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UMD BSCI 437 - Classification and Taxonomy

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Slide 1Slide 2Slide 3Slide 4Slide 5Slide 6Slide 7Classification and NomenclatureSlide 9FamilyOrigins of family namesSubfamiliesGenusSlide 14SpeciesTaxonomy: two examplesSlide 17Further breakdowns not recognized by the ICTVSlide 19Slide 20Satellites virusesSatellite nucleic acidsSlide 23Slide 24Slide 25Classification and Taxonomy Reference site: http://www.ncbi.nlm.nih.gov/ICTVdb/index.htmNaming virusesAnimal viruses1)Diseases that they cause: small pox, foot and mouth disease, hepatitis2)Places where virus was first identifiedNorwalk virus, West Nile virus, Hanta virus3) OtherOrgan virus was isolated from: adnoids -AdenovirusSin NombrePlant viruses an many insect viruses (two components)1) Host2) DiseaseTomato bushy stunt virusCricket paralysis virus3Classification and TaxonomyClassical: morphologyPhysical and chemical compositionGenetic relatednessModern: Phylogenetic, based on nucleic acid sequence analysis.1. Disease symptomsUseful in clinical situations 2. Host organismimplies a fixed link between virus and host-Small pox, HBV3. Physical structure of the virus particleEnvelope vs no envelopeHelical or isocahedralAlls these approaches fail to predict fundamental features of the viruses Classical criteria for classification of animal virusesModern Criteria for classificationBased on genome composition and structureallows you to: 1) deduce the basic steps that must take place to produce mRNA2) simplifies comprehension of the life cycle of virus Baltimore classificationTraditional classification generate thousands of distinct entities but based on genomes can be classified into 7 groupsClassification and NomenclatureICTV-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 genomePresent totals: Family: 73 Subfamily: 9Genus: 287 Species: 1950Taxonomy schemeFamily•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 names1) Symptoms or disease caused by virusesHerpes: produce scaly (snake skin) lesionsPox: infections produce pox lesions Papilloma:infections result in papilla (bumps on skin), e.g. wartsFlavi: Latin for yellow2) Sites of infectionAdeno: infections of respiratory tract3) Physical characteristics of the virusesPicorna: Pico (small) + RNAToga: wearing a togaCorona: wearing a crownRetro: use retrotranspositionFilo: Look fibrous4) Combination Hepadna: hepatitis + DNASubfamilies•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 genusExample from Flaviviridae: •Flavivirus-yellow fever virus•Pestivirus- Bovine Diarrhea virus 1 •Hepacivirus-Hepatitis virus C (HCV)Flavivirus5’ NTRStructural Non-Structural3’ NTRC prM 1E2B 3 B 5AA4cap1)HepacivirusAC E1 E2 2p7 3 B A BIRESStructural Non-Structural3’ NTR5’ NTR4 53)PestivirusANproC ERNSp7 NS2/3 B A BIRESStructural Non-Structural3’ NTR5’ NTR4 5E1 E2NS2)HepacivirusPestivirusFlavivirusSpecies•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 virusTaxonomy: two examplesExample 1: herpes simplex virus 1Family: Herpesviridae or herpesvirus familySubfamily: Alphaherpesvirinae; Genus: Simplexvirus; »Species: herpes simplex virus 1.Taxonomy: two examplesExample 2: PoliovirusFamily: Picornaviridae or picornavirus family; Subfamily: None; Genus: Enterovirus;»Species: poliovirusFurther 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.Special casesSatellites,DI particles,viriods & prions.Satellites and viriods-subviral agentsCommon features : 1) do not encodes enzymes required for replication2)therefore require coinfection with a conventional (helper) virus3) Satellite genome is significantly different from the helper virus4) May affect replication of the helper virus. 5) May increase or decrease severity of diseaseSatellite virus and nucleic acidsSatellites viruses Encodes structural proteins which form the viral capsidThey rely on the helper virus replicative machinery to replicate their genomes. Examples : adeno associated virus (helper: adenovirus)www-ermm.cbcu.cam.ac.uk/ fig002bbr.gifSatellite 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 ParticlesDefective interfering particle: A virus that lacks part of its genome and interferes with the replication of a standard virus.1. Require helper virus2. 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) 3. Interfere with helper virus replication by their ability to out compete for helper virus resources.Viroids: Novel agent of disease in plantsemu.arsusda.gov/ typesof/images/viroid.jpgwww.nature.comSingle circular ssRNA molecule with no protein component70% base-pairedDisease from RNA


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