Classification and Taxonomy

2 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 mRNA 2) 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: 9 Genus: 287 Species: 1950 Taxonomy scheme In 2010 the International Committee on Taxonomy of Viruses (ICTV) formally recognized:International Committee on Taxonomy of Viruses 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) Flavivirus 5’ NTR StructuralNon-Structural 3’ NTR CprM1E 2 B3B5AA 4 cap 1) Hepacivirus ACE1E22p73BA B IRES StructuralNon-Structural 3’ NTR 5’ NTR 45 3) Pestivirus AN pro CE RNS p7NS2/3BA B IRES StructuralNon-Structural 3’ NTR5’ NTR 45 E1E2 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 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 3) Other Organ virus was isolated from: adenoids –Adenovirus

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

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

DNA VIRUS

Dependovirus / Virusoids 卫星病毒 Viroids are small ( nt), 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.