Virus nomenklatur

It is therefore becoming difficult for researchers to be aware of them, and in particular, to know their specific characteristics. Decreasing sequencing costs and ongoing improvements in sequencing technology have led to increased submission of genomic consensus sequences of viruses to databases without associated peer-reviewed descriptive publications and without fulfilling yet undefined minimum standards for sequencing and metadata.

In practice, this means that crucial information about these sequences and the associated viruses is lost when, for instance, the date of isolation or the location of isolation, i. The amount of genomic information for members of the family Filoviridae is unlikely to become overwhelming in the short term.

However, their importance in regard to biodefense measures, and recent calls for genetic filovirus variant standardization to expedite countermeasure development [ 18 ], make them suitable candidates for name standardization trends started by influenzavirus, coronavirus, and rotavirus experts.

Here, we propose guidelines for the establishment of a standardized nomenclature for natural genetic variants of filoviruses, and how to build designations for them from metadata in GenBank records and publications. Several nomenclature schemes have been brought forward for individual virus groups. According to the guidelines of this nomenclature, influenzaviruses are to be designated as.

A similar system was suggested for the naming of avian coronaviruses order Nidovirales , family Coronaviridae , subfamily Coronavirinae , genus Gammacoronavirus , species Avian coronavirus by Cavanagh in [ 6 ]:.

The influenzavirus nomenclature has proven very useful as it allows searching for and identifying particular influenzavirus isolates from the more than , deposited sequences. It is generally accepted within the influenzavirus research community and has the advantage that the isolate designation is mostly self-explanatory, allowing non-influenzavirus specialists to comprehend it quickly.

This system has several disadvantages. Complicating the matter, the species abbreviations used are identical with the virus abbreviations in circulation. Fourth, the system does not differentiate between strains and variants. In , Fauquet and Stanley proposed a nomenclature for geminiviruses family Geminiviridae [ 8 ], which was modified in [ 9 ]:.

Reminiscent of the influenzavirus nomenclature, this system is easily comprehensible in its unabbreviated form. The abbreviated names are more difficult to grasp immediately and raise the question how countries, cities, and hosts should be abbreviated consistently. The most recent comprehensive virus nomenclature was proposed in by the Rotavirus Classification Working Group in conjunction with the development of an NCBI database for rotavirus genome sequences [ 21 ].

This nomenclature is again similar to that used for influenzaviruses:. This taxonomy, summarized in Table 1 , also delineates the proper use of vernacular filovirus names. It is an attempt to ameliorate the confusion that exists generally among virologists regarding the difference between virus species and viruses [ 4 , 7 , 15 , 28 — 30 ] by introducing virus names distinct from species names [ 14 ] as previously requested by some experts [ 15 , 27 ].

Lastly, it accommodates recent developments in filovirology, such as the discovery of two novel filoviruses that require d the establishment of two new species and one new genus [ 14 , 22 , 25 ]. Whereas the demarcation of individual filoviruses Ebola virus vs. Sudan virus vs. Marburg virus, etc. The result is not only inconsistency and the ensuing difficulties for non-specialists to understand manuscripts, seminars, or figures [ 16 ], but also a broad range of different designations referring to the same filovirus, as well as typographical and transliterational errors [ 13 ].

In recent years, filovirus disease outbreaks have been observed more frequently, and an ever-increasing number of isolates and genomic consensus sequences are becoming available. Technological breakthroughs in sequencing also have allowed the identification of a novel filovirus Lloviu virus, LLOV in the absence of replicating isolates [ 22 ].

Fragmented MARV genomes were detected in greater long-fingered bats Miniopterus inflatus Thomas, and eloquent horseshoe bats Rhinolophus eloquens Andersen, [ 24 ]. It is foreseeable that the discovery or creation of novel filoviruses will accelerate in the near future. In this article, a standardized nomenclature and guidelines for its further development are being proposed for natural filoviruses, i. Here, we propose not to add to the existing confusion by constructing radically novel definitions, but rather to employ or extrapolate from the few existing definitions that have been brought forward.

A virus-infected cell will, after only one round or replication, already contain a population of genomes, and virions derived from these genomes will vary slightly from each other quasispecies [ 23 ]. Likewise, a sample taken from a virus culture or an infected animal will contain numerous virions, many of which vary slightly quasispecies [ 23 ]. While single-virion analysis is theoretically possible, it certainly is not done routinely right now it would be meaningless as far as naming is concerned , and even if it were, one would still have to work with virion populations to infect animals—and of course virions are not equal to viruses [ 31 ].

