Computational inference methods for selective sweeps arising in acute HIV infection

Genetics

Volumn 194, Issue 3, 2013, Pages 737-752

  Leviyang, Sivan ^a  

^a GEORGETOWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE;

ARTICLE; CELL DEATH; COMPUTATIONAL INFERENCE METHOD; CYTOTOXIC T LYMPHOCYTE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTED PATIENT; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MUTATION; PRIORITY JOURNAL; STATISTICAL ANALYSIS;

HUMAN IMMUNODEFICIENCY VIRUS 1;

CYTOTOXIC T LYMPHOCYTE; ESCAPE MUTATION; HIV-1; INFERENCE; SELECTIVE SWEEP;

BAYES THEOREM; HIV INFECTIONS; HIV-1; HUMANS; IMMUNITY, INNATE; MODELS, THEORETICAL; MUTATION; T-LYMPHOCYTES, CYTOTOXIC; VIRUS REPLICATION;

EID: 84879772304     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.113.150862     Document Type: Article

References (59)

1. Asquith, B., C. Edwards, M. Lipsitch, and A. McLean, 2006 Inefficient CTL mediated killing of HIV-1 infected cells in-vivo. PLoS Biol. 4: 583-592.
2. Batorsky, R., M. Kearney, S. Palmer, F. Maldarelli, I. Rouzine et al., 2011 Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection. Proc. Natl. Acad. Sci. USA 108: 5661-5666.
3. B. Bimber, B. Burwitz, S. O'Conner, A. Detmer, and E. Gostick et al., 2009 Ultradeep pyrosequencing detects complex patterns of CD8 T-lymphocyte escape in simian immunodeficiency virus-infected macaques. J. Virol. 83: 8247-8253.
4. C. L. Boutwell, M. M. Rolland, J. T. Herbeck, J. L. Mullins, and T. M. Allen, 2010 Viral evolution and escape during acute HIV-1 infection. J. Infect. Dis. 202: 309-314.
5. Cohen, M., G. Shaw, A. McMichael, and B. Haynes, 2011 Acute HIV-1 infection. N. Engl. J. Med. 364: 1943-1954.
6. Conway, J., and D. Coombs, 2011 A stochastic model in latently infected cell reactivation and viral blip generation in treated hiv patients. PLOS Comp. Bio. 7: 1-15.
7. De Boer, R., 2007 Understanding the failure of CD8 T-cell vacci-nation against simian/human immunodeficiency virus. J. Virol. 81: 2838-2848.
8. Desai, M., and D. Fisher, 2007 Beneficial mutation-selection bal-ance and the effect of linkage on positive selection. Genetics 176: 1759-1798.
9. Fernandez, C., I. Stratov, R. De Rose, K. Walsh, C. Dale et al., 2005 Rapid viral escape at an immunodominant simian-human immunodeficiency CTL epitope exacts a dramatic fitness cost. J. Virol. 79: 5721-5731.
10. Fiebig, E., D. Wright, B. Rawal, P. Garrett, R. Schumacher et al., 2003 Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of pri-mary HIV infection. AIDS 17: 1871-1879.
11. Fisher, W., V. Ganusov, E. Giorgi, P. Hraber, B. Keele et al., 2010 Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing. PLoS ONE 5: 1-15.
12. Frost, S. M., R. Nijhuis, R. Schuurman, C. Boucher, and A. L. Brown, 2000 Evolution of lamivudine resistance in HIV-1 infected in-dividuals: the relative roles of drift and selection. J. Virol. 74: 6262-6268.
13. Ganusov, V., and R. De Boer, 2006 Estimating costs and benefits of CTL escape mutations in SIV/HIV infection. PLOS Comput. Biol. 2: 182-187.
14. Ganusov, V., N. Goonetilleke, M. Liu, G. Ferrari, G. Shaw et al., 2011 Fitness costs and diversity of the CTL response deter-mine the rate of CTL escape during acute and chronic phases of HIV infection. J. Virol. 85: 10518-10528.
15. Gilks, W., S. Richardson, and D. Spiegelhalter, 1996 Markov Chain Monte Carlo in Practice. Chapman & Hall, London.
