIX VALUES: `new, split, move, merge, rename, and abolish`. Not prose, not a convention - a controlled field in a SQL schema, stored per taxon per release — “The tables store a controlled vocabulary used for specific fields where the possible data values remain fairly constant. These include taxonomy level (currently species, genus, subfamily, family, and order), possible taxonomic changes from the previous release (new, split, move, merge, rename, and abolish), and virus genome type (e.g. dsDNA, ssDNA, dsRNA, ssRNA(+), ssRNA(–), etc.) that forms part of the annotation available for the member viruses of each species.” | senses[0] |
| sense | `taxonomy` AS A DISCIPLINE - `This process of classification and naming comprises the discipline of taxonomy`. Two acts, one discipline, and the ICTV is unusual in holding authority over both — “The process used to study any new biological entity begins by classifying it in relation to other known biological organisms, and then giving it a name ( 1 – 3 ). This process of classification and naming comprises the discipline of taxonomy, and has been an integral part of biological research since at least the 18th Century when Carl Linnaeus defined the principles of modern taxonomy” | senses[1] |
| sense | `character` - `any property or feature of the virus`, including genome composition, capsid structure, envelopment, gene expression programme, HOST RANGE, PATHOGENICITY and sequence similarity. AND ONE FAMILY OF CHARACTERS HAS WON: `sequence comparisons ... have become one of the primary sets of characters used to define and distinguish virus taxa` — “Classification of viruses is based on the collection and comparison of various characters that describe the virus, and can then be used to distinguish one virus from another ( 1 , 10 – 15 ). Characters can consist of any property or feature of the virus, and include the molecular composition of the genome; the structure of the virus capsid and whether or not it is enveloped; the gene expression program used to produce virus proteins; host range; pathogenicity; and sequence similarity. While all characters are important in determining taxonomic relationships, sequence comparisons using both pairwise sequence similarity and phylogenetic relationships have become one of the primary sets of characters used to define and distinguish virus taxa.” | senses[2] |
| sense | `ICTV` - the committee, which RENAMED ITSELF FROM NAMING TO CLASSIFYING: `established in 1966 as the International Committee on NOMENCLATURE of Viruses, and was RENAMED the International Committee on TAXONOMY of Viruses in 1977` — “The ICTV was established in 1966 as the International Committee on Nomenclature of Viruses, and was renamed the International Committee on Taxonomy of Viruses in 1977” | senses[3] |
| control | annual Executive Committee review followed by ratification by the whole membership — held — “Unlike for other groups of biological organisms, the ICTV charge extends not only to developing the guidelines for naming of taxa, but to establishing guidelines for taxonomic classification of viruses, and approving the proposed taxonomy and names before they become official.” — rules out a single study group's criteria becoming official without scrutiny - the EC 'will either accept a proposal, send it back for modification, or reject it', and only then does the membership ratify — “Every year, virologists submit proposals to the ICTV recommending the creation of new taxa as well as renaming, moving, or abolishing existing taxa. These proposals are submitted to the appropriate study group which then evaluates and modifies the proposal as necessary, in consultation with the original author. Once a year, the ICTV Executive Committee (EC) meets, discusses all submitted proposals, and will either accept a proposal, send it back for modification, or reject it. Then the set of accepted proposals are sent to the ICTV membership for ratification. Once ratified, the newly approved taxonomy is entered in the ICTV taxonomic database.” | controls[0] |
| control | a stored 'previous record' pointer and the filename of the proposal that made each change — held — “The tables store a controlled vocabulary used for specific fields where the possible data values remain fairly constant. These include taxonomy level (currently species, genus, subfamily, family, and order), possible taxonomic changes from the previous release (new, split, move, merge, rename, and abolish), and virus genome type (e.g. dsDNA, ssDNA, dsRNA, ssRNA(+), ssRNA(–), etc.) that forms part of the annotation available for the member viruses of each species.” — rules out the loss of a taxon's history when its name or parent changes - 'a complete history of every taxon can be reconstructed from the database' — “Each record in the taxonomy table stores data on a single taxon including its name, numerical id, parent taxon, release number and date, most recent taxonomic change, filename of the proposal establishing the taxon, and a pointer to its previous record if a change has occurred in taxon data (such as moving a species to another genus). With this information, a complete history of every taxon can be reconstructed from the database.” | controls[1] |
| control | whether the stored change type describes the change that happened — failed — “The tables store a controlled vocabulary used for specific fields where the possible data values remain fairly constant. These include taxonomy level (currently species, genus, subfamily, family, and order), possible taxonomic changes from the previous release (new, split, move, merge, rename, and abolish), and virus genome type (e.g. dsDNA, ssDNA, dsRNA, ssRNA(+), ssRNA(–), etc.) that forms part of the annotation available for the member viruses of each species.” — rules out nothing, and the paper's own worked example shows it: a record of 'creation' that 'in fact ... was not a new species, but was a merging of three existing species ... into one, newly renamed species' that was also moved to a different genus — “the most recent change to this particular taxonomic lineage was the creation of the species Alphacoronavirus 1 in 2009. But in fact, this was not a new species, but was a merging of three existing species (transmissible gastroenteritis virus, feline coronavirus, and canine coronavirus) into one, newly renamed species, Alphacoronavirus 1 . In addition, the species were moved from the now defunct genus coronavirus, into the genus Alphacoronavirus that is a member of the subfamily” | controls[2] |
| control | whether the demarcation criteria are set independently of the people applying them — failed — “Members of the genus Enterovirus (family Picornaviridae ) share more than 42% amino acid identity across the length of their polyprotein.” — rules out nothing - it is the design: study groups 'develop the demarcation criteria used to define each new taxon, and evaluate proposals using those criteria' — “Each subcommittee contains a series of study groups, generally one per virus family, that develop the demarcation criteria used to define each new taxon, and evaluate proposals using those criteria for classification and naming. These demarcation criteria are based upon the genetic and biological properties of the taxon members, and cover each of the taxonomic ranks currently recognized by the ICTV” | controls[3] |
| weight | Linnaean taxonomy, named in the paper as the origin of the principles, applied to entities that are not organisms — 0.8 — “The process used to study any new biological entity begins by classifying it in relation to other known biological organisms, and then giving it a name ( 1 – 3 ). This process of classification and naming comprises the discipline of taxonomy, and has been an integral part of biological research since at least the 18th Century when Carl Linnaeus defined the principles of modern taxonomy” | claim_relations[0] |
