From Quasispecies Theory to Viral Quasispecies: How Complexity has Permeated Virology

E. Domingo; C. Perales

doi:10.1051/mmnp/20127508

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From Quasispecies Theory to Viral Quasispecies: How Complexity has Permeated Virology

E. Domingo ^1,^2,³ ; C. Perales ^1,³

¹ Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM) Campus de Cantoblanco 28049, Madrid, Spain
² Centro de Astrobiología (CSIC-INTA), Instituto Nacional de Técnica Aeroespacial Ctra. de Torrejón a Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
³ Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08036 Barcelona, Spain

Mathematical modelling of natural phenomena, Tome 7 (2012) no. 5, pp. 105-122.

Voir la notice de l'article provenant de la source EDP Sciences

Résumé

RNA viruses replicate as complex and dynamic mutant distributions. They are termed viral quasispecies, in recognition of the fundamental contribution of quasispecies theory in our understanding of error-prone replicative entities. Viral quasispecies have launched a fertile field of transdiciplinary research, both experimental and theoretical. Here we review the origin and some implications of the quasispecies concept, with emphasis on internal interactions among components of the same mutant virus ensemble, a critical fact to design new antiviral strategies. We make the distinction between “intrinsic” and “extrinsic” properties of mutant distributions, and emphasize that there are several levels of complexity that can influence viral quasispecies behavior.

DOI : 10.1051/mmnp/20127508

Affiliations des auteurs :

E. Domingo ^{1, 2, 3} ; C. Perales ^{1, 3}

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E. Domingo; C. Perales. From Quasispecies Theory to Viral Quasispecies: How Complexity has Permeated Virology. Mathematical modelling of natural phenomena, Tome 7 (2012) no. 5, pp. 105-122. doi : 10.1051/mmnp/20127508. http://geodesic.mathdoc.fr/articles/10.1051/mmnp/20127508/

Bibliographie
Cité par

[1] V.I. Agol. Picornaviruses as a model for studying the nature of RNA recombination. In : The Picornaviruses. E. Ehrenfeld, E. Domingo and R.P. Roos, eds, ASM Press, Washington DC. pp. 239–252, 2010.

[2] A. Airaksinen, N. Pariente, L. Menendez-Arias, E. Domingo Virology 2003 339 349

[3] R. Antia, R.R. Regoes, J.C. Koella, C.T. Bergstrom Nature 2003 658 661

[4] A. Arias, R. Agudo, C. Ferrer-Orta, R. Perez-Luque, A. Airaksinen, E. Brocchi, E. Domingo, N. Verdaguer, C. Escarmis J. Mol. Biol. 2005 1021 1032

[5] E. Batschelet, E. Domingo, C. Weissmann Gene 1976 27 32

[6] A. Bernad, L. Blanco, J.M. Lazaro, G. Martin, M. Salas Cell 1989 219 228

[7] C.K. Biebricher, M. Eigen Virus Res. 2005 117 127

[8] B. Borrego, I.S. Novella, E. Giralt, D. Andreu, E. Domingo J. Virol. 1993 6071 6079

[9] M.J. Buzon, T. Wrin, F.M. Codoner, J. Dalmau, P. Phung, A. Bonjoch, E. Coakley, B. Clotet, J. Martinez-Picado Journal of acquired immune deficiency syndromes (1999) 2011 109 117

[10] M. Clementi Clin Microbiol Infect 2008 629 631

[11] L.L. Coffey, Y. Beeharry, A.V. Borderia, H. Blanc, M. Vignuzzi Proc Natl Acad Sci U S A 2011 16038 16043

[12] S. Crowder, K. Kirkegaard Nature Genetics 2005 701 709

[13] K.M. Chumakov, L.B. Powers, K.E. Noonan, I.B. Roninson, I.S. Levenbook Proc. Natl. Acad. Sci. USA 1991 199 203

[14] J.C. De La Torre, J.J. Holland J. Virol. 1990 6278 6281

[15] M.R. Denison, R.L. Graham, E.F. Donaldson, L.D. Eckerle, R.S. Baric RNA biology 2011 270 279

[16] E. Domingo Vet Res 2010 38

[17] E. Domingo, C. Biebricher, M. Eigen, J.J. Holland. Quasispecies and RNA Virus Evolution : Principles and Consequences. Landes Bioscience, Austin, 2001.

