Chapter 2 Virus Taxonomy

2.1 HISTORY

• a. At the turn of the century, the single physio-chemical characteristic measure was filterability. In fact, it was this estimation of the size of the infectious entities that set the virus apart from the "microbes."
• b. The earliest efforts to classify viruses were based on 

• 1. common pathogenic properties (e.g. human "hepatitis viruses," including agents now known as hepatitis A virus, hepatitis B virus, yellow fever virus, and Rift Valley Fever Virus).
• 2. Common organ tropisms (e.g. "respiratory viruses," including agents now known as hepatitis A virus, rhinoviruses, and adenoviruses).
• 3. Common ecologic characteristics (e.g. "arboviruses", including agents now known as togaviruses bunya-viruses, and adenoviruses).

• c. Classification by biochemical and morphological characteristics of viruses. About 1950 the first groupings of viruses on the basis of common physicochemical properties emerged - the myxovirus group, the poxvirus group, and the herpesvirus group.
• d. The International Committee on Nomenclature of Viruses (ICNV) was established in 1966 at the Ninth International Congress for Microbiology to set standards in nomenclature and classification of viruses. Virus nomenclature bears little relationship to disease pathogenesis, diagnoses, therapy and control.

2.2. ICTV-UNIVERSAL SYSTEM OF VIRUS TAXONOMY ( THE INTERNATIONAL COMMITTEE ON NOMENCLATURE OF VIRUSES ICNV BECAME THE INTERNATIONAL COMMITTEE ON TAXONOMY OF VIRUSES ICTV).

2.2.1 Families:

• viruses families are designated by terms ending in - viridae. Families represent clusters of general of viruses with apparently common, evolutionary origin in morphology, genomic structure and strategy in replication. In four families, the poxviridae, the Herpesviridae, the papovaviridae and the Retroviridae subfamilies have been introduced.

2.2.2 Virus Genera:

• virus Genera are designated by terms ending in virus. Viral genera represent populations of species within families that share certain common characteristics and are distinct from other populations of species. The subgenustaxon is used in the family Retroviridae to divide the unnamed genus comprising the type C oncoviruses into three taxa, for the mammalian, avian and reptilian type C oncoviruses, respectively. The subgenus taxas is also used in the family Adenoviridae to distinguish groups of human adenoviruses.

2.2.3 Virus species:

• virus species have not yet been designated formally (except for the family Adenoviridae.) 

2.3 PROPERTIES OF VIRUSES USED IN TAXONOMIC CONSTRUCTIONS

2.3.1 Properties of virions (Morphology) 

• 1. Virion size
• 2. Virion shape
• 3. Presence or absence of an envelope and peplomers
• 4. Capsomeric symmetry and structure

  2.3.2 Properties of genome

• 1. Type of nucleic acid -- DNA or RNA
• 2. Strandedness-single stranded or double stranded
• 3. Linear or circular
• 4. Sense-positive, negative, or ambisense
• 5. Number or segments
• 6. Size of genome or genome segments
• 7. Presence or absence and type of 5' -terminal cap
• 8. Presence or absence of 5' -terminal covalently linked polypeptide
• 9. Presence or absence of 3' -terminal poly(A) tract
• 10. Nucleotide sequence

  2.3.3 Properties of proteins 

• 1. Number of proteins
• 2. Size of proteins
• 3. Functional activities of proteins (especially virion transcriptase, virion reverse transcriptase, virion hemagglutinin, virion neuraminidase, virion fusion protein)
• 4. Amino acid sequence 

  2.3.4 Replication Strategies 

• 1. Strategy of replication of nucleic acid
• 2. Characteristics of transcription
• 3. Characteristics of translation and posttranslational processing
• 4. Site of accumulation of virion proteins, site of assembly, site of maturation and release
• 5. Cytopathology, inclusion body formation E. Physical properties
  • 1. pH stability
  • 2. Thermal stability
  • 3. Cation (Mg2+, Mn2+) stability
  • 4. Solvent stability
  • 5. Detergent stability
  • 6. Radiation stability 

  2.3.6 Biological properties

• 1. Serological relationship
• 2. Host range, natural and experimental
• 3. Pathogenicity, association with disease
• 4. Tissue tropisms, pathology, histopathology
• 5. Transmission
• 6. Vector relationship
• 7. Geographic distribution