Classification and Taxonomy Or the grouping of viruses into an ordered system that indicates relationships There are multiple ways that you can goupr viruses and none of them all have there advantages and disadvantages Add slide about spliiters and lumpers. Reference site: http://www.ncbi.nlm.nih.gov/ICTVdb/index.htm

Naming viruses Animal viruses Diseases that they cause: small pox, foot and mouth disease, hepatitis Places where virus was first identified Norwalk virus, West Nile virus, Hanta virus 3) Other Organ virus was isolated from: adnoids -Adenovirus Sin Nombre Plant viruses an many insect viruses (two components) Host Disease Tomato bushy stunt virus Cricket paralysis virus

Classification and Taxonomy Classical: morphology Physical and chemical composition Genetic relatedness Modern: Phylogenetic, based on nucleic acid sequence analysis.

Classical criteria for classification of animal viruses Disease symptoms Useful in clinical situations Host organism implies a fixed link between virus and host-Small pox, HBV Physical structure of the virus particle Envelope vs no envelope Helical or isocahedral Example- 1)hepatitis, colds, pneumonia---disimilar viruses casue similar disease states 2) Some viruses cause more than one disease state 90-100% of people in this room are infected with HSV-1 For some of us this infection is asympomatic Others will have reoccuring cold soars as a result of the infection. and Approximately 3 in 100,000 people HSV will develop encephalitis from HSV , which is an infection of the brain. erpes virus common cold sore and e ncephalitits, chicken pox Many viruses that don’t cause disease in humans Problems : This approach focus mainly on human viruses and some live stock- ignores viruses that do not cause disease Why not use the type of cell that a virus infects or disease as a criteria for basic science Unrelated viruses can cause similar disease states HAV-ssRNA nonenveloped HBV - dsDNA HCV- (+) RNA, envoloped Related viruses can very different diseases HCV WNV dengue virus However grouping viruses passed on disease is useful in clinical and epidemiological studies Host Small host range Poio and HCv humans and primates Large host range- WNv mosquitos, birds, humans , horsed, cats, dogs etc, Does not imply any other similarity in terms of disease of genetics Structure tell you nothing of the biology, pathology or molecular biology of the virus Classification methods 1 disease focuses on viruses that infect humans and animals many viruses do not cause disease single virus may cause different disease-chickenpox different viruses cause similar diseases some viruses infect multiple a range of hosts-WNV-insects, birds,horses humans, cat etc, infection of a single host does not imply similarities in genetic makeup Morp when first visualized this method was used helica, iscohedron, filamentous similar structure does not allow you to predict anything about the biology,pathology or molecular biology of the virus. Genome-baltimore Sat,viriods,prions Alls these approaches fail to predict fundamental features of the viruses

Baltimore classification Modern Criteria for classification Based on genome composition and structure allows you to: 1) deduce the basic steps that must take place to produce mRNA 2) simplifies comprehension of the life cycle of virus Baltimore classification The first method of sequencing were developed in 1970 and were extremely inefficient. Still use the balitmore classification but add the perameter of genome structure

Traditional classification generate thousands of distinct entities but based on genomes can be classified into 7 groups

Note-all animal viruses that are helical are enveloped Compare old vs new

Classification and Nomenclature ICTV-International Committee on Taxonomy of Viruses (meets every 4 years). Considerations: Host range (eukaryote or prokaryote, animal, plant etc.) Morphological features (enveloped, shape of capsid) Nature of genome Add current total to emphasize that these number are subject to change

Taxonomy scheme Present totals: Family: 73 Subfamily: 9 Genus: 287 Species: 1950

Family A group of genera with common characteristics. Capitalized, Italicized, and end in -viridae. Examples: Picornaviridae (picornavirus family is also acceptable). Herpesviridae (herpesvirus family). Flaviviridae (flavivirus family)

Origins of family names 1) Symptoms or disease caused by viruses Herpes: produce scaly (snake skin) lesions Pox: infections produce pox lesions Papilloma:infections result in papilla (bumps on skin), e.g. warts Flavi: Latin for yellow 2) Sites of infection Adeno: infections of respiratory tract 3) Physical characteristics of the viruses Picorna: Pico (small) + RNA Toga: wearing a toga Corona: wearing a crown Retro: use retrotransposition Filo: Look fibrous 4) Combination Hepadna: hepatitis + DNA

Subfamilies Groups within some large families. Capitalized, Italicized, end in -virinae. Examples Alphaherpesvirinae Betaherpesvirinae Gammaherpesvirinae.

