Virus phylum

The names of groups of viruses belonging to taxa ranked higher than species, such as all members of a family, should be derived from the taxon name e. The ICTV Virus Metadata Resource VMR is a developing resource in which virus names, virus name abbreviations, exemplar isolates, and GenBank accession numbers can be located in association with the taxa to which particular viruses are currently assigned.

Several steps are currently under discussion that, potentially, could bring virus taxonomy in harmony with other biological taxonomies. The acceptance of Negarnaviricota based on the analysis depicted in Fig. In addition, the viruses of several taxa, such as animal viruses of Herpesvirales and the prokaryotic viruses of Caudovirales , have long been considered as related and therefore should be joined at higher ranks.

Consequently, in , Koonin et al. The establishment of the realms was proposed to be justified based on the discovery of specific viral hallmark genes that can be used to evolutionary connect all their constituent viruses: 1 RdRps and RNA-directed DNA polymerases RdDps for most RNA viruses Riboviria ; 2 replication initiator proteins Reps of the His-hydrophobic-His HUH superfamily for all single-stranded DNA viruses; 3 vertical jelly-roll capsid proteins for many double-stranded DNA viruses; and 4 HKfold capsid proteins for viruses classified in Caudovirales and Herpesvirales.

If accepted by the ICTV, virus classification would finally begin to resemble the classification schemes of cellular organisms. Finally, procedural improvements might ensure improved communication of the ICTV with the virology community and thereby increased efficiency of the ICTV.

Such improvements may include automatic classification algorithms, fully online TaxoProp submissions and evaluation systems, harmonization of classification criteria across taxa, and faster ratification cycles.

The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services or of the institution and company affiliated with the author.

National Center for Biotechnology Information , U. Encyclopedia of Virology. Published online Mar 1. Jens H. Guest Editor s : Dennis H. Bamford and Mark Zuckerman. Author information Copyright and License information Disclaimer. Copyright notice. Elsevier hereby grants permission to make all its COVIDrelated research that is available on the COVID resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source.

Abstract Virus taxonomy is the classification of viruses into categories called taxa and the development and implementation of a standardized nomenclature for taxa. Glossary Classification The rational process of assigning viruses to taxa. Inclusion principle Viruses assigned to a lower taxon based on certain virus characteristics must also have the characteristics needed for classification into a higher-ranked taxon that includes the lower taxon. Monophyletic Belonging to a group of viruses that consists of all the descendants from a common ancestor.

Nomenclature The often controversial assignment of names to taxa. Polyphyletic Not being connected to a common ancestor. Polythetic Sharing many, but not all characteristics of a common core set of characteristics.

Species Currently the lowest-ranked taxon in virus taxonomy. Taxon A man-made category for viruses that share certain characteristics. Taxonomy Virus classification into taxa and taxon nomenclature.

Virions Particles produced by some, but not all viruses, during the viral lifecycle for transfer of the viral genome from one host cell to another. History of Virus Taxonomy Early Taxonomic Developments — Virus taxonomy is a virology subspecialty that addresses the grouping classification of viruses physical entities into categories concepts called taxa and the development and implementation of a standardized system of naming nomenclature for taxa.

Baltimore Classification In , David Baltimore published a working classification of viruses that is still used today in parallel with official virus taxonomy. BCs were established based on the type of nucleic acid incorporated into virions, and thereby on the type of virus reproduction: 1.

Current Virus Taxonomy —Present Influenced by the publication of the LHT system, the virology community clearly felt an urgent need for an official virus taxonomy. Open in a separate window. Taxonomic Process Contrary to common perception, the ICTV does not impose taxa on the virology community but instead evaluates, votes on, and administers submitted taxonomic proposals TaxoProps originating from the virology community.

Submitted TaxoProps undergo several steps of scrutiny: 1. Virus Classification Virus classification is the gathering of viruses into progressively more inclusive groups lower taxa included in higher-ranked taxa based on common genomic, phylogenetic, and phenotypic properties that, ideally, are proof of evolutionary relationships or descendance. Differentiating Taxa and Viruses In virus taxonomy, viruses and taxa need to be strictly differentiated.

Nomenclature Virus Taxa In biological taxonomies, nomenclature is the process of assigning specific, ideally unique, names to organisms e. Virus taxon nomenclature is regulated by the rules of the ICVCN, which stipulate, for instance, that 1. Table 2 Rank-specific suffixes for virus taxon names.

Table 3 Species names in non-virologic taxonomies. Thale cress Mycological Pleurotus ostreatus Jacq. Table 4 Non-exhaustive list of currently used species naming formats in virus taxonomy. Future Developments Several steps are currently under discussion that, potentially, could bring virus taxonomy in harmony with other biological taxonomies.

Acknowledgement The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services or of the institution and company affiliated with the author.