[18] E. Domingo, M. Davila, J. Ortin Gene 1980 333 346

[19] E. Domingo, R.A. Flavell, C. Weissmann Gene 1976 3 25

[20] E. Domingo, J.J. Holland, P. Ahlquist. RNA Genetics, CRC Press, Boca Raton, 1988.

[21] E. Domingo, D. Sabo, T. Taniguchi, C. Weissmann Cell 1978 735 744

[22] E. Domingo, J. Sheldon, C. Perales Microbiology and Molecular Biology Reviews 2012 159 216

[23] E. Domingo, S. Wain-Hobson EMBO Rep 2009 444 448

[24] J.W. Drake Nature 1969 1132

[25] J.W. Drake, J.J. Holland Proc. Natl. Acad. Sci. USA 1999 13910 13913

[26] E.A. Duarte, I.S. Novella, S. Ledesma, D.K. Clarke, A. Moya, S.F. Elena, E. Domingo, J.J. Holland J. Virol. 1994 4295 4301

[27] L.D. Eckerle, M.M. Becker, R.A. Halpin, K. Li, E. Venter, X. Lu, S. Scherbakova, R.L. Graham, R.S. Baric, T.B. Stockwell, D.J. Spiro, M.R. Denison PLoS Pathog 2010 e1000896

[28] L.D. Eckerle, X. Lu, S.M. Sperry, L. Choi, M.R. Denison J Virol 2007 12135 12144

[29] M. Eigen Biophys. Chem. 2000 101 123

[30] M. Eigen Naturwissenschaften 1971 465 523

[31] M. Eigen. Steps towards life, Oxford University Press, 1992.

[32] M. Eigen, J. Mccaskill, P. Schuster J. Phys. Chem. 1988 6881 6891

[33] M. Eigen, P. Schuster. The hypercycle. A principle of natural self-organization. Springer, Berlin, 1979.

[34] C. Escarmis, E. Lazaro, A. Arias, E. Domingo J. Mol. Biol. 2008 367 379

[35] G. Feix, R. Pollet, C. Weissmann Proc Natl Acad Sci U S A 1968 145 152

[36] C. Ferrer-Orta, R. Agudo, E. Domingo, N. Verdaguer Current Opinion in Structural Biology 2009 752 758

[37] C. Ferrer-Orta, A. Arias, R. Agudo, R. Perez-Luque, C. Escarmis, E. Domingo, N. Verdaguer EMBO J 2006 880 888

[38] R.A. Flavell, D.L. Sabo, E.F. Bandle, C. Weissmann J Mol Biol 1974 255 272

[39] E.C. Friedberg, G.C. Walker, W. Siede, R.D. Wood, R.A. Schultz, T. Ellenberger. DNA repair and mutagenesis. American Society for Microbiology, Washington, DC, 2006.

[40] M. Gell-Mann. Complex adaptive systems, in : G.A. Cowan, D. Pines, D. Meltzer (Eds.). Complexity. Metaphors, models and reality, Wesley Publishing Co., Reading, MA, 1994, pp. 17–45.

[41] R.F. Gesteland, T.R. Cech, J.F. Atkins. The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2006.

