Virus Nomenclature

Style Rules of Thumb.

A virus term that ends in -virales, -viridae, or -virinae should be capitalized, eg, change paramyxovirinae to Paramyxovirinae. Terms that end in -virus may or may not be formal terms (and may be genuses, species, or subspecific entities); editors should follow author usage. Authors should distinguish formal and common terms and style them accordingly. It is useful to give the formal, taxonomic identity of a virus at first mention in an article; afterward the informal name is typically used (unless the article is discussing taxonomy per se). Formal names are used for species and above, so subspecific viral entities (strains, serotypes, isolates etc) are not capitalized or italicized. Abbreviations may be used for common names.

Reference sources for viral terms include the latest nomenclature reports² and online databases^4,5 (more below). See Table 14 (at the end of the section on viruses) for formal names, common names, and abbreviations of human (and related) viruses.

Background and further style specifics follow.

The Viral Code.

International virus taxonomy dates from 1966 and the first published report from 1971. Viral taxonomy and nomenclature are put forth by the International Committee on Taxonomy of Viruses (ICTV) in the International Code of Virus Classification and Nomenclature of ICTV.^2,6 (The ICTV is a committee of the Virology Division, International Union of Microbiology Societies.) The code is the work of more than 500 virologists worldwide, including 82 study groups.⁷ The eighth report was issued in 2005.²

Official virus names for species and higher taxa are available in book form² with updates published in Archives of Virology. Online, official names and updates are to be available at the ICTV website, http://www.danforthcenter.org/iltab/ictvnet/asp/_MainPage.asp,⁴ and at ICTVdb, http://phene.cpmc.columbia.edu (US mirror site: http://www.ncbi.nlm.nih.gov/ICTVdb/).⁵ The ICTVdb site also provides information about isolates (eg, serotypes, strains) with links to genome sequence databases. (It is hoped that this linkage will bring needed consistency between official viral nomenclature and viral entries in gene sequence databases.⁷)

As with bacterial, animal, and plant nomenclature, viral nomenclature aims for stability and clarity. (See also 15.14.1, Biological Nomenclature.) Names of viral taxa have standing when approved by the members of the full ICTV.⁸ Proposals for new names or changes should be submitted to the ICTV website.⁴

The viral code applies to the ranks of order, family, subfamily, genus, and species (but not lower ranks). A virus may not yet be classified at each rank, eg, a viral species may belong to a family but not a genus, and a viral genus may not be assigned to a family. The rank of species was added to the code in 1991^6,9 and is reflected in the approximately 1950 viral species names found in the eighth report.² (There are around 5500 viruses recognized in the latest report.²) International specialty groups are responsible for viral nomenclature below the rank of species, eg, types, strains. The code does not govern artificially created and laboratory hybrid viruses.

Formal vs Vernacular Virus Names.

Formal virus names are used for taxonomic groups (order, family, subfamily, genus, and species) in the abstract state.^2,10-12 Use of the formal name indicates that the group has official standing according to the ICTV code. Vernacular (common, informal) virus species names are used for actual entities, eg, laboratory material or outbreak specimens: “concrete viral objects that cause diseases.…”^12(p2247)

Style of Virus Names.

For examples of the typographic conventions described in this section, see Table 14, Viruses of Humans, at the end of the section.^2,9,13,14

Typical endings for order, family, subfamily, genus, and species are as follows:

Latin and English Forms.

Formal names of viral genus and above are latinized. Formal names of species “are English names derived from vernacular common names.”^9(p3) English, the scientific lingua franca during the era of viral discovery, is used for formal virus species names no matter what the language of publication.

Initial Capitals.

Formal virus names at each rank have initial capital letters. Other capitals are used when a proper noun is part of the name, eg:

St Louis encephalitis virus

West Nile virus

Vernacular names do not use initial capitals unless a proper noun is part of the name, eg:

La Crosse virus

Italics.