| weight | the position that a scientific vocabulary needs a governing body, a written code and a versioned record - the ICTV has all three and the paper describes each — 0.85 — “The rules governing the ICTV and its operations are defined by the ICTV Statutes ( http://ictv.global/statutes.asp ), while the rules for creating and naming virus taxa are provided in the International Code of Virus Classification and Nomenclature” | claim_relations[1] |
| audit | International Committee on Nomenclature of Viruses —renamed-across-fields→ International Committee on Taxonomy of Viruses — Audit 2026-09-28: DOUBTFUL - read against its span and kept, but a committee renamed itself; renamed-across-fields overstates a renaming within one body. — “The ICTV was established in 1966 as the International Committee on Nomenclature of Viruses, and was renamed the International Committee on Taxonomy of Viruses in 1977” | concept_edges[0] |
| note | International Committee on Nomenclature of Viruses —renamed-across-fields→ International Committee on Taxonomy of Viruses — THE REMIT CHANGED WITH THE NAME: from NOMENCLATURE to TAXONOMY in 1977, and the paper's next claim is that this committee, unlike its counterparts in zoology and bacteriology, also approves each classification — “The ICTV was established in 1966 as the International Committee on Nomenclature of Viruses, and was renamed the International Committee on Taxonomy of Viruses in 1977” | concept_edges[0] |
| weight | International Committee on Nomenclature of Viruses —renamed-across-fields→ International Committee on Taxonomy of Viruses — 0.95 — “The ICTV was established in 1966 as the International Committee on Nomenclature of Viruses, and was renamed the International Committee on Taxonomy of Viruses in 1977” | concept_edges[0] |
| note | ICTV —contrasted-with→ other groups of biological organisms — 'the ICTV charge extends NOT ONLY to developing the guidelines for naming of taxa, BUT to establishing guidelines for taxonomic classification, AND APPROVING the proposed taxonomy and names before they become official'. One body writes the rules and rules on each application — “Unlike for other groups of biological organisms, the ICTV charge extends not only to developing the guidelines for naming of taxa, but to establishing guidelines for taxonomic classification of viruses, and approving the proposed taxonomy and names before they become official.” | concept_edges[1] |
| weight | ICTV —contrasted-with→ other groups of biological organisms — 0.95 — “Unlike for other groups of biological organisms, the ICTV charge extends not only to developing the guidelines for naming of taxa, but to establishing guidelines for taxonomic classification of viruses, and approving the proposed taxonomy and names before they become official.” | concept_edges[1] |
| note | ICTV Statutes —distinct-from→ International Code of Virus Classification and Nomenclature — one document governs the COMMITTEE, the other governs the TAXA. A vocabulary with a constitution and a style guide, kept separate — “The rules governing the ICTV and its operations are defined by the ICTV Statutes ( http://ictv.global/statutes.asp ), while the rules for creating and naming virus taxa are provided in the International Code of Virus Classification and Nomenclature” | concept_edges[2] |
| weight | ICTV Statutes —distinct-from→ International Code of Virus Classification and Nomenclature — 0.95 — “The rules governing the ICTV and its operations are defined by the ICTV Statutes ( http://ictv.global/statutes.asp ), while the rules for creating and naming virus taxa are provided in the International Code of Virus Classification and Nomenclature” | concept_edges[2] |
| note | study groups —part-of→ subcommittee — generally one study group per virus family, and the study group both writes the demarcation criteria and evaluates proposals against them — “Each subcommittee contains a series of study groups, generally one per virus family, that develop the demarcation criteria used to define each new taxon, and evaluate proposals using those criteria for classification and naming. These demarcation criteria are based upon the genetic and biological properties of the taxon members, and cover each of the taxonomic ranks currently recognized by the ICTV” | concept_edges[3] |
| weight | study groups —part-of→ subcommittee — 0.95 — “Each subcommittee contains a series of study groups, generally one per virus family, that develop the demarcation criteria used to define each new taxon, and evaluate proposals using those criteria for classification and naming. These demarcation criteria are based upon the genetic and biological properties of the taxon members, and cover each of the taxonomic ranks currently recognized by the ICTV” | concept_edges[3] |
| note | lower-level taxa —part-of→ higher-level taxa — 'The properties that define higher-level taxa are shared with all lower-level taxa that belong to higher-level taxa' - definitional inheritance, stated as the rule rather than as a fact about any particular pair — “Based on an assessment of characters, a hierarchical relationship is established that groups together viruses with similar properties. The properties that define higher-level taxa are shared with all lower-level taxa that belong to higher-level taxa” | concept_edges[4] |
| weight | lower-level taxa —part-of→ higher-level taxa — 0.95 — “Based on an assessment of characters, a hierarchical relationship is established that groups together viruses with similar properties. The properties that define higher-level taxa are shared with all lower-level taxa that belong to higher-level taxa” | concept_edges[4] |
| audit | classification and naming —part-of→ taxonomy — Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span says classification and naming COMPRISES the discipline of taxonomy; part-of is loose. — “The process used to study any new biological entity begins by classifying it in relation to other known biological organisms, and then giving it a name ( 1 – 3 ). This process of classification and naming comprises the discipline of taxonomy, and has been an integral part of biological research since at least the 18th Century when Carl Linnaeus defined the principles of modern taxonomy” | concept_edges[5] |
| note | classification and naming —part-of→ taxonomy — 'This process of classification and naming comprises the discipline of taxonomy' - two acts, one discipline, and the ICTV is unusual in holding authority over both — “The process used to study any new biological entity begins by classifying it in relation to other known biological organisms, and then giving it a name ( 1 – 3 ). This process of classification and naming comprises the discipline of taxonomy, and has been an integral part of biological research since at least the 18th Century when Carl Linnaeus defined the principles of modern taxonomy” | concept_edges[5] |
| weight | classification and naming —part-of→ taxonomy — 0.95 — “The process used to study any new biological entity begins by classifying it in relation to other known biological organisms, and then giving it a name ( 1 – 3 ). This process of classification and naming comprises the discipline of taxonomy, and has been an integral part of biological research since at least the 18th Century when Carl Linnaeus defined the principles of modern taxonomy” | concept_edges[5] |
