A quantitative quasispecies theory-based model of virus escape mutation under immune selection

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 32, 2012, Pages 12980-12985

  Woo, Hyung June ^a   Reifman, Jaques ^a  

^a U S ARMY MEDICAL RESEARCH AND MATERIEL COMMAND   (United States)

Author keywords

HIV; Next generation sequencing; Population dynamics; Stochastic simulation

Indexed keywords

EPITOPE;

ARTICLE; CELLULAR IMMUNITY; CONTROLLED STUDY; CYTOTOXIC T LYMPHOCYTE; DISEASE COURSE; EVOLUTION; GENETIC VARIABILITY; GENOTYPE PHENOTYPE CORRELATION; HUMAN IMMUNODEFICIENCY VIRUS; MOLECULAR MODEL; MUTATION RATE; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; QUASISPECIES THEORY; SIMIAN IMMUNODEFICIENCY VIRUS; STOCHASTIC MODEL; VIRAL CLEARANCE; VIROGENESIS; VIRUS GENOME; VIRUS MUTATION; VIRUS PATHOGENESIS;

BIOLOGICAL EVOLUTION; COMPUTER SIMULATION; EPITOPES, T-LYMPHOCYTE; GENETIC VARIATION; HUMANS; MODELS, BIOLOGICAL; MUTATION; POPULATION DYNAMICS; SELECTION, GENETIC; SIMIAN IMMUNODEFICIENCY VIRUS; SPECIES SPECIFICITY; STOCHASTIC PROCESSES; T-LYMPHOCYTES, CYTOTOXIC; VIRUS DISEASES; VIRUSES;

HUMAN IMMUNODEFICIENCY VIRUS; SIMIAN IMMUNODEFICIENCY VIRUS;

EID: 84864697529     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1117201109     Document Type: Article

References (43)