Although the viral nomenclature code recommends italicizing all scientific virus names (ie, species through order), codes for other organisms differ on using italics for names of higher taxa. For reasons of internal consistency, JAMA and the Archives Journals do not italicize names of viral taxa above genus. JAMA and the Archives Journals do italicize formal viral genus and species names. (Italicization of species is a change from previous ICTV nomenclature reports that was introduced in 1998, to indicate formal approval.¹⁵ It is consistent with style in other areas of biological nomenclature.) Vernacular names are never italicized.

How to Style a Virus Term.

An editor encountering a term ending in -virales, -viridae, or -virinae would capitalize the term; for instance, an editor would change parvoviridae to Parvoviridae. An editor encountering a term ending in -virus can use context to determine whether it is a formal or vernacular name (more below) and revise as necessary, querying the author. For instance, an editor might leave the term poliovirus as is or might change it to the formal species term Poliovirus. Terms for strains, types, serogroups, isolates, etc, are never italicized or capitalized (see the section on those entities below). In legends to figures depicting actual viral entities, eg, electron micrographs, italics and capitals would not be used for the actual entity depicted.¹⁵ Legends to schematic depictions of viruses, however, probably refer to classes of virus, and formal style should be used.

Formal and Vernacular Names in Articles.

Formal names are used for abstract entities, vernacular names for physical entities:

West Nile virus is a member of the genus Flavivirus. The presence of West Nile virus was confirmed in mosquitoes and dead crows….

“We used polymerase chain reaction assays to detect RNA of West Nile virus (family Flaviviridae, genus Flavivirus, species West Nile virus)…”^16(p505)

It is useful, for purposes of identification, to include the formal name initially in an article discussing actual viral entities (with the vernacular name used thereafter)^2,3,10,11,13:

Hepatitis C virus… hepatitis C virus

Human herpesvirus 4… Epstein-Barr virus

Human herpesvirus 3… varicella-zoster virus

Human immunodeficiency virus 1… HIV-1

In such articles, the virus and its higher taxonomic classification may be usefully included early on, eg:

“Sin Nombre virus (family Bunyaviridae, genus Hantavirus, species Sin Nombre virus) is an etiologic agent of hantavirus pulmonary syndrome, a potentially fatal illness of humans.”^3(p2469)

The formal name remains in English, the vernacular name in the language of publication, eg:

Measles virus…virus de la rougeole…^12,13

Hepatitis B virus…el virus de la hepatitis B

Abbreviations.

Formal viral species names should not be abbreviated. Common names of viral species names may be abbreviated. Recommended abbreviations are given in the international code (see Table 14, Viruses of Humans, at the end of this section).² Note that related gene symbols and virus abbreviations may differ (see 15.6.2, Genetics, Human Gene Nomenclature):

The viral code recommends that rank always be specified with formal names and that it precede the virus name:

the family Paramyxoviridae

the genus Respirovirus (formerly the genus Paramyxovirus)

the species Human parainfluenzavirus 1

Virus names used as adjectives are not italicized,¹⁵ eg:

human immunodeficiency virus infection

murine leukemia virus polymerase

vaccinia immune globulin

West Nile virus surveillance

Official style calls for temporary names (recognized taxa whose names are not yet formally approved) to be presented in roman type within quotation marks:

Sapovirus (formerly “Sapporo-like virus”)

“T4-like viruses”

Formal style is unambiguous. Vernacular style can be ambiguous, because the ending -virus occurs in common names at all taxonomic ranks and in other informal designations (eg, arboviruses, which includes several families). It is therefore helpful for authors to specify rank with vernacular terms as well:

the family of retroviruses

Hantaan virus, a species of the genus Hantavirus

the paramyxovirus family

the paramyxovirus subfamily

Plant Virus Alternative.

Many plant virologists favor a different style for formal species names, which uses a binomial term that includes species and genus.^6,11,17,18 (Despite the designation “binomial,” it may contain more than 2 words.) Plant virus names in this style consist of an English species name followed by the genus name:

Binomial Proposal.