[42] W. Gilbert Nature 1986 618

[43] C. Gonzalez-Lopez, A. Arias, N. Pariente, G. Gomez-Mariano, E. Domingo J. Virol. 2004 3319 3324

[44] A. Grande-Perez, E. Lazaro, P. Lowenstein, E. Domingo, S.C. Manrubia Proc. Natl. Acad. Sci. USA 2005 4448 4452

[45] A. Grande-Perez, S. Sierra, M.G. Castro, E. Domingo, P.R. Lowenstein Proc. Natl. Acad. Sci. USA 2002 12938 12943

[46] B.L. Haagmans, A.C. Andeweg, A.D. Osterhaus PLoS Pathog 2009 e1000557

[47] G.Z. Han, M. Worobey Viruses 2011 1358 1373

[48] J.J. Holland. Continuum of change in RNA virus genomes. In : A.L. Notkins, M.B.A. Oldstone (Eds.). Concepts in Viral Pathogenesis, Springer-Verlag, New York, 1984.

[49] J.J. Holland. Genetic diversity of RNA viruses. Current Topics in Microbiology and Immunology, Springer-Verlag, Berlin, 1992.

[50] J.J. Holland, E.A. Grabau, C.L. Jones, B.L. Semler Cell 1979 495 504

[51] J.J. Holland, K. Spindler, F. Horodyski, E. Grabau, S. Nichol, S. Vandepol Science 1982 1577 1585

[52] K. Horiuchi. Genetic studies of RNA phages, in : N.D. Zinder (Ed.) RNA Phages, Cold Spring Harbor laboratory, Cold Spring Harbor, New York, 1975, pp. 29–50.

[53] J. Iranzo, S.C. Manrubia Europhys. Lett. 2009 18001

[54] J. Iranzo, C. Perales, E. Domingo, S.C. Manrubia Proc Natl Acad Sci U S A 2011 16008 16013

[55] K.S. Kemal, C.M. Kitchen, H. Burger, B. Foley, D. Mayers, T. Klimkait, F. Hamy, K. Anastos, K. Petrovic, V.N. Minin, M.A. Suchard, B. Weiser. Recombination Between Variants from Genital Tract and Plasma : Evolution of Multidrug-Resistant HIV Type 1. AIDS research and human retroviruses, (2012), in press.

[56] G.M. Li Cell research 2008 85 98

[57] T. Loeb, N.D. Zinder Proc Natl Acad Sci U S A 1961 282 289

[58] R. Mateo, A. Diaz, E. Baranowski, M.G. Mateu J Biol Chem 2003 41019 41027

[59] L. Menendez-Arias Viruses 2009 1137 1165

[60] A. Meyerhans, R. Cheynier, J. Albert, M. Seth, S. Kwok, J. Sninsky, L. Morfeldt-Manson, B. Asjo, S. Wain-Hobson Cell 1989 901 910

[61] D.R. Mills, R.L. Peterson, S. Spiegelman Proc. Natl. Acad. Sci. USA 1967 217 224

[62] E. Minskaia, T. Hertzig, A.E. Gorbalenya, V. Campanacci, C. Cambillau, B. Canard, J. Ziebuhr Proc. Natl. Acad. Sci. USA 2006 5108 5113

[63] L. Moutouh, J. Corbeil, D.D. Richman Proc Natl Acad Sci U S A 1996 6106 6111

[64] H. Naegeli. Mechanisms of DNA damage recognition in mammalian cells. Landes Bioscience, Austin, Texas, 1997.

[65] M.A. Nowak, P. Schuster J. Theor. Biol. 1989 375 395

[66] S. Ojosnegros, N. Beerenwinkel, T. Antal, M.A. Nowak, C. Escarmis, E. Domingo Proc Natl Acad Sci U S A 2010 2108 2112

[67] K.M. Page, M.A. Nowak J. Theor. Biol. 2002 93 98

[68] N. Pariente, A. Airaksinen, E. Domingo J. Virol. 2003 7131 7138

[69] N. Pariente, S. Sierra, P.R. Lowenstein, E. Domingo J. Virol. 2001 9723 9730

[70] C. Perales, R. Agudo, S.C. Manrubia, E. Domingo J Mol Biol 2011 60 78

[71] C. Perales, R. Agudo, H. Tejero, S.C. Manrubia, E. Domingo PLoS Pathog 2009 e1000658