1. Eigen M (1971) Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften 58:465-523.
2. Swetina J, Schuster P (1982) Self-replication with errors: A model for polynucleotide replication. Biophys Chem 16:329-345.
3. Loeb LA, et al. (1999) Lethal mutagenesis of HIV with mutagenic nucleoside analogs. Proc Natl Acad Sci USA 96:1492-1497. (Pubitemid 29098478)
4. Iranzo J, Perales C, Domingo E, Manrubia SC (2011) Tempo and mode of inhibitormutagen antiviral therapies: A multidisciplinary approach. Proc Natl Acad Sci USA 108:16008-16013.
5. Domingo E, Holland JJ (1997) RNA virus mutations and fitness for survival. Annu Rev Microbiol 51:151-178. (Pubitemid 27433046)
6. Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387-402.
7. McMichael AJ, Borrow P, Tomaras GD, Goodnetilleke N, Haynes BF (2010) The immune response during acute HIV-1 infection: Clues for vaccine development. Nat Rev Immunol 10:11-23.
8. Mild M, Hedskog C, Jernberg J, Albert J (2011) Performance of ultradeep pyrosequencing in analysis of HIV-1 pol gene variation. PLoS One 6:e22741.
9. +T-lymphocyte escape in simian immunodeficiency virus-infected macaques. J Virol 83:8247-8253.
10. Bimber BN, et al. (2010) Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing. J Virol 84:12087-12092.
11. Fischer W, et al. (2010) Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultradeep sequencing. PLoS One 5:e12303.
12. + T lymphocytes cross-recognize mutant simian immunodefieciency virus (SIV) sequences but fail to contain very early evolution and eventual fixation of epitope escape mutations during SIV infection. J Virol 85:3746-3757.
13. Moore CB, et al. (2002) Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level. Science 296:1439-1443. (Pubitemid 34553083)
14. Bhattacharya T, et al. (2007) Founder effects in the assessment of HIV polymorphisms and HLA allele associations. Science 315:1583-1586. (Pubitemid 46449476)
15. Kawashima Y, et al. (2009) Adaptation of HIV-1 to human leukocyte antigen class I. Nature 458:641-645.
16. Addo MM, et al. (2003) Comprehensive epitope analysis of human immunodeficiency virus type 1 (HIV-1)-specific T-cell responses directed against the entire expressed HIV-1 genome demonstrate broadly directed responses, but no correlation to viral load. J Virol 77:2081-2092. (Pubitemid 36110021)
17. Goodnetilleke N, et al. (2009) The first T-cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J Exp Med 206:1253-1272.
18. Nowak MA, Bangham CR (1996) Population dynamics of immune responses to persistent viruses. Science 272:74-79. (Pubitemid 26110757)
19. Nowak MA, May RM (2001) Virus Dynamics: Mathematical Principles of Immunology and Virology (Oxford Univ Press, New York).
20. Nowak MA, et al. (1995) Antigenic oscillations and shifting immunodominance in HIV-1 infections. Nature 375:606-611.
21. Althaus CL, De Boer RJ (2008) Dynamics of immune escape during HIV/SIV infection. PLoS Comput Biol 4:e1000103.
22. + T-lymphocyte responses exert strong selective pressure in simian immunodeficiency virus-infected macaques but still fail to clear founder epitope sequences. J Virol 84:5802-5814.
23. Lee HY, et al. (2009) Modeling sequence evolution in acute HIV-1 infection. J Theor Biol 261:341-360.
24. Lee HY, Perelson AS, Park S-C, Leitner T (2008) Dynamic correlation between intrahost HIV-1 quasispecies evolution and disease progression. PLoS Comput Biol 4:e1000240.
25. Keele BF, et al. (2008) Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci USA 105:7552-7557. (Pubitemid 351830056)
26. Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81:2340-2361.
27. 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.
28. Yang Z, Bielawski JP (2000) Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15:496-503.
29. Aguirre J, Buldu JM, Stich M, Manrubia SC (2011) Topological structure of the space of phenotypes: The case of RNA neutral networks. PLoS One 6:e26324.
30. Burch CL, Chao L (2000) Evolvability of an RNA virus is determined by its mutational neighborhood. Nature 406:625-628. (Pubitemid 30641048)
31. Schuster P, Fontana W (1999) Chance and necessity in evolution: Lessons from RNA. Physica D 133:427-452.
32. Hietpas RT, Jensen JD, Bolon DN (2011) Experimental illumination of a fitness landscape. Proc Natl Acad Sci USA 108:7896-7901.
33. Stich M, Briones C, Manrubia SC (2008) On the structural repertoire of pools of short, random RNA sequences. J Theor Biol 252:750-763.
34. Pitt JN, Ferre-D'Amare AR (2010) Rapid construction of empirical RNA fitness landscapes. Science 330:376-379.
35. Duarte EA, et al. (1994) Subclonal components of consensus fitness in an RNA virus clone. J Virol 68:4295-4301. (Pubitemid 24183022)
36. Sanjuan R, Moya A, Elena SF (2004) The distribution of fitness effects caused by singlenucleotide substitutions in an RNA virus. Proc Natl Acad Sci USA 101:8396-8401. (Pubitemid 38736586)
37. Fernandez G, Clotet B, Martinez MA (2007) Fitness landscape of human immunodeficiency virus type 1 protease quasispecies. J Virol 81:2485-2496.
38. Allen TM, et al. (2000) Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia. Nature 407:386-390.
39. Mansky LM, Temin HM (1995) Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J Virol 69:5087-5094.
40. Schuster P, Swetina J (1988) Stationary mutant distributions and evolutionary optimization. Bull Math Biol 50:635-660. (Pubitemid 18268678)
41. Wilke CO, Wang JL, Ofria C, Lenski RE, Adami C (2001) Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature 412:331-333. (Pubitemid 32691846)
42. Gaschen B, et al. (2002) Diversity considerations in HIV-1 vaccine selection. Science 296:2354-2360. (Pubitemid 34734202)
43. Dahirel V, et al. (2011) Coordinate linkage of HIV evolution reveals regions of immunological vulnerability. Proc Natl Acad Sci USA 108:11530-11535.