| outcome | control — held — “Every year, virologists submit proposals to the ICTV recommending the creation of new taxa as well as renaming, moving, or abolishing existing taxa. These proposals are submitted to the appropriate study group which then evaluates and modifies the proposal as necessary, in consultation with the original author. Once a year, the ICTV Executive Committee (EC) meets, discusses all submitted proposals, and will either accept a proposal, send it back for modification, or reject it. Then the set of accepted proposals are sent to the ICTV membership for ratification. Once ratified, the newly approved taxonomy is entered in the ICTV taxonomic database.” — “Unlike for other groups of biological organisms, the ICTV charge extends not only to developing the guidelines for naming of taxa, but to establishing guidelines for taxonomic classification of viruses, and approving the proposed taxonomy and names before they become official.” | controls[0] |
| outcome | control — held — “Each record in the taxonomy table stores data on a single taxon including its name, numerical id, parent taxon, release number and date, most recent taxonomic change, filename of the proposal establishing the taxon, and a pointer to its previous record if a change has occurred in taxon data (such as moving a species to another genus). With this information, a complete history of every taxon can be reconstructed from the database.” — “The tables store a controlled vocabulary used for specific fields where the possible data values remain fairly constant. These include taxonomy level (currently species, genus, subfamily, family, and order), possible taxonomic changes from the previous release (new, split, move, merge, rename, and abolish), and virus genome type (e.g. dsDNA, ssDNA, dsRNA, ssRNA(+), ssRNA(–), etc.) that forms part of the annotation available for the member viruses of each species.” | controls[1] |
| outcome | control — failed — “the most recent change to this particular taxonomic lineage was the creation of the species Alphacoronavirus 1 in 2009. But in fact, this was not a new species, but was a merging of three existing species (transmissible gastroenteritis virus, feline coronavirus, and canine coronavirus) into one, newly renamed species, Alphacoronavirus 1 . In addition, the species were moved from the now defunct genus coronavirus, into the genus Alphacoronavirus that is a member of the subfamily” — “The tables store a controlled vocabulary used for specific fields where the possible data values remain fairly constant. These include taxonomy level (currently species, genus, subfamily, family, and order), possible taxonomic changes from the previous release (new, split, move, merge, rename, and abolish), and virus genome type (e.g. dsDNA, ssDNA, dsRNA, ssRNA(+), ssRNA(–), etc.) that forms part of the annotation available for the member viruses of each species.” | controls[2] |
| outcome | control — failed — “Each subcommittee contains a series of study groups, generally one per virus family, that develop the demarcation criteria used to define each new taxon, and evaluate proposals using those criteria for classification and naming. These demarcation criteria are based upon the genetic and biological properties of the taxon members, and cover each of the taxonomic ranks currently recognized by the ICTV” — “Members of the genus Enterovirus (family Picornaviridae ) share more than 42% amino acid identity across the length of their polyprotein.” | controls[3] |
| limitation | THE DEMARCATION CRITERIA ARE WRITTEN BY THE PEOPLE WHO APPLY THEM, BY DESIGN: `Each subcommittee contains a series of study groups, generally one per virus family, that develop the demarcation criteria used to define each new taxon, and evaluate proposals using those criteria`. One committee per family writes the rule and judges the application - `the definer never fixes their own terms`, institutionalised — “Each subcommittee contains a series of study groups, generally one per virus family, that develop the demarcation criteria used to define each new taxon, and evaluate proposals using those criteria for classification and naming. These demarcation criteria are based upon the genetic and biological properties of the taxon members, and cover each of the taxonomic ranks currently recognized by the ICTV” | limitations[0] |
| limitation | AND ONE OF THOSE CRITERIA IS A BARE PERCENTAGE: `members of the genus Enterovirus share MORE THAN 42% AMINO ACID IDENTITY across the length of their polyprotein`. No derivation is offered for 42, and the sentence stating it carries no definitional language at all - it is a fact about members, doing the work of a criterion — “Members of the genus Enterovirus (family Picornaviridae ) share more than 42% amino acid identity across the length of their polyprotein.” | limitations[1] |
| limitation | AND THE CHANGE TYPE STORED CAN MISREPRESENT THE CHANGE: `the most recent change ... was the creation of the species Alphacoronavirus 1 in 2009. But in fact, this was not a new species, but was a merging of three existing species ... into one, newly renamed species ... In addition, the species were moved from the now defunct genus coronavirus`. THREE OF THE SIX OPERATIONS AT ONCE, RECORDED AS ONE, and the paper has to say `but in fact` to correct its own database — “the most recent change to this particular taxonomic lineage was the creation of the species Alphacoronavirus 1 in 2009. But in fact, this was not a new species, but was a merging of three existing species (transmissible gastroenteritis virus, feline coronavirus, and canine coronavirus) into one, newly renamed species, Alphacoronavirus 1 . In addition, the species were moved from the now defunct genus coronavirus, into the genus Alphacoronavirus that is a member of the subfamily” | limitations[2] |
| limitation | and the hierarchy is expected to move: `As new data are obtained either on the organisms previously studied, or on related organisms, the classification hierarchy may change`. A vocabulary that is correct at a release number rather than simply correct — “This research process is driven by individual scientists who publish their work, providing their evidence for the proposed classification. As new data are obtained either on the organisms previously studied, or on related organisms, the classification hierarchy may change.” | limitations[3] |
finding · quantity · variable · definition · key-term — grounded in the full text| finding | — “The tables store a controlled vocabulary used for specific fields where the possible data values remain fairly constant. These include taxonomy level (currently species, genus, subfamily, family, and order), possible taxonomic changes from the previous release (new, split, move, merge, rename, and abolish), and virus genome type (e.g. dsDNA, ssDNA, dsRNA, ssRNA(+), ssRNA(–), etc.) that forms part of the annotation available for the member viruses of each species.” | content_tags.findings[0] |
| finding | — “Each record in the taxonomy table stores data on a single taxon including its name, numerical id, parent taxon, release number and date, most recent taxonomic change, filename of the proposal establishing the taxon, and a pointer to its previous record if a change has occurred in taxon data (such as moving a species to another genus). With this information, a complete history of every taxon can be reconstructed from the database.” | content_tags.findings[1] |
| finding | — “the most recent change to this particular taxonomic lineage was the creation of the species Alphacoronavirus 1 in 2009. But in fact, this was not a new species, but was a merging of three existing species (transmissible gastroenteritis virus, feline coronavirus, and canine coronavirus) into one, newly renamed species, Alphacoronavirus 1 . In addition, the species were moved from the now defunct genus coronavirus, into the genus Alphacoronavirus that is a member of the subfamily” | content_tags.findings[2] |
