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Quasispecies Theory and the Behavior of RNA Viruses
A large number of medically important viruses, including HIV, hepatitis C virus, and influenza, have RNA genomes. These viruses replicate with extremely high mutation rates and exhibit significant genetic diversity. This diversity allows a viral population to rapidly adapt to dynamic environments and evolve resistance to vaccines and antiviral drugs. For the last 30 years, quasispecies theory has provided a population-based framework for understanding RNA viral evolution. A quasispecies is a cloud of diverse variants that are genetically linked through mutation, interact cooperatively on a functional level, and collectively contribute to the characteristics of the population. Many predictions of quasispecies theory run counter to traditional views of microbial behavior and evolution and have profound implications for our understanding of viral disease. Here, we discuss basic principles of quasispecies theory and describe its relevance for our understanding of viral fitness, virulence, and antiviral therapeutic strategy.
Vyšlo v časopise: Quasispecies Theory and the Behavior of RNA Viruses. PLoS Pathog 6(7): e32767. doi:10.1371/journal.ppat.1001005
Kategorie: Review
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1001005Souhrn
A large number of medically important viruses, including HIV, hepatitis C virus, and influenza, have RNA genomes. These viruses replicate with extremely high mutation rates and exhibit significant genetic diversity. This diversity allows a viral population to rapidly adapt to dynamic environments and evolve resistance to vaccines and antiviral drugs. For the last 30 years, quasispecies theory has provided a population-based framework for understanding RNA viral evolution. A quasispecies is a cloud of diverse variants that are genetically linked through mutation, interact cooperatively on a functional level, and collectively contribute to the characteristics of the population. Many predictions of quasispecies theory run counter to traditional views of microbial behavior and evolution and have profound implications for our understanding of viral disease. Here, we discuss basic principles of quasispecies theory and describe its relevance for our understanding of viral fitness, virulence, and antiviral therapeutic strategy.
