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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1. Airaksinen, A.,, N. Pariente,, L. Menendez-Arias, and, E. Domingo. 2003. Curing of foot-and-mouth disease virus from persistently infected cells by ribavirin involves enhanced mutagenesis. Virology 311:339349.
2. Andrei, G.,, D. B. Gammon,, P. Fiten,, E. De Clercq,, G. Opdenakker,, R. Snoeck, and, D. H. Evans. 2006. Cidofovir resistance in vaccinia virus is linked to diminished virulence in mice. J. Virol. 80:93919401.
3. Arias, A.,, J. J. Arnold,, M. Sierra,, E. D. Smidansky,, E. Domingo, and, C. E. Cameron. 2008. Determinants of RNA-dependent RNA polymerase (in)fidelity revealed by kinetic analysis of the polymerase encoded by a foot-and-mouth disease virus mutant with reduced sensitivity to ribavirin. J. Virol. 82:1234612355.
4. Arnold, J. J., and, C. E. Cameron. 2000. Poliovirus RNA-dependent RNA polymerase (3Dpol). Assembly of stable, elongation-competent complexes by using a symmetrical primer-template substrate (sym/sub). J. Biol. Chem. 275:53295336.
5. Arnold, J. J., and, C. E. Cameron. 2004. Poliovirus RNA-dependent RNA polymerase (3Dpol): pre-steady-state kinetic analysis of ribonucleotide incorporation in the presence of Mg2+. Biochemistry 43:51265137.
6. Arnold, J. J.,, M. Vignuzzi,, J. K. Stone,, R. Andino, and, C. E. Cameron. 2005. Remote site control of an active site fidelity checkpoint in a viral RNA-dependent RNA polymerase. J. Biol. Chem. 280:2570625716.
7. Baltera, R. F., Jr., and, D. R. Tershak. 1989. Guanidine-resistant mutants of poliovirus have distinct mutations in peptide 2C. J. Virol. 63:44414444.
8. Batschelet, E.,, E. Domingo, and, C. Weissmann. 1976. The proportion of revertant and mutant phage in a growing population, as a function of mutation and growth rate. Gene 1:2732.
9. Brown, S. P. 2006. Cooperation: integrating evolutionary and ecological perspectives. Curr. Biol. 16:R960R961.
10. Castro, C.,, J. J. Arnold, and, C. E. Cameron. 2005. Incorporation fidelity of the viral RNA-dependent RNA polymerase: a kinetic, thermodynamic and structural perspective. Virus Res. 107:141149.
11. Contreras, A. M.,, Y. Hiasa,, W. He,, A. Terella,, E. V. Schmidt, and, R. T. Chung. 2002. Viral RNA mutations are region specific and increased by ribavirin in a full-length hepatitis C virus replication system. J. Virol. 76:85058517.
12. Crotty, S.,, C. Cameron, and, R. Andino. 2002. Ribavirin’s antiviral mechanism of action: lethal mutagenesis? J. Mol. Med. 80:8695.
13. Crotty, S.,, C. E. Cameron, and, R. Andino. 2001. RNA virus error catastrophe: direct molecular test by using ribavirin. Proc. Natl. Acad. Sci. USA 98:68956900.
14. Crotty, S.,, D. Maag,, J. J. Arnold,, W. Zhong,, J. Y. Lau,, Z. Hong,, R. Andino, and, C. E. Cameron. 2000. The broad-spectrum antiviral ribonucleoside ribavirin is an RNA virus mutagen. Nat. Med. 6:13751379.
15. Crotty, S.,, M. C. Saleh,, L. Gitlin,, O. Beske, and, R. Andino. 2004. The poliovirus replication machinery can escape inhibition by an antiviral drug that targets a host cell protein. J. Virol. 78:33783386.
16. Cuconati, A.,, A. Molla, and, E. Wimmer. 1998. Brefeldin A inhibits cell-free, de novo synthesis of poliovirus. J. Virol. 72:64566464.