| finding | — “The ICTV was established in 1966 as the International Committee on Nomenclature of Viruses, and was renamed the International Committee on Taxonomy of Viruses in 1977” | content_tags.findings[3] |
| finding | — “Unlike for other groups of biological organisms, the ICTV charge extends not only to developing the guidelines for naming of taxa, but to establishing guidelines for taxonomic classification of viruses, and approving the proposed taxonomy and names before they become official.” | content_tags.findings[4] |
| finding | — “The rules governing the ICTV and its operations are defined by the ICTV Statutes ( http://ictv.global/statutes.asp ), while the rules for creating and naming virus taxa are provided in the International Code of Virus Classification and Nomenclature” | content_tags.findings[5] |
| finding | — “Every year, virologists submit proposals to the ICTV recommending the creation of new taxa as well as renaming, moving, or abolishing existing taxa. These proposals are submitted to the appropriate study group which then evaluates and modifies the proposal as necessary, in consultation with the original author. Once a year, the ICTV Executive Committee (EC) meets, discusses all submitted proposals, and will either accept a proposal, send it back for modification, or reject it. Then the set of accepted proposals are sent to the ICTV membership for ratification. Once ratified, the newly approved taxonomy is entered in the ICTV taxonomic database.” | content_tags.findings[6] |
| finding | — “Each subcommittee contains a series of study groups, generally one per virus family, that develop the demarcation criteria used to define each new taxon, and evaluate proposals using those criteria for classification and naming. These demarcation criteria are based upon the genetic and biological properties of the taxon members, and cover each of the taxonomic ranks currently recognized by the ICTV” | content_tags.findings[7] |
| finding | — “Members of the genus Enterovirus (family Picornaviridae ) share more than 42% amino acid identity across the length of their polyprotein.” | content_tags.findings[8] |
| finding | — “Classification of viruses is based on the collection and comparison of various characters that describe the virus, and can then be used to distinguish one virus from another ( 1 , 10 – 15 ). Characters can consist of any property or feature of the virus, and include the molecular composition of the genome; the structure of the virus capsid and whether or not it is enveloped; the gene expression program used to produce virus proteins; host range; pathogenicity; and sequence similarity. While all characters are important in determining taxonomic relationships, sequence comparisons using both pairwise sequence similarity and phylogenetic relationships have become one of the primary sets of characters used to define and distinguish virus taxa.” | content_tags.findings[9] |
| finding | — “Based on an assessment of characters, a hierarchical relationship is established that groups together viruses with similar properties. The properties that define higher-level taxa are shared with all lower-level taxa that belong to higher-level taxa” | content_tags.findings[10] |
| finding | — “The principles, procedures, and nomenclature used to name taxa, is handled by one of the international organizations charged with developing the necessary guidelines. For example, naming of animal species is subject to the principles established by the International Commission on Zoological Nomenclature ( 2 , 5 ). Naming of bacterial species is guided by the International Committee on Systematic Bacteriology ( 3 ). The taxonomic classification of viruses and naming of virus taxa is the responsibility of the International Committee on Taxonomy of Viruses (ICTV)” | content_tags.findings[11] |
| finding | — “This research process is driven by individual scientists who publish their work, providing their evidence for the proposed classification. As new data are obtained either on the organisms previously studied, or on related organisms, the classification hierarchy may change.” | content_tags.findings[12] |
| finding | — “No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy.” | content_tags.findings[13] |
| quantity | 6 operations — the enumerated change types - new, split, move, merge, rename, abolish — “The tables store a controlled vocabulary used for specific fields where the possible data values remain fairly constant. These include taxonomy level (currently species, genus, subfamily, family, and order), possible taxonomic changes from the previous release (new, split, move, merge, rename, and abolish), and virus genome type (e.g. dsDNA, ssDNA, dsRNA, ssRNA(+), ssRNA(–), etc.) that forms part of the annotation available for the member viruses of each species.” | content_tags.quantities[0] |
| quantity | 42 per cent — amino acid identity across the polyprotein, the demarcation criterion for the genus Enterovirus — “Members of the genus Enterovirus (family Picornaviridae ) share more than 42% amino acid identity across the length of their polyprotein.” | content_tags.quantities[1] |
| quantity | 1966 — the committee's founding, as the International Committee on Nomenclature of Viruses; renamed in 1977 — “The ICTV was established in 1966 as the International Committee on Nomenclature of Viruses, and was renamed the International Committee on Taxonomy of Viruses in 1977” | content_tags.quantities[2] |
| variable | demarcation criteria — “Each subcommittee contains a series of study groups, generally one per virus family, that develop the demarcation criteria used to define each new taxon, and evaluate proposals using those criteria for classification and naming. These demarcation criteria are based upon the genetic and biological properties of the taxon members, and cover each of the taxonomic ranks currently recognized by the ICTV” | content_tags.variables[0] |
| definition | taxonomy — “The process used to study any new biological entity begins by classifying it in relation to other known biological organisms, and then giving it a name ( 1 – 3 ). This process of classification and naming comprises the discipline of taxonomy, and has been an integral part of biological research since at least the 18th Century when Carl Linnaeus defined the principles of modern taxonomy” | content_tags.definitions[0] |
| definition | demarcation criteria — “Each subcommittee contains a series of study groups, generally one per virus family, that develop the demarcation criteria used to define each new taxon, and evaluate proposals using those criteria for classification and naming. These demarcation criteria are based upon the genetic and biological properties of the taxon members, and cover each of the taxonomic ranks currently recognized by the ICTV” | content_tags.definitions[1] |
| definition | controlled vocabulary — “The tables store a controlled vocabulary used for specific fields where the possible data values remain fairly constant. These include taxonomy level (currently species, genus, subfamily, family, and order), possible taxonomic changes from the previous release (new, split, move, merge, rename, and abolish), and virus genome type (e.g. dsDNA, ssDNA, dsRNA, ssRNA(+), ssRNA(–), etc.) that forms part of the annotation available for the member viruses of each species.” | content_tags.definitions[2] |
