Monitoring sequence space as a test for the target of selection in viruses

Journal of Molecular Biology

Volumn 345, Issue 3, 2005, Pages 451-459

  Perales, Celia ^a   Martín, Verónica ^a   Ruiz Jarabo, Carmen M ^a   Domingo, Esteban ^a  

^a UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

Author keywords

foot and mouth disease virus; monoclonal antibody escape; target of selection; viral quasispecies

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; CONTROLLED STUDY; FOOT AND MOUTH DISEASE VIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROGENY; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; VIRUS GENOME; VIRUS MUTANT;

FOOT-AND-MOUTH DISEASE VIRUS;

EID: 9644273913     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.10.066     Document Type: Article

References (55)

1. M. Eigen, and P. Schuster The hypercycle. A principle of natural self-organization 1979 Springer Berlin
2. M. Eigen, and C.K. Biebricher Sequence space and quasispecies distribution E. Domingo P. Ahlquist J.J. Holland RNA Genetics Vol. 3 1988 CRC Press Boca Raton, FL 211 245
3. E. Domingo, C. Biebricher, M. Eigen, and J.J. Holland Quasispecies and RNA virus evolution: principles and consequences 2001 Landes Bioscience Austin
4. M. Eigen, J. McCaskill, and P. Schuster Molecular quasi-species J. Phys. Chem. 92 1988 6881 6891
5. P. Schuster, and P.F. Stadler Nature and evolution of early replicons E. Domingo R.G. Webster J.J. Holland Origin and Evolution of Viruses 1999 Academic Press San Diego 1 24
6. M. Eigen Natural selection: a phase transition? Biophys. Chem. 85 2000 101 123
7. C.O. Wilke, C. Ronnewinkel, and T. Martinetz Dynamic fitness landscapes in molecular evolution Phys. Rep. 349 2001 395 446
8. E. Domingo Quasispecies A. Granoff R.G. Webster Encyclopedia of Virology 1999 Academic Press London 1431 1436
9. E.A. Duarte, I.S. Novella, S.C. Weaver, E. Domingo, S. Wain-Hobson, and D.K. Clarke RNA virus quasispecies: significance for viral disease and epidemiology Infect. Agents Dis. 3 1994 201 214
10. E. Domingo Quasispecies and the development of new antiviral strategies Prog. Drug Res. 60 2003 133 158
11. E. Baranowski, C.M. Ruíz-Jarabo, N. Pariente, N. Verdaguer, and E. Domingo Evolution of cell recognition by viruses: a source of biological novelty with medical implications Advan. Virus Res. 62 2003 19 111
12. J.C. de la Torre, and J.J. Holland RNA virus quasispecies populations can suppress vastly superior mutant progeny J. Virol. 64 1990 6278 6281
13. K.M. Chumakov, L.B. Powers, K.E. Noonan, I.B. Roninson, and I.S. Levenbook Correlation between amount of virus with altered nucleotide sequence and the monkey test for acceptability of oral poliovirus vaccine Proc. Natl Acad. Sci. USA 88 1991 199 203
14. B. Borrego, I.S. Novella, E. Giralt, D. Andreu, and E. Domingo Distinct repertoire of antigenic variants of foot-and-mouth disease virus in the presence or absence of immune selection J. Virol. 67 1993 6071 6079
15. M.N. Teng, M.B. Oldstone, and J.C. de la Torre Suppression of lymphocytic choriomeningitis virus - induced growth hormone deficiency syndrome by disease-negative virus variants Virology 223 1996 113 119
16. C. González-López, A. Arias, N. Pariente, G. Gómez-Mariano, and E. Domingo Preextinction viral RNA can interfere with infectivity J. Virol. 78 2004 3319 3324
17. A. Arias, E. Lázaro, C. Escarmís, and E. Domingo Molecular intermediates of fitness gain of an RNA virus: characterization of a mutant spectrum by biological and molecular cloning J. Gen. Virol. 82 2001 1049 1060
