KSN - Vol 53, No 1 - Classification of VirusesVolume 53, Number 1 - April 2006

Classification of Viruses

by Claude M. Fauquet and John R. Schrock

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ABOUT THIS ISSUE

Kansas School Naturalist

ISSN: 0022-877X

Published by EMPORIA STATE UNIVERSITY

Editor: JOHN RICHARD SCHROCK

Editorial Committee: TOM EDDY, GAYLEN NEUFELD, GREG SMITH

Editors Emeritus: ROBERT BOLES, ROBERT F. CLARKE

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Press Composition: John Decker & Claude Fauquet

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Authors:
Picture - Dr. Claude M. FauquetDr. Claude M. Fauquet
is the director of ILTAB (International Laboratory for Tropical Agricultural Biotechnology), located at the Danforth Plant Science Center (St. Louis, Missouri, USA). He graduated from the University Louis Pasteur of Strasburg in France. Dr. Fauquet is a leading expert on virus taxonomy, virus diversity and control of plant viruses, as well as an expert on cassava biotechnology. Dr. C. Fauquet worked for 32 years as a plant virologist dedicated to developing countries. Dr. Fauquet is the co-chair of the Global Cassava Partnership, a world alliance to invest research and development in cassava, and a leading expert in the BioCassava Plus project of the Grand Challenge for Global Health (Funded by the Gates Foundation and NIH).


Dr. John Richard Schrock
received his doctorate from the University of Kansas where he studied insect systematics and ecology. He was associate director and publications manager at the Association of Systematics Collections before joining E.S.U. He wrote the comparative systematics portion of the text.


Cover and contents: The cover is designed using a variety of original photographs published in Virus Taxonomy: the VIIIth Report of the International Committee on Taxonomy of Viruses (ICTV), edited by Claude M. Fauquet et al., 2005 by Elsevier, Inc. 1259 pages. This issue of the Kansas School Naturalist primarily simplifies the content of the new viral taxonomic work of the ICTV as presented in the VIIIth Edition. Permission to published all the graphs and diagrams has been given by Dr. C. Fauquet, who designed and drew them, and source of the original figures is given in the legends.


VIRUS CLASSIFICATION

by Claude M. Fauquet and John R. Schrock

WHAT IS A VIRUS?
Viruses are not living cells. They cannot move, metabolize, respond, or evolve on their own. Viruses have a central core of nucleic acid (DNA or RNA) surrounded by a protein sheath, or capsid. Animal viruses also often have an additional envelope made of proteins, glycoproteins, or lipids.

WHY DO VIRUSES APPEAR TO BE ALIVE?
Viruses invade and are reproduced inside living cells. Some do not disturb this host cell, but others may damage or destroy their host cell. If a specific virus infects a variety of hosts, it is said to have a wide host range. See an example of virus cell cycle in Figure 3.

WHY CLASSIFY VIRUSES?
When a new virus is discovered, it is important to describe or characterize the virus and provide a name so that additional research and properties can be associated with the species. This is done by following the rules of nomenclature and taxonomy found in The International Code of Virus Classification and Nomenclature of ICTV. The main purpose of nomenclature is to provide a stable and uniform naming system.

To "classify" means "to group." The process of grouping viruses by similarities is the complex task of virus systematics, a study that utilizes information about the viral genome, structural and metabolic variations, hosts, and biology. The purpose of classification is to reflect shared characteristics and possible evolutionary history of the members of species.

WHAT IS The International Code of Virus Classification and Nomenclature of ICTV?
Both virus nomenclature and classification are subject to the rules of The International Code of Virus Classification and Nomenclature. This code is independent of the more commonly known botanical and zoological codes, and varies from them in many important aspects:
- Names of species and taxa must be approved by the ICTV.
- No levels above Order are yet recognized.
- Virus names are not required to be Latinized and are not restricted to binomial nomenclature.
- All taxa names are italicized.