| concept | controlled vocabulary — not defined in this paper's own words; the database's own term for the enumerated fields - taxonomy level, change type, genome type — “The tables store a controlled vocabulary used for specific fields where the possible data values remain fairly constant. These include taxonomy level (currently species, genus, subfamily, family, and order), possible taxonomic changes from the previous release (new, split, move, merge, rename, and abolish), and virus genome type (e.g. dsDNA, ssDNA, dsRNA, ssRNA(+), ssRNA(–), etc.) that forms part of the annotation available for the member viruses of each species.” | concepts[0] |
| concept | International Committee on Nomenclature of Viruses — not defined in this paper's own words; the committee's name from 1966 to 1977, when its remit was naming — “The ICTV was established in 1966 as the International Committee on Nomenclature of Viruses, and was renamed the International Committee on Taxonomy of Viruses in 1977” | concepts[1] |
| concept | International Committee on Taxonomy of Viruses — not defined in this paper's own words; the same committee after 1977, when its remit extended to classification — “The ICTV was established in 1966 as the International Committee on Nomenclature of Viruses, and was renamed the International Committee on Taxonomy of Viruses in 1977” | concepts[2] |
| concept | ICTV Statutes — not defined in this paper's own words; the rulebook governing the committee and its operations — “The rules governing the ICTV and its operations are defined by the ICTV Statutes ( http://ictv.global/statutes.asp ), while the rules for creating and naming virus taxa are provided in the International Code of Virus Classification and Nomenclature” | concepts[3] |
| concept | International Code of Virus Classification and Nomenclature — not defined in this paper's own words; the rulebook governing the creation and naming of taxa - a second document, for the objects rather than the committee — “The rules governing the ICTV and its operations are defined by the ICTV Statutes ( http://ictv.global/statutes.asp ), while the rules for creating and naming virus taxa are provided in the International Code of Virus Classification and Nomenclature” | concepts[4] |
| concept | demarcation criteria — not defined in this paper's own words; the per-family criteria used to define each new taxon, written and applied by the same study group — “Each subcommittee contains a series of study groups, generally one per virus family, that develop the demarcation criteria used to define each new taxon, and evaluate proposals using those criteria for classification and naming. These demarcation criteria are based upon the genetic and biological properties of the taxon members, and cover each of the taxonomic ranks currently recognized by the ICTV” | concepts[5] |
| concept | study groups — not defined in this paper's own words; one per virus family, writing the demarcation criteria and evaluating proposals against them — “Each subcommittee contains a series of study groups, generally one per virus family, that develop the demarcation criteria used to define each new taxon, and evaluate proposals using those criteria for classification and naming. These demarcation criteria are based upon the genetic and biological properties of the taxon members, and cover each of the taxonomic ranks currently recognized by the ICTV” | concepts[6] |
| concept | subcommittee — not defined in this paper's own words; one of six, each covering a host type and genome composition — “Each subcommittee contains a series of study groups, generally one per virus family, that develop the demarcation criteria used to define each new taxon, and evaluate proposals using those criteria for classification and naming. These demarcation criteria are based upon the genetic and biological properties of the taxon members, and cover each of the taxonomic ranks currently recognized by the ICTV” | concepts[7] |
| concept | classification and naming — not defined in this paper's own words; the two acts that together comprise taxonomy — “The process used to study any new biological entity begins by classifying it in relation to other known biological organisms, and then giving it a name ( 1 – 3 ). This process of classification and naming comprises the discipline of taxonomy, and has been an integral part of biological research since at least the 18th Century when Carl Linnaeus defined the principles of modern taxonomy” | concepts[8] |
| concept | taxonomy — not defined in this paper's own words; the discipline comprising classification and naming, dated by this paper to Linnaeus — “The process used to study any new biological entity begins by classifying it in relation to other known biological organisms, and then giving it a name ( 1 – 3 ). This process of classification and naming comprises the discipline of taxonomy, and has been an integral part of biological research since at least the 18th Century when Carl Linnaeus defined the principles of modern taxonomy” | concepts[9] |
| concept | lower-level taxa — not defined in this paper's own words; taxa that inherit the defining properties of the taxa above them — “Based on an assessment of characters, a hierarchical relationship is established that groups together viruses with similar properties. The properties that define higher-level taxa are shared with all lower-level taxa that belong to higher-level taxa” | concepts[10] |
| concept | higher-level taxa — not defined in this paper's own words; taxa whose defining properties are shared by everything below them — “Based on an assessment of characters, a hierarchical relationship is established that groups together viruses with similar properties. The properties that define higher-level taxa are shared with all lower-level taxa that belong to higher-level taxa” | concepts[11] |
| concept | ICTV — not defined in this paper's own words; the committee holding both the naming rules and the classification approval — “Unlike for other groups of biological organisms, the ICTV charge extends not only to developing the guidelines for naming of taxa, but to establishing guidelines for taxonomic classification of viruses, and approving the proposed taxonomy and names before they become official.” | concepts[12] |
| concept | other groups of biological organisms — not defined in this paper's own words; zoology and bacteriology, whose bodies set naming rules without approving each classification — “Unlike for other groups of biological organisms, the ICTV charge extends not only to developing the guidelines for naming of taxa, but to establishing guidelines for taxonomic classification of viruses, and approving the proposed taxonomy and names before they become official.” | concepts[13] |