17. Cuevas, J. M.,, F. Gonzalez-Candelas,, A. Moya, and, R. Sanjuan. 2009. Effect of ribavirin on the mutation rate and spectrum of hepatitis C virus in vivo. J. Virol. 83:57605764.
18. de la Torre, J. C.,, C. Giachetti,, B. L. Semler, and, J. J. Holland. 1992. High frequency of single-base transitions and extreme frequency of precise multiple-base reversion mutations in poliovirus. Proc. Natl. Acad. Sci. USA 89:25312535.
19. de la Torre, J. C.,, E. Wimmer, and, J. J. Holland. 1990. Very high frequency of reversion to guanidine resistance in clonal pools of guanidine-dependent type 1 poliovirus. J. Virol. 64:664671.
20. Dougherty, J. P., and, H. M. Temin. 1988. Determination of the rate of base-pair substitution and insertion mutations in retrovirus replication. J. Virol. 62:28172822.
21. Dougherty, J. P., and, H. M. Temin. 1986. High mutation rate of a spleen necrosis virus-based retrovirus vector. Mol. Cell. Biol. 6:43874395.
22. Drake, J. W. 1993. Rates of spontaneous mutation among RNA viruses. Proc. Natl. Acad. Sci. USA 90:41714175.
23. Drake, J. W. 1999. The distribution of rates of spontaneous mutation over viruses, prokaryotes, and eukaryotes. Ann. N. Y. Acad. Sci. 870:100107.
24. Drake, J. W.,, B. Charlesworth,, D. Charlesworth, and, J. F. Crow. 1998. Rates of spontaneous mutation. Genetics 148:16671686.
25. Drake, J. W., and, J. J. Holland. 1999. Mutation rates among RNA viruses. Proc. Natl. Acad. Sci. USA 96:1391013913.
26. Drosopoulos, W. C., and, V. R. Prasad. 1998. Increased misin-corporation fidelity observed for nucleoside analog resistance mutations M184V and E89G in human immunodeficiency virus type 1 reverse transcriptase does not correlate with the overall error rate measured in vitro. J. Virol. 72:42244230.
27. Eriksson, N.,, L. Pachter,, Y. Mitsuya,, S. Y. Rhee,, C. Wang,, B. Gharizadeh,, M. Ronaghi,, R. W. Shafer, and, N. Beerenwinkel. 2008. Viral population estimation using pyrosequencing. PLoS Comput. Biol. 4:e1000074.
28. Fox, M. P.,, M. J. Otto, and, M. A. McKinlay. 1986. Prevention of rhinovirus and poliovirus uncoating by WIN 51711, a new antiviral drug. Antimicrob. Agents Chemother. 30:110116.
29. Gammon, D. B.,, R. Snoeck,, P. Fiten,, M. Krecmerova,, A. Holy,, E. De Clercq,, G. Opdenakker,, D. H. Evans, and, G. Andrei. 2008. Mechanism of antiviral drug resistance of vaccinia virus: identification of residues in the viral DNA polymerase conferring differential resistance to antipoxvirus drugs. J. Virol. 82:1252012534.
30. Gohara, D. W.,, S. Crotty,, J. J. Arnold,, J. D. Yoder,, R. Andino, and, C. E. Cameron. 2000. Poliovirus RNA-dependent RNA polymerase (3Dpol): structural, biochemical, and biological analysis of conserved structural motifs A and B. J. Biol. Chem. 275:2552325532.
31. Gonzalez-Lopez, C.,, G. Gomez-Mariano,, C. Escarmis, and, E. Domingo. 2005. Invariant aphthovirus consensus nucleotide sequence in the transition to error catastrophe. Infect. Genet. Evol. 5:366374.
32. Graci, J. D., and, C. E. Cameron. 2004. Challenges for the development of ribonucleoside analogues as inducers of error catastrophe. Antivir. Chem. Chemother. 15:113.