16. Gillespie, D., 2001 Approximate accelerated simulation of chem-ically reaction systmes. J. Chem. Phys. 81: 1716-1733.
17. Gillespie, J., 1991 The Causes of Molecular Evolution. Oxford Uni-versity Press, Oxford, UK.
18. Goonetilleke, N., M. Liu, J. Salazar-Gonzalez, G. Ferrari, E. Giorgi et al., 2009 The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infec-tion. J. Exp. Med. 206: 1253-1272.
19. Goulder, P., and D. Watkins, 2004 HIV and SIV CTL escape: im-plications for vaccine design. Nat. Rev. Immunol. 4: 630-640.
20. Henn, M. R., C. L. Boutwell, P. Charlebois, N. J. Lennon, K. A. Power, et al., 2012 Whole genome sequencing of HIV-1 reveals impact of early minor immune variants on immune recognition during acute infection. PLoS Pathog. 8: 1-14.
21. Kaplan, N., T. Darden, and R. Hudson, 1988 The coalescent pro-cess in models with selection. Genetics 120: 819-829.
22. Keele, B., E. Giorgi, J. Salazar-Gonzalez, J. Decker, K. Pham 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.
23. Krone, S., and C. Neuhauser, 1997 Ancestral processes with se-lection. Theor. Popul. Biol. 51: 210-237.
24. Lemey, P., M. Salemi, and A.-M. Vandamme, 2009 The Phyloge-netic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, Ed. 2. Cambridge University Press, Cam-bridge, UK.
25. Leviyang, S., 2012 Sampling HIV intrahost genealogies based on a model of acute stage CTL response. Bull. Math. Biol. 3: 509-535.
26. Liu, Y. et al., 2006 Selection on the human immunodeficiency virus type 1 proteome following primary infection. J. Virol. 80: 9519-9529.
27. Mansky, L., 1996 Forward mutation rate of human immunodefi-ciency virus type 1 in a T lymphoid cell line. AIDS Res. Hum. Retroviruses 12: 307-314.
28. Mehandru, S., M. Poles, K. Tenner-Racz, A. Horowitz, A. Hurley et al., 2004 Primary HIV-1 infection is associated with prefer-ential depletion of CD4+ T lymphocytes from effector sites in the gastrointestinal tract. J. Exp. Med. 200: 761-770.
29. Mehandru, S., M. Poles, and K. Tenner-Racz, V. Manuellil, P. Jean-Pierre et al., 2007 Mechanisms of gastrointestinal CD4+ T-cell depletion during acute and early human immunodeficiency vi-rus type 1 infection. J. Virol. 81: 599-612.
30. Merrill, S., 2005 The stochastic dance of early HIV infection. J. App. Comp. Math. 184: 242-257.
31. Miao, H., X. Xia, A. Perelson, and H. Wu, 2011 On identifiability of nonlinear ODE models with application in viral dynamics. SIAM Rev. 53: 3-39.
32. Nielsen, R., and Z. Yang, 1998 Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929-936.
33. Nowak, M., 2000 Evolutionary Dynamics: Exploring the Equations of Life. Oxford University Press, Oxford.
34. Nowak, M., and R. May, 2000 Virus Dynamics: Mathematical Prin-ciples of Immunology and Virology. Oxford University Press, Ox-ford.
35. Pennings, P., and J. Hermisson, 2006 Soft sweeps iii: the signa-ture of positive selection from recurrent mutation. PLoS Genet. 2: 1998-2012.
36. Perelson, A., 2002 Modeling viral and immune system dynamics. Natl. Rev. 2: 28-36.
37. Perelson, A., D. Kirschner, and R. De Boer, 1993 Dynamics of HIV infection of CD4+ T cells. Math. Biosci. 114: 81-125.
38. Perelson, A., A. Neumann, M. Markowitz, J. Leonard, and D. Ho, 1996 HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science 271: 1582-1586.
39. Ribeiro, R., and S. Bonhoeffer, 1999 A stochastic model for pri-mary HIV infection: optimal timing of therapy. AIDS 13: 351-357.
