Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection

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

Volumn 108, Issue 14, 2011, Pages 5661-5666

  Batorsky, Rebecca ^a   Kearney, Mary F ^b   Palmer, Sarah E ^b   Maldarelli, Frank ^b   Rouzine, Igor M ^c   Coffin, John M ^c  

^a TUFTS UNIVERSITY   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c TUFTS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Background selection; Clonal interference; Haplotype; Hitchhiking; Modeling

Indexed keywords

ADULT; CASE REPORT; CONFERENCE PAPER; EVOLUTIONARY ADAPTATION; GENE LINKAGE DISEQUILIBRIUM; GENE MUTATION; GENE SEQUENCE; GENETIC DRIFT; GENETIC LINKAGE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; NONHUMAN; PRIORITY JOURNAL; STRUCTURAL GENE; VIRUS RECOMBINATION;

EID: 79955043851     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1102036108     Document Type: Article

References (51)

1. Salazar-Gonzalez JF, et al. (2009) Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. J Exp Med 206:1273-1289.
2. Kearney M, et al. (2009) Human immunodeficiency virus type 1 population genetics and adaptation in newly infected individuals. J Virol 83:2715-2727.
3. 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)
4. Goonetilleke N, et al.; CHAVI Clinical Core B (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.
5. Rouzine IM, Coffin JM(1999) Search for the mechanism of genetic variation in the pro gene of human immunodeficiency virus. J Virol 73:8167-8178. (Pubitemid 29441678)
6. Achaz G, et al. (2004) A robust measure of HIV-1 population turnover within chronically infected individuals. Mol Biol Evol 21:1902-1912. (Pubitemid 39331637)
7. Asquith B, Edwards CT, Lipsitch M, McLean AR (2006) Inefficient cytotoxic T lymphocyte-mediated killing of HIV-1-infected cells in vivo. PLoS Biol 4:e90.
8. Brown AJ (1997) Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population. Proc Natl Acad Sci USA 94:1862-1865. (Pubitemid 27113927)
9. Rouzine IM, Coffin JM (1999) Linkage disequilibrium test implies a large effective population number for HIV in vivo. Proc Natl Acad Sci USA 96:10758-10763. (Pubitemid 29442217)
10. Rouzine IM, Rodrigo A, Coffin JM (2001) Transition between stochastic evolution and deterministic evolution in the presence of selection: General theory and application to virology. Microbiol Mol Biol Rev 65:151-185. (Pubitemid 32204292)
11. Frost SD, Nijhuis M, Schuurman R, Boucher CA, Brown AJ (2000) Evolution of lamivudine resistance in human immunodeficiency virus type 1-infected individuals: The relative roles of drift and selection. J Virol 74:6262-6268. (Pubitemid 30429790)
12. Frost SD, Dumaurier MJ, Wain-Hobson S, Brown AJ (2001) Genetic drift and withinhost metapopulation dynamics of HIV-1 infection. Proc Natl Acad Sci USA 98: 6975-6980. (Pubitemid 32538327)
13. Rice WR (2002) Experimental tests of the adaptive significance of sexual recombination. Nat Rev Genet 3:241-251. (Pubitemid 34279793)
14. Fisher RA (1958) The Genetical Theory of Natural Selection (Clarendon, Oxford).
15. Muller HJ (1932) Some genetic aspects of sex. Am Nat 66:118-128.
16. Hill WG, Robertson A (1966) The effect of linkage on limits to artificial selection. Genet Res 8:269-294.
17. Otto SP, Barton NH (1997) The evolution of recombination: Removing the limits to natural selection. Genetics 147:879-906. (Pubitemid 27418594)
18. Felsenstein J (1974) The evolutionary advantage of recombination. Genetics 78: 737-756.
19. Smith JM (1971) What use is sex? J Theor Biol 30:319-335.
20. Rouzine IM, Wakeley J, Coffin JM (2003) The solitary wave of asexual evolution. Proc Natl Acad Sci USA 100:587-592. (Pubitemid 36126096)
21. Rouzine IM, Brunet E, Wilke CO (2008) The traveling-wave approach to asexual evolution: Muller's ratchet and speed of adaptation. Theor Popul Biol 73:24-46.
22. Desai MM, Fisher DS (2007) Beneficial mutation selection balance and the effect of linkage on positive selection. Genetics 176:1759-1798. (Pubitemid 47105232)
23. Brunet E, Rouzine IM, Wilke CO (2008) The stochastic edge in adaptive evolution. Genetics 179:603-620.
24. Tsimring LS, Levine H, Kessler DA (1996) RNA virus evolution via a fitness-space model. Phys Rev Lett 76:4440-4443. (Pubitemid 126639096)
