Classification and Taxonomy

Naming virusesAnimal viruses 1Diseases that they cause: small pox, foot and mouth disease, hepatitis 2Places where virus was first identified Norwalk virus, West Nile virus, Hanta virus

Classification and Taxonomy

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

Naming viruses

Animal viruses

1)Diseases that they cause:

small pox, foot and mouth disease, hepatitis

2)Places where virus was first identified

Norwalk virus, West Nile virus, Hanta virus

1 Disease symptoms

Useful in clinical situations

2 Host organism

implies a fixed link between virus and host -Small pox, HBV

3 Physical structure of the virus particle

Envelope vs no envelope Helical 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 mRNA 2) 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

• A group of genera with common characteristics

• Capitalized, Italicized, and end in - viridae

Examples:

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

• Groups within some large families

• Capitalized, Italicized, end in - virinae

• Examples

• 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

4 5

E1 E2

NS

2)

Flavivirus

• 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

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 cases Satellites,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)

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Satellite nucleic acids

- encode only nonstructural proteins or no proteins at

DI Particles

Defective 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