33. Graci, J. D.,, D. A. Harki,, V. S. Korneeva,, J. P. Edathil,, K. Too,, D. Franco,, E. D. Smidansky,, A. V. Paul,, B. R. Peterson,, D. M. Brown,, D. Loakes, and, C. E. Cameron. 2007. Lethal mutagenesis of poliovirus mediated by a mutagenic pyrimidine analogue. J. Virol. 81:1125611266.
34. Grande-Perez, A.,, G. Gomez-Mariano,, P. R. Lowenstein, and, E. Domingo. 2005. Mutagenesis-induced, large fitness variations with an invariant arenavirus consensus genomic nucleotide sequence. J. Virol. 79:1045110459.
35. Grande-Perez, A.,, S. Sierra,, M. G. Castro,, E. Domingo, and, P. R. Lowenstein. 2002. Molecular indetermination in the transition to error catastrophe: systematic elimination of lymphocytic choriomeningitis virus through mutagenesis does not correlate linearly with large increases in mutant spectrum complexity. Proc. Natl. Acad. Sci. USA 99:1293812943.
36. Griffiths, A., and, D. M. Coen. 2003. High-frequency phenotypic reversion and pathogenicity of an acyclovir-resistant herpes simplex virus mutant. J. Virol. 77:22822286.
37. Hall, J. D.,, D. M. Coen,, B. L. Fisher,, M. Weisslitz,, S. Randall,, R. E. Almy,, P. T. Gelep, and, P. A. Schaffer. 1984. Generation of genetic diversity in herpes simplex virus: an antimutator phenotype maps to the DNA polymerase locus. Virology 132:2637.
38. Hall, J. D.,, P. A. Furman,, M. H. St. Clair, and, C. W. Knopf. 1985. Reduced in vivo mutagenesis by mutant herpes simplex DNA polymerase involves improved nucleotide selection. Proc. Natl. Acad. Sci USA 82:38893893.
39. Hamburgh, M. E.,, W. C. Drosopoulos, and, V. R. Prasad. 1998. The influence of 3TC-resistance mutations E89G and M184V in the human immunodeficiency virus reverse transcriptase on mispair extension efficiency. Nucleic Acids Res. 26:43894394.
40. Hansen, J. L.,, A. M. Long, and, S. C. Schultz. 1997. Structure of the RNA-dependent RNA polymerase of poliovirus. Structure 5:11091122.
41. Harki, D. A.,, J. D. Graci,, J. P. Edathil,, C. Castro,, C. E. Cameron, and, B. R. Peterson. 2007. Synthesis of a universal 5-nitroindole ribonucleotide and incorporation into RNA by a viral RNA-dependent RNA polymerase. ChemBioChem 8:13591362.
42. Harki, D. A.,, J. D. Graci,, J. E. Galarraga,, W. J. Chain,, C. E. Cameron, and, B. R. Peterson. 2006. Synthesis and antiviral activity of 5-substituted cytidine analogues: identification of a potent inhibitor of viral RNA-dependent RNA polymerases. J. Med. Chem. 49:61666169.
43. Harris, K. S.,, W. Brabant,, S. Styrchak,, A. Gall, and, R. Daifuku. 2005. KP-1212/1461, a nucleoside designed for the treatment of HIV by viral mutagenesis. Antiviral Res. 67:19.
44. Holland, J. J.,, J. C. de la Torre,, D. A. Steinhauer,, D. Clarke,, E. Duarte, and, E. Domingo. 1989. Virus mutation frequencies can be greatly underestimated by monoclonal antibody neutralization of virions. J. Virol. 63:50305036.
45. Hsu, M.,, P. Inouye,, L. Rezende,, N. Richard,, Z. Li,, V. R. Prasad, and, M. A. Wainberg. 1997. Higher fidelity of RNA-dependent DNA mispair extension by M184V drug-resistant than wild-type reverse transcriptase of human immunodeficiency virus type 1. Nucleic Acids Res. 25:45324536.
