1. Classification and Taxonomy Reference site: http://www.ncbi.nlm.nih.gov/ICTVdb/index.htm

2. 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

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

4. 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 Alls these approaches fail to predict fundamental features of the viruses

5. 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

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

8. 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

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

10. 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)

11. 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

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

13. Structural Non-Structural 5’ NTR 3’ NTR 4 5 C E1 E2 p7 2 3 A B A B IRES Flavivirus 1) Structural Non-Structural 5’ NTR 3’ NTR 2 4 C prM E 1 A B 3 A B 5 cap NS Structural Non-Structural 5’ NTR 3’ NTR 4 5 Hepacivirus Npro C ERNS E1 E2 p7 NS2/3 A B A B 3) IRES Pestivirus 2) 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)

14. Hepacivirus Pestivirus Flavivirus

15. 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

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

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

18. 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.

19. Special cases Satellites,DI particles,viriods & prions. Satellites and viriods-subviral agents

20. 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

21. 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) www-ermm.cbcu.cam.ac.uk/ fig002bbr.gif

22. 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.

23. 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.

24. 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

25. 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