classification and taxonomy. 2 classical: morphology physical and chemical composition genetic...

Classification and Taxonomy

2

Classification and Taxonomy

Classical: morphology

Physical and chemical composition

Genetic relatedness

Modern: Phylogenetic, based on nucleic acid sequence analysis.

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

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

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

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

Order Family Caudovirales

• Myoviridae  • Podoviridae  • Siphoviridae

Herpesvirales

• • Alloherpesviridae  • Herpesviridae  • Malacoherpesviridae

Mononegavirales

• Bornaviridae   • Filoviridae   • Paramyxoviridae   • Rhabdoviridae

Picornavirales

• • Dicistroviridae •   Iflaviridae  • Marnaviridae  • Picornaviridae  • Secoviridae

• Papillomaviridae• Polyomaviridae

Papovaviridae

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)

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

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

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

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.

Classification of human viruses

DNAVIRUS

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.

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

• 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).

• 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.