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Scientific Nomenclature

Italics are used for bacterial and viral taxa at the level of family and below. All bacterial and many viral genes are italicized. Serovars of Salmonella enterica are not italicized.

For organisms other than bacteria, fungi, and viruses, scientific names of taxa above the genus level (families, orders, etc.) should be in roman type.

Because abbreviations for restriction endonucleases are derived from the name of the organism (usually bacteria) from which they are isolated, they should be italicized.

SmaI was isolated from Serratia marcescens.

Taq polymerase, which is used in PCRs, was isolated from Thermus aquaticus.

Use italics for genus and species in virus names.

A/Cygnus cygnus/Germany/R65/2006

Italicize species, variety or subspecies, and genus when used in the singular. Do not italicize or capitalize genus name when used in the plural.

Listeria monocytogenes is

…listeria are; salmonellae; mycobacteria

The genus Salmonella consists of only 2 species: S. enterica (divided into 6 subspecies) and S. bongori. Most salmonellae encountered in EID will be serotypes (serovars) belonging to S. enterica. Put the genus and species in italics, followed by initially capped serotype in Roman (e.g., Salmonella enterica serotype Paratyphi). The genus shorthand “S.” should never be used without a species name

Correct: S. enterica

Correct: S. enterica serovar Typhimurium

Correct: S. enterica ser. Typhimurium

Incorrect: Salmonella Typhimurium

Incorrect: S. Typhimurium

Serotypes belonging to other subspecies are designated by their antigenic formulae following the subspecies name (e.g., S. enterica subspecies diarizonae 60:k:z or S. IIIb 60:k:z).

For an article about 1 genus, the author can use abbreviation to introduce new species.

We studied Pseudomonas aeruginosa, P. putida, P. fluorescens, and P. denitrificans.

For an article about multiple genera that each have a different abbreviation, the author can use abbreviation to introduce new species.

We studied Pseudomonas aeruginosa, Streptococcus pyogenes, P. putida, and S. felis.

For an article about multiple genera, some of which have the same abbreviation, write out first mention of new species.  Abbreviate later.

We studied the relationship between Trypanosoma cruzi and Triatoma infestans.

We found the relationship between T. infestans and T. cruzi to be...

For an article about several species of the same genus, the genus must be spelled out only in the title and at first use in the abstract, text, tables, and figures. It may subsequently be abbreviated for other species.

We studied Pseudomonas aeruginosa, P. putida, and P. fluorescens.

However, if >1 genus begins with the same letter in an article, the full genus name must be spelled out the first time it is used with a new species. On subsequent mentions of a species, the genus may be abbreviated.

Ticks were discovered on Canis lupus, Canis latrans, Cerdocyon thous, and Chrysocyon brachyurus, but C. lupus hosted the greatest number of ticks.

Bacteria

Italicize family, genus, species, and variety or subspecies. Begin family and genus with a capital letter. Kingdom, phylum, class, order, and suborder begin with a capital letter but are not italicized. If a generic plural for an organism exists (see Dorland’s), it is neither capitalized nor italicized.

Mycobacterium tuberculosis

family Mycobacteriaceae, order Actinomycetales

mycobacteria

Binary genus-species combinations are always used in the singular. Genus used alone (capitalized and italicized) is usually used in the singular, but it may be used in the plural (not italicized) if it refers to all species within that genus.

Salmonella enterica is…

Salmonellae are ubiquitous…

Do not use spaces for MRSA isolates.

Preferrred: USA300

Avoid: USA 300

Fungi

Use Valley fever, not Valley Fever, when referring coccidioidomycosis. The use of a lowercase “f” in “fever” is consistent with use in the Communicable Diseases Manual and with AMA style for Rift Valley fever.

Genes

Gene designations are generally italicized, which helps clarify whether the writer is referring to a gene or to another entity that might be confused with a gene. Style for genes varies according to organism.

There is no real consensus on style of depicting acronyms for Plasmodium genes, except that when referred to as genes, they are italicized; when referred to as proteins, they are not. The style is more dependent on the particular journal. In molecular microbiology the gene and species abbreviation, i.e., pf, is italicized and all of the term is in lowercase; pfmdr1, pfatp6, pvdhfr. This particular gene was presented in The Lancet as PfATPase6. The main idea is to be consistent throughout the manuscript.

Acronyms for Plasmodium genes are italicized when referring to a gene. When referring to a protein they are not italicized.