A strain is therefore a genetically stable virus variant that differs from a natural reference virus type variant in that it causes a significantly different, observable, phenotype of infection different kind of disease, infecting a different kind of host, being transmitted by different means etc. The extent of genomic sequence variation is irrelevant for the classification of a variant as a strain since a distinct phenotype sometimes arises from few mutations. The designation of a virus variant as a virus strain would be the responsibility of international expert groups.

All described genetic variants of EBOV, for instance, cause a similar hemorrhagic fever in humans and even experimental animals and are transmitted similarly. None of the known EBOV genetic variants can be distinguished from others on clinical grounds alone. In fact, their variety seems to be limited to subtle differences in growth kinetics and plaque formation in vitro or subtle changes in the duration of disease in experimental animals, and ultimately derives from limited, but often stable, differences in genomic sequence [ 13 ].

Van Regenmortel defined a virus variant as an isolate or a set of isolates whose genomic consensus sequence s differ s from that of a reference virus [ 30 ], i. According to Fauquet et al. We suggest adopting the latter definition for filoviruses, as advancement in sequencing now allows for the partial characterization of an instance of a virus variant in the absence of culturing.

A natural filovirus isolate is an instance of a particular natural filovirus or of a particular genetic variant. Isolates can be identical or slightly different in consensus or individual sequence from each other.

A novel isolate of a virus may at first be grouped with a particular genetic filovirus variant based on sequence information but later reclassified as a strain after experimental infections reveal it to behave phenotypically differently from a reference variant for instance, if the filovirus did not cause viral hemorrhagic fever in a laboratory nonhuman primate but rather caused encephalitis. It would be the decision of international expert groups to change the designation under such circumstances.

We explicitly do not recommend labelling every instance of a filovirus culture in the laboratory as a separate isolate.

Ideally, filovirus taxonomy below the species level would follow an existing general scheme. Unfortunately, as described above, such a global nomenclature does not exist—but the influenzavirus, avian coronavirus, and rotavirus nomenclatures are sufficiently similar to serve as examples.

We suggest following the rotavirus proposal, and propose the following general template for filoviruses, to be used in the Materials and Methods sections of manuscripts:. The virus name should be given in full, as outlined recently [ 14 , 17 ]. If an isolation host can only be identified to a taxon level higher than species, then the entire name of the lowest known taxon should be used. See below for suffixes. The country of sampling field should contain an alpha-3 three-letter country code as outlined in ISO according to present country designations.

The year of sampling field should contain the year of sampling according to the Gregorian calendar in four digits. The genetic variant designation-isolate designation field should contain a unique genetic variant name or acronym an abbreviation that can be pronounced connected by a hyphen to an isolate descriptor. Furthermore, we propose following the suggestions of Fauquet et al. We suggest using the following medium-length designation for virus names in figures, such as phylograms, sequence alignments or diagrams:.

The year of sampling field should contain the year of sampling according to the Gregorian calendar in two digits. The genetic variant designation-isolate designation should contain a unique genetic variant abbreviation connected by a hyphen to an isolate abbreviation.

The genetic variant designation-isolate designation should contain a unique genetic variant abbreviation connected by a hyphen to an isolate abbreviation if the article addresses several different isolates of the same genetic variant.

The isolate descriptor should be left blank if the latter is not the case. The virus name described above and the rest of the full-length designation described above i.

This means that future developments in filovirology may result in the demand for a modified or different nomenclature, which, however, should not be difficult to create based on the metadata collected and archived for the current system. A logical consequence of this system is therefore also the development of a database that contains the information suggested here in conjunction with metadata available from publications, other databases, or research records.

In fact, as many data as possible should be added to GenBank records, and metadata ought to be updated on a constant basis. Maniloff therefore extended to virology what has long been held in bacteriology, namely that the majority of infectious entities in nature most likely cannot be propagated in the laboratory due to their special adaptation to particular cell types and replication conditions. Furthermore, sequence information from uncultured viruses even if they could be cultured is strongly desired because the virus in question could quickly adapt to culture conditions and therefore mutate rapidly.

The exact passaging history should be provided in GenBank metadata fields and also in the methods section of manuscripts next to the virus designation. We agree that the amplification of short stretches of filovirus genomes and their phylogenetic placement using adequate homologous sequences derived from existing filoviruses is not sufficient to recognize truly novel viruses. As genetic variant assignment could change upon further accumulation of data, the genetic variant names ought to be placed in quotation marks to denote the fact that they are considered temporary.