Zdroje
1. DomingoE
BaranowskiE
Ruiz-JaraboCM
Martin-HernandezAM
SaizJC
1998 Quasispecies structure and persistence of RNA viruses. Emerg Infect Dis 4 521 527
2. DomingoE
MartinV
PeralesC
Grande-PerezA
Garcia-ArriazaJ
2006 Viruses as quasispecies: biological implications. Curr Top Microbiol Immunol 299 51 82
3. DuffyS
ShackeltonLA
HolmesEC
2008 Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet 9 267 276
4. BeigelJH
FarrarJ
HanAM
HaydenFG
HyerR
2005 Avian influenza A (H5N1) infection in humans. N Engl J Med 353 1374 1385
5. DawoodFS
JainS
FinelliL
ShawMW
LindstromS
2009 Emergence of a novel swine-origin influenza A (H1N1) virus in humans. N Engl J Med 360 2605 2615
6. RambautA
PosadaD
CrandallKA
HolmesEC
2004 The causes and consequences of HIV evolution. Nat Rev Genet 5 52 61
7. FieldsBN
KnipeDM
HowleyPM
2007 Fields' virology Philadelphia Wolters Kluwer Health/Lippincott Williams & Wilkins2 v. (xix, 3091, I-3086 p.)
8. GeisbertTW
JahrlingPB
2004 Exotic emerging viral diseases: progress and challenges. Nat Med 10 S110 121
9. GerrishPJ
Garcia-LermaJG
2003 Mutation rate and the efficacy of antimicrobial drug treatment. Lancet Infect Dis 3 28 32
10. HollandJ
SpindlerK
HorodyskiF
GrabauE
NicholS
1982 Rapid evolution of RNA genomes. Science 215 1577 1585
11. EigenM
1971 Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften 58 465 523
12. BiebricherCK
EigenM
2006 What is a quasispecies? Curr Top Microbiol Immunol 299 1 31
13. EigenM
1993 Viral quasispecies. Sci Am 269 42 49
14. DomingoE
SaboD
TaniguchiT
WeissmannC
1978 Nucleotide sequence heterogeneity of an RNA phage population. Cell 13 735 744
15. BatscheletE
DomingoE
WeissmannC
1976 The proportion of revertant and mutant phage in a growing population, as a function of mutation and growth rate. Gene 1 27 32
16. SteinhauerDA
HollandJJ
1987 Rapid evolution of RNA viruses. Annu Rev Microbiol 41 409 433
17. VignuzziM
StoneJK
AndinoR
2005 Ribavirin and lethal mutagenesis of poliovirus: molecular mechanisms, resistance and biological implications. Virus Res 107 173 181
18. WilkeCO
2005 Quasispecies theory in the context of population genetics. BMC Evol Biol 5 44
19. OrrHA
2009 Fitness and its role in evolutionary genetics. Nat Rev Genet 10 531 539
20. Quinones-MateuME
ArtsEJ
2006 Virus fitness: concept, quantification, and application to HIV population dynamics. Curr Top Microbiol Immunol 299 83 140
21. DomingoE
HollandJJ
1997 RNA virus mutations and fitness for survival. Annu Rev Microbiol 51 151 178
22. de la TorreJC
HollandJJ
1990 RNA virus quasispecies populations can suppress vastly superior mutant progeny. J Virol 64 6278 6281
23. AaskovJ
BuzacottK
ThuHM
LowryK
HolmesEC
2006 Long-term transmission of defective RNA viruses in humans and Aedes mosquitoes. Science 311 236 238
24. WilkeCO
WangJL
OfriaC
LenskiRE
AdamiC
2001 Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature 412 331 333
25. BurchCL
ChaoL
2000 Evolvability of an RNA virus is determined by its mutational neighbourhood. Nature 406 625 628
26. CodoñerFM
DarósJ-A
SoléRV
ElenaSF
2006 The fittest versus the flattest: experimental confirmation of the quasispecies effect with subviral pathogens. PLoS Pathog 2 e136 doi:10.1371/journal.ppat.0020136
27. SanjuanR
CuevasJM
FurioV
HolmesEC
MoyaA
2007 Selection for Robustness in Mutagenized RNA Viruses. PLoS Genet 3 e93 doi:10.1371/journal.pgen.0030093
28. QuerJ
HersheyCL
DomingoE
HollandJJ
NovellaIS
2001 Contingent neutrality in competing viral populations. J Virol 75 7315 7320
29. DraghiJA
ParsonsTL
WagnerGP
PlotkinJB
2010 Mutational robustness can facilitate adaptation. Nature 463 353 355
30. AriënKK
TroyerRM
GaliY
ColebundersRL
ArtsEJ
2005 Replicative fitness of historical and recent HIV-1 isolates suggests HIV-1 attenuation over time. AIDS 19 1555 1564
31. RichmanDD
2006 Antiviral drug resistance. Antiviral Res 71 117 121
32. RollandM
BranderC
NickleDC
HerbeckJT
GottliebGS
2007 HIV-1 over time: fitness loss or robustness gain? Nat Rev Microbiol 5 1 2
33. KoelleK
CobeyS
GrenfellB
