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
Viral particles (virions) are designed to:
protect the viral genome
A small genome must be used effectively:
One genetic code can encode small subunits which construct a large capsid
What does genetic economy dictate?
• Genetic economy dictates the construction of capsids from small subunits
Describe virus particles.
• Virus particles are metastable structures – they can be inactivated
Functions of virion proteins: Protection of the genome
Assembly of stable protective protein shell
Specific recognition and packaging of nucleic acid genome
Interaction with host cell membranes to form the envelope – when the enveloped virus is budding from the host cell
Functions of virion proteins: Delivery of the genome
Binding to external receptors of the host cell
Transmission of signals that induce uncoating of the genome
Induction of fusion with host cell membranes
Interaction with internal components of the infected cell to direct transport of the genome to the appropriate site
Additional functions of virion proteins:
Interaction with cellular components for transport to intracellular sites of assembly
Interaction with cellular components to ensure an efficient infectious cycle
Methods of studying virus structure:
- Electron microscopy
- Physical methods
- Chemical methods
What does electron microscopy enable?
Electron microscopy enables the examination of the structure and morphology of virus particles
What does electron microscopy overcome?
Electron microscopy overcomes the shortcomings of light microscopy
The 2 types of electron microscopy:
- Transmission electron microscope (TEM) – Valuable – TEM provides a lot info on the virus particle
- Scanning electron microscope (SEM) – Beautiful – SEM provides more info on the surface of the virus particles
Information received from an electron microscope:
- Absolute number of virus particles present in any preparation (total count)
- Appearance and structure of the virions
Name the viruses that infect the gastrointestinal tract and cause outbreaks of diarrhoea
- Adenovirus
- Calicivirus
- Astrovirus
- Rotavirus
Physical methods - what occurred in the 1930s?
• Historical (1930s) – filtration through colloidal membranes of various pore sizes – 1st estimates of the size of virus particles
Physical methods: what happened in the 60s?
• In the 60s – sedimentation properties of viruses in ultracentrifuge
Differential centrifugation:
Obtain purified and highly concentrated preparations of viruses, free of contamination from host cell components
What does the relative density of particles measured in solutions of sucrose reveal?
• Relative density of particles, measured in solutions of sucrose reveals information about the proportions of nucleic acid and protein
Spectroscopy:
Use ultraviolet light to examine the nucleic acid content of the particle
Electrophoretic analysis:
Study viral proteins or nucleic acids by gel electrophoresis
What can be determined by X - ray diffraction?
- Structures of viruses can be determined
- Resolution of images measured in angstroms (Å)
- Not suitable for all viruses
What occurs during X - ray diffraction?
- Have to propagate virus to a high titre
- Have to purify the virus to a high degree
- The purified virus must also be able to form crystals large enough to diffract radiation
What is Nuclear magnetic resonance imaging based in?
Nuclear magnetic resonance imaging is based in the absorption of radio-frequency radiation by atomic nuclei in the presence of an external magnetic field
Chemical methods: Example
- Classical methods
- Example stepwise disruption of particles by slow alteration of pH or the gradual addition of protein – denaturing agents such as urea, phenol, or detergents
What do chemical methods indicate?
Chemical methods indicate the basis of the stable interactions between its components
Chemical methods can also be used to…
observe alteration or loss of antigenic sites on the surface of particles
What do viruses (ALL) possess?
• All viruses possess a capsid or nucleocapsid (aka ‘core’)
How do most viral particles appear?
• Most viral particles appear rod shaped or spherical under an electron microscope
Small coding capacity of viral genomes -
Capsid is constructed from small number of proteins, regularly and repetitively arranged:
- Maximal contact
- Non – covalent bonds
- Results in a symmetrical structure
- Helical symmetry
- Icosahedral symmetry
The virus can form…
spontaneously – i.e., it is in a free energy minimum state
Helical symmetry (examples):
• Examples: influenza, measles, rabies
What do helical animal viruses happen to have?
• All helical animal viruses happen to have single stranded RNA genomes, and all are enveloped
How do helical viruses look?
Filamentous or rod - like
A helical virus is an open structure:
Meaning it can enclose any volume by varying the length
What can the longer helical particles do?
• The longer helical particles can curve or bend – strength through flexibility
Where and how does each helix subunit bind?
• Each helix subunit binds identically with each other and on the inside of the helix binds identically with nucleotides of the genome
Icosahedral symmetry (Examples):
• Examples: Herpesviruses, adenovirus, picornaviruses
Describe icosahedral symmetry:
• Closed structure – restricted volume
Define the term ‘icosahedron’
• An icosahedron is a shape consisting of 20 triangular faces around a sphere
Which method first noticed the icosahedral symmetry?
Electron microscopy
What are most icosahedral viruses made of?
• Most icosahedral viruses are made of 60 protein subunits (3 subunits (i.e., a trimer) per face). This is the simplest conformation, and each subunit binds with the neighbours identically. E.g., AAV [Adeno-associated virus]
What do simple icosahedrons display?
• Simple icosahedrons display 2 – 3 – 5 rotational symmetries
Triangulation number (T): how many subunits is each face of the icosahedron made of? How many faces are there?
- Each face of the icosahedron is made of at least 3 subunits
- There are 20 faces
- Therefore, larger icosahedral viruses will need to make up the faces with multiples of 60 subunits
- Total number of subunits in a structure is 60T
Quasiequivalence:
When a capsid contains greater than 60 subunits, each occupies a more or less equivalent position and forms bonds with their neighbours in a similar fashion
Other capsid architectures:
- Most viruses are helical or icosahedral
* Some exceptions to the rule e.g., retroviruses (HIV), poxviruses (vaccinia)
Retroviridae:
- Two single strands of RNA genome
- Surrounded by matrix protein
- Encapsidated by a spherical, cylindrical or conical capsid (e.g., HIV)
Poxviridae
- Large, brick – shaped particles 200 – 400 nm long
- Extracellular form contains 2 envelopes
- More than 100 proteins
- Dumbbell shaped core with icosahedral heads with T = 7 symmetry
Packaging nucleic acid genome - Encapsidation of a viral genome:
• Encapsidation of viral genome is specific process mediated by packaging signals encoded within the viral genome (non – structural proteins)
Packaging is mediated by:
- Direct contact with the viral genome, condensing and proctecting the genome OR
- Packaging by cellular proteins (nucleosomes)
2 major advantages of packaging nucleic acid genome:
- None of the limited viral genetic information needs to be devoted to DNA – binding proteins
- Viral genome is transcribed by cellular RNAs and enters the infected cell nucleus as nucleoprotein closely resembling cellular templates
Envelope:
- Some viruses exit the cell without destroying it
* They instead ‘bud’ from the surface of the cell, acquiring a lipid envelope in the process
What is embedded in the envelope?
• Embedded in the envelope are:
Contain hydrophobic domains
Form a channel through the envelope e.g., ion channels
Enables the virus to control the permeability of the membrane
e.g., influenza M2 protein [Influenza A virus (IAV) matrix protein 2 (M2)]
External proteins: Location and association
Sits outside the membrane, but anchored with a transmembrane domain
- Can be associated with each other – multimeric spikes – visible on EM
External proteins may be….
glycosylated – glycoproteins
External proteins (important):
- Major antigens
- Receptor binding
- Membrane fusion
- Haemagglutination