46. Hwang, C. B., and, H. J. Chen. 1995. An altered spectrum of herpes simplex virus mutations mediated by an antimutator DNA polymerase. Gene 152:191193.
47. Hwang, Y. T.,, B. Y. Liu, and, C. B. Hwang. 2002. Replication fidelity of the supF gene integrated in the thymidine kinase locus of herpes simplex virus type 1. J. Virol. 76:36053614.
48. Irurzun, A.,, L. Perez, and, L. Carrasco. 1992. Involvement of membrane traffic in the replication of poliovirus genomes: effects of brefeldin A. Virology 191:166175.
49. Jonckheere, H.,, E. De Clercq, and, J. Anne. 2000. Fidelity analysis of HIV-1 reverse transcriptase mutants with an altered amino-acid sequence at residues Leu74, Glu89, Tyr115, Tyr183 and Met184. Eur. J. Biochem. 267:26582665.
50. Korneeva, V. S., and, C. E. Cameron. 2007. Structure-function relationships of the viral RNA-dependent RNA polymerase: fidelity, replication speed, and initiation mechanism determined by a residue in the ribose-binding pocket. J. Biol. Chem. 282:1613516145.
51. Kuss, S. K.,, C. A. Etheredge, and, J. K. Pfeiffer. 2008. Multiple host barriers restrict poliovirus trafficking in mice. PLoS Pathog. 4:e1000082.
52. Lanford, R. E.,, D. Chavez,, B. Guerra,, J. Y. Lau,, Z. Hong,, K. M. Brasky, and, B. Beames. 2001. Ribavirin induces error-prone replication of GB virus B in primary tamarin hepatocytes. J. Virol. 75:80748081.
53. Lee, C. H.,, D. L. Gilbertson,, I. S. Novella,, R. Huerta,, E. Domingo, and, J. J. Holland. 1997. Negative effects of chemical mutagenesis on the adaptive behavior of vesicular stomatitis virus. J. Virol. 71:36363640.
54. Lutchman, G.,, S. Danehower,, B. C. Song,, T. J. Liang,, J. H. Hoofnagle,, M. Thomson, and, M. G. Ghany. 2007. Mutation rate of the hepatitis C virus NS5B in patients undergoing treatment with ribavirin monotherapy. Gastroenterology 132:17571766.
55. Marguerat, S.,, B. T. Wilhelm, and, J. Bahler. 2008. Next-generation sequencing: applications beyond genomes. Biochem. Soc. Trans. 36:10911096.
56. Maynell, L. A.,, K. Kirkegaard, and, M. W. Klymkowsky. 1992. Inhibition of poliovirus RNA synthesis by brefeldin A. J. Virol. 66:19851994.
57. Mitsuya, Y.,, V. Varghese,, C. Wang,, T. F. Liu,, S. P. Holmes,, P. Jayakumar,, B. Gharizadeh,, M. Ronaghi,, D. Klein,, W. J. Fessel, and, R. W. Shafer. 2008. Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutations. J. Virol. 82:1074710755.
58. Monk, R. J.,, F. G. Malik,, D. Stokesberry, and, L. H. Evans. 1992. Direct determination of the point mutation rate of a murine retrovirus. J. Virol. 66:36833689.
59. Moriyama, K.,, T. Suzuki,, K. Negishi,, J. D. Graci,, C. N. Thompson,, C. E. Cameron, and, M. Watanabe. 2008. Effects of introduction of hydrophobic group on ribavirin base on mutation induction and anti-RNA viral activity. J. Med. Chem. 51:159166.
60. Nadell, C. D.,, J. B. Xavier, and, K. R. Foster. 2009. The socio-biology of biofilms. FEMS Microbiol. Rev. 33:206224.
61. Otto, M. J.,, M. P. Fox,, M. J. Fancher,, M. F. Kuhrt,, G. D. Diana, and, M. A. McKinlay. 1985. In vitro activity of WIN 51711, a new broad-spectrum antipicornavirus drug. Antimicrob. Agents Chemother. 27:883886.
