Virology 1.2: Spring, 2014. Components of a virus and some definitions. Virion -an individual virus particle (on the left). Minimal virion. Essential components (not necessarily the only ones) Capsid (the cargo container) Genome (the cargo). Two simple examples of capsids.
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Virology 1.2: Spring, 2014 Components of a virus and some definitions
Minimal virion • Essential components (not necessarily the only ones) Capsid (the cargo container) Genome (the cargo)
Two simple examples of capsids Rod-shaped and isometric
Some characteristics of genomes • DNA or RNA • Single or double stranded (ss or ds) • Linear or circular • Haploid or diploid
Some more characteristics of genomes • Size and genetic content varies • One or more pieces of nucleic acid (aka multipartite or segmented genome) • May have genome-linked protein or VpG • May be (+) or (-) sense or ambisense
Viral Nucleic Acids Have Secondary Structure Predicted Structure of Uncoated NS1 RNA from Influenza A H5N1 Left: Swine Right: Duck Citation:Pallavi S, Vijai S, M Arshad (2008) Modeling of RNA Secondary Structure of Non Structural Gene and Evolutionary Stability of the Influenza Virus Through In Silico Methods. J Proteomics Bioinform 1: 219-226. doi:10.4172/jpb.1000026
Some characteristics of capsids • Multiple copies of capsid protein • Capsid protein is aka the structural subunit of the capsid • May be more than one type of capsid protein in the capsid • A capsid protein may be a lipo- or glycoprotein
Double layer capsids • Human rotavirus- a reovirus
Geminiviruses Contains one small DNA molecule in each twin capsid
Virions may contain additional components • Envelope or membrane • Host-derived • Membrane proteins • Complex virions may have more than one membrane
Features of enveloped virions Influenza A, an Orthomyxovirus Membrane and membrane proteins SARS virus - a coronavirus
Segmented genome Orthomyxovirus on right
Other components • Matrix (layer inside envelope) • Tegument (herpesviruses only) • Core or nucleocapsid
Herpesvirus virion • Human herpesvirus 1 (HHV-1) aka herpes simplex virus 1
Virion may contain other proteins • Non-structural proteins • Regulatory proteins • Enzymes required for viral replication
Non-genomic nucleic acids • Primers for replication • tRNAs in retroviruses
Features of more complex capsids • Adenovirus
A highly complex and functional capsid • Bacteriophage T4-a myovirus
Tails-Another interesting feature Phage lambda and its relatives, the siphoviruses Corndog phage-a mycobacteriophage
Bacilliform capsids Rabies virus – a Rhabdovirus
Core of HIV-1 Diagnostic shape “Core” is actually the virus capsid
Multicomponent viruses • Aka multipartite viruses or coviruses • Segmented genome viruses in which the genome segments are distributed among more than one particle • Usually plant viruses
Defective/helper viruses • Defective virus cannot complete “life” cycle • Helper virus provides missing functions • Complementation • May or may not be related viruses • Defective interfering (DI) particles are different and are usually laboratory artifacts (next!)
Defective Interfering (DI) Particles 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 virus(definition from Field’s Virology) • Type of defective virus • Stable ecological relationship • Satellite (of) tobacco necrosis virus • STNV • Replication-defective • But competent for capsid protein • Minimal identity
Satellite nucleic acid (RNA) • Helper provides capsid • Satellite may provide some of own replication functions or part of its own core • Hepatitis delta agent aka HDV CMV Associated RNA 5 aka CARNA5 (satellite RNA may change symptoms)
Satellite Viruses and Satellite RNAs Both are defective!!! Satellite RNAs Packaged in the coat protein of the helper Virus. Satellite viruses Encode a coat protein that encapsidates the Satellite Genome. 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.
Satellites never found without helper But helper may be found without satellites
Virophages • Look like a cross between a satellite virus and a bacteriophage • dsDNA agents with ~20 kbp genome • Only found associated with giant viruses of protozoa • “Sputnik”, “Maverick”
Viroids • Infectious RNAs-no capsids whatsoever • Small • Ss • Circular • Infect plants • Not defective, not satellites-they are different entities!
Provirus or prophage • Viral genome inserted (integrated) into host genome • Lambda forms a prophage, retroviruses form proviruses
Prions 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 particles • Proteinaceous infectious particle • No detectable nucleic acid • Can it really replicate? • Stanley Prusiner, 1982 • Prions are not viruses
Retroid family • Reverse transcriptase step • Some “true viruses” included such as HIV or cauliflower mosaic virus • Retrotransposons, some introns
Some Controversial Terms to be Avoided Virusoid - has no recognized meaning Slow virus – historical, old-fashioned, archaic term, not a lentivirus