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Original Articles

On the role of the degradation rates for the dominance of the fittest in Eigen's quasispecies model

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Pages 531-548 | Received 28 Sep 2010, Accepted 26 Nov 2010, Published online: 20 Apr 2011

References

  • Alves , K. , Canzian , M. and Delwart , E. L. 2002 . HIV type 1 envelope quasispecies in the thymus and lymph nodes of AIDS patients . AIDS Res. Hum. Retroviruses , 18 : 161 – 165 .
  • Belshaw , R. , Gardner , A. , Rambaut , A. and Pybus , O. 2008 . Pacing a small cage: Mutation and RNA viruses . Trends Ecol. Evol , 23 ( 4 ) : 188 – 193 .
  • Berman , A. and Plemmons , R. J. 1970 . Nonnegative Matrices in the Mathematical Sciences , New York : Academic Press .
  • Boden , D. , Pusch , O. , Lee , F. , Tucker , L. and Ramratnam , B. 2003 . Human Immunodeficiency Virus Type 1 Escape from RNA Interference . J. Virol , 77 ( 21 ) : 11531 – 11535 .
  • Bull , J. J. , Meyers , L. A. and Lachmann , M. 2005 . Quasispecies made simple . PLoS Comput. Biol , 1 : 450 – 460 .
  • Cases-Gonzalez , C. , Arribas , M. , Domingo , E. and Lazaro , E. 2008 . Beneficial effects of population bottlenecks in an RNA virus evolving at increased error rate . J. Mol. Biol , 384 ( 5 ) : 1120 – 1129 .
  • Crotty , S. , Cameron , C. E. and Andino , R. 2001 . RNA virus error catastrophe: Direct molecular test by using ribavirin . PNAS , 98 ( 12 ) : 6895 – 6900 .
  • Domingo , E. 2007 . “ Virus evolution ” . In Fields Virology , 5 , Edited by: Knipe , D. M. , Howley , P. M. , Griffin , D. E. , Lamb , R. A. , Martin , M. A. , Roizman , B. and Straus , S. E. 389 – 421 . Philadelphia : Lippincott Williams and Wilkins .
  • Domingo , E. , Biebricher , C. , Eigen , M. and Holland , J. J. 2001 . Quasispecies and RNA Virus Evolution: Principles and Consequences , Georgetown, TX : Eurekah.com/Landes Bioscience .
  • Domingo , E. , Escarmis , C. , Lazaro , E. and Manrubia , S. C. 2005 . Quasispecies dynamics and RNA virus extinction . Virus Res. , 107 ( 2 ) : 129 – 39 .
  • Drake , J. W. and Holland , J. J. 1999 . Mutation rates among RNA viruses . Proc Natl. Acad. Sci. USA , 96 ( 24 ) : 13910 – 13913 .
  • Eigen , M. 1971 . Selforganization of matter and the evolution of biological macromolecules . Naturwissenschaften , 58 : 465 – 523 .
  • Eigen , M. 2000 . Natural selection: A phase transition? . Biophys. Chem , 85 : 101 – 123 .
  • Eigen , M. and Schuster , P. 1977 . A principle of natural self-organization . Naturwissenschaften , 64 : 541 – 565 .
  • Eigen , M. , McCaskill , J. and Schuster , P. 1989 . The molecular quasispecies . Adv. Chem. Phys , 75 : 149 – 263 .
  • Farci , P. , Shimoda , A. , Coiana , A. , Diaz , G. , Peddis , G. , Melpolder , J. C. , Strazzera , A. , Chien , D. Y. , Munoz , S. J. , Balestrieri , A. , Purcell , R. H. and Alter , H. J. 2000 . The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies . Science , 288 : 339 – 344 .
  • Ghosh , Z. , Bibekanand , M. and Jayprokas , C. 2009 . Cellular versus viral microRNAs in host-virus interaction . Nucleic Acids Res , 37 ( 4 ) : 1035 – 1048 .
  • Gitlin , L. , Stone , J. K. and Andino , R. 2005 . Poliovirus escape from RNA interference: Short interfering RNA-target recognition and implications for therapeutic approaches . J. Virol , 79 : 1027 – 1035 .
  • Holmes , E. C. 2009 . “ The Evolution and Emergence of RNA Viruses ” . In Oxford Series in Ecology and Evolution , New York : Oxford Press .
  • Iranzo , J. and Manrubia , S. C. 2009 . Stochastic extinction of viral infectivity through the action of defectors . Europhys. Lett , 85 ( 1 ) : p1 – p6 . 18001
  • Jerzak , G. , Bernard , K. A. , Kramer , L. D. and Ebel , G. D. 2005 . Genetic variation in West Nile virus from naturally infected mosquitoes and birds suggests quasispecies structure and strong purifying selection . J. Gen. Virol , 86 : 2175 – 2183 .
  • Jones , L. R. , Zandomeni , R. and Weber , E. L. 2002 . Quasispecies in the 59 untranslated genomic region of bovine viral diarrhoea virus from a single individual . J. Gen. Virol , 83 : 2161 – 2168 .
  • Jonsson , C. B. , Miligan , B. C. and Arterburn , J. B. 2005 . Potential importance of error catastrophe to the development of antiviral strategies for hantaviruses . Virus Res , 107 : 195 – 205 .