Many virus gene names are written in italics and are traditionally 3 letters, lowercase, although some will be written in all caps, roman. No definitive rules exist for naming such genes, and you will see them described in a variety of different ways.

src gene, myc gene, HA, NA

Bacteria gene names are always written in italics.

lacZ gene

Fungus gene names are generally treated the same as virus gene names (i.e., 3 italicized letters, lowercase). With a multigene family, a numeric notation is included. When different alleles of the same gene are noted, the terminology allows for a superscript.

Mitochondrial genes add an “mt” prefix to the 3- or 4-letter gene, which may or may not be in lowercase. Drug target genes are all capped, no italics.

msg1, msg2, msg3 (multigene)

xyz1 (different alleles of same gene)

mtLSU (mitochondrial genes)

DHPS and DHFR (drug target genes)

Cholera toxin gene is written as ctx, and cholera toxin gene subunit A is written as ctxA.

Insertion sequences are written as “IS” plus an italicized number (IS6110).

Human gene names are all caps and italicized. May be all uppercase Latin letters or a combination of uppercase letters and Arabic numbers, ideally no longer than 6 characters. Initial character is always a letter. No subscript, superscript, roman numerals, or Greek letters are used.

Similar gene names may exist for humans and mice. For example, AMA Manual of Style lists the following genes:

β2-microglobulin: B2m (mice) and B2M (humans)

CD5 antigen: Cd5 (mice) and CD5 (humans)

A list of human gene names is available at http://www.genenames.org/guidelines.html

Proteins

Proteins, the combinations of amino acids that make up plants and animals, including humans, often have the same name as a gene but are not italicized and always begin with a capital letter. For example, 1 of the outer surface proteins of Borrelia burgdorferi is named outer surface protein A. It is encoded by ospA (the gene), and the protein is OspA.

Proteins often have common names (e.g., β-galactosidase is the gene product of lacZ).

How to tell difference between proteins and genes? If a term is combined with 1 of the following words, it is probably describing a gene:

Promoter (e.g., P2 core promoter [of myc gene]); promoters are parts of genes, not proteins

Terminator, operator, attenuator sites

If term is combined with one of following words, it is probably describing a protein.

Repress—a protein represses, a gene doesn’t.

React—a protein reacts, a gene doesn’t

Heterodimerization

Elevated levels of ____ [A common usage error is for authors to write “elevated myc” when they mean: “elevated levels of myc.”]

Italicizing MMR is another common usage error. This term, which means “mismatch repair,” is never a gene, just an abbreviation for a process. But you may see “Mice with specific alterations in a number of MMR genes have been developed…”

Restriction Enzymes

Restriction enzymes are identified with a 3-letter designation of the bacterium from which they are isolated, plus a single-letter strain designation (as needed) and a roman numeral showing the order in which it was identified. The 3-letter bacterium designation should begin with a capital letter and is italicized; the rest of the enzyme name is set roman.

SmaI, EcoRI, BamHI

Viruses

Italics Use with Virus Names

A virus is not a species; a virus belongs to a species. Italicize species, genus, and family of a virus when used in a taxonomic sense. Note however, that it is fine to not mention taxonomy of a virus, especially one like dengue or polio that is well known.

Do not italicize a virus name when used generically. If you capitalize a virus name (other than one that has a proper name in it so that you must capitalize it), then you need to italicize it.

bovine kobuviruses, a kobuvirus, kobuviruses, but Kobuvirus spp.

The presence of West Nile virus was confirmed in mosquitoes and dead crows. (AMA Style Guide, p. 758).

Epidemic transmission of West Nile virus (WNV)…prompted aerial application.

The species West Nile virus is a member of the genus Flavivirus.

Family Bunyaviridae, genus Phlebovirus, species Rift Valley fever virus

Recent attention has been drawn to Toscana virus (family Bunyaviridae, genus Phlebovirus, species Sandfly fever Naples virus) in countries…

Acronyms Use with Virus names

It is permissible to use an acronym for a virus (e.g., WNV for West Nile virus), after defining it. However, do not abbreviate a species (including the species West Nile virus). In short, if you do italicize, don’t use an acronym.

Correct: West Nile virus (WNV; family Flaviviridae, genus Flavivirus) is transmitted to humans [here the virus is being transmitted, not the species name; so West Nile virus is roman type and may be abbreviated]. 

For viruses that begin with a Greek letter, write it out and close up space between the letter and the rest of the word.

            Betaherpesvirus

For human coronavirus, use the abbreviation hCoV. Be aware that there is a genus/species named Human coronavirus, which should be abbreviated as H. coronavirus, not hCoV.

For numbered echoviruses (e.g., echovirus 13), use the following format: E13 (do not use EV)

For hepatitis E virus, use the acryonym HEV.