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Abstract. Abstract The International Committee on Taxonomy of Virusesterm (ICTVterm) is charged with the task of developing, refining, and maintaining a universal virus taxonomyterm. This task encompasses the classification of virus species and higher-level taxaterm according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomyterm; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTVterm web site ( http://ictvterm.global ) provides access to the current taxonomyterm database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971date. The ICTVterm has also published the ICTVterm Report on Virus Taxonomyterm starting in 1971date. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTVterm report, published in 2012, is available as an open-access online publication from the ICTVterm web site. The current, 10th report ( http://ictvterm.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 taxonomyterm. INTRODUCTION The process used to study any new biological entity begins by classifying it in relation to other known biological organisms, and then giving it a name ( 1 – 3 ). This process of classification and namingterm comprises the discipline of taxonomyterm, and has been an integral part of biological research since at least the 18th Century when Carl Linnaeus defined the principles of modern taxonomyterm ( 4 ). Taxonomic classification is a scientific endeavor whereby biological organisms are grouped together and placed into their proper taxonomic hierarchy based on the characteristics that form a unique descriptor identifying a particular organism. This research process is driven by individual scientists who publish their work, providing their evidence for the proposed classification. As new data are obtained either on the organisms previously studied, or on related organisms, the classification hierarchy may change. The principles, procedures, and nomenclature used to name taxa, is handled by one of the international organizations charged with developing the necessary guidelines. For example, naming of animal species is subject to the principles established by the International Commission on Zoological Nomenclature ( 2 , 5 ). Naming of bacterial species is guided by the International Committee on Systematic Bacteriology ( 3 ). The taxonomic classification of viruses and naming of virus taxa is the responsibility of the International Committee on Taxonomy of Virusesterm (ICTVterm) ( 6 ). The ICTVterm is charged with the task of developing, refining, and maintaining a universal virus taxonomyterm by the Virology Division of the International Union of Microbiological Societies ( 7 ). Unlike for other groups of biological organismsterm, the ICTVterm charge extends not only to developing the guidelines for naming of taxa, but to establishing guidelines for taxonomic classification of viruses, and approving the proposed taxonomyterm and names before they become official. The rules governing the ICTVterm and its operations are defined by the ICTV Statutesterm ( http://ictvterm.global/statutes.asp ), while the rules for creating and naming virus taxa are provided in the International Code of Virus Classification and Nomenclatureterm ( http://ictvterm.global/codeOfVirusClassification.asp ). The ICTVterm was established in 1966 as the International Committee on Nomenclature of Virusesterm, and was renamed the International Committee on Taxonomy of Virusesterm in 1977 ( 6 , 8 , 9 ). The ICTVterm consists of a series of officers, subcommitteeterm chairs, and elected members that oversee taxonomic classification and namingterm. There are six subcommitteesterm, each of which covers a different group of viruses, differentiated by the type of host the virus infects (animal, plant, fungal and protist, or bacterial and archaeal) and the molecular composition of the virus genome (DNA, RNA, double or single stranded and translational polarity). Each subcommitteeterm contains a series of study groupsterm, generally one per virus family, that develop the demarcation criteriaterm used to define each new taxon, and evaluate proposals using those criteria for classification and namingterm. These demarcation criteriaterm are based upon the genetic and biological properties of the taxon members, and cover each of the taxonomic ranks currently recognized by the ICTVterm: order, family, subfamily, genus and species. In addition to overseeing taxonomic decisions, the ICTVterm is also charged with disseminating these decisions to the scientific community. Therefore, the ICTVterm maintains a database that stores the virus taxonomyterm, taxon names, and associated metadata, including information on exemplar viruses for each named species. The ICTVterm web site ( http://ictvterm.global ) provides access to its taxonomyterm database and also provides an extensive collection of information supporting its overall activities, including the ICTVterm Report that provides a complete description of every defined virus taxon. DATABASE AND WEB SITE Virus classification Classification of viruses is based on the collection and comparison of various characters that describe the virus, and can then be used to distinguish one virus from another ( 1 , 10 – 15 ). Characters can consist of any property or feature of the virus, and include the molecular composition of the genome; the structure of the virus capsid and whether or not it is enveloped; the gene expression program used to produce virus proteins; host range; pathogenicity; and sequence similarity. While all characters are important in determining taxonomic relationships, sequence comparisons using both pairwise sequence similarity and phylogenetic relationships have become one of the primary sets of characters used to define and distinguish virus taxa. Based on an assessment of characters, a hierarchical relationship is established that groups together viruses with similar properties. The properties that define higher-level taxaterm are shared with all lower-level taxaterm that belong to higher-level taxaterm ( 15 ). For example, viruses of the order Picornavirales all are non-enveloped, icosahedral particles containing one or two segments of positive-sense RNA ( 16 ). The family Picornaviridae is one of (currently) five families belonging to the order Picornavirales . Members of the family Picornaviridae contain a single monocistronic genome with conserved genome organization (arrangement of encoded polypeptides). Members of the genus Enterovirus (family Picornaviridae ) share more than 42% amino acid identity across the length of their polyprotein. Finally, members of the species Enterovirus C , share a limited range of hosts and host receptors, have similar polyprotein processing programs, and share more than 70% amino acid identity in the polyprotein. Once these criteria for grouping similar viruses into common taxa are established, they are used as demarcation criteriaterm to determine if newly discovered viruses are members of an existing species (and therefore also in existing higher-level taxaterm), or if the new viruses warrant creation of a new species (and potentially new higher-level taxaterm), if their properties are sufficiently distinct from the viruses in an existing species. The ICTVterm database of virus taxonomyterm Every year, virologists submit proposals to the ICTVterm recommending the creation of new taxa as well as renaming, moving, or abolishing existing taxa. These proposals are submitted to the appropriate study groupterm which then evaluates and modifies the proposal as necessary, in consultation with the original author. Once a year, the ICTVterm Executive Committee (EC) meets, discusses all submitted proposals, and will either accept a proposal, send it back for modification, or reject it. Then the set of accepted proposals are sent to the ICTVterm membership for ratification. Once ratified, the newly approved taxonomyterm is entered in the ICTVterm taxonomic database. The database utilizes a relational schema built using Microsoft SQL Server. The tables store a controlled vocabularyterm used for specific fields where the possible data values remain fairly constant. These include taxonomyterm level (currently species, genus, subfamily, family, and order), possible taxonomic changes from the previous release (new, split, move, merge, rename, and abolish), and virus genome type (e.g. dsDNA, ssDNA, dsRNA, ssRNA(+), ssRNA(–), etc.) that forms part of the annotation available for the member viruses of each species. Each record in the taxonomyterm table stores data on a single taxon including its name, numerical id, parent taxon, release number and date, most recent taxonomic change, filename of the proposal establishing the taxon, and a pointer to its previous record if a change has occurred in taxon data (such as moving a species to another genus). With