18. A. Arias, C.M. Ruiz-Jarabo, C. Escarmis, and E. Domingo Fitness increase of memory genomes in a viral quasispecies J. Mol. Biol. 339 2004 405 412
19. C. Briones, E. Domingo, and C. Molina-París Memory in retroviral quasispecies: experimental evidence and theoretical model for human immunodeficiency virus J. Mol. Biol. 331 2003 213 229
20. C.M. Ruíz-Jarabo, A. Arias, E. Baranowski, C. Escarmís, and E. Domingo Memory in viral quasispecies J. Virol. 74 2000 3543 3547
21. C.M. Ruíz-Jarabo, A. Arias, C. Molina-París, C. Briones, E. Baranowski, C. Escarmís, and E. Domingo Duration and fitness dependence of quasispecies memory J. Mol. Biol. 315 2002 285 296
22. C.M. Ruíz-Jarabo, E. Miller, G. Gómez-Mariano, and E. Domingo Synchronous loss of quasispecies memory in parallel viral lineages: a deterministic feature of viral quasispecies J. Mol. Biol. 333 2003 553 563
23. E. Batschelet, E. Domingo, and C. Weissmann The proportion of revertant and mutant phage in a growing population, as a function of mutation and growth rate Gene 1 1976 27 32
24. J.W. Drake, and J.J. Holland Mutation rates among RNA viruses Proc. Natl Acad. Sci. USA 96 1999 13910 13913
25. D.J. Rowlands ed. Foot-and-mouth disease Virus Res. 91 2003 1 161
26. F. Sobrino E. Domingo Foot and Mouth Disease: Current Perspectives 2004 Horizon Bioscience Wymondham
27. R. Acharya, E. Fry, D. Stuart, G. Fox, D. Rowlands, and F. Brown The three-dimensional structure of foot-and-mouth disease virus at 2.9 Å resolution Nature 337 1989 709 716
28. M.G. Mateu Antibody recognition of picornaviruses and escape from neutralization: a structural view Virus Res. 38 1995 1 24
29. F. Sobrino, M. Dávila, J. Ortín, and E. Domingo Multiple genetic variants arise in the course of replication of foot-and-mouth disease virus in cell culture Virology 128 1983 310 318
30. E. Baranowski, N. Sevilla, N. Verdaguer, C.M. Ruíz-Jarabo, E. Beck, and E. Domingo Multiple virulence determinants of foot-and-mouth disease virus in cell culture J. Virol. 72 1998 6362 6372
31. E. Baranowski, C.M. Ruíz-Jarabo, N. Sevilla, D. Andreu, E. Beck, and E. Domingo Cell recognition by foot-and-mouth disease virus that lacks the RGD integrin-binding motif: flexibility in aphthovirus receptor usage J. Virol. 74 2000 1641 1647
32. C.M. Ruíz-Jarabo, N. Pariente, E. Baranowski, M. Dávila, G. Gómez-Mariano, and E. Domingo Expansion of host-cell tropism of foot-and-mouth disease virus despite replication in a constant environment J. Gen. Virol. 85 2004 2289 2297
33. E. Baranowski, C.M. Ruiz-Jarabo, and E. Domingo Evolution of cell recognition by viruses Science 292 2001 1102 1105
34. B. Baxt, D.O. Morgan, B.H. Robertson, and C.A. Timpone Epitopes on foot-and-mouth disease virus outer capsid protein VP1 involved in neutralization and cell attachment J. Virol. 51 1984 298 305
35. 3) inhibit binding and infection of foot-and-mouth disease virus to cultured cells J. Virol. 69 1995 2664 2666
36. T. Jackson, A.M. King, D.I. Stuart, and E. Fry Structure and receptor binding Virus Res. 91 2003 33 46
37. M.G. Mateu, M.A. Martínez, L. Capucci, D. Andreu, E. Giralt, and F. Sobrino A single amino acid substitution affects multiple overlapping epitopes in the major antigenic site of foot-and-mouth disease virus of serotype C J. Gen. Virol. 71 1990 629 637
38. N. Verdaguer, M.G. Mateu, D. Andreu, E. Giralt, E. Domingo, and I. Fita Structure of the major antigenic loop of foot-and-mouth disease virus complexed with a neutralizing antibody: direct involvement of the Arg-Gly-Asp motif in the interaction EMBO J. 14 1995 1690 1696
