Human Immunodeficiency Virus Infection : from Biological Observations to Mechanistic Mathematical Modelling

 Access to full text

 Full (PDF)

1. Q. Abdool Karim, S.S. Abdool Karim, J.A. Frohlich, A.C. Grobler, C. Baxter, L.E. Mansoor, A.B. Kharsany, S. Sibeko, K.P. Mlisana, Z. Omar, T.N. Gengiah, S. Maarschalk, N. Arulappan, M. Mlotshwa, L. Morris, D. Taylor. Effectiveness and safety of tenofovir gel, an antiretroviral microbicide, for the prevention of HIV infection in women. Science, 329(5996) (2010), 1168–74.  
2. B.M. Adams, H.T. Banks, M. Davidian, H.D. Kwon, H.T. Tran, S.N. Wynne, E.S. Rosenberg. HIV dynamics : Modeling, data analysis, and optimal treatment protocols. Journal of Computational and Applied Mathematics, 184 (2005), 10–49.  
3. B.M. Adams, H.T. Banks, M. Davidian, E.S. Rosenberg. Estimation and prediction with HIV-treatment interruption data. Bulletin of mathematical biology, 69(2) (2007), 563–84.  
4. B.M. Adams, H.T. Banks, H.D. Kwon, H.T. Tran. Dynamic multidrug therapies for hiv : optimal and sti control approaches. Mathematical biosciences and engineering, 1(2) (2004), 223–41.  
5. M. Alizon, S. Wain-Hobson, L. Montagnier, P. Sonigo. Genetic variability of the AIDS virus : nucleotide sequence analysis of two isolates from African patients. Cell, 46(1) (1986), 63–74.  
6. G. Alter, D. Heckerman, A. Schneidewind, L. Fadda, C.M. Kadie, J.M. Carlson, C. Oniangue-Ndza, M. Martin, B. Li, S. I. Khakoo, M. Carrington, T.M. Allen, M. Altfeld. HIV-1 adaptation to NK-cell-mediated immune pressure. Nature, 476(7358) (2011), 96–100.  
7. P. Arora, N.M. Dixit. Timing the emergence of resistance to anti-HIV drugs with large genetic barriers. PLoS computational biology, 5(3) (2009), p. e1000305.  
8. J. Arthos, C. Cicala, E. Martinelli, K. Macleod, D. Van Ryk, D. Wei, Z. Xiao, T.D. Veenstra, T.P. Conrad, R.A. Lempicki, S. McLaughlin, M. Pascuccio, R. Gopaul, J. McNally, C.C. Cruz, N. Censoplano, E. Chung, K.N. Reitano, S. Kottilil, D.J. Goode, A.S. Fauci. HIV-1 envelope protein binds to and signals through integrin alpha4beta7, the gut mucosal homing receptor for peripheral T cells. Nature immunology, 9(3) (2008), 301–9.  
9. E.J. Arts, D.J. Hazuda. HIV-1 Antiretroviral Drug Therapy. Cold Spring Harbor perspectives in medicine, 2(4) (2012), p. a007161.  
10. M.S.Ascher, H.W. Sheppard. AIDS as immune system activation : a model for pathogenesis. Clinical and experimental immunology, 73(2) (1988), 165–7.  
11. B. Asquith. The evolutionary selective advantage of HIV-1 escape variants and the contribution of escape to the HLA-associated risk of AIDS progression. PLoS One, 3(10) (2008), p. e3486.  
12. B. Asquith, C.T. Edwards, M. Lipsitch, A.R. McLean. Inefficient cytotoxic T lymphocyte-mediated killing of HIV-1-infected cells in vivo. PLoS biology, 4(4) (2006), p. e90.  
13. B. Autran, G. Carcelain, T.S. Li, C. Blanc, D. Mathez, R. Tubiana, C. Katlama, P. Debre, J. Leibowitch. Positive effects of combined antiretroviral therapy on CD4+ T cell homeostasis and function in advanced HIV disease. Science, 277(5322) (1997), 112–6.  
14. B. Auvert, D. Taljaard, E. Lagarde, J. Sobngwi-Tambekou, R. Sitta, A. Puren. Randomized, controlled intervention trial of male circumcision for reduction of HIV infection risk : the ANRS 1265 Trial. PLoS medicine, 2(11) (2005), p. e298.  
15. E. Baake. Mutation and recombination with tight linkage. Journal of mathematical biology, 42(5) (2001), 455–88.  
16. R.C. Bailey, S. Moses, C.B. Parker, K. Agot, I. Maclean, J.N. Krieger, C.F. M. Williams, R.T. Campbell, J.O. Ndinya-Achola. Male circumcision for HIV prevention in young men in Kisumu, Kenya : a randomised controlled trial. Lancet, 369(9562) (2007), 643–56.  
17. H.T. Banks, M. Davidian, S. Hu, G.M. Kepler, E.S. Rosenberg. Modeling HIV Immune Response and Validation with Clinical Data. Journal of biological dynamics, 2(4) (2008), 357–85.  
18. H.T. Banks, H.-D. Kwon, J.A. Toivanen, H.T. Tran. A state-dependent Riccati equation-based estimator approach for HIV feedback control. Optim. Control Appl. Meth., 27 (2006), 93–121.  
19. D.L. Barber, E.J. Wherry, D. Masopust, B. Zhu, J.P. Allison, A. H. Sharpe, G.J. Freeman, R. Ahmed. Restoring function in exhausted CD8 T cells during chronic viral infection. Nature, 439(7077) (2006), 682–7.  
20. F. Barre-Sinoussi, J.C. Chermann, F. Rey, M.T. Nugeyre, S. Chamaret, J. Gruest, C. Dauguet, C. Axler-Blin, F. Vezinet-Brun, C. Rouzioux, W. Rozenbaum, L. Montagnier. Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science, 220(4599) (1983), 868–71.  