this information, a complete history of every taxon can be reconstructed from the database. Table 1 displays an example set of database records for the species Measles morbillivirus . Table 1. Database Records for the Species Measles morbillivirus Table Field Record 1 Record 2 taxon_name Measles virus Measles morbillivirus taxon_level Species Species release_number 30 31 release_year 2015 2016 taxon_id (stable) 19750163 19750163 node_id (new with each release) 20151044 20161044 parent_taxon Morbillivirus Morbillivirus last_change move rename proposal 2015.011a-iM.A.v2.Pneumoviridae.pdf 2016.011aM.A.v2.Paramyxoviridae_spren.pdf The two most recent records in the ICTVterm database are displayed, detailing changes in the taxonomic classification and namingterm of virus members of this species. Data stored in the taxonomyterm database can be accessed visually from the ICTVterm web site ( http://ictvterm.global/virusTaxonomy.asp ) using the taxonomyterm browser: a hierarchical series of expandable, tabular rows, with each row containing information on a single taxon (Figure 1 ). Each taxon is presented in its proper position in the taxonomic hierarchy (Figure 2 ). Each row is labeled with the number of lower-level taxaterm belonging to each higher-level taxon, and a link is provided to the complete history of each taxon (see below). A search box is available to search the current, or current and historical taxonomyterm releases for any taxon that includes the text entered in the search box ( Supplementary Figure S1 ). Each search result is linked to the identified taxon in the hierarchical taxonomyterm browser. Figure 1. Taxonomyterm Web Page. A screen shot of the ICTVterm web page ( http://ictvterm.global/virusTaxonomy.asp ) that contains the taxonomyterm browser and search form. Figure 2. Taxonomyterm browser. The online taxonomyterm browser, showing an expanded view of the taxonomic hierarchy of the species Measles morbillivirus . The ‘history’ links to the right of each row are colored green if there has been a change in the indicated taxon since the last release. Clicking on any ‘history’ link will take the user to the taxon history page (Figure 3 ). The complete taxonomyterm for any one release (the Master Species List) is also available for download as an Excel spreadsheet ( http://ictvterm.global/msl.asp ). These spreadsheets are available for every release back to 2008. Each new taxonomyterm release is also shared with the National Center for Biotechnology Information (NCBI) of the National Institutes of Health so that the taxonomyterm database they maintain and use for the annotation of virus sequence records can be kept up-to-date with the most recent ICTVterm taxonomyterm. Historical taxonomyterm releases The ICTVterm database contains the complete taxonomyterm for every release since the taxonomyterm was first produced in 1971date (Table 2 ) ( 6 , 8 ). Each of these releases can be accessed using the taxonomyterm browser by following the appropriate link on the release history web page ( http://ictvterm.global/taxonomyReleases.asp ). In addition, by selecting the ‘history’ link from the taxonomyterm browser (Figure 2 ), a page displaying the complete history of the selected taxon is displayed (Figure 3 ). This history is constructed from the complete set of database records that are part of the historical path leading to the selected taxon, and to the most recent child of that taxon in the last release recording a change. For example, in Figure 3 , the most recent change to this particular taxonomic lineage was the creation of the species Alphacoronavirus 1 in 2009. But in fact, this was not a new species, but was a merging of three existing species (transmissible gastroenteritis virus, feline coronavirus, and canine coronavirus) into one, newly renamed species, Alphacoronavirus 1 . In addition, the species were moved from the now defunct genus coronavirus, into the genus Alphacoronavirus that is a member of the subfamily Coronavirinae . This particular history goes back to the first ICTVterm data release in 1971date when the species transmissible gastro-enteritis virus of swine was created as a member of the genus coronavirus. (The species concept in virus taxonomyterm was not defined until 1996 ( 8 ). Therefore any ‘species’ present in the database between 1971date and 1995 represents an informal taxonomic rank, existing to contain the viruses that are members of each genus and higher-level ranks.) Table 2. Taxonomyterm Release History. Information on each release of the approved ICTVterm taxonomyterm is displayed including the date and location of the ICTVterm meeting where proposals were discussed; the Master Species List (MSL) release number and the number of taxa belonging to each taxon rank present in the ICTVterm database for the indicated release Number of Taxa Year Release Information Order Family Subfamily Genus Species 2016 EC 48, Budapest, Hungary, August 2016; Email ratification 2017 (MSL #31) 8 122 35 735 4404 2015 EC 47, London, UK, July 2015; Email ratification 2016 (MSL #30) 7 111 27 609 3704 2014 EC 46, Kingston and Montreal, Canada, July 2014, Email ratification 2015 (MSL #29) 7 104 23 505 3185 2013 EC 45, Edinburgh, July 2013; Email ratification 2014 (MSL #28) 7 103 22 455 2827 2012 EC 44, Leuven, July 2012; Email ratification 2013 (MSL #27) 7 96 22 420 2617 2011 EC 42: Paris, June 2010; EC43: Sapporo, September 2011; Email ratification 2012 (MSL #26) 6 94 22 395 2480 2009 ICTVterm 9th Report; EC41: Leiden, June 2009; Email ratification 2009 (MSL #25) 6 87 19 349 2285 2008 EC 39: Kingston, June 2007; EC 40: Istanbul, August 2008; Email ratification 2008 (MSL #24) 5 82 11 307 2079 2005 ICTVterm 8th Report (MSL #23) 3 73 11 289 1899 2004 Postal vote 2004 (MSL #22) 3 73 11 290 1832 2002 Plenary session, July 2002, Paris (MSL #21) 3 70 11 251 1619 2002 Postal vote spring 2002 (MSL #20) 3 70 9 247 1602 1999 Plenary session, August 1999, Sydney (MSL #19) 3 64 9 239 1550 1999 ICTVterm 7th Report (MSL #18) 3 64 9 234 1551 1998 Postal vote autumn 1998 (MSL #17) 3 63 9 233 2370 1997 Postal vote autumn 1997 (MSL #16) 2 56 9 197 2267 1996 Plenary session, August 1996, Jerusalem (MSL #15) 2 53 9 182 2253 1995 ICTVterm 6th Report (MSL #14) 1 50 9 166 2220 1993 Plenary session, August 1993, Glasgow (MSL #13) 1 49 9 160 1700 1991 ICTVterm 5th Report (MSL #12) 1 40 9 142 1674 1990 Plenary session, August 1990, Berlin (MSL #11) 1 40 9 137 1290 1987 Plenary session, August 1987, Edmonton (MSL #10) 0 37 8 116 1275 1984 Plenary session, September 1984, Sendai (MSL #09) 0 35 8 103 1222 1982 ICTVterm 4th Report (MSL #08) 0 29 8 97 1209 1981 Plenary session, August 1981, Strasbourg (MSL #07) 0 29 8 93 1091 1979 ICTVterm 3rd Report (MSL #06) 0 24 8 84 1008 1978 Plenary session, August 1978, The Hague (MSL #05) 0 24 7 76 760 1976 ICTVterm 2nd Report (MSL #04) 0 17 3 67 754 1975 Plenary session, September 1975, Madrid (MSL #03) 0 17 1 63 309 1974 Postal vote April-May 1974 (MSL #02) 0 5 0 49 298 1971date ICTVterm 1st Report (MSL #01) 0 2 0 43 290 Figure 3. Taxon history. Complete history of the species Alphacoronavirus 1 . The bottom of the figure displays the earliest taxon (transmissible gastro-enteritis virus of swine) into which viruses belonging to the current taxon, Alphacoronavirus 1 , were classified. Moving up the page provides an account of every change that has occurred including moves to new higher-level taxaterm, new names, and merges with other existing species. Within a particular release, a grayed-out row indicates that there was no change to that taxon, while other rows depict changes as indicated by the label above the row (New, Moved, Renamed and Merged). Each change indicated in the historical