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Bio 260
Viruses!!!
Chapter 13
Viruses, and a half a second about
viroids and prions
Viral topics today
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Characteristics
Structure
Classification
Culturing
Replication
Things that aren’t viruses
Some questions first
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How big is a virus?
What is its structure?
How does it get into cells?
Can you tell viral relatedness based on symptoms?
How big?
5 um
General Characteristics of Viruses
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Obligatory intracellular parasites
DNA or RNA
Protein coat
Some enclosed by envelope
Some have spikes
Most infect only specific types of cells in one host
Host range determined by specific host
attachment sites and cellular factors
Virus Sizes
Figure 13.1
Filtration – will it remove viruses?
• Membrane
filtration
removes
microbes
>0.22 µm
Other methods:
Autoclaving (steam heat)
Chemicals
Dry heat (longer time)
Figure 7.4
Virion Structure
• What’s a virus made of?
• Chemical composition?
• Structural components?
Figure 13.2a
Virion Structure
• Nucleic acid
– DNA or RNA
• Capsid (protein)
– Capsomeres
• Attachment proteins
– spikes
• Optional extras
– Envelope (lipid)
Figure 13.2a
Virus – naked or enveloped
• Naked viruses: outer coat is
protein capsid made of
capsomeres (subunits)
(eg.phages and some animal)
• WHY repeating subunits?
• Enveloped viruses: lipid bilayer
covers protein capsid
(some animal)
• WHERE did envelope come from?
• Attachment proteins (spikes)
either in capsid or envelope
• WHAT determines host
specificity?
Virus Morphologies
• polyhedral: composed of flat
equilateral triangles
– Icosahedral: 20 faces
• Helical: filamentous or rod-like
appearance
• Enveloped: irregular shape
• Complex: Isometric head and
helical sheath or tail eg. phages
Morphology of a Polyhedral Virus
• Nucleic acid (DNA or RNA)
• Capsid (triangular faces)
made of capsomeres
• Spikes (for what?)
Adenovirus –
common cold
Check the size
Morphology of a Helical Virus
What’s this
subunit?
Morphology of a Helical Virus
What’s this
subunit?
Morphology
of an
Enveloped
Virus
Morphology of a Complex Virus
If you were to guess, which viruses would be the most complex?
• Bacteriophages
• Animal viruses
• Plant viruses
Figure 13.5
Morphology of a Complex Virus
Figure 13.5
Viral Genome
• Usually very small, few genes
• RNA or DNA, ss or ds
(matters for replication and
transcription)
• What GENES will the virus
need? (what proteins…)
Viral Genome
• Usually very small, few genes
• RNA or DNA, ss or ds
(matters for replication and
transcription)
• Genome must code for three
things:
– 1) Viral protein coat
– 2) Replication of viral
nucleic acids
– 3) Movement into and out
of host cells
Genome structure matters
• Genome structure: ss or ds DNA or RNA
– Only (+) mRNA is translated into protein
– Other genomes need to be transcribed to (+) mRNA
• RNA replication unique to viruses; usually in cytoplasm
• DNA replication usually in nucleus
Different strategies to achieve two goals
• Make new genome (how??)
• Make new capsid and other proteins
(process??)
Different strategies to achieve two goals
• Make new genome – DNA or RNA polymerase
• Make new capsid and other proteins –
transcription and translation aka expression
• Viruses are all about genetics!
• Terminology note: “viral replication” means all
of the above (genome replication plus gene
expression plus capsid assembly)
Preview of viral replication and gene
expression
But don’t worry… we’ll talk more
about that later. Meanwhile…
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Characteristics
Structure
Classification
Culturing
Replication
Things that aren’t viruses
Classification of Viruses based on structure
• Virus particle structure
– Isometric, helical, pleomorphic, complex (bacteriophages)
• Naked vs. enveloped
• Genome structure
– DNA or RNA; ss or ds; one molecule or segmented
Classification based on transmission
• Enteric viruses: fecal-oral route  YAY!
– (e.g., poliovirus, norovirus)
• Respiratory viruses: inhaled droplets
– (e.g., influenza virus, rhinovirus)
• Sexually transmitted viruses
– (e.g., herpes, papillomaviruses, HIV)
• Zoonotic viruses: animal or arthropod vector
– transmission can occur to humans or other animals
– (e.g., rabies, West Nile virus, cowpox, dengue)
Growing Viruses - phage
• Obligate intracellular
parasite… meaning?