WHAT IS THE ICTV?
In 1966, at the International Congress of Microbiology the International Committee on Taxonomy of Viruses (ICTV) was created to bring order to the growing numbers of viruses being described. ICTV began a series of reports in 1971 to update the state of virus taxonomy. ICTV is a committee of the Virology Division, itself part of the International Union of Microbiological Societies (IUMS).

This summary is mostly based on the VIIIth ICTV Report (Fauquet et al., Elsevier, London, pp1259) which includes decisions made at the most recent International Congress of Virology. ICTV has subcommittees working with plant, prokaryote, fungal, vertebrate and invertebrate viruses as well as virus data. More than 78 Study-Groups subdivide the work further, mostly by families.

KSN - Vol. 53, No. 1 - Figure 1 - Distribution of Identity Percentages L1 Papillomaviruses
Figure 1: Distribution of pairwise identity percentages calculated for the sequences of the L1 gene of members of the family Papillomaviridae (Courtesy of C.M. Fauquet). Comparison of virus sequences to define species demarcation criteria.

WHAT IS A VIRUS "SPECIES"?
The VIIth ICTV Report established "a virus species is a polythetic class of viruses that constitute a replicating lineage and occupy a particular ecological niche." The term "polythetic class" indicates that the members of the species will share many traits in common, but they may not all possess a specific defining trait. While this may seem a strange situation to plant and animal systematists where universal or essential traits are required for membership in a taxon, a virus genome can be highly variable and rapidly evolve. While some botanists and zoologists might contend that the species level is real and higher categories are abstractions, the situation with viruses is discussed in a 2003 article by M.H.V. van Regenmortel: "Viruses are real, virus species are man-made, taxonomic constructions".

HOW DO WE RECOGNIZE A VIRUS SPECIES?
The "species concept" often used for living animals and plants requires knowledge of whether two organisms can interbreed and have fertile offspring. Such definitions that rely on living organisms that reproduce sexually are obviously useless for viruses.

Virus taxonomy relies on comparison of traits, such as biological, structural, or genomic-like nucleic and amino acid sequences. When sequences are very similar, they are considered strains. When they have substantial differences, this indicates species. And ever greater differences cluster genera in a family, as shown in Figure 1. Establishing such demarcation criteria is an important part of describing species. The Code does not govern the naming of virus isolates, strains, variants, types, sub-types or serotypes.

KSN - Vol. 53, No. 1 - pg 5 of issue
KSN - Vol. 53, No. 2 - Figure 2: The similarities in the genes coding for glycoproteins show this relationships among filoviruses
Figure 2: The similarities in the genes coding for glycoproteins show this relationships among filoviruses. This analysis suggests a common evolutionary origin for this family. It also confirms that there are major differences between the four species of ebolaviruses. These viruses are highly fatal when they infect humans. (Redrawn from A. Sanchez, Center for Disease Control and Prevention, Atlanta, USA).

HOW IS A VIRUS SPECIES NAMED?
New species of plants or animals are established when an author publishes a description in a scientific journal. However, names of virus species (and higher virus taxa) have no official status until approved by the ICTV. The ICTV has forms and procedures for submitting taxonomic proposals. A consensus among virologists controls the ever expanding classification of viruses.

There is a priority rule; a virus name once accepted by ICTV cannot be replaced by an another name. Soon an electronic system will be put in place to avoid authors entering non-ICTV approved names on databases. No virus name incorporates a person's name, only proper names of localities can be used.

Taxa names may be formed from letter combinations made from compound terms. One example is Reovirus which is formed from "R" from "Respiratory, "e" from "enteric" and "o" from "orphan."

HOW IS A TAXONOMIC NAME CONSTRUCTED?
Unlike plant and animal names, viral names need not be binomials. Plant viruses often consist of host + symptom + "virus" as in Tobacco mosaic virus. Others may be built from the location where the virus was discovered as in Cote d'Ivoire ebolavirus which is an ebolavirus first isolated in the Ivory Coast. Letters or numbers may be included but may not comprise the whole species epithet in new names, as in Saccharomyces cerevisiae virus L-A.

A species name is italicized and the first word is capitalized. If a proper noun is involved, it is also capitalized as in Murray River encephalitis virus.

