Virology 1.2: Fall, 2015
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
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
RNA
Secondary
Structure
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
Some more complex views of
isometric capsids
Double layer capsids

Human
rotavirusa 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
Paramyxovirus 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.
Tobacco mosaic virus and a satellite
Satellites never found without helper
But helper may be found without satellites
Viroids
 Infectious
RNAs-no capsids whatsoever
 Small
 Ss
 Circular
 Infect
plants
 Not defective, not satellites-they are
different entities!
Avocado sunblotch viroid infection of avocado
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
Some prion diseases
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, oldfashioned, archaic term, not a
lentivirus