• Viruses must be
grown in living cells
– Bacteriophages form
plaques on a lawn of
bacteria
Figure 13.6
Growing Viruses - animal
• Animal viruses
– may be grown in
living animals OR
– embryonated eggs
Figure 13.7
Growing Viruses - common
• Animal and plant viruses can grow in cell culture
– Continuous cell lines maintained indefinitely
Figure 13.8
Virus Identification
• Cytopathic effects
• Serological tests
• DNA or RNA sequence
Virus Identification –cytopathic effect
Any detectable change after infection – range from shape change to death
Which is the infected side? A or B
Figure 13.9
Virus Identification –cytopathic effect
Any detectable change after infection – range from shape change to death
Uninfected – monolayer
VSV infection: rounded
Figure 13.9
Serological tests
• Detect antibodies against viruses in a patient
• Use antibodies to identify viruses in
neutralization tests, viral hemagglutination, and
Western blot
How do viruses replicate?
Virus life cycle in brief
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Get in
Make more
Get out
Some variations on this theme
Figure 13.9
A Viral One-Step Growth Curve
Figure 13.10
Bacteriophage replication
• DNA genomes
• Lytic cycle
• Lysogenic cycle
Lytic cycle
• Attachment and penetration
• Biosynthesis and maturation
• Lysis and release
get in
make more
get out
The Lytic Cycle (bacteriophage)
• Attachment: Phage attaches by tail fibers to host cell
• Penetration: Phage lysozyme opens cell wall; tail
sheath contracts to force tail core and DNA into cell
• Biosynthesis: Production of phage DNA and proteins
• Maturation: Assembly of phage particles
• Release: Phage lysozyme breaks cell wall
Lytic Cycle of a T-Even Bacteriophage
1
attachment
2
penetration
3
biosynthesis
Figure 13.11
Lytic Cycle of a T-Even Bacteriophage
maturation
4
release
Figure 13.11
Viral infection of bacteria
• Lytic cycle
– Phage causes lysis and death of host cell
• Lysogenic cycle
– Prophage DNA incorporated in host DNA
The Lysogenic Cycle
“prophage” – when the phage DNA is in the host bacterial chromosome
Figure 13.12
The Lysogenic Cycle
• phage DNA incorporated in host DNA  ________
• A form of horizontal gene transfer  ___________
Figure 13.12
The Lysogenic Cycle
• phage DNA incorporated in host DNA  Prophage
• A form of horizontal gene transfer  Transduction
Figure 13.12
Why should we care about lysogeny
(or transduction)
• This exchange mediated by bacterial viruses is
responsible for pathogenicity of many bacteria
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Botulism toxin of C. botulinum originally from a virus
C. diphtheriae, also originally a viral (phage) source
Shiga toxin of E. coli, from Shigella
toxic shock syndrome of Streptococcus
I could go on…
Multiplication of Animal Viruses
• Attachment: Viruses attach to cell membrane
(spikes not tail fibers)
• Penetration by endocytosis or fusion
• Uncoating by viral or host enzymes
• Biosynthesis: Production of nucleic acid and
proteins
• Maturation: Nucleic acid and capsid proteins
assemble
• Release by budding (enveloped viruses) or
rupture
Getting in…
• Animal virus options
If you’re naked…
• Attachment (how?)
• Penetration by endocytosis
• Uncoating (what’s coming off?)
Figure 13.14a
Attachment, Penetration, Uncoating
• By fusion (enveloped)
Figure 13.14b
A question about entry
• Do both naked and enveloped viruses need to
remove their coats?? A for yes, B for no
Getting OUT
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What do you think?
Animal virus 2 options – depend on structure
LYSIS
BUDDING
The dramatic way… lysis
Budding of an Enveloped Virus
How is viral structure related to entry/exit?
ENTER BY
NAKED VIRUS
ENVELOPED VIRUS
EXIT BY
How is viral structure related to entry/exit?
NAKED VIRUS
ENVELOPED VIRUS
ENTER BY
EXIT BY
ENDOCYTOSIS  
LYSIS
FUSION  
BUDDING
What happens in between
• Biosynthesis, maturation – what’s the point?
• Make new virus particles!!!
Multiplication of DNA Virus
release
uncoat
maturation
“early” proteins
(viral replication)
“late” proteins
(capsid)
Get into
nucleus
Figure 13.15
If you’re a DNA virus
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What is copying your genome?
What’s making your mRNA?
DNA  DNA by host DNA polymerase
DNA m RNA by host RNA polymerase
mRNA  protein by host ribosomes
If you’re an RNA virus
• What is copying your genome?
• What’s making your mRNA?
• Are these obvious or simple questions to answer?
Some RNA virus terms
• Single stranded “+” RNA
• Single stranded “-” RNA
• Double stranded RNA
Types of RNA genome
Multiplication of RNA-Containing Viruses
Only (+) mRNA is
translated into protein
Other genomes need
to be transcribed to
(+) mRNA
Genome + mRNA  translate to protein and transcribe to –RNA
-RNA  + RNA for mRNA and genome
RNA to RNA HOW?
