VIRAL TAXONOMY

By Bikram Kumar Das

INTRODUCTION• Virus classification is the process of naming viruses and placing them into

a taxonomic system. • Viruses are mainly classified by phenotypic characteristics, such as

morphology, nucleic acid type, mode of replication, host organisms, and the type of disease they cause.

• Currently there are two main schemes used for the classification of viruses:

1. The International Committee on Taxonomy of Viruses (ICTV) system and 2. Baltimore classification system,

which places viruses into one of seven groups. Accompanying this broad method of classification are specific naming conventions and further classification guidelines set out by the ICTV.

International Committee on Taxonomy of Viruses (ICTV)

• The ICTV (originally the International Committee on the Nomenclature of Viruses, ICNV) was established in 1966.

• The only body charged by the International Union of Microbiological Societies with the task of developing, refining, and maintaining a universal virus taxonomy.

• this system of nomenclature differs from other taxonomic codes on several points.

• A minor point is that names of orders and families are italicized, unlike in the International Code of Nomenclature for algae, fungi, and plants and International Code of Zoological Nomenclature.

International Committee on Taxonomy of Viruses (ICTV)

• The ICTV had adopted the principle that A VIRUS SPECIES IS A POLYTHETIC* CLASS OF VIRUSES THAT CONSTITUTES A REPLICATING LINEAGE AND OCCUPIES A PARTICULAR ECOLOGICAL NICHE.

• The formal definition of a polythetic class is “a class whose members always have several properties in common although no single common attribute is present in all of its members”

• The qualification of a replicating lineage implies that members of a species experience evolution over time with consequent variation, but that members share a common ancestor.

• The qualification of occupation of an ecologic niche acknowledges that the biology of a virus, including such properties as host range, pathogenesis, transmission, and habitat, are fundamental components of the characterization of a virus.

International Committee on Taxonomy of Viruses (ICTV)

• In the most recent report of the ICTV, study group members have listed the criteria that identify each species, then listed species according to the criteria.

• In addition, some viruses are listed as tentative species because their taxonomic status cannot currently be unambiguously determined.

• Last, a type species, the species used to define the taxon, has been identified for each genus.

International Committee on Taxonomy of Viruses (ICTV)

The official objectives of the ICTV are:• To develop an internationally agreed taxonomy for viruses• To develop internationally agreed names for virus taxa,

including species and sub-viral agents• To communicate taxonomic decisions to all users of virus

names, in particular the international community of virologists, by publications and via the Internet

• To maintain an index of virus names• To maintain an ICTV database on the Internet, that records

the data that characterize each named viral taxon, together with the common names of each taxon in all major languages

International Committee on Taxonomy of Viruses (ICTV)

The ICTV's essential principles of virus nomenclature are:• Stability• To avoid or reject the use of names which

might cause error or confusion• To avoid the unnecessary creation of names

International Committee on Taxonomy of Viruses (ICTV)

• In July 2013, the ICTV definition of species changed to state: "A species is a monophyletic group of viruses whose properties can be distinguished from those of other species by multiple criteria.“

Viral classification starts at the level of order and continues as follows, with the taxon suffixes given in italics:• Order (-virales)• Family (-viridae)• Subfamily (-virinae)• Genus (-virus)• SpeciesSpecies names generally take the form of [Disease] virus.

**Of, pertaining to, or affecting a single phylum (or other taxon) of organisms.

International Committee on Taxonomy of Viruses (ICTV)

• The establishment of an order is based on the inference that the virus families it contains have most likely evolved from a common ancestor.

• The majority of virus families remain unplaced. • Currently (2012), 7 orders, 96 families, 22 subfamilies, 420

genera, and 2,618 species (2,619 acc. to ICTV master species list) of viruses have been defined by the ICTV.

• The orders are the Caudovirales, Herpesvirales, Ligamenvirales, Mononegavirales, Nidovirales, Picornavirales, and Tymovirales.

• These orders span viruses with varying host ranges. The Ligamenvirales, infecting archaea, are the most recent addition to the classification system.

International Committee on Taxonomy of Viruses (ICTV)

As an example, the full formal written description of human respiratory syncytial virus is • Order: Mononegavirales• Family: Paramyxoviridae• Subfamily: Pneumovirinae• Genus: Pneumovirus• Species: Human respiratory syncytial virus.

International Committee on Taxonomy of Viruses (ICTV)

• Caudovirales are tailed dsDNA (group I) bacteriophages.• Herpesvirales contain large eukaryotic dsDNA viruses.• Ligamenvirales contains linear, dsDNA (group I) archaean viruses.• Mononegavirales include nonsegmented (-) strand ssRNA (Group V)

plant and animal viruses.• Nidovirales are composed of (+) strand ssRNA (Group IV) viruses with

vertebrate hosts.• Picornavirales contains small (+) strand ssRNA viruses that infect a

variety of plant, insect and animal hosts.• Tymovirales contain monopartite (+) ssRNA viruses that infect plants.• Other variations occur between the orders: Nidovirales, for example, are

isolated for their differentiation in expressing structural and nonstructural proteins separately.

Structure-based virus classification

• It has been suggested that similarity in virion assembly and structure observed for certain viral groups infecting hosts from different domains of life (e.g., bacterial tectiviruses and eukaryotic adenoviruses or prokaryotic Caudovirales and eukaryotic herpesviruses) reflects an evolutionary relationship between these viruses.

• Therefore, structural relationship between viruses has been suggested to be used as a basis for defining higher-level taxa - structure-based viral lineages - that could complement the existing ICTV classification scheme

BALTIMORE CLASSIFICATION

Baltimore classification (first defined in 1971) is a classification system that places viruses into one of seven groups depending on• a combination of their nucleic acid (DNA or RNA), • strandedness (single-stranded or double-stranded),• Sense (+ or -), and • method of replication.Named after David Baltimore, a Nobel Prize-winning biologist, these groups are designated by Roman numerals

BALTIMORE CLASSIFICATION

BALTIMORE CLASSIFICATION

• I: dsDNA viruses (e.g. Adenoviruses, Herpesviruses, Poxviruses)

• II: ssDNA viruses (+ strand or "sense") DNA (e.g. Parvoviruses)• III: dsRNA viruses (e.g. Reoviruses)• IV: (+)ssRNA viruses (+ strand or sense) RNA (e.g.

Picornaviruses, Togaviruses)• V: (−)ssRNA viruses (− strand or antisense) RNA (e.g.

Orthomyxoviruses, Rhabdoviruses)• VI: ssRNA-RT viruses (+ strand or sense) RNA with DNA

intermediate in life-cycle (e.g. Retroviruses)• VII: dsDNA-RT viruses (e.g. Hepadnaviruses)

BALTIMORE CLASSIFICATION

HOLMES CLASSIFICATION

Holmes (1948) used Carolus Linnaeus's system of binomial nomenclature to classify viruses into 3 groups under one order, Virales. They are placed as follows:• Group I: Phaginae (attacks bacteria)• Group II: Phytophaginae (attacks plants)• Group III: Zoophaginae (attacks animals)

LHT System of Virus Classification

• The LHT System of Virus Classification is based on chemical and physical characters like nucleic acid (DNA or RNA), Symmetry (Helical or Icosahedral or Complex), presence of envelope, diameter of capsid, number of capsomers.

• This classification was approved by the Provisional Committee on Nomenclature of Virus (PNVC) of the International Association of Microbiological Societies (1962)