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Part of the book series: Current Topics in Microbiology and Immunology ((CT MICROBIOLOGY,volume 299))

Abstract

In recent years, quasispecies theory in time-dependent (that is, dynamically changing) environments has made dramatic progress. Several groups have addressed questions such as how the time scale of the changes affect viral adaptation and quasispecies formation, how environmental changes affect the optimal mutation rate, or how virus and host co-evolve. Here, we review these recent developments, and give a nonmathematical introduction to the most important concepts and results of quasispecies theory in time-dependent environments. We also compare the theoretical results with results from evolution experiments that expose viruses to successive regimes of replication in two or more different hosts.

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References

  • Ahmed R, Canning WM, Kauffman RS, Sharpe AH, Hallum JV, Fields BN (1981) Role of the host cell in persistent viral infection—coevolution of L cells and reovirus during persistent infection. Cell 25:325–332

    Article  CAS  PubMed  Google Scholar 

  • Bangham CRM, Kirkwood TBL (1990) Defective interfering particles: effects in modulating virus growth and persistence. Virology 179:821–826

    Article  CAS  PubMed  Google Scholar 

  • Borzakian S, Couderc T, Barbier Y, Attal G, Pelletier I, Colberegarapin F (1992) Persistent poliovirus infection — establishment and maintenance involve distinct mechanisms. Virology 186:398–408

    Article  CAS  PubMed  Google Scholar 

  • Brumer Y, Shakhnovich EI (2004) Host-parasite coevolution and optimal mutation rates for semiconservative quasispecies. Phys Rev E Stat Nonlin Soft Matter Phys 69:061909

    PubMed  Google Scholar 

  • Bürger R (2000) The mathematical theory of selection, recombination, and mutation. Wiley, Chichester, UK

    Google Scholar 

  • Chen W, Baric RS (1996) Molecular anatomy of mouse hepatitis virus persistence: Coevolution of increased host cell resistance and virus virulence. J Virol 70:3947–3960

    CAS  PubMed  Google Scholar 

  • Chen W-J, Wu H-R, Chiou S-S (2003) E/NS1 modifications of dengue 2 virus after serial passages in mammalian and/or mosquito cells. Intervirology 46:289–295

    Article  CAS  PubMed  Google Scholar 

  • Cooper LA, Scott TW(2001) Differential evolution of eastern equine encephalitis virus populations in response to host cell type. Genetics 157:1403–1412

    CAS  PubMed  Google Scholar 

  • De la Torre JC, MartÍnez-Salas E, Diez J, Villaverde A, Gebauer F, Rocha E, Dávila M, Domingo E (1988) Coevolution of cells and viruses in a persistent infection of foot-and-mouth disease virus in cell culture. J Virol 62:2050–2058

    PubMed  Google Scholar 

  • DePolo NJ, Giachetti C, Holland JJ (1987) Continuing coevolution of virus and defective interfering particles and of viral genome sequences during undiluted passages — virus mutants exhibiting nearly complete resistance to formerly dominant defective interfering particles. J Virol 61:454–464

    CAS  PubMed  Google Scholar 

  • Dermody TS, Nibert ML, Wetzel JD, Tong X, Fields BN (1993) Cells and viruses with mutations affecting viral entry are selected during persistent infections of L cells with mammalian reoviruses. J Virol 67:2055–2063

    CAS  PubMed  Google Scholar 

  • Eigen M, Schuster P (1979) The hypercycle—principle a of natural self-organization. Springer, Berlin Heidelberg New York

    Google Scholar 

  • Eigen M, McCaskill J, Schuster P (1988) Molecular quasi-species. Phys J Chem 92:6881–6891

    CAS  Google Scholar 

  • Eigen M, McCaskill J, Schuster P (1989) The molecular quasi-species. Adv Chem Phys 75:149–263

    CAS  Google Scholar 

  • Frank SA (2000) Within-host spatial dynamics of viruses and defective interfering particles. Theor J Biol 205:279–290