PascualM
2006 Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science 314 1898 1903
34. OverbaughJ
BanghamCR
2001 Selection forces and constraints on retroviral sequence variation. Science 292 1106 1109
35. SanjuánR
MoyaA
ElenaSF
2004 The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc Natl Acad Sci USA 101 8396 8401
36. ElenaSF
SanjuánR
2005 Adaptive value of high mutation rates of RNA viruses: separating causes from consequences. J Virol 79 11555 11558
37. HolmesEC
2003 Error thresholds and the constraints to RNA virus evolution. Trends Microbiol 11 543 546
38. BiebricherCK
EigenM
2005 The error threshold. Virus Res 107 117 127
39. EigenM
2002 Error catastrophe and antiviral strategy. Proc Natl Acad Sci USA 99 13374 13376
40. HollandJJ
DomingoE
de la TorreJC
SteinhauerDA
1990 Mutation frequencies at defined single codon sites in vesicular stomatitis virus and poliovirus can be increased only slightly by chemical mutagenesis. J Virol 64 3960 3962
41. LeeCH
GilbertsonDL
NovellaIS
HuertaR
DomingoE
1997 Negative effects of chemical mutagenesis on the adaptive behavior of vesicular stomatitis virus. J Virol 71 3636 3640
42. CrottyS
CameronCE
AndinoR
2001 RNA virus error catastrophe: direct molecular test by using ribavirin. Proc Natl Acad Sci U S A 98 6895 6900
43. CrottyS
MaagD
ArnoldJJ
ZhongW
LauJY
2000 The broad-spectrum antiviral ribonucleoside ribavirin is an RNA virus mutagen. Nat Med 6 1375 1379
44. DomingoE
ParienteN
AiraksinenA
Gonzaĺez-LopezC
SierraS
2005 Foot-and-mouth disease virus evolution: exploring pathways towards virus extinction. Curr Top Microbiol Immunol 288 149 173
45. Grande-PerezA
Gomez-MarianoG
LowensteinPR
DomingoE
2005 Mutagenesis-induced, large fitness variations with an invariant arenavirus consensus genomic nucleotide sequence. J Virol 79 10451 10459
46. Grande-PerezA
LazaroE
LowensteinP
DomingoE
ManrubiaSC
2005 Suppression of viral infectivity through lethal defection. Proc Natl Acad Sci U S A 102 4448 4452
47. Grande-PerezA
SierraS
CastroMG
DomingoE
LowensteinPR
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 U S A 99 12938 12943
48. SierraS
DávilaM
LowensteinPR
DomingoE
2000 Response of foot-and-mouth disease virus to increased mutagenesis: influence of viral load and fitness in loss of infectivity. J Virol 74 8316 8323
49. MalimMH
2009 APOBEC proteins and intrinsic resistance to HIV-1 infection. Philos Trans R Soc Lond, B, Biol Sci 364 675 687
50. SheehyAM
GaddisNC
ChoiJD
MalimMH
2002 Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein. Nature 418 646 650
51. HarrisRS
BishopKN
SheehyAM
CraigHM
Petersen-MahrtSK
2003 DNA deamination mediates innate immunity to retroviral infection. Cell 113 803 809
52. MangeatB
TurelliP
CaronG
FriedliM
PerrinL
2003 Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts. Nature 424 99 103
53. ZhangH
YangB
PomerantzRJ
ZhangC
ArunachalamSC
2003 The cytidine deaminase CEM15 induces hypermutation in newly synthesized HIV-1 DNA. Nature 424 94 98
54. VartanianJP
MeyerhansA
SalaM
Wain-HobsonS
1994 G→A hypermutation of the human immunodeficiency virus type 1 genome: evidence for dCTP pool imbalance during reverse transcription. Proc Natl Acad Sci U S A 91 3092 3096
55. KiefferTL
KwonP
NettlesRE
HanY
RaySC
2005 G→A hypermutation in protease and reverse transcriptase regions of human immunodeficiency virus type 1 residing in resting CD4+ T cells in vivo. J Virol 79 1975 1980
56. JaniniM
RogersM
BirxDR
McCutchanFE
2001 Human immunodeficiency virus type 1 DNA sequences genetically damaged by hypermutation are often abundant in patient peripheral blood mononuclear cells and may be generated during near-simultaneous infection and activation of CD4(+) T cells. J Virol 75 7973 7986
57. HolmesRK
MalimMH
BishopKN
2007 APOBEC-mediated viral restriction: not simply editing? Trends Biochem Sci 32 118 128
58. AndersonJP
DaifukuR
LoebLA
2004 Viral error catastrophe by mutagenic nucleosides. Annu Rev Microbiol 58 183 205
59. SeversonWE
SchmaljohnCS
JavadianA
JonssonCB