40. Rouzine, I., and J. Coffin, 2010 Many-site adaptation in the pres-ence of infrequent recombination. Theor. Popul. Biol. 77: 189-204.
41. Rouzine, I., A. Rodrigo, and J. Coffin, 2001 Transition between stochastic evolution and deterministic evolution in the presence of selection: general theory and application to virology. Micro-biol. Mol. Biol. Rev. 65: 151-185.
42. Slatkin, M., and R. Hudson, 1991 Pairwise comparisons of mito-chondrial DNA sequences in stable and exponentially growing populations. Genetics 129: 555-562.
43. Stafford, M., L. Corey, Y. Cao, E. Daar, D. Ho et al., 2000 Modeling plasma virus concentration during primary HIV infection. J. Theor. Biol. 203: 285-301.
44. Tajima, F., 1989 Statistical method for testing the neutral muta-tion hypothesis by DNA polymorphism. Genetics 123: 585-595.
45. Tuckwell, H., P. Shipman, and A. Perelson, 2008 The probability of HIV infection in a new host and its reduction with micro-bicides. Math. Biosci. 214: 81-86.
46. Wick, D. and S. G. Self, 2000 Early HIV infection in vivo: branch-ing-process model for studying timing of immune responses and drug therapy. Math. Biosci. 165: 115-134.
47. Zhuo, H., and K. Dorman, 2005 A branching process model of drug resistant HIV, pp. 457-496 in Deterministic and Stochastic Mod-els of AIDS Epidemics and HIV infections with Intervention, Chap. 18 edited by T. Wai-Yuan, and H. Wu. World Scientific Publish-ing Co., Singapore.
48. J. CONWAY and D. COOMBS, A stochastic model in latently infected cell reactivation and viral blip generation in treated hiv patients, PLOS Comp. Bio., 7 (2011).
49. R. DE BOER, Understanding the failure of cd8 t-cell vaccination against simian/human im-munodeficiency virus, J. Virology, 81 (2007), pp. 2838-2848.
50. M. DESAI and D. FISHER, Beneficial mutation-selection balance and the effect of linkage on positive selection, Genetics, 176 (2007), pp. 1759-1798.
51. V. GANUSOV, N. GOONETILLEKE, M. LIU, G. FERRARI, G. SHAW, ET AL., Fitness costs and diversity of the ctl response determine the rate of ctl escape during acute and chronic phases of hiv infection, J. Virology, 85 (2011), pp. 10518-10528.
52. S. LEVIYANG, Sampling hiv intrahost genealogies based on a model of acute stage ctl re-sponse, Bull. Math. Bio., 3 (2012), pp. 509-35.
53. H. MIAO, X. XIA, A. PERELSON, and H. WU, On identifiability of nonlinear ode models with application in viral dynamics, SIAM Review, 53 (2011), pp. 3-39.
54. M. NOWAK, Evolutionary Dynamics: Exploring the Equations of Life, Oxford University Press, 2000.
55. A. PERELSON, D. KIRSCHNER, and R. DE BOER, Dynamics of hiv infection of cd4+ t cells, Math. Biosci., 114 (1993), pp. 81-125.
56. A. PERELSON, A. NEUMANN, M. MARKOWITZ, J. LEONARD, and D. HO, Hiv-1 dynam-ics in vivo: Virion clearance rate, infected cell life-span, and viral generation time, Science, 271 (1996), pp. 1582-1586.
57. I. ROUZINE, A. RODRIGO, and J. COFFIN, Transition between stochastic evolution and de-terministic evolution in the presence of selection: General theory and application to virology, Microbiology and Molecular Biology Reviews, (2001), pp. 151-185.
58. M. STAFFORD, L. COREY, Y. CAO, E. DAAR, D. HO, et al., Modeling plasma virus concentration during primary hiv infection, J. Theor. Biol., 203 (2000), pp. 285-301.
59. S. TAVARE, Line-of-descent and genealogical processes, and their applications in population genetics models, Theo. Pop. Bio., 26 (1984), pp. 119-163.