Viral RNA-dependent RNA polymerase (in the genome)
Figure 13.17
“+” stranded RNA genetics
Multiplication of RNA-Containing Viruses
Only (+) mRNA is
translated into protein
Other genomes need
to be transcribed to
(+) mRNA
Genome - RNA  transcribe to +RNA
+RNA translate to protein, transcribe to –RNA genome
RNA to RNA HOW?
Viral RNA-dep RNA pol IN THE CAPSID
Figure 13.17
“-” stranded RNA genetics
Multiplication of RNA-Containing Viruses
Only (+) mRNA is
translated into protein
Other genomes need
to be transcribed to
(+) mRNA
Genome dsRNA  use +RNA to make protein
RNA polymerase transcribes both strands to make new ds genome
RNA to RNA HOW?
RNA-dep RNA pol in the genome (+ side of ds RNA can be mRNA)
Figure 13.17
“ds” stranded RNA genetics
How is viral genome related to replication?
GENOME
dsDNA
FUNCTION
REPLICATION requires
DNA polymerase
“+” RNA or dsRNA Genome is an mRNA Gene for RDRP (RNA
dependent RNA pol)
“-” stranded RNA
RDRP protein loaded into
the capsid
Anything ELSE???
Of COURSE there is. :D
Multiplication of a Retrovirus
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HIV, leukemia, animal tumors
Single-stranded, enveloped, RNA viruses
reverse transcriptase: ss RNA  ds DNA
NO PROOFREADING, mistakes made, capsid proteins
highly variable
 ds DNA integrated into host chromosome = provirus
Figure 13.19
Multiplication of a Retrovirus
Release by budding
Viral proteins to
cell surface
Entry by fusion
Uncoating releases
genome
enzymes
like RT,
integrase
RT ssDNAdsDNA
transcription 
viral genome
and proteins
Integration of provirus
Figure 13.19
Retrovirus replication
How animal viruses get mRNA and genomes
• DNA viruses
– DNA  DNA
– DNA mRNA
host DNA polymerase
sometimes also viral DNA polymerase
host RNA polymerase
• “+” RNA or ds RNA – their genome is already an mRNA
– Genome is an mRNA used directly by ribosome
– Encodes a Viral RNA RNA pol; makes more genomes
• “-” RNA – their genome is NOT an mRNA
– In capsid: viral RNA RNA pol makes mRNA
– This RNA RNA polymerase also makes more genomes
• Retroviruses – not “+” or “-” because of life cycle
– In capsid: RNA DNA reverse transcriptase
– Enters nucleus, incorporates into chromosome as provirus
– Now treated as a gene so mRNA is made by host RNA pol
Cancer
• oncogenes
– transform normal cells into cancer cells
– normal cell protein that is overactive or has extra functions
due to mutation or misregulation
– oncogenes are the result of mutation – radiation,
chemicals, and 10% of the time gene transfer by viruses
• Transformed cells how can you tell
– Change shape: increased growth, loss of contact inhibition
– Cell surface: tumor-specific transplant antigens
– Genetic: oncogenic virus’ DNA integrated into host DNA
Do plants get viruses?
• Yes!
• Is their life
cycle the
same?
Figure 13.23
Plant Viruses
-Very common
- instead of attaching to receptors on
cells enter through cell wall wounds
- Many extremely hardy
- Human, insect, worm, fungal vectors
Things that aren’t cells or viruses
• But still cause disease
• And they are REALLY REALLY small
Viroids are infectious RNAs in plants
• It’s not PTSD, it’s PSTD: potato spindle tuber disease
Figure 13.23
Viroids
Circular ssRNA ~300 to 400 nucleotides
Replicate autonomously within susceptible cells using
host RNA polymerase
Single viroid capable of infecting cell
Resistant to digestion by nucleases
So far only host is plants
Sequences similar to introns
- Many questions: how do they replicate, how do they cause
disease, how did they originate (“RNA world”), are they
restricted to plants?
Prions
• Proteinaceous Infectious particle
• No nucleic acids!
• Inherited and transmissible by ingestion,
transplant, and surgical instruments
– Spongiform encephalopathies: Sheep scrapie,
Creutzfeldt-Jakob disease, Gerstmann-SträusslerScheinker syndrome, fatal familial insomnia, mad cow
disease
 PrPC: Normal cellular prion protein, on cell surface
 PrPSc: Scrapie protein; accumulates in brain cells, forming plaques
Sphongiform encephalopathies
 PrPC: Normal cellular prion protein, on cell surface
 PrPSc: Scrapie protein; accumulates in brain cells, forming plaques
How a Protein Can Be Infectious
Figure 13.22