Genus A group of virus species sharing common characteristics. Capitalized, Italicized, ends in -virus. type member: a single virus designated by the ICTV that serves as a reference for the genus Example from Flaviviridae: Flavivirus-yellow fever virus Pestivirus- Bovine Diarrhea virus 1 Hepacivirus-Hepatitis virus C (HCV) Flavivirus 5’ NTR Structural Non-Structural 3’ NTR C prM 1 E 2 B 3 5 A 4 cap 1) Hepacivirus E1 E2 p7 A B IRES 3) Pestivirus Npro ERNS NS2/3 NS 2) HCV as example of classification based on sequence. Give two examples; go over flavivirus in detail.

Hepacivirus Pestivirus Flavivirus

Species A cluster of strains from a variety of sources or a population of strains from one particular source, all of which have in common a set pattern of stable properties that separates the cluster from other clusters or strains. Not capitalized, unless a geographical location. Not italicized. Examples: poliovirus human immunodeficiency virus West Nile virus Add slide on names- disease, place of isolation- Plants- plant infected and disease.

Taxonomy: two examples Example 1: herpes simplex virus 1 Family: Herpesviridae or herpesvirus family Subfamily: Alphaherpesvirinae; Genus: Simplexvirus; Species: herpes simplex virus 1.

Taxonomy: two examples Example 2: Poliovirus Family: Picornaviridae or picornavirus family; Subfamily: None; Genus: Enterovirus; Species: poliovirus

Further breakdowns not recognized by the ICTV Strain- different lines of isolates of the same virus. Example: Isolated from different geographical locations. Type- different serotype (different antigenic specificity) of the same virus. Example: Influenza type A or B. There may also be “subtypes” within a particular type. Group- sub-category of species, division often based on genomic sequence similarities or origin. Example: HIV group M (Main), N (Neither M or O), or O (Outlier). There may also be “subgroups” (sometimes called clades) within a particular group (subgroups A-J of group M HIV). Varient-Virus whose phenotype differs from original wild type strain but where the genetic basis for the difference is not known. Add or isolated at different times; example 1918 flu. Spend more time on this. Type or serogroups-switch to WNV as a sampe and include the whole description of classification-

Satellites,DI particles,viriods & prions. Special cases Satellites,DI particles,viriods & prions. Satellites and viriods-subviral agents Hbv enhnced pathology in HBV infectins

Satellite virus and nucleic acids Common features : 1) do not encodes enzymes required for replication 2)therefore require coinfection with a conventional (helper) virus 3) Satellite genome is significantly different from the helper virus 4) May affect replication of the helper virus. 5) May increase or decrease severity of disease Require both the host cell and another virus for replciaton Add DI particles to lecture Most common in plants

www-ermm.cbcu.cam.ac.uk/ fig002bbr.gif Satellites viruses Encodes structural proteins which form the viral capsid They rely on the helper virus replicative machinery to replicate their genomes. Examples : adeno associated virus (helper: adenovirus) Aav-used in gene therapy HDv- associated with increase disease state in HVB infections www-ermm.cbcu.cam.ac.uk/ fig002bbr.gif

Satellite nucleic acids encode only nonstructural proteins or no proteins at all. rely upon a helper virus for replication, and caspid formation. often found in plants.

DI Particles Defective interfering particle: A virus that lacks part of its genome and interferes with the replication of a standard virus. Require helper virus Derived from helper virus: They tend to be deletion mutants that have lost their ability to encode proteins, but retain their ability to be replicated by the helper virus replicative machinery. (defective) Interfere with helper virus replication by their ability to out compete for helper virus resources.

Viroids: Novel agent of disease in plants Single circular ssRNA molecule with no protein component 70% base-paired Disease from RNA interfering with essential host cell mechanisms www.nature.com emu.arsusda.gov/ typesof/images/viroid.jpg

Prions Agents of disease characterized by slow progressive neurological degeneration Aberrant form of normal cellular proteins that induce changes in the shape of the normal homologs