For instance, Marburg virus R. Storage of viruses is not always optimal, thereby resulting in their inactivation over time. Furthermore, virus-infected samples, such as formalized, paraffin-embedded, or frozen tissues are often discarded when storage space is limited. It is therefore no surprise that once-isolated viruses have been inadvertently or deliberately destroyed. A considerable percentage of the early filovirus literature reports experiments performed with these virus isolates.

Their natural history often allows their closest still-available relatives to be inferred, thereby allowing for extrapolation of scientific data to virus isolates used today. We would like to emphasize the importance of studies done with now unavailable viruses while urging that it should be made clear to readers that viruses used for said studies are not available anymore and that results of experiments done at present with a closely related isolate may therefore not necessarily fit historical results.

In addition, 16 plant virus groups were designated, as reported by Matthews in The fifth ICTV report, edited by Francki et al in , described one order, 40 families, nine subfamilies, genera, two floating genera and two subgenera for vertebrate, invertebrate, bacterial and fungal viruses, and 32 groups and seven subgroups for plant viruses.

It was only in , as described in the sixth ICTV report, that the ICTV proposed a uniform system for all viruses, with two orders, 50 families, nine subfamilies, genera, 23 floating genera and four subgenera encompassing assigned viruses.

It is a general trend that the number of described taxa and the number of species of viruses is increasing steadily, easily explained by the increasing complexity of the virus classification and by the amount of data available to demarcate viruses. Therefore, the ICTV classification is not only a taxonomic exercise for virus evolutionists but also a valuable diagnostic tool and educational system for virologists, teachers, medical doctors and epidemiologists.

The ICTV is a nonprofit-making organization composed of prominent virologists representing countries from throughout the world who work to designate virus names and taxa through a democratic process. The ICTV operates through a number of committees, subcommittees and study groups consisting of more than eminent virologists with expertise in viruses infecting humans, animals, insects, protozoa, archaea, bacteria, mycoplasma, fungi, algae, yeasts and plants.

Taxonomic proposals are initiated and formulated by individuals or by the study groups. These proposals are revised and accepted by the corresponding subcommittees and presented for executive committee approval.

All decisions are then ratified at a plenary session or also now by postal vote held at each Virology Congress where all members of ICTV and more than 50 representatives of national microbiological societies are represented. At present, there are 47 study groups working in concert with six subcommittees — namely, the vertebrate, invertebrate, plant, bacteria, fungus and virus data subcommittees. The ICTV regularly publishes reports describing all existing virus taxa with a list of classified viruses as well as descriptions of virus families and genera.

An Internet web site, where the most important information relative to virus taxonomy is made available, is updated regularly. The sixth report was published by Murphy et al and the seventh by van Regenmortel et al The increasing number of virus species and virus strains being identified, together with the explosion of data on many descriptive aspects of viruses and viral diseases, and particularly sequence data, has led the ICTV to launch an international virus database project.

This project, termed ICTVdB, is scheduled to be fully operational and accessible to the scientific community around the year The ICTVdB, in addition to the taxonomic descriptions of all the taxa, will comprise all the information available about each virus species, and later each virus strain, for all the descriptors necessary to identify and recognize all viruses. There are currently two systems in use for classifying organisms: the linnean and the adansonian systems.

The former is the monothetic hierarchical classification applied by Linnaeus to plants and animals, while the adansonian is a polythetic hierarchical system initially proposed by Adanson in In Maurin and collaborators suggested applying the linnean classification system to the viruses. Although convenient to use, this system has shortcomings when applied to the classification of viruses. Firstly, it is difficult to appreciate the validity of a particular criteria. For example, it may not be appropriate to use the number of genomic components as a hierarchical criteria.

Secondly, there are no obvious reasons for prioritizing criteria, and in consequence it is difficult to rank all the available criteria. The adansonian system considers all available criteria at once and makes several classifications, taking the criteria into consideration successively.

The criteria leading to the same classifications are considered as correlated and are therefore not discriminatory. Subsequently, a subset of criteria are considered, and the process is repeated until all criteria can be ranked to provide the best discrimination of the species. This system has not been used frequently in the past owing to its labor-intensive nature, but this situation has changed as a result of the power and availability of today's computer technology.

Furthermore, qualitative and quantitative data can be simultaneously considered when generating such a classification. In the case of viruses, it was determined by Harrison and collaborators in that at least 60 characters could be used for a complete virus description Table 1. Thus, the limiting factor for applying the adansonian system is now not its labor-intensive nature but the lack of data for many of the viruses.

