Chapter 13 : Biological Implications of Picornavirus Fidelity Mutants

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That RNA viruses have extreme mutation frequencies that permit them to rapidly adapt and evolve to changing environments is a well-established fact. The first description of viral polymerase fidelity variants and their effects on mutation frequency was made in 1974, with mutator and antimutator strains of DNA bacteriophage T4. Since RNA viruses are notorious for generating resistance to virtually every antiviral compound, it was not surprising that the isolation of ribavirin-resistant poliovirus would soon follow the demonstration of this compound as an RNA mutagen. The reasoning was that a population that was passaged several times in tissue culture would have had the opportunity to expand into a diverse quasispecies. Lower-fidelity viruses, which would expectedly be more sensitive to RNA mutagens, would likely be the first variants to be removed from the population in the screens used above to identify higher-fidelity polymerases. The identification and characterization of G64S polymerase have already unlocked a wealth of knowledge on how viral RdRps dictate copying fidelity and mutation rate. Importantly, the data obtained using these first RdRp fidelity variants revealed that the polymerase error rate does indeed play a key role in the observed mutation frequencies of RNA viruses. The recent isolation and characterization of higher- and lower-fidelity RdRps of picornaviruses suggest that viral RNA polymerase fidelity is more flexible than once thought and that nature has indeed selected for a less-than-perfect fidelity to benefit adaptation.

Citation: Vignuzzi M, Andino R. 2010. Biological Implications of Picornavirus Fidelity Mutants, p 213-227. In Ehrenfeld E, Domingo E, Roos R (ed), The Picornaviruses. ASM Press, Washington, DC. doi: 10.1128/9781555816698.ch13
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Image of Figure 1.
Figure 1.

Treatment of poliovirus with ribavirin. Sequencing individual viruses in a wild-type poliovirus population reveals that, on average, each progeny genome bears two mutations with respect to the consensus sequence. Treatment with ribavirin increases the mutation frequency of poliovirus. Even moderate increases in the mutation frequency (>2-fold) result in significant reductions of specific infectivity and can lead to extinction of the virus population by lethal mutagenesis. The studies revealed that poliovirus exists very close to an extinction threshold, where genetic diversity is at a maximum but beyond which the mutational load is too high to sustain the viral population. LI0, 50% loss of specific infectivity. (Adapted from [ ] with permission. Copyright 2001, National Academy of Sciences, USA.)

Citation: Vignuzzi M, Andino R. 2010. Biological Implications of Picornavirus Fidelity Mutants, p 213-227. In Ehrenfeld E, Domingo E, Roos R (ed), The Picornaviruses. ASM Press, Washington, DC. doi: 10.1128/9781555816698.ch13
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Image of Figure 2.
Figure 2.

Schematics of the virus quasispecies. (Top left) The sequence space occupied by a wild-type poliovirus population presenting a genetically diverse quasispecies. The center point (black circle) represents the consensus sequence that, because of high polymerase error, is presented by fewer than half of the virus population. Radiating from the center of the sequence space (black circle) are mutants bearing a 1-nucleotide difference from the consensus (open circles), two mutations (small gray circles), three mutations (small black circles), and so on. The diverse quasispecies is such that most mutants are already present at low frequency in the population: mutants that may become enriched by selection from immune responses, tissue-specific constraints (tropism), or bottlenecks (anatomical or during transmission). Because of a high mutation frequency, wild-type virus can regenerate its diversity, even if one such subpopulation is favored at some point in the infection. A wild-type population might favor a quasispecies that allows for a maximum of “movement” along the sequence space. (Top right) Representation of the G64S population, in which the majority of members are perfect copies of the consensus. This population does not have potentially beneficial mutations already present within its repertoire. It is “stuck” in sequence space. Even if the required adaptive or escape mutants were generated, the population might not be able to return to consensus following the selective pressure because of its lower mutation frequency. The race against time and the immune response might be lost as a result. (Bottom left) Possible structures of quasispecies bearing the same consensus sequence. Due to the limitations of classic Sanger sequencing, it is not possible to determine whether the distribution of mutants present within a quasispecies is “symmetrical” or whether it resembles more a constellation of minority variants built around a central consensus sequence. New sequencing technologies are needed to better describe how viruses occupy sequence space. (Bottom right) Study of the population dynamics of RNA viruses in vivo. The majority of work in virology has focused on consensus sequence studies and often describes infection in terms of input virus and virus at the end point. The field has not explored how a virus population expands and contracts, and possibly compartmentalizes, during infection. (Further information is available at http://www.vignuzzilab.eu; see also Chapter 12.)

Citation: Vignuzzi M, Andino R. 2010. Biological Implications of Picornavirus Fidelity Mutants, p 213-227. In Ehrenfeld E, Domingo E, Roos R (ed), The Picornaviruses. ASM Press, Washington, DC. doi: 10.1128/9781555816698.ch13
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