Classification and Taxonomy

Reference site: http://www.ncbi.nlm.nih.gov/ICTVdb/index.htm

Naming virusesAnimal viruses1)Diseases that they cause:

small pox, foot and mouth disease, hepatitis

2)Places where virus was first identifiedNorwalk virus, West Nile virus, Hanta virus

3) OtherOrgan virus was isolated from: adnoids -

AdenovirusSin Nombre

Plant viruses an many insect viruses (two components)

1) Host2) Disease

Tomato bushy stunt virusCricket paralysis virus

3

Classification and Taxonomy

Classical: morphology

Physical and chemical composition

Genetic relatedness

Modern: 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, HBV

3. Physical structure of the virus particleEnvelope vs no envelopeHelical or isocahedral

Alls these approaches fail to predict fundamental features of the viruses

Classical criteria for classification of animal

viruses

Modern Criteria for classification

Based on genome composition and structure

allows you to: 1) deduce the basic steps that must take place to produce mRNA2) simplifies comprehension of the life cycle of virus

Baltimore classification

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

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

Present totals: Family: 73

Subfamily: 9Genus: 287

Species: 1950

Taxonomy scheme

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 names1) Symptoms or disease caused by viruses

Herpes: produce scaly (snake skin) lesionsPox: infections produce pox lesions Papilloma:infections result in papilla (bumps on skin), e.g. wartsFlavi: Latin for yellow

2) Sites of infectionAdeno: infections of respiratory tract

3) Physical characteristics of the virusesPicorna: Pico (small) + RNAToga: wearing a toga

Corona: wearing a crownRetro: use retrotranspositionFilo: 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)

Flavivirus5’ NTR Structural Non-Structural 3’ NTR

C prM 1E

2

B 3 B 5AA

4

cap

1)

Hepacivirus

AC E1 E2 2p7 3 B A BIRES

Structural Non-Structural 3’ NTR5’ NTR4 5

3)

Pestivirus

ANpro C ERNS p7 NS2/3 B A BIRES

Structural Non-Structural 3’ NTR5’ NTR4 5

E1 E2

NS

2)

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

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.

Special casesSatellites,DI particles,viriods &

prions.

Satellites and viriods-subviral agents

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

Satellite virus and nucleic acids

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

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 ParticlesDefective interfering particle: A virus that lacks part of its genome and interferes with the replication of a standard virus.

1. Require helper virus

2. 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 plants

emu.arsusda.gov/ typesof/images/viroid.jpg

www.nature.com

Single circular ssRNA molecule with no protein component

70% base-paired

Disease from RNA interfering with essential host cell mechanisms

PrionsAgents of disease characterized by slow progressive

neurological degeneration

Aberrant form of normal cellular proteins that induce changes in the shape of the normal homologs