[72] C. Perales, M. Henry, E. Domingo, S. Wain-Hobson, J.P. Vartanian Lethal mutagenesis of foot-and-mouth disease virus involves shifts in sequence space J Virol 2011 12227 12240

[73] C. Perales, R. Lorenzo-Redondo, C. Lopez-Galandez, M.A. Martinez, E. Domingo Future Virology 2010 679 698

[74] C. Perales, R. Mateo, M.G. Mateu, E. Domingo J. Mol. Biol. 2007 985 1000

[75] J.K. Pfeiffer, K. Kirkegaard PLoS Pathogens 2005 102 110

[76] M.E. Quinones-Mateu, E. Arts Current Topics in Microbiol. and Immunol. 2006 83 140

[77] D.B. Saakian, C.K. Biebricher, C.K. Hu Physical review 2009 041905

[78] D.B. Saakian, E. Munoz, C.K. Hu, M.W. Deem Physical Review E 2006 041913

[79] R. Sanjuan, M.R. Nebot, N. Chirico, L.M. Mansky, R. Belshaw J Virol 2010 9733 9748

[80] D. Shriner, A.G. Rodrigo, D.C. Nickle, J.I. Mullins Genetics 2004 1573 1583

[81] S. Sierra, M. Davila, P.R. Lowenstein, E. Domingo J. Virol. 2000 8316 8323

[82] P. Simmonds. Recombination in the Evolution of Picornaviruses. In : The Picornaviruses. E. Ehrenfeld, E. Domingo and R.P. Roos, eds, ASM Press, Washington, D.C. p.p. 229–238, 2010.

[83] P. Simmonds, S. Midgley J Virol 2005 15467 15476

[84] H.A. Simon. The Sciences of the Artificial (3rd edition). The MIT Press, Cambridge, Massachusetts, 1996.

[85] F. Sobrino, M. Davila, J. Ortin, E. Domingo Virology 1983 310 318

[86] R. Solé, B. Goodwin. Signs of Life. How Complexity Pervades Biology. Basic Books, New York, 2000.

[87] R. Sousa Trends Biochem. Sci. 1996 186 190

[88] D.A. Steinhauer, E. Domingo, J.J. Holland Gene 1992 281 288

[89] T.A. Steitz J. Biol. Chem. 1999 17395 17398

[90] J. Swetina, P. Schuster Biophys. Chem. 1982 329 345

[91] J. Sztuba-Solinska, A. Urbanowicz, M. Figlerowicz, J.J. Bujarski Annual review of phytopathology 2011 415 443

[92] M.N. Teng, M.B. Oldstone, J.C. De La Torre Virology 1996 113 119

[93] R.C. Valentine, R. Ward, M. Strand Adv. Virus Res. 1969 1 59

[94] M. Vignuzzi, R. Andino. in : E. Ehrenfeld, E. Domingo, R.F. Roos (Eds.). The Picornaviruses. ASM Press, Washington DC, 2010, pp. 213–228.

[95] M. Vignuzzi, J.K. Stone, J.J. Arnold, C.E. Cameron, R. Andino Nature 2006 344 348

[96] C. Weissmann, M.A. Billeter, H.M. Goodman, J. Hindley, H. Weber Annu Rev Biochem 1973 303 328

[97] C. Weissmann, T. Tanaguchi, E. Domingo, D. Sabo, R.A. Flavell. Site-directed mutagenesis as a tool in genetics, in : J. Schultz, Z. Brada (Eds.). Genetic manipulation as it affects the cancer problem, Academic Press, New York, 1977, pp. 11–36.

[98] C.O. Wilke, C. Ronnewinkel, T. Martinetz Physics Reports 2001 395 446

[99] S. Wright Proc. of the VI International Congress of Genetics 1932 356 366

[100] M. Yarus. Life from an RNA world. The ancestor within. Harvard University Press, Cambridge, Massachusetts and London, England, 2010.

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