62. Palmenberg, A., and, J. Sgro. 2002. Alignments and comparative profiles of picornavirus genera, p. 149–155. In B. Semler and, E. Wimmer (ed.), Molecular Biology of Picornaviruses. ASM Press, Washington, DC.
63. Pandey, V. N.,, N. Kaushik,, N. Rege,, S. G. Sarafianos,, P. N. Yadav, and, M. J. Modak. 1996. Role of methionine 184 of human immunodeficiency virus type-1 reverse transcriptase in the polymerase function and fidelity of DNA synthesis. Biochemistry 35:21682179.
64. Pariente, N.,, S. Sierra,, P. R. Lowenstein, and, E. Domingo. 2001. Efficient virus extinction by combinations of a mutagen and antiviral inhibitors. J. Virol. 75:97239730.
65. Parvin, J. D.,, A. Moscona,, W. T. Pan,, J. M. Leider, and, P. Palese. 1986. Measurement of the mutation rates of animal viruses: influenza A virus and poliovirus type 1. J. Virol. 59:377383.
66. Pathak, V. K., and, H. M. Temin. 1990. Broad spectrum of in vivo forward mutations, hypermutations, and mutational hotspots in a retroviral shuttle vector after a single replication cycle: deletions and deletions with insertions. Proc. Natl. Acad. Sci. USA 87:60246028.
67. Pathak, V. K., and, H. M. Temin. 1990. Broad spectrum of in vivo forward mutations, hypermutations, and mutational hot-spots in a retroviral shuttle vector after a single replication cycle: substitutions, frameshifts, and hypermutations. Proc. Natl. Acad. Sci. USA 87:60196023.
68. Pfeiffer, J. K., and, K. Kirkegaard. 2003. A single mutation in poliovirus RNA-dependent RNA polymerase confers resistance to mutagenic nucleotide analogs via increased fidelity. Proc. Natl. Acad. Sci. USA 100:72897294.
69. Pfeiffer, J. K., and, K. Kirkegaard. 2006. Bottleneck-mediated quasispecies restriction during spread of an RNA virus from inoculation site to brain. Proc. Natl. Acad. Sci. USA 103:55205525.
70. Pfeiffer, J. K., and, K. Kirkegaard. 2005. Increased fidelity reduces poliovirus fitness and virulence under selective pressure in mice. PLoS Pathog. 1:e11.
71. Pfister, T., and, E. Wimmer. 1999. Characterization of the nucleoside triphosphatase activity of poliovirus protein 2C reveals a mechanism by which guanidine inhibits poliovirus replication. J. Biol. Chem. 274:69927001.
72. Pincus, S. E.,, D. C. Diamond,, E. A. Emini, and, E. Wimmer. 1986. Guanidine-selected mutants of poliovirus: mapping of point mutations to polypeptide 2C. J. Virol. 57:638646.
73. Pincus, S. E., and, E. Wimmer. 1986. Production of guanidine-resistant and -dependent poliovirus mutants from cloned cDNA: mutations in polypeptide 2C are directly responsible for altered guanidine sensitivity. J. Virol. 60:793796.
74. Rezende, L. F.,, K. Curr,, T. Ueno,, H. Mitsuya, and, V. R. Prasad. 1998. The impact of multidideoxynucleoside resistance-conferring mutations in human immunodeficiency virus type 1 reverse transcriptase on polymerase fidelity and error specificity. J. Virol. 72:28902895.
75. Rezende, L. F.,, W. C. Drosopoulos, and, V. R. Prasad. 1998. The influence of 3TC resistance mutation M184I on the fidelity and error specificity of human immunodeficiency virus type 1 reverse transcriptase. Nucleic Acids Res. 26:30663072.
76. Rezende, L. F., and, V. R. Prasad. 2004. Nucleoside-analog resistance mutations in HIV-1 reverse transcriptase and their influence on polymerase fidelity and viral mutation rates. Int. J. Biochem. Cell Biol. 36:17161734.
