Virus classification and structure Flashcards
History of Taxonomy
Viruses were named according to:
- The disease - rabies, hepatitis viruses
- The cause - influenza
- The body site - rhinovirus
- The area it was discovered - Rift Valley fever virus
- The person who discovered it: Epstein - Barr (EBV)
What happened in the 60s?
The advent of a highly powered electron microscope led to researchers becoming more scientific the way in which they named viruses
What was the new hierarchical system that was developed based on?
- The nature of the nucleic acid in the virion
- The symmetry of the protein shell
- The presence or absence of a lipid membrane
- The dimensions of the virion and capsid
What happened in the 70s?
Sequencing technologies were discovered
Genomics started playing a role in taxonomy:
Not only were nucleic acids described as DNA or RNA, but the genetic code was illustrated. • Therefore, the classification system needed to be adjusted and reclassified
Which international committee was developed?
• The international committee on the taxonomy of viruses (ICTV) was developed. • Simultaneously, David Baltimore developed an alternative classification system
Baltimore Classification system:
Is based on the type of genome (whether it is DNA or RNA; if it is positive or negative), and how it replicates
Taxonomy concepts: Monothetic system
- Based on a single characteristic or a series of single characteristics
- The characteristics are both necessary and sufficient in order to identify members of a category
- The monothetic system is good for plants and animals. It lends itself to hierarchy
Polythetic system:
- Akin to family resemblance: some virus may have a certain characteristic, while others don’t have that characteristic
- Criteria are neither necessary nor sufficient
- There is a set of criteria. A minimum number of criteria must be satisfied. No single criterion is essential
- The polythetic system is good for viruses as it accounts for various properties simultaneously
How does the international committee on taxonomy of viruses deal with viral species?
ICTV deals with viral species in a polythetic fashion
What does the ICTV require?
The ICTV requires the consideration of various properties of viruses
What do a group of virologists have to?
A group of virologists has to rationalise the assignment properties to groups viruses
As more information becomes available,
the system has to evolve over time
Virus species are the…
Lowest taxon in the hierarchy of classification
Virus species were first formally defined in 2000:
• A polythetic class of viruses that constitute a replicating lineage and occupy a particular ecological niche
Members (of a virus species) have several properties in common, e.g.,
genome relatedness tropism, antigenic properties, and mode of transmission but they don’t necessarily all share a single common defining property
Virus species differ from the higher viral taxa,
which are “universal” classes and as such are defined by properties that are necessary for membership
What should viruses (including virus isolates, strains, variants, types, sub - types, serotypes, etc.) be assigned as?
• Viruses (including virus isolates, strains, variants, types, sub – types, serotypes, etc.) should where possible be assigned as members of the appropriate virus species, although many viruses remain unassigned because they are inadequately characterised
What must all virus species be represented by?
• All virus species must be represented by at least one virus isolate – if you attempting to gear a strain or a subtype, a new species’ name. You must be able to isolate that virus and characterize it by genomic characterisation or broymeta
Almost all virus species are members of…
recognized genera
Some genera are members of…
recognized sub - family
Distinguishing properties of genera, families and orders:
- Virus morphology
- Genome organization (positive or negative, DNA or RNA, single strand or double strand)
- Method of replication
- Size of proteins
All sub - families and most genera are members of…
recognized families
An order is the…
highest taxonomic level into which viruses can be classified
Some families are members of recognized orders:
Nidovirales, Mononegavirales, Herpesvirales and Picornavirales
Hierarchy levels of viruses:
(Order) Family (Sub – family) Genus Species
Nomenclature: Taxon and Suffix
Order (-virales) Family (-viridae) Subfamily (-virinae) Genus (-virus) Specie ( No specific suffix)
Rules for taxa:
- Should be capitalized
- Written in Italics
- Preceded by the name of the taxon
Species
• First word shouldn’t be capitalized, unless there are proper nouns
Example: Formal description of the human respiratory syncytial virus:
This virus belongs to the order Mononegavirales, family Paramyxoviridae, subfamily Pneumovirinae, genus Pneumovirus, species Human respiratory syncytial virus
Virologists may use informal names for some of the viruses, example
herpesvirus = any member of the family Herpesviridae
The Baltimore classification is based on the:
Nature of the genome (DNA or RNA)
Polarity of genome (positive vs negative sense)
Reverse transcription (yes or no)
the nature of the pathway from the nucleic acid to MRNA synthesis
DNA → RNA → Protein
7 Categories of the Baltimore classification:
- Groups 1&2: DNA, replicates via DdDp (DNA-dependent DNA polymerase)
- Group 3: dsRNA (ds: double stranded), replicates in the cytoplasm
- Groups 4&5: ssRNA (ss: single stranded), polarity of the genome
- Group 6: +sense RNA viruses that replicate via a DNA intermediate
- Group 7: dsDNA (ds: double stranded) viruses that replicate via a ssRNA (single stranded) intermediate
Nomenclature used in virus structure
Term Synonym Definition
Subunit Single, folded polypeptide chain
Structural unit Unit from which a capsid or nucleocapsid are built (maybe made up of one or more protein subunits)
Capsid Coat Protein shell surrounding the viral nucleic acid
Nucleocapsid Core Nucleic acid – protein assembly packaged within the virion
Envelope Viral membrane Host cell – derived lipid bilayer with viral glycoproteins
Virion Viral particle Infectious viral particle
Principles of viral structure
• Viral particles (virions) are made up of structural proteins and non-structural components including enzymes, small RNAs (sRNAs) and cellular macromolecules
• Primary functions of a virion:
Protects the viral genome
Enables the effective transmission of viral genome from one host cell to another