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