Classification and Taxonomy
Reference site: http://www.ncbi.nlm.nih.gov/ICTVdb/index.htm
Animal viruses
Naming 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
3)
Other
Organ virus was isolated from: adnoids -Adenovirus
Sin Nombre
Plant viruses an many insect viruses (two
components)
1) Host
2) 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.
3
Classical criteria for classification
of animal viruses
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
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
Taxonomy scheme
Family:
Subfamily:
Genus:
Species:
Present totals:
73
9
287
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
1)
5’ NTR
Structural
2
cap
C prM E
Non-Structural
4
1 A B
3
A B
3’ NTR
5
Pestivirus
2)
5’ NTR NS
IRES
Structural
Non-Structural
4
5
Npro C ERNS E1 E2 p7 NS2/3 A B
3’ NTR
A B
Hepacivirus
3)
5’ NTR
IRES
Structural
C E1 E2 p7 2
Non-Structural
4
5
3
A B
A B
3’ NTR
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 cases
Satellites,DI particles,viriods &
prions.
Satellites and viriods-subviral agents
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
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 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
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