    Google Scholar 

  • Holland JJ (1991) Defective viral genomes. In Fields B, Knipe D (eds) Fundamental virology. Raven Press, New York, pp 151–165

    Google Scholar 

  • Holmes EC, Moya A (2002) Is the quasispecies concept relevant to RNA viruses? J Virol J 76:460–462

    CAS  Google Scholar 

  • Jenkins GM, Worobey M, Woelk CH, Holmes EC (2001) Evidence for the nonquasispecies evolution of RNA viruses. Mol Biol Evol 18:987–994

    CAS  PubMed  Google Scholar 

  • Kamp C (2003) A quasispecies approach to viral evolution in the context of an adaptive immune system. Microbes Infect 5:1397–1405

    Article  CAS  PubMed  Google Scholar 

  • Kamp C, Bornholdt S (2002) Co-evolution of quasispecies: B-cell mutation rates maximize viral error catastrophes. Phys Rev Lett 88:068104

    Article  PubMed  Google Scholar 

  • Kamp C, Wilke CO, Adami C, Bornholdt S (2002) Viral evolution under the pressure of an adaptive immune system—optimal mutation rates for viral escape. Complexity 8:28–33

    Article  Google Scholar 

  • Kimura M (1967) On the evolutionary adjustment of spontaneous mutation rates. Genet Res 9:23–34

    Google Scholar 

  • Kirkwood TB, Bangham CR (1994) Cycles, chaos, and evolution in virus cultures: a model of defective interfering particles. Proc Natl Acad Sci U S A 91:8685–8689

    CAS  PubMed  Google Scholar 

  • Li Y, Wilke CO (2004) Digital evolution in time-dependent fitness landscapes. Artificial Life 10:123–134

    Article  PubMed  Google Scholar 

  • MartÍn Hernández MAM, Carrillo EC, Sevilla N, Domingo E (1994) Rapid cell variation can determine the establishment of a persistent viral infection. Proc Natl Acad Sci U S A 91:3705–3709

    PubMed  Google Scholar 

  • Nilsson M, Snoad N (2000) Error thresholds on dynamic fitness landscapes. Phys Rev Lett 84:191–194

    Article  CAS  PubMed  Google Scholar 

  • Nilsson M, Snoad N (2002a) Optimal mutation rates in dynamic environments. Bull Math Biol 64:1033–1043

    Article  CAS  PubMed  Google Scholar 

  • Nilsson M, Snoad N (2002b) Quasispecies evolution on a fitness landscape with a fluctuating peak. Phys Rev E 65:031901

    Article  Google Scholar 

  • Novella IS, Clarke DK, Quer J, Duarte EA, Lee CH, Weaver SC, Elena SF, Moya A, Domingo E, Holland JJ (1995) Extreme fitness differences in mammalian and insect hosts after continuous replication of vesicular stomatitis virus in sandfly cells. J Virol 69:6805–6809

    CAS  PubMed  Google Scholar 

  • Novella IS, Hershey CL, EscarmÍs C, Domingo E, Holland J (1999) Lack of evolutionary stasis during alternating replication of an arbovirus in insect and mammalian cells. J Mol Biol 287:459–465

    Article  CAS  PubMed  Google Scholar 

  • Nowak M, Schuster P (1989) Error thresholds of replication in finite populations— mutation frequencies and the onset of Muller’s ratchet. J Theor Biol 137:375–395

    CAS  PubMed  Google Scholar 

  • Nowak MA, May RM (2000) Virus dynamics. Oxford University Press, Oxford

    Google Scholar 

  • O’Hara PJ, Nichol ST, Horodyski FM, Holland JJ (1984)Vesicular stomatitis virus defective interfering particles can contain extensive genomic sequence rearrangements and base substitutions. Cell 36:915–924