77. Rigola, D.,, J. van Oeveren,, A. Janssen,, A. Bonne,, H. Schneiders,, H. J. van der Poel,, N. J. van Orsouw,, R. C. Hogers,, M. T. de Both, and, M. J. van Eijk. 2009. High-throughput detection of induced mutations and natural variation using KeyPoint technology. PLoS One 4:e4761.
78. Ruiz-Jarabo, C. M.,, C. Ly,, E. Domingo, and, J. C. de la Torre. 2003. Lethal mutagenesis of the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV). Virology 308:3747.
79. Sabo, D. L.,, E. Domingo,, E. F. Bandle,, R. A. Flavell, and, C. Weissmann. 1977. A guanosine to adenosine transition in the 3′ terminal extracistronic region of bacteriophage Q beta RNA leading to loss of infectivity. J. Mol. Biol. 112:235252.
80. Sedivy, J. M.,, J. P. Capone,, U. L. RajBhandary, and, P. A. Sharp. 1987. An inducible mammalian amber suppressor: propagation of a poliovirus mutant. Cell 50:379389.
81. Severson, W. E.,, C. S. Schmaljohn,, A. Javadian, and, C. B. Jonsson. 2003. Ribavirin causes error catastrophe during Hantaan virus replication. J. Virol. 77:481488.
82. Shah, F. S.,, K. A. Curr,, M. E. Hamburgh,, M. Parniak,, H. Mitsuya,, J. G. Arnez, and, V. R. Prasad. 2000. Differential influence of nucleoside analog-resistance mutations K65R and L74V on the overall mutation rate and error specificity of human immunodeficiency virus type 1 reverse transcriptase. J. Biol. Chem. 275:2703727044.
83. Shapiro, J. A. 1998. Thinking about bacterial populations as multicellular organisms. Annu. Rev. Microbiol. 52:81104.
84. Sierra, M.,, A. Airaksinen,, C. Gonzalez-Lopez,, R. Agudo,, A. Arias, and, E. Domingo. 2007. Foot-and-mouth disease virus mutant with decreased sensitivity to ribavirin: implications for error catastrophe. J. Virol. 81:20122024.
85. Sierra, S.,, M. Dávila,, P. R. Lowenstein, and, E. Domingo. 2000. Response of foot-and-mouth disease virus to increased mutagenesis: influence of viral load and fitness in loss of infectivity. J. Virol. 74:83168323.
86. Siwinska, M. E.,, M. Tabaczynski, and, W. J. Kunicki-Goldfinger. 1974. Effects of mutator, antimutator and wild-type DNA polymerase of T4 bacteriophage on mutation rates in rII cistrons of its own genome and in complemented amber mutants of gene 43. Acta Microbiol. Pol. A 6:6369.
87. Solmone, M.,, D. Vincenti,, M. C. Prosperi,, A. Bruselles,, G. Ippolito, and, M. R. Capobianchi. 2009. Use of massively parallel ultradeep pyrosequencing to characterize the genetic diversity of hepatitis B virus in drug-resistant and drug-naive patients and to detect minor variants in reverse transcriptase and hepatitis B S antigen. J. Virol. 83:17181726.
88. Steinhauer, D. A.,, J. C. de la Torre, and, J. J. Holland. 1989. High nucleotide substitution error frequencies in clonal pools of vesicular stomatitis virus. J. Virol. 63:20632071.
89. Suarez, P.,, J. Valcarcel, and, J. Ortin. 1992. Heterogeneity of the mutation rates of influenza A viruses: isolation of mutator mutants. J. Virol. 66:24912494.
90. Taddie, J. A., and, P. Traktman. 1991. Genetic characterization of the vaccinia virus DNA polymerase: identification of point mutations conferring altered drug sensitivities and reduced fidelity. J. Virol. 65:869879.
91. Tam, R. C.,, J. Y. Lau, and, Z. Hong. 2001. Mechanisms of action of ribavirin in antiviral therapies. Antivir. Chem. Chemother. 12:261272.