WHAT IS A "TYPE SPECIES"?
"A type species is a species whose name is linked to the use of a particular genus name. The genus so typified will always contain the type species." This proposed definition establishes the 'nomenclatural type' for the genus.

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Figure 3
Figure 3: Overview of the life cycle of Equine arteritis virus (EAV). The virus particles are absorbed across the cell membrane (on the left) and uncoated from their capsid. The viral RNA is then available for translation and replication. The genome organization, including replicase cleavage sites (arrowheads) is shown at the top of the figure. The synthesis of more viral RNA, along with the production of membrane proteins, is shown on the right. The assembly of new virus particles, their maturation and release is shown in the center of the figure. (ER, endoplasmic reticulum; PM, plasma membrane; DMV, double membrane vesicle; NC, nucleocapsid). Redrawn from a diagram courtesy of E.J. Snijder.

WHAT IS A "VIRION"?
A virion is a "morphologically and genetically complete virus particle."

WHAT IS A "VIROPLASM"?
Viroplasm is "a modified region within the infected cell in which virus replication occurs...."

WHAT ARE "PSEUDOTYPES"?
Pseudotypes are "enveloped virus particles in which the envelope is derived from one virus and the internal constituents from another."

WHAT ARE "ISOLATES"?
Isolates do not have taxonomic meaning, but simply signify that a virus sample has been identified and this biological and viral entity constitutes a virus isolate.

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WHAT TAXONOMIC LEVELS ARE USED?
Virus clusters are generally built up from the species level. The Linnaean ranks of kingdom, phylum and class are not used. Recognized viral taxa are placed in the following ranks:

(Order)

Family

(Subfamily)

Genus

Species

No other ranks are recognized by the ICTV. All taxa names are capitalized and (in contrast to other codes of nomenclature) printed in italics. Similar to zoological nomenclature, family names end in "-dae." Some families are members of the three currently recognized orders, but many clustering end at the family level. Some species are not yet assigned to genera, and some genera are unassigned to families. Subfamilies are only used when more clusterings are needed at that level.

HOW ARE TAXONOMIC CHANGES MADE?
When virologists want to make a taxonomic change, they must access the ICTV website, called ICTVnet at: www.danforthcenter.org/iltab/ictvnet. Once the correct template is completed, the proposal is posted on the website for public exposure, then circulated to the members of the corresponding Study Group for that virus family, then to the ICTV Executive Committee. After adequate review, successful proposals are submitted for ratification to the full ICTV. Approved proposals are incorporated into the ICTV Taxonomic Reports published every three years, or the Virology Division News section of the Archives of Virology.

A new electronic procedure is being elaborated, called Taxonomic Proposal Management System (TPMS) which will allow a quicker decision process and which will become an electronic reference for all virus databases in the near future.

Figure 4
Figure 4: Phylogenetic analysis of conserved regions of the polymerase genes of retroviruses (Courtesy of Quackenbush, S and Casey, J.), based on an alignment of the aa residues contained within domains 1 through 4 and part of domain 5 (Xiong, Y. and Eickbush, T.H. (1990). EMBO J., 9, 3353-3362) of reverse transcriptase genes of several retroviruses.

WHY IS THE HIGHER VIRUS TAXONOMY NOT CONNECTED?
Biologists are accustomed to seeing phylogenies or "family trees" that branch from an ancient stem, indicating a common ancestor. Efforts are underway to graft all the branches of the "tree of life" that would have originated from a primitive "protocell."

Viruses have very diverse types of genomes (using ss and dsDNA or ss or dsRNA as genetic support), with variable strategies of replication (positive, negative or ambisense and retro-transcribing strategies). In addition viruses use a variety of strategies for their genome transcription and translation. Their genome may be composed of a single nuclei acid molecule or several. During the replication subgenomic size nucleic acids may be produced. All of this suggests viruses almost certainly have many origins and therefore are certainly not derived from a unique "protovirus."

