Lecture 3 Flashcards
What is taxonomy?
“In the end, all nature is a continuum, and the business of taxonomy has the unfortunate obligation of drawing boundaries within this continuum, an artificial and illogical east, but necessary nevertheless”
Explain the Linnaeus classification system
In the 1700s, which classified plants and animals
What is the classification system used today?
It is the three domain system, which classifies bacteria, archaea, and eukarya
What is the Homes legacy?
Homes attempted to adopt the Linnaean system to classify and name viruses: failed
What did Homes attempt to do?
Homes classified the order virales:
Group I: Phagine (viruses that infect bacteria)
Group II: Phytophaginae (viruses that infect plants)
Group III: Zoophaginae (viruses that infect animals
Faced strong criticism and was rejected
Explain how the hepatitis virus was classified
Hepatitis virus causes different types of hepatitis:
1) Hep A: Hep A virus, family Picornaviridae
2) Hep B: Hep B virus, family Hepadnaviridae
3) Hep C: Hep C virus, family Flaviviridae
These 3 are entirely different viruses
Explain how the mosaic viruses are classified
1) TMV –> family Virgaviridae
2) Cauliflower mosaic virus –> family Caulimoviridae
3) Cucumber mosaic virus –> family Bromoviridae
4) Turnip yellow mosaic virus –> family Tymoviridae
What is the difference between virus and disease?
Viruses are the living organisms and agents that causes an infection or disease
Diseases are the final outcome and manifestation of an infection resulting from interactions between a virus and its host
Infection can lead to disease, but does not necessarily cause disease
What happened in the later days with taxonomy?
There was more emphasis on virus over disease
Viruses was based on morphology, capsid structure, chemical composition, and type go genome. All viruses were classified into groups
In the later days with taxonomy, how were viruses classified into ‘groups’?
1) Herpesvirus group: dsDNA, icosahedral capsids, large virion size, enveloped
2) Poxvirus group: dsDNA, complex & irregular virion structure, 200 nm or larger, enveloped
3) Myxovirus group: (-)ssRNA, helical nucleocapsids, spherical virion, enveloped
What happened with classification in the modern days?
In 1966, the International Committee on the Taxonomy of Viruses was established. Two approaches were considered: Monthetic and polythetic
What is the monothetic approach being considered by the ICTV?
Based on one characteristic at a time: the nature of viral genome (nucleic acid), capsid symmetry, presence or absence of envelope. The issue however is that this assumes all members in a group originated from the same and only one ancestor, and this is unable to capture and reflect the vast diversity of viruses
What is the polythetic approach being considered by the ICTV?
This considers multiple properties and characteristics. Individual viruses in a group share most, but not all, of a set of common characteristics, this does not assume that all viruses in a group evolved from a common ancestor
This ultimately how viruses were classified.
What is the older definition of a virus?
A polythetic class of viruses that constitute a replicating lineage and occupy a particular ecological niche
What is the new definition of a virus?
A monophyletic group of viruses whose properties can be distinguished from those of other species by multiple criteria
How is a virus species defined?
Viruses are defined by relatedness in sequences in a specific gene or a set of genes
Values of sequence identity used for species demarcation differ vastly among different families of viruses
How does classification work?
Taxon, order, family (subfamily), genus, and species
Subspecies designations: strains, serotypes, genotypes, subtypes, variants (Not official taxonomic names)
Quasi-species is a term used specifically for RNA viruses and retroviruses, and it has nothing to do with classification
Here is an example of classification
Order: virales, family: virile, genus: virus, species: virus
What are the rules on writing virus names?
The name of the taxon must be italicized
The first letter of the taxon name must be capitalized
The first letter of each word in a place name must also be capital
We do not italicize the acronym of a virus name
How are bacterial viruses named?
Based on a specific coding
How are plant viruses named?
Based on the host in which the virus was first identified, followed by a description of symptoms
How are insect viruses named?
Based on the Latin name of the host and an indication of the effects of viral infection
How are vertebrate viruses?
Based on disease and symptoms
How are viral species named?
Many are based on names of the place where the prototype member of the group was first identified or many will be based on properties of virions or diseases
What are the characteristics for a genus/family?
1) Nature and organization of viral genomes
2) Virion morphology and architecture of capsids/nucleocapsids
3) Strategies for genome replication and expression
4) Number and size of structural and non-structural proteins
5) Enzymes
Explain how the nature and organization of viral genomes are used?
1) DNA or RNA
2) Strandedness (ss or ds)
3) Polarity [positive(+) or negative (-); how to distinguish them]
4) Segmented or non-segmented
5) Topology (linear or circular, closed circle, or open circle)
Explain how virion morphology and architecture of capsids/nucleocapsids are used?
1) Symmetry of capsids or nucleocapsids (helical, icosahedral, or complex)
2) Shape and size of virion
3) Envelope (presence or absence)
What are the characteristics used to define species?
1) Natural host range
2) Cell and tissue tropism
3) Pathology and cytopathology
4) Mode of transmission
5) Physico-chemical properties of virions
6) Antigenic properties of viral proteins
7) Sequence relatedness of genes and genomes
What is phylogeny?
The prediction of evolutionary relatedness among viruses based on comparison of their sequences using computer and mathematical algorithms
Full genomes, specific genes, set of genes or partial gene sequences can be used
Phylogenetic analysis can be done using either nucleotide sequence, amino acid sequences, or both
There has been fast evolution of viral taxa as a function of time
What methods can be used to generating phylogenetic trees?
1) Neighbour joining (NJ)
2) Maximum likelihood (ML)
3) Maximum parsimony (MP)
4) Bayesian inference
How did viral taxonomy go viral?
ICTV Taxonomy Reports are available online, free of charge
There are overviews, new taxa, and updates on classification will be published in JGV by the respective Study groups
What is the internal code of virus taxonomy and nomenclature?
The first attempt to conform to the classification of cellular organisms; there was a five rank structure (1991-2017) , and then 8 additional levels for higher taxa were added; and then a 15 rank structure from (2019- onwards) –> realm, kingdom, phylum, class, and sub levels designations were added to taxonomy
What is the Baltimore classification system?
It is based on transcription:
+RNA –> - DNA –> +/- DNA
+RNA –> - RNA –> + mRNA +/-DNA –> +mRNA
-RNA –> +mRNA
What is the revised Baltimore classification system?
PICTURE
Explain viruses with -ssRNA genomes
Viruses with negative strand RNA genomes all have helical symmetry
The - ssRNA genomes of this group are all linear
This group contains some of the highly pathogenic viruses of humans
Explain viruses with ssDNA genomes
Genomes are small, 2-9 kilo bases
All these viruses are naked
All have circular genomes, with the exception of Parvoviridae
All have icosahedral symmetry, except for the family Inoviridae
