virology 1.2: fall, 2015 components of a virus and some definitions
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Virology 1.2: Fall, 2015Virology 1.2: Fall, 2015
Components of a virus and some Components of a virus and some definitionsdefinitions
Virion-an individual virus particle Virion-an individual virus particle (on the left)(on the left)
Minimal virionMinimal virion
Essential components (not necessarily the Essential components (not necessarily the only ones)only ones)
Capsid (the cargo container)Capsid (the cargo container)
Genome (the cargo)Genome (the cargo)
Two simple examples of Two simple examples of capsidscapsids
Rod-shaped and isometric
Some characteristics of genomesSome characteristics of genomes
DNA or RNADNA or RNA Single or double stranded (ss or ds)Single or double stranded (ss or ds) Linear or circularLinear or circular Haploid or diploidHaploid or diploid
Some more characteristics of Some more characteristics of genomesgenomes
Size and genetic content variesSize and genetic content varies One or more pieces of nucleic acid (aka One or more pieces of nucleic acid (aka
multipartite or segmented genome)multipartite or segmented genome) May have genome-linked protein or VpGMay have genome-linked protein or VpG May be (+) or (-) sense or ambisenseMay be (+) or (-) sense or ambisense
RNARNASecondarySecondaryStructureStructure
Viral Nucleic Acids Have Secondary StructureViral Nucleic Acids Have Secondary Structure
Predicted Structure of Uncoated NS1 RNA from Influenza A H5N1Predicted Structure of Uncoated NS1 RNA from Influenza A H5N1
Left: Swine Left: Swine Right: DuckRight: Duck
Citation:Citation: Pallavi S, Vijai S, M Arshad (2008) Modeling of RNA Secondary Structure of Non Structural Pallavi S, Vijai S, M Arshad (2008) Modeling of RNA Secondary Structure of Non Structural Gene and Evolutionary Stability of the Influenza Virus Through Gene and Evolutionary Stability of the Influenza Virus Through In SilicoIn Silico Methods. J Proteomics Methods. J Proteomics Bioinform 1: 219-226. doi:10.4172/jpb.1000026Bioinform 1: 219-226. doi:10.4172/jpb.1000026
Some characteristics of capsidsSome characteristics of capsids
Multiple copies of capsid proteinMultiple copies of capsid protein Capsid protein is aka the structural subunit Capsid protein is aka the structural subunit
of the capsidof the capsid May be more than one type of capsid May be more than one type of capsid
protein in the capsidprotein in the capsid A capsid protein may be a lipo- or A capsid protein may be a lipo- or
glycoproteinglycoprotein
Some more complex views of Some more complex views of isometric capsidsisometric capsids
Double layer capsidsDouble layer capsids
Human Human rotavirus-rotavirus-
a reovirusa reovirus
GeminivirusesGeminiviruses
Contains one small DNA molecule in each twin capsid
Virions may contain additional Virions may contain additional componentscomponents
Envelope or membraneEnvelope or membrane
Host-derivedHost-derived Membrane proteinsMembrane proteins Complex virions may have more than one Complex virions may have more than one
membranemembrane
Features of enveloped virionsFeatures of enveloped virionsInfluenza A, an OrthomyxovirusInfluenza A, an Orthomyxovirus
Membrane and membrane Membrane and membrane proteins proteins
SARS virus - a coronavirusSARS virus - a coronavirus
Segmented genomeSegmented genome
Paramyxovirus on Paramyxovirus on rightright
Other componentsOther components
Matrix (layer inside envelope)Matrix (layer inside envelope) Tegument (herpesviruses only)Tegument (herpesviruses only) Core or nucleocapsidCore or nucleocapsid
Herpesvirus virionHerpesvirus virion
Human herpesvirus 1Human herpesvirus 1
(HHV-1)(HHV-1)
aka herpes simplex aka herpes simplex virus 1virus 1
Virion may contain other proteinsVirion may contain other proteins
Non-structural proteinsNon-structural proteins
• Regulatory proteinsRegulatory proteins• Enzymes required for viral replicationEnzymes required for viral replication
Non-genomic nucleic acidsNon-genomic nucleic acids
Primers for replicationPrimers for replication tRNAs in retrovirusestRNAs in retroviruses
Features of more complex capsidsFeatures of more complex capsids
AdenovirusAdenovirus
A highly complex and functional A highly complex and functional capsidcapsid
Bacteriophage T4-a Bacteriophage T4-a myovirusmyovirus
Tails-Another interesting featureTails-Another interesting feature
Phage lambda Phage lambda
and its relatives, theand its relatives, the
siphovirusessiphoviruses
Corndog phage-a Corndog phage-a mycobacteriophagemycobacteriophage
Bacilliform capsidsBacilliform capsids
Rabies virus – aRabies virus – a
RhabdovirusRhabdovirus
Core of HIV-1Core of HIV-1
Diagnostic Diagnostic shapeshape
““Core” is Core” is
actually theactually the
virus capsidvirus capsid
Multicomponent virusesMulticomponent viruses
Aka multipartite viruses or covirusesAka multipartite viruses or coviruses Segmented genome viruses in which the Segmented genome viruses in which the
genome segments are distributed among genome segments are distributed among more than one particlemore than one particle
Usually plant virusesUsually plant viruses
Defective/helper virusesDefective/helper viruses
Defective virus cannot complete “life” cycleDefective virus cannot complete “life” cycle Helper virus provides missing functionsHelper virus provides missing functions Complementation Complementation May or may not be related virusesMay or may not be related viruses
Defective interfering (DI) particles are Defective interfering (DI) particles are different and are usually laboratory different and are usually laboratory artifacts (next!)artifacts (next!)