Further Reading Abudurexiti A. Taxonomy of the order Bunyavirales : Update Archives of Virology. Taxonomy of the order Mononegavirales : Update Expression of animal virus genomes. Bacteriological Reviews. Nomina ad infinitum. Chronica Botanica. Over een Contagium vivum fluidum als oorzaak van de Vlekziekte der Tabaksbladen. The nomenclature of plant viruses. Bunyavirus taxonomy: Limitations and misconceptions associated with the current ICTV criteria used for species demarcation.

The morphology and physiology of bacteriophages as revealed by the electron microscope. Journal of the Royal Microscopical Society. Classification of elongated plant viruses on the basis of particle morphology.

Strengthening the interaction of the virology community with the international committee on taxonomy of viruses ICTV by linking virus names and their abbreviations to virus species. Systematic Biology. Taxonomy: Get it right or leave it alone. A chemical basis for the classification of animal viruses. Improved clarity of meaning from the use of both formal species names and common vernacular virus names in virological literature.

Virus taxonomy. Classification and nomenclature of viruses. Second report of the International Committee on Taxonomy of Viruses. Springer-Verlag; Archives of virology supplement. Classification and Nomenclature of Viruses.

Fifth report of the International Committee on Taxonomy of Viruses. Increasing the number of available ranks in virus taxonomy from five to ten and adopting the Baltimore classes as taxa at the basal rank. Contributions to characterization and classification of animal viruses. Experimental Biology and Medicine. Order virales — The filterable viruses. In: Breed R. Symmetry in virus architecture. International Association for Plant Taxonomy. International Commission on Zoological Nomenclature.

In the extracellular environment, the virus will be exposed to enzymes that could break down or degrade nucleic acid.

Physical stresses, such as the flow of air or liquid, could also shear the nucleic acid strands into pieces. In addition, viral genomes are susceptible to damage by ultraviolet radiation or radioactivity, much in the same way that our DNA is. If the nucleic acid genome of the virus is damaged, then it will be unable to produce progeny virions. This repeating structure forms a strong but slightly flexible capsid.

Combined with its small size, the capsid is physically very difficult to break open and sufficiently protects the nucleic acid inside of it. Together, the nucleic acid and the capsid form the nucleocapsid of the virion Fig. Viral capsid proteins protect the fragile genome, composed of nucleic acid, from the harsh environment. The capsid and nucleic acid together are known as the nucleocapsid. Remember that the genomes of most viruses are very small.

Genes encode the instructions to make proteins, so small genomes cannot encode many proteins. It is for this reason that the capsid of the virion is composed of one or only a few proteins that repeat over and over again to form the structure.

The nucleic acid of the virus would be physically too large to fit inside the capsid if it were composed of more than just a few proteins. In the same way that a roll of magnets will spontaneously assemble together, capsid proteins also exhibit self-assembly. The first to show this were H.

Fraenkel-Conrat and Robley Williams in They separated the RNA genome from the protein subunits of tobacco mosaic virus, and when they put them back together in a test tube, infectious virions formed automatically. This indicated that no additional information is necessary to assemble a virus: the physical components will assemble spontaneously, primarily held together by electrostatic and hydrophobic forces.

Most viruses also have an envelope surrounding the capsid. Virus capsids are held together by some of the same bonds that are found in living organisms. Rarely are covalent bonds found in capsids; these are the strongest of bonds that are formed when atoms share electrons with each other.

Hydrogen bonds are also weak electrostatic forces that occur between slightly charged atoms, usually between hydrogen slightly positively charged and another atom that is partially negatively charged, such as oxygen. Van der Waals forces are weak interactions that occur when an atom becomes slightly charged due to random asymmetry of its electrons. The properties of water also contribute to virus assembly and attachment to cells.

Water is a polar molecule, meaning that the molecule has two distinct ends, much like a battery or magnet has a positive and a negative end.

Molecules that do not have distinct ends are termed nonpolar. Other polar molecules are attracted to water, since water is polar too. This explains the phenomenon of oil nonpolar not mixing with water polar. These viruses often have proteins, called matrix proteins , that function to connect the envelope to the capsid inside. A virus that lacks an envelope is known as a nonenveloped or naked virus Fig. Each virus also possesses a virus attachment protein embedded in its outer-most layer.

This will be found in the capsid, in the case of a naked virus, or the envelope, in the case of an enveloped virus. The virus attachment protein is the viral protein that facilitates the docking of the virus to the plasma membrane of the host cell, the first step in gaining entry into a cell. The capsid of an enveloped virion is wrapped with a lipid membrane derived from the cell. Virus attachment proteins located in the capsid or envelope facilitate binding of the virus to its host cell. Each virus possesses a protein capsid to protect its nucleic acid genome from the harsh environment.

Virus capsids predominantly come in two shapes: helical and icosahedral. The helix plural: helices is a spiral shape that curves cylindrically around an axis.

It is also a common biological structure: many proteins have sections that have a helical shape, and DNA is a double-helix of nucleotides. In the case of a helical virus, the viral nucleic acid coils into a helical shape and the capsid proteins wind around the inside or outside of the nucleic acid, forming a long tube or rod-like structure Fig. The nucleic acid and capsid constitute the nucleocapsid. In fact, the protein that winds around the nucleic acid is often called the nucleocapsid protein.