    CAS  PubMed  Google Scholar 

  • Orr HA (2000) The rate of adaptation in asexuals. Genetics 155:961–968

    CAS  PubMed  Google Scholar 

  • Perelson AS (2002) Modelling viral and immune system dynamics. Nature Rev Immunol 2:28–36

    CAS  Google Scholar 

  • Perelson AS, Essunger P, Ho DD (1997) Dynamics of HIV-1 CD4+ lymphocytes in vivo. AIDS 11:S17–S24

    PubMed  Google Scholar 

  • Ronnewinkel C, Wilke CO, Martinetz T (2001) Genetic algorithms in time-dependent environments. In Kallel L, Naudts B, Rogers A (eds) Theoretical aspects of evolutionary computing. Springer, Berlin Heidelberg New York, pp 261–285

    Google Scholar 

  • Szathmáry E (1992) Natural selection and dynamical coexistence of defective and complementing virus segments. J Theor Biol 157:383–406

    PubMed  Google Scholar 

  • Turner PE, Elena SF (2000) Cost of host radiation in an RNA virus. Genetics 156:1465–1470

    CAS  PubMed  Google Scholar 

  • Kamp C (2003) A quasispecies approach to viral evolution in the context of an adaptive immune system. Microbes Infect 5:1397–1405

    Article  CAS  PubMed  Google Scholar 

  • Kamp C, Bornholdt S (2002) Co-evolution of quasispecies: B-cell mutation rates maximize viral error catastrophes. Phys Rev Lett 88:068104

    Article  PubMed  Google Scholar 

  • Kamp C, Wilke CO, Adami C, Bornholdt S (2002) Viral evolution under the pressure of an adaptiveimmune system—optimalmutation rates for viral escape. Complexity 8:28–33

    Article  Google Scholar 

  • Kimura M (1967) On the evolutionary adjustment of spontaneous mutation rates. Genet Res 9:23–34

    Google Scholar 

  • Kirkwood TB, Bangham CR (1994) Cycles, chaos, and evolution in virus cultures: a model of defective interfering particles. Proc Natl Acad Sci U S A 91:8685–8689

    CAS  PubMed  Google Scholar 

  • Li Y, Wilke CO (2004) Digital evolution in time-dependent fitness landscapes. Artificial Life 10:123–134

    Article  PubMed  Google Scholar 

  • MartÍn Hernández MAM, Carrillo EC, Sevilla N, Domingo E (1994) Rapid cell variation can determine the establishment of a persistent viral infection. Proc Natl Acad Sci U S A 91:3705–3709

    PubMed  Google Scholar 

  • Nilsson M, Snoad N (2000) Error thresholds on dynamic fitness landscapes. Phys Rev Lett 84:191–194

    Article  CAS  PubMed  Google Scholar 

  • Nilsson M, Snoad N (2002a) Optimal mutation rates in dynamic environments. Bull Math Biol 64:1033–1043

    Article  CAS  PubMed  Google Scholar 

  • Nilsson M, Snoad N (2002b) Quasispecies evolution on a fitness landscape with a fluctuating peak. Phys Rev E 65:031901

    Article  Google Scholar 

  • Novella IS, Clarke DK, Quer J, Duarte EA, Lee CH, Weaver SC, Elena SF, Moya A, Domingo E, Holland JJ (1995) Extreme fitness differences in mammalian and insect hosts after continuous replication of vesicular stomatitis virus in sandfly cells. J Virol 69:6805–6809

    CAS  PubMed  Google Scholar 

  • Novella IS, Hershey CL, EscarmÍs C, Domingo E, Holland J (1999) Lack of evolutionary stasis during alternating replication of an arbovirus in insect and mammalian cells. J Mol Biol 287:459–465

    Article  CAS  PubMed  Google Scholar 

  • Nowak M, Schuster P (1989) Error thresholds of replication in finite populations— mutation frequencies and the onset of Muller’s ratchet. J Theor Biol 137:375–395