taxonomic record is documented by the taxonomyterm proposal that was submitted to the ICTVterm proposing that change. These proposals are accessible from the ICTVterm web site, and can be downloaded as pdf files ( Supplementary Figure S2 ). Links to each relevant proposal are provided from the taxonomyterm history web page (Figure 3 ). Proposals are available for all taxonomic changes since 2008; though many earlier proposals are also available. ICTVterm Online (10th) Report on virus taxonomyterm In addition to providing current and historical access to the ICTVterm taxonomyterm through the web-based browser and the Master Species List, the ICTVterm has also published a compendium, the ‘ICTVterm Reports on Virus Taxonomyterm: The Classification and Nomenclature of Viruses’ since 1971date, providing a description of all virus taxa existing at the time of publication ( 1 , 9 , 17 , 18 ). This has been published as a hard-copy book, and contains a complete listing of all taxa, along with a list of exemplar viruses corresponding to each species. In addition, these reports provide extensive information on each taxon, describing the properties and characteristics of the virus members of each taxon. These reports also contain a description of the demarcation criteriaterm used to determine whether a particular virus should be classified into an existing species, or whether the creation of a new species (and potentially higher-level taxaterm) is warranted. The last hard-copy ICTVterm Report published was the ninth Report, published in 2012 ( 1 ). (Due to the length of time required to compile the report, the ninth Report was based on the 2009 ICTVterm taxonomyterm release.) The ninth report is currently available as an open-source publication from the ICTVterm web site ( http://ictvterm.global/9th-report/ ). The ICTVterm 10th Report on Virus Taxonomyterm is being published in an online format, and is available from the ICTVterm web site ( http://ictvterm.global/report/ ). The 10th report is being published sequentially as chapters are released at the rate of ∼25 a year. Report chapters provide a thorough description of each virus taxon, and are generally organized by taxonomic family (Figure 4 ). Within each family, separate sections describe each genus and the member species of that genus. Each of these sections contains a member species table that provides a list of species, and one exemplar virus corresponding to that species. These exemplars are not meant to be a comprehensive listing of all member viruses of the species, but comprise viruses that can serve as a prototypic member of each species. These tables are populated from information stored within the ICTVterm database, and may also provide names of additional prototypic virus isolates, as well as accession number-based links to available GenBank ( 19 ) sequence records ( Supplementary Table S1 ). Accession numbers for RefSeq ( 20 ) sequence records are also stored in the database and will be made available in a future update of the web site. Figure 4. ICTVterm Report chapter. A screen shot of the web page depicting the Flaviviridae chapter of the ICTVterm Online (10th) Report ( http://ictvterm.global/report/flaviviridae/ ). In addition to the Online Report, the ICTVterm is also partnering with the Journal of General Virology to publish short summaries of each report chapter ( 21 ). These ICTVterm Virus Taxonomyterm Profiles are published at the same time as the Online Report chapters, and consist of a two to three-page review of the properties of each virus family. These profiles serve as citable references for the Online Report chapters ( 22 ). FUTURE DEVELOPMENTS A number of challenges currently exist for the ICTVterm and virus taxonomyterm that generally derive from our nascent understanding of the true extent of worldwide virus diversity, arising from new and more efficient technologies for discovering, measuring, and characterizing that diversity ( 10 , 23 – 29 ). Virus discovery has been one of the areas of emphasis of large environmental sampling and metagenomic sequencing projects. The goal of these projects is to more thoroughly assess, in an unbiased manner, the true diversity of biological organisms in a particular environment at a particular place in time, by sequencing the genomes of all organisms present in a sample using high-throughput sequencing technologies. For viruses, this entails utilizing methods that sequence not only DNA-based organisms, but organisms (viruses) with RNA genomes, by including a reverse transcription step in the metagenomic isolation and sequencing pipeline. Once the sequence reads have been generated, efficient sequence assemblers are then able to then identify the reads unique to a single virus genome, and assemble them into a complete, or almost complete, genomic sequence. These metagenomic sequencing projects have resulted in the assembly of thousands of new virus genomes that when classified, should result in the creation of thousands of new virus species and higher-level taxaterm. In June of 2016, the ICTVterm helped organize a meeting to discuss metagenomic sequencing and its impact on virus classification. 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 namingterm ( 30 , 31 ). The ICTVterm concurred with that recommendation. Therefore, the ICTVterm is now accepting proposals for new virus taxa supported solely by metagenomic sequence information. This policy should ensure that the official ICTVterm virus taxonomyterm 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 ICTVterm database, and browsing and searching for these taxa from the ICTVterm web pages, be streamlined and made capable of handling the many thousands of new taxa that will need to be created. The ICTVterm 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 ICTVterm has continually modified and modernized its approach to virus taxonomyterm 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 ( 30 ). 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 ICTVterm will be able to remain current and continue to be relevant to the scientific community. AVAILABILITY The ICTVterm web site and all applications accessing the ICTVterm database are available from http://ictvterm.global/ . The database and web site are the responsibility of the ICTVterm Data Secretary, an elected position of the ICTVterm membership serving a 6-year term. This position, and the provision of the database and web site are defined within and required by the ICTV Statutesterm ( http://ictvterm.global/statutes.asp ), thus assuring the long-term existence of this resource. Unless otherwise noted, all information provided by the ICTVterm from its web site are provided under the Creative Commons Attribution-ShareAlike 4.0 International license ( https://creativecommons.org/licenses/by-sa/4.0/ ). Supplementary Material Supplementary Data Click here for additional data file. ACKNOWLEDGEMENTS We would like to acknowledge the assistance and support of the entire ICTVterm Executive Committee, and the extensive work of the ICTVterm Study Groupterm chairs and members, for their work preparing and reviewing taxonomyterm proposals, and in preparing the Online (10th) Report chapters. SUPPLEMENTARY DATA Supplementary Data are available at NAR online. FUNDING The ICTVterm is supported by a grant from the Wellcome Trust [WT108418AIA]; contributions from the Virology Division of the International Union of Microbiological Societies, the American Society of Virology, and the Microbiology Society; and support from Archives of Virology. Funding for open access charge: Department of Microbiology, University of Alabama at Birmingham (to E.J.L.). Conflict of interest statement . None declared.