25. Kessler DA, Levine H, Ridgway D, Tsimring L (1997) Evolution on a smooth landscape. J Stat Phys 87:519-544.
26. Rouzine IM, Coffin JM (2005) Evolution of human immunodeficiency virus under selection and weak recombination. Genetics 170:7-18. (Pubitemid 40799967)
27. Gheorghiu-Svirschevski S, Rouzine IM, Coffin JM (2007) Increasing sequence correlation limits the efficiency of recombination in a multisite evolution model. Mol Biol Evol 24:574-586. (Pubitemid 46204389)
28. Rouzine IM, Coffin JM (2007) Highly fit ancestors of a partly sexual haploid population. Theor Popul Biol 71:239-250. (Pubitemid 46186465)
29. Rouzine IM, Coffin JM (2010) Multi-site adaptation in the presence of infrequent recombination. Theor Popul Biol 77:189-204.
30. Iles MM, Walters K, Cannings C (2003) Recombination can evolve in large finite populations given selection on sufficient loci. Genetics 165:2249-2258. (Pubitemid 38040304)
31. Brandin E, Thorstensson R, Bonhoeffer S, Albert J (2006) Rapid viral decay in simian immunodeficiency virus-infected macaques receiving quadruple antiretroviral therapy. J Virol 80:9861-9864. (Pubitemid 44435660)
32. Markowitz M, et al. (2003) A novel antiviral intervention results in more accurate assessment of human immunodeficiency virus type 1 replication dynamics and T-cell decay in vivo. J Virol 77:5037-5038. (Pubitemid 36402857)
33. 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.
34. Levy DN, Aldrovandi GM, Kutsch O, Shaw GM (2004) Dynamics of HIV-1 recombination in its natural target cells. Proc Natl Acad Sci USA 101:4204-4209. (Pubitemid 38405907)
35. Nowak MA, Bangham CRM (1996) Population dynamics of immune responses to persistent viruses. Science 272:74-79.
36. Müller V, Marée AF, De Boer RJ (2001) Small variations in multiple parameters account for wide variations in HIV-1 set-points: A novel modelling approach. Proc Biol Sci 268:235-242. (Pubitemid 32154501)
37. Wodarz D (2001) Helper-dependent vs. helper-independent CTL responses in HIV infection: Implications for drug therapy and resistance. J Theor Biol 213:447-459. (Pubitemid 34014409)
38. Rouzine IM, Sergeev RA, Glushtsov AI (2006) Two types of cytotoxic lymphocyte regulation explain kinetics of immune response to human immunodeficiency virus. Proc Natl Acad Sci USA 103:666-671. (Pubitemid 43153083)
39. Sergeev RA, Batorsky RE, Rouzine IM (2010) Model with two types of CTL regulation and experiments on CTL dynamics. J Theor Biol 263:369-384.
40. Neher RA, Shraiman BI, Fisher DS (2010) Rate of adaptation in large sexual populations. Genetics 184:467-481.
41. Jung A, et al. (2002) Recombination: Multiply infected spleen cells in HIV patients. Nature 418:144. (Pubitemid 34773761)
42. Shriner D, Rodrigo AG, Nickle DC, Mullins JI (2004) Pervasive genomic recombination of HIV-1 in vivo. Genetics 167:1573-1583. (Pubitemid 39265897)
43. Neher RA, Leitner T (2010) Recombination rate and selection strength in HIV intrapatient evolution. PLOS Comput Biol 6:e1000660.
44. McVean G, Awadalla P, Fearnhead P (2002) A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160:1231-1241. (Pubitemid 34263482)
45. Burch CL, Turner PE, Hanley KA (2003) Patterns of epistasis in RNA viruses: A review of the evidence from vaccine design. J Evol Biol 16:1223-1235. (Pubitemid 37379290)
46. Ayme V, Petit-Pierre J, Souche S, Palloix A, Moury B (2007) Molecular dissection of the potato virus Y VPg virulence factor reveals complex adaptations to the pvr2 resistance allelic series in pepper. J Gen Virol 88:1594-1601. (Pubitemid 46723245)
47. Novella IS (2004) Negative effect of genetic bottlenecks on the adaptability of vesicular stomatitis virus. J Mol Biol 336:61-67. (Pubitemid 38102329)
48. Weinreich DM, Watson RA, Chao L (2005) Perspective: Sign epistasis and genetic constraint on evolutionary trajectories. Evolution 59:1165-1174. (Pubitemid 40870413)
49. Bonhoeffer S, Chappey C, Parkin NT, Whitcomb JM, Petropoulos CJ (2004) Evidence for positive epistasis in HIV-1. Science 306:1547-1550. (Pubitemid 39564948)
50. Poon AF, et al. (2010) Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1. Mol Biol Evol 27:819-832.
51. Palmer S, et al. (2005) Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis. J Clin Microbiol 43:406-413. (Pubitemid 40096331)