Formal virus species names do not currently follow the binomial style typical of other organisms (see 15.14.1, Biological Nomenclature), which includes the genus name and a specific epithet. Confusion exists between terms for abstract virus species and actual virus entities, which often are distinguished only typographically. Virologists have indicated a preference for a binomial style for official virus species names.^10,12 Such a style would resemble the plant style described above, giving species and then genus. (For instance, Measles virus would become Measles morbillivirus. The vernacular term measles virus would remain in use for actual measles-virus entities.) That proposal is under study.^10,11,12,17

Derivations.

For derivations of virus names, consult the reports of the ICTV.²

Some virus names are combinations of words; such names are known as sigla. Examples include echovirus (e nteric cytopathic human orphan virus) and picorna-virus (pico-, RNA virus). Variant capitalization—eg, ECHOvirus, picoRNAvirus—is not used.

Strains, Types, and Isolates.

In clinical and laboratory articles dealing with actual entities, most terms will refer to strains, serotypes, serogroups, or viral isolates, ie, ranks below species. Such terms are not capitalized (unless they include proper nouns) or italicized. Such terms often contain numbers, letters, or names, eg:

coxsackievirus A1, coxsackievirus A24

Desert Shield virus (a strain of Norwalk virus)

human adenovirus 2 (a strain of Human adenovirus C)

human astrovirus 3, Berlin isolate

Hantaan virus 76–118 (a serotype of Hantaan virus)

hepatitis C virus (HCV) genotype 1

HCV subtype (or genotype) 3a

hepatitis D virus genotype 1

human poliovirus 1, poliovirus 1, or poliovirus type 1

human poliovirus 2, poliovirus 2, or poliovirus type 2

human poliovirus 3, poliovirus 3, or poliovirus type 3

human respiratory syncytial virus A2

La Crosse virus (a serotype of California encephalitis virus)

Norwalk virus (a strain of Norwalk virus)

rotavirus B strain IDIR

tick-borne encephalitis virus European subtype

Formal species names may also include numbers or letters (eg, Human herpesvirus 1, hepatitis B virus; see Table 14, Viruses of Humans, at the end of this section).

Hepatitis Terms.

Antigens of hepatitis B virus and antibodies to hepatitis B virus are expressed as follows:

Do not confuse hepatitis e antigen with hepatitis E virus or anti-HBe with anti-hepatitis E virus (anti-HEV).

Influenza Types and Strains.

Strains of influenza A virus are identified by antigenic sub-types, defined by the surface proteins hemagglutinin (H) and neuraminidase (N), eg:

influenza A(H3N2)

The H,N suffix is used only for influenza A, but the 3 species of influenza virus may also contain suffixes with terms for the host of origin (if nonhuman), geographic origin (or a proper name in older strains), laboratory strain number, and year of isolation, separated by virgules (forward slashes) and, in the case of influenza A, followed by the H and N designations in parentheses:

influenza A/New York/55/2004(H3N2)

influenza A/chicken/Hong Kong/317.5/01(H5N1)

influenza B/Jiangsu/10/2003

influenza C/California/78

Phages.

Phages are viruses that infect bacteria. The term phage is shortened from “bacteriophage.” Although the current ICTV nomenclature code prohibits Greek letters in new virus names, older names with Greek letters have not been changed. Spelled-out Greek letters are also found, and letters may be uppercase or lowercase; follow author style. Vernacular terms often include the word phage, eg:

phage T4 or T4 phage

Phage groups or genera are sometimes referred to with general terms such as the following: T-even phages, actinophages, coliphages, T7 phage group.

Examples of formal phage names include the following:

All of the above phage viruses have identically named strains, and many more strains belong to species of similar names. Follow author usage.

Enterobacteria phages Qβ and M11 are strains of Enterobacteria phage Qβ.

(For phage cloning vectors, see 15.6.1, Nucleic Acids and Amino Acids, “Cloning Vectors.”)

Genes.

For genes related to human viruses, see 15.6.2, Human Gene Nomenclature. For retrovirus gene terms, see 15.6.3, Oncogenes and Tumor Suppressor Genes, and 15.6.5, Nonhuman Genetic Terms.