    CAS  PubMed  Google Scholar 

  • Nowak MA, May RM (2000) Virus dynamics. Oxford University Press, Oxford

    Google Scholar 

  • O’Hara PJ, Nichol ST, Horodyski FM, Holland JJ (1984)Vesicular stomatitis virus defective interfering particles can contain extensive genomic sequence rearrangements and base substitutions. Cell 36:915–924

    CAS  PubMed  Google Scholar 

  • Orr HA (2000) The rate of adaptation in asexuals. Genetics 155:961–968

    CAS  PubMed  Google Scholar 

  • Perelson AS (2002) Modelling viral and immune system dynamics. Nature Rev Immunol 2:28–36

    CAS  Google Scholar 

  • Perelson AS, Essunger P, Ho DD(1997) Dynamics of HIV-1 CD4+ lymphocytes in vivo. AIDS 11:S17–S24

    PubMed  Google Scholar 

  • Ronnewinkel C, Wilke CO, Martinetz T (2001) Genetic algorithms in time-dependent environments. In Kallel L, Naudts B, Rogers A (eds) Theoretical aspects of evolutionary computing. Springer, Berlin Heidelberg New York, pp 261–285

    Google Scholar 

  • Szathmáry E (1992) Natural selection and dynamical coexistence of defective and complementing virus segments. J Theor Biol 157:383–406

    PubMed  Google Scholar 

  • Turner PE, Elena SF (2000) Cost of host radiation in an RNA virus. Genetics 156:1465–1470

    CAS  PubMed  Google Scholar 

  • Van Nimwegen E, Crutchfield JP, Mitchell M (1999a) Statistical dynamics of the royal road genetic algorithm. Theoretical Computer Science 229:41–102

    Google Scholar 

  • Van Nimwegen E, Crutchfield JP, Huynen M (1999b) Neutral evolution of mutational robustness. Proc Natl Acad Sci U S A 96:9716–9720

    PubMed  Google Scholar 

  • Weaver SC, Brault AC, Kang W, Holland JJ (1999) Genetic and fitness changes accompanying adaptation of an arbovirus to vertebrate and invertebrate cells. J Virol 73:4316–4326

    CAS  PubMed  Google Scholar 

  • Wilke CO (2001a) Adaptive evolution on neutral networks. Bull Math Biol 63:715–730

    Article  CAS  PubMed  Google Scholar 

  • Wilke CO (2001b) Selection for fitness versus selection for robustness in RNA secondary structure folding. Evolution 55:2412–2420

    CAS  PubMed  Google Scholar 

  • Wilke CO, Ronnewinkel C (2001) Dynamic fitness landscapes: expansions for small mutation rates. Physica A 290:475–490

    Article  Google Scholar 

  • Wilke CO, Adami C (2002) The biology of digital organisms. Trends Ecol Evol 17:528–532

    Article  Google Scholar 

  • Wilke CO, Adami C (2003) Evolution of mutational robustness. Mut Res 522:3–11

    CAS  Google Scholar 

  • Wilke CO, Ronnewinkel C, Martinetz T (2001a) Dynamic fitness landscapes in molecular evolution. Phys Rep 349:395–446

    Article  CAS  Google Scholar 

  • Wilke CO, Wang JL, Ofria C, Lenski RE, Adami C (2001b) Evolution of digital organisms at high mutation rate leads to survival of the flattest. Nature 412:331–333

    Article  CAS  PubMed  Google Scholar 

  • Zárate S, Novella IS (2004) Vesicular stomatitis virus evolution during alternation between persistent infection in insect cells and acute infection in mammalian cells is dominated by the persistence phase. J Virol 78:12236–12242

    PubMed  Google Scholar 

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© 2006 Springer-Verlag Berlin Heidelberg

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Wilke, C.O., Forster, R., Novella, I.S. (2006). Quasispecies in Time-Dependent Environments. In: Domingo, E. (eds) Quasispecies: Concept and Implications for Virology. Current Topics in Microbiology and Immunology, vol 299. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-26397-7_2

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