Virology 1.3 Classification of viruses

Virus names are so cute Why not stop there? Why bother to classify at all? Some actual virus names Cricket paralysis virus Molluscum contagiosum Bean golden mosaic virus Barley yellow dwarf virus

1) Classification appeals to sense of logic or beauty There is an intrinsic simplicity of nature, and the ultimate contribution of science resides in the discovery of unifying and simplifying generalizations, rather than in the description of isolated situations—in the visualization of simple overall patterns rather than in the analysis of patchworks. “Salvador Luria”, General Virology, Wiley:New York 1953

2. Understanding Virus Evolution Charles DarwinTree of Life Viruses infect members of all three kingdoms and their evolution is intimately tied to the evolution of their hosts.

3. Utility and Practicality- a. Historical method…. Places where viruses were found or people who discovered them: e.g.: Epstein-Barr virus, Rous sarcoma virus, Rift Valley fever virus

Utility and practicality b. social impact  Viruses cause diseases  Suffering, economic damage, etc.  Classification may aid in understanding

The pragmatic approach tends to win out A time-honored method is to base names on disease properties…… Diseases viruses are associated with, e.g.: Poxvirus, Hepatitis virus, HIV, Measles virus. Cytopathology occuring during infection, e.g.: Respiratory Syncytial virus, Cytomegalovirus. Site of infection, e.g.: Adenovirus, Rhinovirus, Enterovirus

“ Hepatitis” Viruses illustrate some of the problems with this pragmatic approach  Hepatitis A Virus- a picornavirus  Hepatitis B Virus- a hepatovirus  Hepatitis C Virus- a flavivirus (Partial listing only! There are more viruses that cause hepatitis.) Similar diseases but different viruses Similar diseases but different viruses

Related Herpesviruses Cause Different Diseases  HSVHerpes Simplex VirusCold sores (type 1), Genital lesions (type 2)  VZVVaricella Zoster VirusChicken pox  CMVCytomegalovirusOrgan failure  EBVEpstein-Barr VirusMononucleosis, Burkitt’s lymphoma, Nasopharyngeal carcinoma and HHV-6, HHV-7, HHV-8….. Similar viruses-different diseases Therefore if these viruses were classified based on their symptoms their relationships would be missed.

Different viruses can cause (nearly) the same symptoms. e.g., the hepatitis viruses However, distinct members of the same group can cause different symptoms. e.g., the herpes viruses “Simple” classification systems did not work well Virologists had to devise more orderly systems

“informal” systems proliferated “national” naming systems Host-based naming systems Strong personalities were involved A profusion of data The problems with virus nomenclature and classification led to chaos by the 1960s

Federation of European Microbiology Societies (FEMS) Federation of European Microbiology Societies (FEMS) Virology Division International Committee International Committee on the Nomenclature of Viruses (1966) Renamed in 1971 International Committee on the Taxonomy of Viruses (ICTV)

The ICTV is charged to devise an internationally-acceptable system for naming and classification of viruses and to communicate that system. The ICTV seeks input from a wide range of virologists and meets every three years to revise the taxa. Study groups practice the opinionated use of data. Seven orders, 104 families, 23 subfamilies, >350 genera, >2,500 species

Characteristics of the ICTV system  “Non-systematic”  Polythetic  Hierarchical w/species as lowest level  Universal  Limited (very conservative)  Uses “order of presentation” not a universal tree  Latinized, but no binomials  Preserves common or trivial names at species level

ICTV Definition The virus species is the fundamental unit. A virus species (or quasi-species) is defined as a polythetic class of viruses that constitutes a replicating lineage and occupies a particular ecological niche.

Polythetic class IndividualProperties 1ABCD 2ABCE 3ABDE 4ACDE 5BCDE All Viruses 1-5 are in the same virus species

ICTV Hierarchical nomenclature Taxonomic Level ICTV Suffix Order-virales Family-viridae Subfamily-virinae Genus-virus Species none (trivial name preserved)

Example 1 Taxonomic Level ICTV Name Order(none-conservative!) FamilyPoxviridae SubfamilyChordopoxvirinae GenusOrthopoxvirus Species Vaccinia virus

Example 2 Taxonomic Level ICTV Name OrderMononegavirales FamilyRhabdoviridae Subfamily GenusNucleorhabdovirus Species Potato yellow dwarf virus

Order of Presentation XXXXXXXXXXXXXXXXXXXXX

Virus Classification is Based Primarily on Properties of the Virus Particle (see virosphere) Genetic material Is Most Important!!! (See Baltimore Scheme) form of nucleic acid (RNA, DNA, ss or ds) genetic organization sequence homology Morphology: by electron microscopy Serology: antigenic cross-reactivity Biological Properties have a low priority

Baltimore classification of viral genomes  Based on gene expression  Relationship to mRNA is central feature- defined by properties of genome nucleic acid  All viruses divided into classes based on genome structure  Molecular property

Classes in the Baltimore Scheme Class Virion nucleic acid Example 1dsDNAAdenoviridae 2a+ssDNAMicroviridae 2b-ssDNAParvoviridae 3dsRNAReoviridae 4+ssRNAPicornaviridae 5-ssRNAFiloviridae 6 +ssRNA (RT) Retroviridae 7 dsDNA (RT) Caulimoviridae

Diagram of Baltimore scheme

Comparisons of Vertebrate and Plant Viruses Vertebrate Infecting Viruses Plant Infecting Viruses

Hi Dr. Luciano, I'm getting some terrific questions from your virology class about TWiV episodes. Thanks so much for having them do that as an assignment - I think it's a great way for the students to get someone else's perspective. We'll likely read many of these s over the next several shows, starting this Friday - first names only of course. Would you prefer that I respond by as well? ______________________________ Vincent Racaniello, Ph.D. | Higgins Professor Department of Microbiology & Immunology Columbia University, New York virology.ws | twiv.tv | microbeworld.org/twip "Tanto sa ciascuno quanto opera"