Quasispecies Theory and the Behavior of RNA
Viruses
Sumeeta Singh, Steve Bowers, Greg Rice, Tom McCarty
BINF 70402/19/13
What is a virus?
• Viruses are obligate intracellular parasites.
• Small infectious agents bearing nucleic acid instructions.
• Classified based on the form of nucleic acid, DNA or RNA.
Virus types
• Plus strand RNA virus• Minus strand RNA virus• Double strand RNA virus
• Retrovirus
• Single strand DNA virus• Double strand DNA virus
RNA Virus types
DNA Virus types
“Quasispecies Theory”
• Mathematical framework describing evolution of macromolecules (Eigen, 1971)
• Extends the classic population genetics ideas of mutation-selection into quasispecies (Eigen, Schuster, 1977)
• Eventually borrowed to describe RNA virus evolution dynamics
Virus Replication Error
• Plus strand RNA virus• Minus strand RNA virus • Double strand RNA virus
• Retrovirus
• Single strand DNA virus• Double strand DNA virus
RNA dependent- RNA polymeraseError rate =10-3 to 10-5
DNA polymeraseError rate =10-7 to 10-9
Reverse TranscriptaseError rate =10-4 to 10-5
Requirements and Consequences
• Polymerase responsible for high error rates.
• Estimated that each single and some double nucleotide sequence changes occur.
• Resulting in a collection of related sequences around a “master” sequence.
• Variation is related to ability to survive (population genetics) AND probability of occurring based on sequence neighbors (quasispecies).
Virus Replication Swarm
Virus Replication Swarm
“Quasispecies Theory”
1971
1977
Quasispecies and RNA viruses
• Survival of the “flattest”
• Error Catastrophe
• Fidelity and Fitness
Survival of the Fittest or Survival of the FlattestA flat species is a species which exists in a genetically diverse group. Not dominated by one variant.
A quasispecies must be a flat species.
A fit species (in this part of the presentation) is a species which reproduces very fast.
Flat Species
Properties of a flat species
A flat species will have high mutation rates.
A flat species is able to mutate without a major effect on fitness.
Advantages of a flat species
Different mutants in a flat quasispecies can help each other.
Flat species are better able to adapt.
Dengue-1 VirusLives as a quasispeciesOne variant of the virus which is
found in high concentrations cannot survive on its own.
It can only survive because other viruses (infecting the same cell) create the protein which it lacks.
Viroid ExperimentTheory: More genetically diverse
(flatter) species are better able to adapt to mutations.
Viroid 1 - CSVd – very fitViroid 2- CChVMd – more flat, but less
fitProcedure: Infect plants with each viroid Subject the plants to two environment either normal, or UVC light
Results UVC light will cause mutationsResults: Under normal conditions the fitter viroid did better, then the flatter viroid. Under the UVC light the two were about equal Under the UVC light the flatter became more diverse. The fitter did not become more diverse.
Fitter or Flatter, which is better able to survive?The fit species will grow faster in
an ideal environment.The flat species will be able to
adapt more quickly.
Error ThresholdRNA Viruses have a high mutation rate
The point at which accumulated mutations reduce fitness:
- Too much mutation can lead to loss of vital information
- Too little mutation can lead to host defenses overcoming the virus
Error Threshold: position in informational space where a phase transition occurs such that the genomic sequence information can no longer be perpetuated.
The greatest fitness is when mutation rates approach the error threshold
Model of Error Catastrophe
http://www.pnas.org/content/98/12/6895.full
Error CatastropheExtinction of a virus as a result of excessive
RNA mutations – lethal mutagenesis
Decrease viral fitness by increasing the rate at which new mutations appear.
There is an intrinsic limit to the maximum variability of viral genetic information before it loses meaning. If an RNA virus quasispecies
goes beyond that mutation limit, the population will no longer be viable.
Increasing Mutation RateIonizing radiation (eg X-rays) –
cause mutations by damaging DNA.
Base Analogs – chemicals that replace one of the usual nucleotides in the DNA. These mutagens cause copying errors.
APOBEC3GHumans have the ability to
induce lethal mutagenesis Protein found inside cells that has
a very specific antiviral roleCytidine deaminase enzymeUnfortunately, HIV has the ability
to bind to APOBEC3G proteins and cause their degradation
APOBEC3G
It de-aminates the cytosine base, thus mutating it to a uracil base
APOBEC3G
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Fidelity and Fitness: Mutation Rate
• Evolutionary Theory: viral error rates
• RNA Virus: low fidelity generates diverse population of variants
• Homogenous population vs dynamic environment
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Fidelity and Fitness: Mutation Rate
• Ribavirin and Lethal Mutagenesis
• Hypothesis: mutant with low mutation rate less sensitive to LM and resistant to ribavirin
• Poliovirus experimental groups: G64S polymerase mutation
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Fidelity and Fitness: Mutation Rate/Pathogenicity
3D-G64S Virus Is Less Pathogenic than Wild-Type Virus in Mice
Competition between 3D-G64S and Wild-Type Virus in Mice
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Fidelity and Fitness: Virulence
• G64S species attenuated in transgenic mouse model for poliovirus infection
• Virulence determined by diversity of coinfecting population
• Quasispecies diversity, rather than the selection of individual variants, correlates with enhanced virulence
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Fidelity and Fitness: Attenuation
• Vaccine Design• Vignuzzi(2008): G64
engineered mutants stimulated high titers of neutralizing antibodies in mice
• Fidelity modulation as therapeutic strategy
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Future Perspectives
• How do models apply to infected hosts?• What is best measure of viral fitness in
dynamic population?• How does population diversity influence
pathogenesis (subpopulation cooperation)?
• Improved assays for characterizing viral populations
• Modern techniques: Deep sequencing, Molecular barcoding
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