39. M.G. Mateu, M.L. Valero, D. Andreu, and E. Domingo Systematic replacement of amino acid residues within an Arg-Gly-Asp-containing loop of foot-and-mouth disease virus and effect on cell recognition J. Biol. Chem. 271 1996 12814 12819
40. E. Baranowski, C.M. Ruíz-Jarabo, P. Lim, and E. Domingo Foot-and-mouth disease virus lacking the VP1 G-H loop: the mutant spectrum uncovers interactions among antigenic sites for fitness gain Virology 288 2001 192 202
41. C.M. Ruíz-Jarabo, N. Sevilla, M. Dávila, G. Gómez-Mariano, E. Baranowski, and E. Domingo Antigenic properties and population stability of a foot-and-mouth disease virus with an altered Arg-Gly-Asp receptor-recognition motif J. Gen. Virol. 80 1999 1899 1909
42. M.A. Martínez, C. Carrillo, F. González-Candelas, A. Moya, E. Domingo, and F. Sobrino Fitness alteration of foot-and-mouth disease virus mutants: measurement of adaptability of viral quasispecies J. Virol. 65 1991 3954 3957
43. A. Holguín, J. Hernández, M.A. Martínez, M.G. Mateu, and E. Domingo Differential restrictions on antigenic variation among antigenic sites of foot-and-mouth disease virus in the absence of antibody selection J. Gen. Virol. 78 1997 601 609
44. E. Domingo Viruses at the edge of adaptation Virology 270 2000 251 253
45. C. Escarmís, M. Dávila, and E. Domingo Multiple molecular pathways for fitness recovery of an RNA virus debilitated by operation of Muller's ratchet J. Mol. Biol. 285 1999 495 505
46. C. Escarmís, G. Gómez-Mariano, M. Dávila, E. Lázaro, and E. Domingo Resistance to extinction of low fitness virus subjected to plaque-to-plaque transfers: diversification by mutation clustering J. Mol. Biol. 315 2002 647 661
47. E. Lázaro, C. Escarmís, E. Domingo, and S.C. Manrubia Modeling viral genome fitness evolution associated with serial bottleneck events: evidence of stationary states of fitness J. Virol. 76 2002 8675 8681
48. E. Lazaro, C. Escarmis, J. Perez-Mercader, S.C. Manrubia, and E. Domingo Resistance of virus to extinction on bottleneck passages: study of a decaying and fluctuating pattern of fitness loss Proc. Natl Acad. Sci. USA 100 2003 10830 10835
49. S. Maisnier-Patin, and D.I. Andersson Adaptation to the deleterious effects of antimicrobial drug resistance mutations by compensatory evolution Res. Microbiol. 155 2004 360 369
50. M. Nijhuis, R. Schuurman, D. de Jong, J. Erickson, E. Gustchina, J. Albert, and P. Schipper Increased fitness of drug resistant HIV-1 protease as a result of acquisition of compensatory mutations during suboptimal therapy AIDS 13 1999 2349 2359
51. M.A. Martínez, N. Verdaguer, M.G. Mateu, and E. Domingo Evolution subverting essentiality: dispensability of the cell attachment Arg-Gly-Asp motif in multiply passaged foot-and-mouth disease virus Proc. Natl Acad. Sci. USA 94 1997 6798 6802
52. E. Domingo, M. Dávila, and J. Ortín Nucleotide sequence heterogeneity of the RNA from a natural population of foot-and-mouth-disease virus Gene 11 1980 333 346
53. C. Escarmís, M. Dávila, N. Charpentier, A. Bracho, A. Moya, and E. Domingo Genetic lesions associated with Muller's ratchet in an RNA virus J. Mol. Biol. 264 1996 255 267
54. M. Toja, C. Escarmis, and E. Domingo Genomic nucleotide sequence of a foot-and-mouth disease virus clone and its persistent derivatives. Implications for the evolution of viral quasispecies during a persistent infection Virus Res. 64 1999 161 171
55. N. Charpentier, M. Dávila, E. Domingo, and C. Escarmís Long-term, large-population passage of aphthovirus can generate and amplify defective noninterfering particles deleted in the leader protease gene Virology 223 1996 10 18