  • Knipe , D. , Lodish , H. F. and Baltimore , D. 1977 . Analysis of the defects of temperature-sensitive mutants of vesicular stomatitis virus: Intracellular degradation of specific viral proteins . J. Virol , 21 ( 3 ) : 1140 – 1148 .
  • Lee , C. W. and Jackwood , M. W. 2000 . Evidence of genetic diversity generated by recombination among avian coronavirus IBV . Arch. Virol , 145 : 2135 – 2148 .
  • Mas , A. , Ulloa , E. , Bruguera , M. , Furcic , I. , Garriga , D. , Fabregas , S. , Andreu , D. , Saiz , J. C. and Diez , J. 2004 . Hepatitis C virus population analysis of a single-source nosocomial outbreak reveals an inverse correlation between viral load and quasispecies complexity . J. Gen. Virol , 85 ( 12 ) : 3619 – 3626 .
  • Peery , T. and Mathews , M. B. 2007 . “ Viral conquest of the host cell ” . In Fields Virology , 5 , Edited by: Knipe , D. M. , Howley , P. M. Griffin , D. E. Philadelphia : Lippincott Williams and Wilkins .
  • Pfeiffer , J. and Kirkegaard , K. 2003 . A single mutation in poliovirus RNA-dependent RNA polymerase confers resistance to mutagenic nucleotide analogs via increased fidelity . Proc. Natl. Acad. Sci , 100 ( 12 ) : 7289 – 7294 .
  • Plyusnin , A. , Cheng , Y. , Lehvaslaiho , H. and Vaheri , A. 1996 . Quasispecies in wild-type Tula hantavirus populations . J. Virol , 70 : 9060 – 9063 .
  • Pult , I. , Abbott , N. , Zhang , Y. Y. and Summers , J. 2001 . Frequency of spontaneous mutations in an avian hepadnavirus infection . J. Virol , 75 ( 20 ) : 9623 – 9632 .
  • Runkler , N. , Poh , C. , Schneider-Schaulies , S. , Klenk , H. D. and Maisner , A. 2007 . Measles virus nucleocapsid transport to the plasma membrane requires stable expression and surface accumulation of the viral matrix protein . Cell. Microbiol , 9 ( 5 ) : 1203 – 1214 .
  • Schikora , B. M. , Shih , L. M. and Hietala , S. K. 2003 . Genetic diversity of avian infectious bronchitis virus California variants isolated between 1988 and 2001, based on the S1 subunit of the spike glycoprotein . Arch. Virol , 148 : 115 – 136 .
  • Schneider , W. L. and Roosnick , M. J. 2001 . Genetic diversity in RNA virus quasispecies is controlled by host-virus interactions . J. Virol , 75 ( 14 ) : 6566 – 6571 .
  • Sierra , M. , Airaksinen , A. , Gonzalez-Lopez , C. , Agudo , R. , Arias , A. and Domingo , E. 2006 . Foot-and-mouth disease virus mutant with decreased sensitivity to ribavirin: Implications for error catastrophe . J. Virol , 81 ( 4 ) : 2012 – 2024 .
  • Sole , R. V. , Sardanyes , J. , Diez , J. and Mas , A. 2006 . Information catastrophe in RNA viruses through replication thresholds . J. Theor. Biol , 240 : 353 – 359 .
  • Summers , J. and Litwin , S. 2006 . Examining the theory of error catastrophe . J. Virol , 80 ( 1 ) : 20 – 26 .
  • Swetina , J. and Schuster , P. 1982 . Self-replication with errors – a model for polynucleotide replication . Biophys. Chem , 16 : 329 – 345 .
  • Umbach , J. L. and Cullen , B. R. 2009 . The role of RNAi and microRNAs in animal virus replication and antiviral immunity . Genes Dev , 23 : 1151 – 1164 .
  • Vignuzzi , M. , Stone , J. K. and Andino , A. 2005 . Ribavirin and lethal mutagenesis of poliovirus: Molecular mechanisms, resistance and biological implications . Virus Res , 107 : 173 – 181 .
  • Vignuzzi , M. , Stone , J. K. , Arnold , J. J. , Cameron , C. E. and Andino , R. 2006 . Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population . Nature , 439 ( 19 ) : 344 – 348 .
  • Vignuzzi , M. , Wendt , E. and Andino , R. 2008 . Engineering attenuated virus vaccines by controlling replication fidelity . Nat. Med , 14 ( 2 ) : 154 – 161 .
  • Wagner , G. P. and Krall , P. 1993 . What is the difference between models of error threshold and Muller's ratchet? . J. Math. Biol , 32 : 33 – 44 .
  • Wiehe , T. 1997 . Model dependency of error thresholds: The role of fitness functions and contrasts between the finite and infinite sites models . Genet. Res , 69 ( 2 ) : 127 – 136 .
  • Wilke , C. O. , Ronnewinkel , C. and Martinetz , T. 2000 . Dynamic fitness landscapes in molecular evolution , Available at arXiv:physics/9912012v2

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