Use a capital H for human virus abbreviations (e.g., HMPV, not hMPV), unless otherwise directed by author or precedent (see human coronavirus above).

For human enterovirus, use human EV, not HEV.  For numbered enteroviruses, use the following format: EV75.

For influenza virus, see separate section (i.e., following West Nile virus below).

For polyomaviruses, use the following:

KIPyV for KI polyomaviruses (formerly known as Karolinska Institute polyomavirus)

MCPyV, not MCV, for Merkel cell polyomavirus, and

WUPyV for WU polyomaviruses (formerly known as Washington University polyomavirus).

For West Nile virus, use WNV.

Influenza

On October 18, 2011, WHO published guidelines for the standardization of terminology of the pandemic A(H1N1)2009 virus (see http://www.who.int/influenza/gisrs_laboratory/terminology_ah1n1pdm09/en/index.html). The guidelines are intended to minimize confusion and differentiate the pandemic virus from the old seasonal A (H1N1) viruses circulating in humans before pandemic A(H1N1)2009 virus. In agreement with WHO guidelines, EID will use the following nomenclature for the pandemic A(H1N1)2009 virus:

influenza A(H1N1)pdm09 virus

 After a first mention of the full virus name, including the word “influenza,” it is sufficient to use “A(H1N1)pdm09”;  however, the word “virus,”  “infection,” or “outbreak” should be added to the name, as appropriate. If the term appears frequently, the abbreviation “pH1N1” may be used.

Examples of other influenza virus nomenclature used by EID:

avian influenza A(H7N9) virus

avian influenza A(H5N1) virus

As stated above for influenza A(H1N1)pdm09 virus, other influenza virus names can be shortened after a first mention that includes the word “influenza,” but, as appropriate, the word word “virus,”  “infection,” or “outbreak” should be added to the name. Examples: A(H7N9) virus, A(H7N9) infection, A(H7N9) outbreak.

The H and N subtype should always be in parentheses when it follows “influenza”: 

influenza virus A (H5N1) (for “influenza virus A subtype H5N1”)

A (H3N2)v (for “variant influenza A (H3N2)”)

When used alone, subtypes do not need parentheses but must be accompanied by the word “subtype.”

The H5N1 subtype is…

Different subtypes, such as H5N1…

Note: H5N1 is neither a virus, nor a disease; it is merely a subtype designation of influenza virus type A. If you want to drop anything later in the article, you may leave out the subtype designation. If only 1 virus is being studied, you can say in the Methods that influenza virus means influenza virus A subtype H5N1, and leave the subtype out from then on.

Influenza virus (H5N1) can have high or low pathogenicity. It is not redundant to include "highly pathogenic" in the title.

For information on this virus nomenclature style, adopted by several international organizations, see International Committee on Taxonomy of Viruses.

For influenza virus isolates, include the virus subtype, write out in full the host of origin (omit if human), include the site of isolation and strain number, and use the 4-digit year if the virus was isolated in 2000 or later. For viruses isolated during the 1900s, use the 2-digit year.

Incorrect: dk/Laos/3295/06

Correct: A/duck/Laos/3295/2006

Italicize genus and species of the host in isolate names.

A/Cygnus cygnus/Germany/R65/2006

The formal nomenclature for the designation of influenza viruses was revised and published by the World Health Organization (WHO). (WHO. A revision of the system of nomenclature for influenza viruses: a WHO memorandum. Bull.World Health Organ. 1980;58;585–9). The full and correct nomenclature includes the type of virus (A, B, or C), the host of origin (except for human), the geographic site of isolation, the strain number, the year of isolation (4-digit year for viruses isolated in 2000 or later; 2-digit year for viruses isolated during the 1900s), and the subtype (16 possible H and 9 possible N subtypes).

Thus a type A virus isolated in 1995 from a Mallard duck in Memphis Tennessee with a strain number of 123 and an H5N1 subtype is designated:

Influenza A/mallard/Memphis/123/95 (H5N1).

Site can be abbreviated in human viruses, as in the following for which PR (Puerto Rico) and FM (Fort Monmouth) are well known and not written out.

Influenza viruses used were A/PR/8/34 (H1N1), A/FM/1/47 (H1N1), and
A/Thailand/SP-83/2004 (H5N1).

When referring to avian influenza viruses that have low pathogenicity, use the term “low pathogenicity avian influenza” not “low pathogenic avian influenza.” If used 3 or more times, the term can be abbreviated as LPAI.

When referring to avian influenza viruses that have high pathogenicity, use the term “highly pathogenic avian influenza” not “high pathogenicity avian influenza.” If used ≥3 times, the term can be abbreviated as HPAI.

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