In addition, the increasing number of viral nucleic acid sequences being reported, in combination with the appropriate computer software, allows the comparison of viruses to generate different phylogenetic trees, according to the gene or set of genes used, as for example proposed by Koonin in , Dolja and Koonin in and Dolja et al in However, to date, none of them has satisfactorily provided a clear classification of all viruses. A multidimensional classification, taking into account all the criteria necessary to describe viruses, would probably be the most appropriate way of representing a virus classification, but again the shortcomings of data for some viruses would prevent the use of this system in the foreseeable future.

For almost 25 years, the ICTV has been classifying viruses essentially at the family and genus levels using a nonsystematic polythetic approach.

Viruses were clustered first in genera and then in families. A subset of characters, including physicochemical, structural, genomic and biological criteria, is then used to compare and group viruses. This subset of characters may change from one family to another, according to the availability of the data and the importance of a particular character for a particular family. It is obvious that there is no homogeneity in this respect throughout the virus classification and that virologists weigh the criteria differently in this subjective process, leading to the generation of a nonhomogeneous classification.

Nevertheless, over time we can see stability of the current ICTV classification at the genus and family level. When sequence, genomic organization and replicative cycle data are subsequently used for taxonomic purposes, they usually confirm the actual classification. It is also obvious that hierarchical classifications above the family level will encounter conflicts between phenotypic and genotypic criteria and that virologists will have to consider the entire classification process in order to progress in this direction.

Currently, and for practical reasons only, virus classification is structured according to the presentation indicated in Table 2 , Table 3. Since a taxonomic structure above the level of family with the exception of the orders Mononegavirales, Caudovirales and Nidovirales has not been developed extensively, any listing must be arbitrary.

The order of presentation of virus families and genera follows four criteria: 1 the nature of the viral nucleic acid; 2 the strandedness of the nucleic acid; 3 the use of a reverse transcription process DNA or RNA ; and 4 the positive or negative sense of gene coding on the encapsidated genome.

These four criteria give rise to six clusters comprising the 86 families and floating genera of viruses. In the past, two other criteria were also taken in account: the presence or absence of a lipid envelope and the segmentation of the genome as mono-, bi-, tri-, tetra- or multipartite.

However, it has become clear that the presence of an envelope was entirely related to the nature of the host and that families could comprise genera having viruses with segmented or nonsegmented genomes, but sharing all other properties, including genome organization and sequence homology.

These criteria have been therefore abandoned. Orders, families and floating genera of viruses according to the seventh ICTV report Viruses are then differentiated in species and tentative species according to this list of criteria and the availability of information to demarcate the species. First, it is intended to define for each genus the criteria demarcating a virus species, and, second, to compare these criteria from one genus to the next, searching for homogeneity throughout the virus classification.

Naturally this list of criteria should follow the polythetic nature of the species definition and more than one criteria should be used to determine a new species. It is obvious that most of the criteria in the list of demarcating criteria are shared amongst the different genera, within and across families; namely, host range, serological relationships, vector transmission type, tissue tropism, genome rearrangement and sequence homology Table 4.

However, if the types of criteria are similar, the levels of demarcation clearly differ from one family to another. This may reflect differences in appreciation from one family to another but also the differential ranking of a particular criterion in different families. The levels of demarcation may even change from one gene to another within the same family. Homogenization of the application of the species definition concept throughout the virus definition will be the next challenge of ICTV for the eighth report to be published by This, in turn, will contribute to homogeneity of the genus and family demarcation criteria Table 4 and will permit creation of new families or merging of existing families.

However, it is important to note that the nature of the demarcating criteria at the genus level will probably not change as these have passed the test of time. Despite the fact that they were mostly established using biochemical and structural criteria, they remained valid when correlated with genome organization and sequence data.

The present universal system of virus taxonomy is set arbitrarily at hierarchical levels of order, family in some cases subfamily , genus and species. The species taxon is always regarded as the most important taxonomic level in classification but it has proved to be the most difficult to apply to the viruses. This was a general definition, which was in fact not very useful for practically delineating species in a particular family.

Furthermore, this definition directly addressed the definition of a virus strain, which had never been attempted in the history of virus taxonomy. Members of a polythetic class are defined by more than one property and no single property is absolutely essential and necessary. The ICTV is currently conducting this exercise throughout all virus families. We studied Pseudomonas aeruginosa, P.

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. 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. 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.

Use Valley fever, not Valley Fever, when referring coccidioidomycosis. 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. 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. Fungus gene names are generally treated the same as virus gene names i. With a multigene family, a numeric notation is included. When different alleles of the same gene are noted, the terminology allows for a superscript. Drug target genes are all capped, no italics.

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.

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 osp A the gene , and the protein is OspA.

Proteins often have common names e. 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. Italicizing MMR is another common usage error. 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.

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.