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Classification and Taxonomy
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2
Classification and Taxonomy
Classical: morphology
Physical and chemical composition
Genetic relatedness
Modern: Phylogenetic, based on nucleic acid sequence analysis.
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CLASSIFICATION OF VIRUSES-------basis of classification
• Virion morphology• Physicochemical properties of the virion• Virus genome properties• Virus protein proteries• Genome organization and replication• Antigenic properties• Biologic properties
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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
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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
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Present totals: Family: 73
Subfamily: 9Genus: 287
Species: 1950
Taxonomy scheme
In 2010 the International Committee on Taxonomy of Viruses (ICTV)
formally recognized: 6 Orders
87 Families 19 Subfamilies
348 Genera and 2285 Species of viruses
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Order Family Caudovirales
• Myoviridae • Podoviridae • Siphoviridae
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Herpesvirales
• • Alloherpesviridae • Herpesviridae • Malacoherpesviridae
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Mononegavirales
• Bornaviridae • Filoviridae • Paramyxoviridae • Rhabdoviridae
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Picornavirales
• • Dicistroviridae • Iflaviridae • Marnaviridae • Picornaviridae • Secoviridae
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• Papillomaviridae• Polyomaviridae
Papovaviridae
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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)
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Subfamilies
• Groups within some large families. • Capitalized, Italicized, end in -virinae. • Examples
– Alphaherpesvirinae– Betaherpesvirinae– Gammaherpesvirinae.
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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)
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Hepacivirus
Pestivirus
Flavivirus
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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
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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: adenoids –
Adenovirus
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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
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Taxonomy: two examples
Example 1: herpes simplex virus 1 Family: Herpesviridae or herpesvirus family
Subfamily: Alphaherpesvirinae; Genus: Simplexvirus;
» Species: herpes simplex virus 1.
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Taxonomy: two examples
Example 2: Poliovirus Family: Picornaviridae or picornavirus family;
Subfamily: None; Genus: Enterovirus;
» Species: poliovirus
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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.
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Classification of human viruses
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DNAVIRUS
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Dependovirus /Virusoids卫星病毒
• Viroids are small (200-400nt), circular RNA molecules with a rod-like secondary structure which possess no capsid or envelope which are associated with certain plant diseases. Their replication strategy like that of viruses - they are obligate intracellular parasites.
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Five genera of Family Bunyaviridae
• Genus Bunyavirus– Prototype Bunyawera virus; mosquito vectored
• Genus Hantavirus– Hantaanvirus
• Genus Nairovirus– Cause hemorrhagic fevers; tick-borne
• Genus Phlebovirus– Cause Rift Valley Fever and similar disease; sandfly
vectored• Genus Tospovirus
– Important plant pathogen with the widest host range of any plant virus; thrips vectored
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• A parvovirus that does not require a helper virus was• discovered in serum from a healthy blood donor. The• virus, named after a batch of blood labelled B19, infects• red blood cell precursors. Many infections with B19 are• without signs or symptoms, but some result in disease,
• such as fifth disease (erythema infectiosum), in which• affected children develop a ‘slapped-cheek’ appearance• (Figure 12.2).• Other diseases caused by B19 virus include
• • acute arthritis• • aplastic anaemia in persons with chronic haemolytic• anaemia• • hydrops foetalis (infection may be transmitted from• a pregnant woman to the foetus and may kill the• foetus).
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• In 2005 a new human parvovirus was discovered using a technique for molecular screening of nasopharyngeal aspirates from children with lower respiratory tract disease. The virus is related to known parvoviruses in the genus Bocavirus.
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