Some viruses undergo recombination and reassortment, producing genomes that may be constituted from several different ancestors. In addition, viruses sometimes are incorporated into the host cell's genome, and host genes may become incorporated into the viral genome. Therefore, viral taxonomy consists of lower ranks that are not connected to each other because there is no common "protovirus" ancestor.

HOW BIG ARE VIRUSES?
Viruses vary in size of their genome between 2kb to 1.2Mb and their virions diameter between 20 nm to 600 nm. The smallest virus, Tobacco necrosis satellite virus, codes for 2 genes, while the largest virus, Acanthamoeba polyphaga mimivirus codes for 1,135 genes. The latter is bigger than the smallest bacteria and codes for many host genes, including a number from host origin.

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Figure 5
Figure 5: Phylogenetic tree showing the relationships of the polymerases of virus families in the "picornavirus-like supercluster", including Picornaviridae, Dicistroviridae, Sequiviridae, Comoviridae, Caliciviridae, Potyviridae, Coronaviridae, Roniviridae, Arteriviridae, the genus Iflavirus and unclassified insect viruses. Redrawn from a diagram courtesy of T.N. Hanzlik.

WHAT ARE ds AND ss FORMS OF DNA AND RNA?
In the charts that group virus families and genera by hosts, these taxa are grouped according to whether the viral genome is DNA or RNA. DNA consists of the nucleotides cytosine, guanine, adenosine, and thymine. RNA also uses the nucleotides cytosine, guanine, and adenosine, but uses uracil instead of thymine.
If the genome is double stranded, it is labeled dsDNA or dsRNA. If it is single stranded, it is ssDNA or ssRNA.

WHAT ARE POSITIVE SENSE AND NEGATIVE SENSE DNA AND RNA?
Positive-sense RNA is "the strand that contains the coding triplets that are translated by ribosomes" and is also called the plus strand or the message strand.

Positive-sense DNA is "the strand that contains the same base sequence as the mRNA. However, mRNAs of some dsDNA viruses hare transcribed from both strands and the transcribed regions may overlap. For such viruses this definition is inappropriate.

Negative sense RNA or DNA is "the strand with base sequence complementary to the positive-sense strand."

HOW MANY DIFFERENT VIRUSES EXIST?
In 2005, the VIIIth Report of the ICTV recognized more than 6,147 isolates belonging to 1,950 virus species, classified in 287 genera, and 76 families and 3 orders. The number of taxa increases exponentially and it is correlated to sequencing. The reorganization of virus taxonomy in a new era of computers and online communication should clear the way for organized exploration of the virus world.

WHAT IS THE ICTV DATABASE?
The ICTV database (ICTVdB) strives to be "a comprehensive and universal database containing virus isolate data." It is to be used to provide researchers with on-line tools to identify viruses from their many traits, and to link to both the taxonomic system and genome sequence databases. At this date, the ICTVdB website can be found at http://phene.cpmc.columbia.edu.

WHAT IS "PHENETICS"?
There are many schools of thought on how to classify organisms. Many give priority to classification based on evolutionary relationships and showing the sequence of changes that have occurred compared to a shared common ancestor.

In contrast, phenetics groups entities based only on their current similarities and was first promoted as numerical taxonomy by Sokal and Sneath a half century ago. Since virus taxonomy uses a "constellation of characteristics," especially viral gene sequences, and does not attempt to locate a common ancestor for all viruses, it is one of the few cases where this methodology is still used.

FURTHER READING
Fauquet, C. M. and Fargette, D. (2005). ICTV and the 3,142 unnamed species. Virology Journal, 2: 64. doi:10.1186/1743-422X-2-64.

Lawrence, J. G., Hatfull, G. F. and Hendrix, R. W. (2002). Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. Journal of Bacteriology, 184: 4891-4905.

van Regenmortel, M. H. V (2003) Viruses are real, virus species are man-made, taxonomic constructions. Archives of Virology, 148: 2483-2490.

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Back cover
Electron micrograph of Acanthamoeba polyphaga mimivirus particle, the largest virus known so far. The bar represents 200 nm. Photo courtesy of D. Raoult, Rickettsia Laboratory, La Timone, Marseille, France.

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