2003 Ribavirin causes error catastrophe during Hantaan virus replication. J Virol 77 481 488
60. HofmannWP
HerrmannE
SarrazinC
ZeuzemS
2008 Ribavirin mode of action in chronic hepatitis C: from clinical use back to molecular mechanisms. Liver Int 28 1332 1343
61. Ruiz-JaraboCM
LyC
DomingoE
de la TorreJC
2003 Lethal mutagenesis of the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV). Virology 308 37 47
62. McCormickJB
KingIJ
WebbPA
ScribnerCL
CravenRB
1986 Lassa fever. Effective therapy with ribavirin. N Engl J Med 314 20 26
63. LoebLA
EssigmannJM
KazaziF
ZhangJ
RoseKD
1999 Lethal mutagenesis of HIV with mutagenic nucleoside analogs. Proc Natl Acad Sci USA 96 1492 1497
64. LoebLA
MullinsJI
2000 Lethal mutagenesis of HIV by mutagenic ribonucleoside analogs. AIDS Res Hum Retroviruses 16 1 3
65. HarrisKS
BrabantW
StyrchakS
GallA
DaifukuR
2005 KP-1212/1461, a nucleoside designed for the treatment of HIV by viral mutagenesis. Antiviral Res 67 1 9
66. Gonzalez-LopezC
AriasA
ParienteN
Gomez-MarianoG
DomingoE
2004 Preextinction viral RNA can interfere with infectivity. J Virol 78 3319 3324
67. SpringmanR
KellerT
MolineuxI
BullJ
2009 Evolution at a High Imposed Mutation Rate: Adaptation Obscures the Load in Phage T7. Genetics
68. GiffordRJ
RheeS-Y
ErikssonN
LiuTF
KiuchiM
2008 Sequence editing by Apolipoprotein B RNA-editing catalytic component [corrected] and epidemiological surveillance of transmitted HIV-1 drug resistance. AIDS 22 717 725
69. PillaiSK
WongJK
BarbourJD
2008 Turning up the volume on mutational pressure: is more of a good thing always better? (A case study of HIV-1 Vif and APOBEC3). Retrovirology 5 26
70. MulderLCF
HarariA
SimonV
2008 Cytidine deamination induced HIV-1 drug resistance. Proc Natl Acad Sci USA 105 5501 5506
71. ParienteN
SierraS
AiraksinenA
2005 Action of mutagenic agents and antiviral inhibitors on foot-and-mouth disease virus. Virus Res 107 183 193
72. ParienteN
AiraksinenA
DomingoE
2003 Mutagenesis versus inhibition in the efficiency of extinction of foot-and-mouth disease virus. J Virol 77 7131 7138
73. ArnoldJJ
VignuzziM
StoneJK
AndinoR
CameronCE
2005 Remote site control of an active site fidelity checkpoint in a viral RNA-dependent RNA polymerase. J Biol Chem 280 25706 25716
74. PfeifferJK
KirkegaardK
2003 A single mutation in poliovirus RNA-dependent RNA polymerase confers resistance to mutagenic nucleotide analogs via increased fidelity. Proc Natl Acad Sci U S A 100 7289 7294
75. PfeifferJK
KirkegaardK
2005 Increased fidelity reduces poliovirus fitness and virulence under selective pressure in mice. PLoS Pathog 1 e11 doi:10.1371/journal.ppat.0010011
76. VignuzziM
StoneJK
ArnoldJJ
CameronCE
AndinoR
2006 Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population. Nature 439 344 348
77. VignuzziM
WendtE
AndinoR
2008 Engineering attenuated virus vaccines by controlling replication fidelity. Nat Med 14 154 161
78. RacanielloVR
2006 One hundred years of poliovirus pathogenesis. Virology 344 9 16
79. RenRB
CostantiniF
GorgaczEJ
LeeJJ
RacanielloVR
1990 Transgenic mice expressing a human poliovirus receptor: a new model for poliomyelitis. Cell 63 353 362
80. BushmanFD
HoffmannC
RonenK
MalaniN
MinkahN
2008 Massively parallel pyrosequencing in HIV research. Aids 22 1411 1415
81. ErikssonN
PachterL
MitsuyaY
RheeSY
WangC
2008 Viral population estimation using pyrosequencing. PLoS Comput Biol 4 e1000074 doi:10.1371/journal.pcbi.1000074
82. Margeridon-ThermetS
ShulmanNS
AhmedA
ShahriarR
LiuT
2009 Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients. J Infect Dis 199 1275 1285
83. MazurkiewiczP
TangCM
BooneC
HoldenDW
2006 Signature-tagged mutagenesis: barcoding mutants for genome-wide screens. Nat Rev Genet 7 929 939
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Článek The Role of Coupled Positive Feedback in the Expression of the SPI1 Type Three Secretion System inČlánek A Systems Immunology Approach to Plasmacytoid Dendritic Cell Function in Cytopathic Virus Infections
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