BSCI437 Lecture 5: Taxonomy
Classification/Taxonomy.
Excellent reference. http://www.ncbi.nlm.nih.gov/ICTVdb/index.htm
Criteria for classification:
1. Disease symptoms
2. Physical structure of the virus particle.
3. Genome composition and structure
Classical:
1. Morphology first,
2. followed by grouping according to physical and chemical composition,
3. followed by genetic relatedness.
Molecular: Classification is currently moving toward nucleic acid sequence analysis.
Classification and Nomenclature:
ICTV-International Committee on Taxonomy of Viruses (meets every 4 years).
Present totals (2000): 3 orders, 56 families, 9 subfamilies, 233 genera, and 1550 species.
Family- A group of genera with common characteristics.
 Capitalized, Italicized, and end in -viridae.
 Examples-Picornaviridae (picornavirus family is also acceptable), Herpesviridae
(herpesvirus family).
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.
 Examples-Rhinovirus, Simplexvirus
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 or italicized.
 Examples: poliovirus, human immunodeficiency virus.
Example with a common virus (herpes simplex virus 1)
 Family: Herpesviridae or herpesvirus family;
 Subfamily: Alphaherpesvirinae;
 Genus: Simplexvirus;
 Species: herpes simplex virus 1.
Another example: 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. 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. 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.
Origins of some viral names
• Picorna: Pico (small) + RNA
• Toga: wearing a toga
• Corona: wearing a crown
• Retro: use retrotransposition
• Filo: Look fibrous
• Papilloma: infections result in papilla (bumps on skin), e.g. warts
• Adeno: infections of respiratory tract
• Hepadna: hepatitis + DNA
• Herpes: produce scaly (snake skin) lesions
• Pox: infections produce pox lesions
Special cases: Satellite viruses, Satellite RNAs and Defective Interfering Elements.
Consider the world of viruses as an ecological habitat. In such habitats, organisms tend
to evolve relationships with one another: mutualistic, commensalistic, symbiotic, and
parasitic. Viruses are no different.
 Satellite viruses
o Viruses with separate genomes that are encapsidated inside viral particles
produced by a “helper” virus.
o They also rely on the helper virus replicative machinery to replicate their
genomes.
o Example: the M1 virus of yeast is the satellite, and the L-A virus is the
helper. M1 encodes a toxin. The M1 dsRNA genome is encapsidated


inside of viral particles produced by L-A, and is replicated by the L-A
RNA-dependent RNA polymerase.
Satellite RNAs:
o Naked RNAs that are not encapsidated inside of viral particles.
o However, they do rely upon a helper virus for replication.
o Often found in plants.
Defective Interfering Elements (DI’s):
o Genomes are derived from a helper virus.
o 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.
o Called defective interfering because they are
 defective in their ability to produce proteins, and
 they tend to interfere with satellite viruses/RNAs by their ability to
out compete for helper virus resources.