92. Thompson, A. A.,, R. A. Albertini, and, O. B. Peersen. 2007. Stabilization of poliovirus polymerase by NTP binding and fingers-thumb interactions. J. Mol. Biol. 366:14591474.
93. Thompson, A. A., and, O. B. Peersen. 2004. Structural basis for proteolysis-dependent activation of the poliovirus RNA-dependent RNA polymerase. EMBO J. 23:34623471.
94. Tian, W.,, Y. T. Hwang,, Q. Lu, and, C. B. Hwang. 2009. Finger domain mutation affects enzyme activity, DNA replication efficiency, and fidelity of an exonuclease-deficient DNA polymerase of herpes simplex virus type 1. J. Virol. 83:71947201.
95. Tsibris, A. M.,, B. Korber,, R. Arnaout,, C. Russ,, C. C. Lo,, T. Leitner,, B. Gaschen,, J. Theiler,, R. Paredes,, Z. Su,, M. D. Hughes,, R. M. Gulick,, W. Greaves,, E. Coakley,, C. Flexner,, C. Nusbaum, and, D. R. Kuritzkes. 2009. Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo. PLoS One 4:e5683.
96. Varela-Echavarria, A.,, N. Garvey,, B. D. Preston, and, J. P. Dougherty. 1992. Comparison of Moloney murine leukemia virus mutation rate with the fidelity of its reverse transcriptase in vitro. J. Biol. Chem. 267:2468124688.
97. Vignuzzi, M.,, J. K. Stone, and, R. Andino. 2005. Ribavirin and lethal mutagenesis of poliovirus: molecular mechanisms, resistance and biological implications. Virus Res. 107:173181.
98. Vignuzzi, M.,, J. K. Stone,, J. J. Arnold,, C. E. Cameron, and, R. Andino. 2006. Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population. Nature 439:344348.
99. Vignuzzi, M.,, E. Wendt, and, R. Andino. 2008. Engineering attenuated virus vaccines by controlling replication fidelity. Nat. Med. 14:154161.
100. Wainberg, M. A.,, W. C. Drosopoulos,, H. Salomon,, M. Hsu,, G. Borkow,, M. Parniak,, Z. Gu,, Q. Song,, J. Manne,, S. Islam,, G. Castriota, and, V. R. Prasad. 1996. Enhanced fidelity of 3TC-selected mutant HIV-1 reverse transcriptase. Science 271:12821285.
101. Wang, C.,, Y. Mitsuya,, B. Gharizadeh,, M. Ronaghi, and, R. W. Shafer. 2007. Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res. 17:11951201.
102. Ward, C. D., and, J. B. Flanegan. 1992. Determination of the poliovirus RNA polymerase error frequency at eight sites in the viral genome. J. Virol. 66:37843793.
103. Whitney, J. B.,, M. Oliveira,, M. Detorio,, Y. Guan, and, M. A. Wainberg. 2002. The M184V mutation in reverse transcriptase can delay reversion of attenuated variants of simian immunodeficiency virus. J. Virol. 76:89588962.
104. Winters, M. A.,, R. W. Shafer,, R. A. Jellinger,, G. Mamtora,, T. Gingeras, and, T. C. Merigan. 1997. Human immunodeficiency virus type 1 reverse transcriptase genotype and drug susceptibility changes in infected individuals receiving dideoxyinosine monotherapy for 1 to 2 years. Antimicrob. Agents Chemother. 41:757762.
105. Zeichhardt, H.,, M. J. Otto,, M. A. McKinlay,, P. Willingmann, and, K. O. Habermehl. 1987. Inhibition of poliovirus uncoating by disoxaril (WIN 51711). Virology 160:281285.
106. Zhou, S.,, R. Liu,, B. M. Baroudy,, B. A. Malcolm, and, G. R. Reyes. 2003. The effect of ribavirin and IMPDH inhibitors on hepatitis C virus subgenomic replicon RNA. Virology 310:333342.

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