Defective Interfering (DI) Defective Interfering (DI) ParticlesParticles
Defective Interfering particles originate from parental viruses by deletions of
the viral genome and subsequent evolution for replication fitness of the
defective particle. DI particles compete with the competent, parental virus.
Satellite virusSatellite virus(definition from Field’s Virology)(definition from Field’s Virology)
Type of defective virusType of defective virus Stable ecological relationshipStable ecological relationship Satellite (of) tobacco necrosis virusSatellite (of) tobacco necrosis virus STNVSTNV Replication-defectiveReplication-defective But competent for capsid proteinBut competent for capsid protein Minimal identityMinimal identity
Satellite nucleic acid (RNA)Satellite nucleic acid (RNA)
Helper provides capsidHelper provides capsid Satellite may provide some of own Satellite may provide some of own
replication functions or part of its own corereplication functions or part of its own core Hepatitis delta agent aka HDVHepatitis delta agent aka HDV
CMV Associated RNA 5 aka CARNA5CMV Associated RNA 5 aka CARNA5
(satellite RNA may change symptoms)(satellite RNA may change symptoms)
Satellite Viruses and Satellite RNAs
Satellite virusesEncode a coat protein that encapsidates the Satellite Genome.
Satellite RNAsPackaged in the coat protein of the helperVirus.
Satellite RNAs: Satellite RNAs are small RNA molecules that require a host virus for replication. They may or may not reduce the titer of the host virus. Satellite RNAs ranges from 200 to 1700 nt. Larger satellite RNAs may encode a protein (not capsid).
Satellite viruses: Defective viruses which can multiply only by association with a helper virus which complements the defective gene. Satellite viruses may be associated with certain plant viruses, animal viruses, or bacteriophages. They differ from satellite RNA (RNA, satellite) in that satellite viruses encode their own coat protein.
Both are defective!!!
Tobacco mosaic virus and a satelliteTobacco mosaic virus and a satellite
Satellites never found without helperSatellites never found without helper
But helper may be found without satellitesBut helper may be found without satellites
ViroidsViroids
Infectious RNAs-no capsids whatsoeverInfectious RNAs-no capsids whatsoever SmallSmall SsSs CircularCircular Infect plantsInfect plants Not defective, not satellites-they are Not defective, not satellites-they are
different entities!different entities!
Avocado sunblotch viroid infection of avocado
Provirus or prophageProvirus or prophage
Viral genome inserted (integrated) into Viral genome inserted (integrated) into host genomehost genome
Lambda forms a prophage, retroviruses Lambda forms a prophage, retroviruses form provirusesform proviruses
PrionsPrions
Scrapie—Germany (1759)
“Some sheep also suffer from scrapie, which can be identified by the fact that affected animals lie down, bite at their feet and legs, rub their backs against posts, fail to thrive, stop feeding and finally become lame. They drag themselves along gradually become emaciated and die. Scrapie is incurable. The best solution, therefore, is for a shepherd who notices that one of his animals is suffering from scrapie, to dispose of it quickly and slaughter it away from the manorial lands for consumption by the servants of the nobleman. A shepherd must isolate such an animal from healthy stock immediately because it is infectious and can cause serious harm to the flock.”
Prion particlesPrion particles
Proteinaceous infectious particleProteinaceous infectious particle No detectable nucleic acidNo detectable nucleic acid Can it really replicate?Can it really replicate? Stanley Prusiner, 1982Stanley Prusiner, 1982 Prions are not virusesPrions are not viruses
Some prion diseasesSome prion diseases
Retroid familyRetroid family
Reverse transcriptase stepReverse transcriptase step Some “true viruses” included such as HIV Some “true viruses” included such as HIV
or cauliflower mosaic virusor cauliflower mosaic virus Retrotransposons, some intronsRetrotransposons, some introns
Some Controversial Terms Some Controversial Terms to be Avoidedto be Avoided
VirusoidVirusoid - has no recognized - has no recognized meaningmeaning
Slow virusSlow virus – historical, old- – historical, old-fashioned, archaic term, not a fashioned, archaic term, not a
lentiviruslentivirus
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