Once in the cell, the helical nucleocapsid uncoils and the nucleic acid becomes accessible. A Viral capsid proteins wind around the nucleic acid, forming a helical nucleocapsid. B Helical structure of tobacco mosaic virus. Graph , 12, —44 using a 2xea PDB assembly J. There are several perceived advantages to forming a helical capsid. First, only one type of capsid protein is required. This protein subunit is repeated over and over again to form the capsid. This structure is simple and requires less free energy to assemble than a capsid composed of multiple proteins.

In addition, having only one nucleocapsid protein means that only one gene is required instead of several, thereby reducing the length of nucleic acid required. Because the helical structure can continue indefinitely, there are also no constraints on how much nucleic acid can be packaged into the virion: the capsid length will be the size of the coiled nucleic acid.

Helical viruses can be enveloped or naked. The first virus described, tobacco mosaic virus, is a naked helical virus. In fact, most plant viruses are helical, and it is very uncommon that a helical plant virus is enveloped. In contrast, all helical animal viruses are enveloped. These include well-known viruses such as influenza virus, measles virus, mumps virus, rabies virus, and Ebola virus Fig. A Vesicular stomatitis virus forms bullet-shaped helical nucleocapsids. Fred A. B Tobacco mosaic virus forms long helical tubes.

C The helical Ebola virus forms long threads that can extend over nm in length. Of the two major capsid structures, the icosahedron is by far more prevalent than the helical architecture.

In comparison to a helical virus where the capsid proteins wind around the nucleic acid, the genomes of icosahedral viruses are packaged completely within an icosahedral capsid that acts as a protein shell.

Initially these viruses were thought to be spherical, but advances in electron microscopy and X-ray crystallography revealed these were actually icosahedral in structure. An icosahedron is a geometric shape with 20 sides or faces , each composed of an equilateral triangle. An icosahedron has what is referred to as 2—3—5 symmetry , which is used to describe the possible ways that an icosahedron can rotate around an axis.

If you hold an icosahedral die in your hand, you will notice there are different ways of rotating it Fig. A helix is mathematically defined by two parameters, the amplitude and the pitch, that are also applied to helical capsid structures. The amplitude is simply the diameter of the helix and tells us the width of the capsid.

The pitch is the height or distance of one complete turn of the helix. In the same way that we can determine the height of a one-story staircase by adding up the height of the stairs, we can figure out the pitch of the helix by determining the rise , or distance gained by each capsid subunit. A staircase with 20 stairs that are each 6 inches tall results in a staircase of 10 feet in height; a virus with This is the architecture of tobacco mosaic virus. Your pencil would be right in the middle of a triangle facing up and a triangle facing down.

If you rotate the icosahedron clockwise, you will find that in degrees you encounter the same arrangement symmetry : a triangle facing up and a triangle facing down. Continuing to rotate the icosahedron brings you back to where you began. This is known as the twofold axis of symmetry, because as you rotate the shape along this axis your pencil , you encounter your starting structure twice in one revolution: once when you begin, and again when rotated degrees.

On the other hand, if you put your pencil axis directly through the center one of the small triangle faces of the icosahedron, you will encounter the initial view two additional times as you rotate the shape, for a total of three times. This is the threefold axis. Similarly, if your pencil axis goes through a vertex or tip of the icosahedron, you will find symmetry five times in one rotation, forming the fivefold axis. It is for this reason that an icosahedron is known to have 2—3—5 symmetry, because it has twofold, threefold, and fivefold axes of symmetry.

This terminology is useful when dealing with an icosahedral virus because it can be used to indicate specific locations on the virus or where the virion has interactions with the cell surface.

For instance, if a virus interacts with a cell surface receptor at the threefold axis, then you know this interaction occurs at one of the faces of the icosahedron. A protein protruding from the capsid at the fivefold axis will be found at one of the vertices tips of the icosahedron. All of the illustrations of viruses in Fig. How many twofold axes of symmetry are found in one icosahedron?

How about the number of threefold or fivefold axes? How many faces, edges, and vertices are found in an icosahedron? A Icosahedron faces fuchsia triangles , edges red rectangles , and vertices violet pentagons are indicated on the white icosahedron. B The twofold axis of symmetry occurs when the axis is placed through the center of an edge.

The threefold axis occurs when the axis is placed in the center of a face C , and the fivefold axis passes through a vertex of the icosahedron D. Viral proteins form each face small triangle of the icosahedral capsid. 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. 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.

The presence of West Nile virus was confirmed in mosquitoes and dead crows. AMA Style Guide, p. 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…. It is permissible to use an acronym for a virus e. However, do not abbreviate a species including the species West Nile virus. 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. For human coronavirus , use the abbreviation hCoV. For numbered echoviruses e. Use a capital H for human virus abbreviations e. For numbered enteroviruses, use the following format: EV 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 virus.

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 or later.