21. R. Batorsky, M.F. Kearney, S.E. Palmer, F. Maldarelli, I.M. Rouzine, J.M. Coffin. 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, 108(14) (2011), 5661–6.  
22. V. Baumgartel, S. Ivanchenko, A. Dupont, M. Sergeev, P.W. Wiseman, H.G. Krausslich, C. Brauchle, B. Muller, D.C. Lamb. Live-cell visualization of dynamics of HIV budding site interactions with an ESCRT component. Nature cell biology, 13(4) (2011), 469–74.  
23. G. Bello, C.A. Velasco-de-Castro, V. Bongertz, C.A. Rodrigues, C.B. Giacoia-Gripp, J.H. Pilotto, B. Grinsztejn, V.G. Veloso, M.G. Morgado. Immune activation and antibody responses in non-progressing elite controller individuals infected with HIV-1. Journal of medical virology, 81(10) (2009), 1681–90.  
24. Z. Bentwich, A. Kalinkovich, Z. Weisman, Z. Grossman. Immune activation in the context of HIV infection. Clinical and experimental immunology, 111(1) (1998), 1–2.  
25. E. Berntorp, A.D. Shapiro. Modern haemophilia care. Lancet, 379(9824) (2012), 1447–56.  
26. G. Bocharov, N.J. Ford, J. Edwards, T. Breinig, S. Wain-Hobson, A. Meyerhans. A genetic-algorithm approach to simulating human immunodeficiency virus evolution reveals the strong impact of multiply infected cells and recombination. The Journal of general virology, 86(Pt 11) (2005), 3109–18.  
27. M.C. Boily, R.F. Baggaley, L. Wang, B. Masse, R.G. White, R.J. Hayes, M. Alary. Heterosexual risk of HIV-1 infection per sexual act : systematic review and meta-analysis of observational studies. The Lancet infectious diseases, 9(2) (2009), 118–29.  
28. J. Bongaarts, P. Reining, P. Way, F. Conant. The relationship between male circumcision and HIV infection in African populations. AIDS, 3(6) (1989), 373–7.  
29. P. Borrow. Innate immunity in acute HIV-1 infection. Current opinion in HIV and AIDS, 6(5) (2011), 353–63.  
30. S.E. Bosinger, Q. Li, S.N. Gordon, N.R. Klatt, L. Duan, L. Xu, N. Francella, A. Sidahmed, A.J. Smith, E.M. Cramer, M. Zeng, D. Masopust, J.V. Carlis, L. Ran, T.H. Vanderford, M. Paiardini, R.B. Isett, D.A. Baldwin, J.G. Else, S.I. Staprans, G. Silvestri, A.T. Haase, D.J. Kelvin. Global genomic analysis reveals rapid control of a robust innate response in SIV-infected sooty mangabeys. The Journal of clinical investigation, 119(12) (2009), 3556–72.  
31. S. Bouchat, J. S. Gatot, K. Kabeya, C. Cardona, L. Colin, G. Herbein, S. de Wit, N. Clumeck, O. Lambotte, C. Rouzioux, O. Rohr, C. van Lint. Histone methyltransferase inhibitors induce HIV-1 recovery in resting CD4+ T cells from HIV-1+ HAART-treated patients. AIDS, (2012).  
32. A.L. Brass, D.M. Dykxhoorn, Y. Benita, N. Yan, A. Engelman, R.J. Xavier, J. Lieberman, S.J. Elledge. Identification of host proteins required for HIV infection through a functional genomic screen. Science, 319(5865) (2008), 921–6.  
33. J.M. Brenchley, D.A. Price, T.W. Schacker, T.E. Asher, G. Silvestri, S. Rao, Z. Kazzaz, E. Bornstein, O. Lambotte, D. Altmann, B.R. Blazar, B. Rodriguez, L. Teixeira-Johnson, A. Landay, J.N. Martin, F.M. Hecht, L.J. Picker, M.M. Lederman, S.G. Deeks, D.C. Douek. Microbial translocation is a cause of systemic immune activation in chronic HIV infection. Nature medicine, 12(12) (2006), 1365–71.  
34. J.M. Brenchley, T.W. Schacker, L.E. Ruff, D.A. Price, J.H. Taylor, G.J. Beilman, P.L. Nguyen, A. Khoruts, M. Larson, A.T. Haase, D.C. Douek. CD4+ T cell depletion during all stages of HIV disease occurs predominantly in the gastrointestinal tract. The Journal of experimental medicine, 200(6) (2004), 749–59.  
35. J.E. Brinchmann, J. Albert, F. Vartdal. Few infected CD4+ T cells but a high proportion of replication-competent provirus copies in asymptomatic human immunodeficiency virus type 1 infection. Journal of virology, 65(4) (1991), 2019–23.  
36. A.J. Brown. Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population. Proceedings of the National Academy of Sciences of the United States of America, 94(5) (1997), 1862–5.  
37. F. Brun-Vezinet, C. Rouzioux, F. Barre-Sinoussi, D. Klatzmann, A.G. Saimot, W. Rozenbaum, D. Christol, J.C. Gluckmann, L. Montagnier, J.C. Chermann. Detection of IgG antibodies to lymphadenopathy-associated virus in patients with AIDS or lymphadenopathy syndrome. Lancet, 1(8389) (1984), 1253–6.  
38. S.P. Buchbinder, D.V. Mehrotra, A. Duerr, D.W. Fitzgerald, R. Mogg, D. Li, P.B. Gilbert, J.R. Lama, M. Marmor, C. Del Rio, M.J. McElrath, D.R. Casimiro, K.M. Gottesdiener, J.A. Chodakewitz, L. Corey, M.N. Robertson. Efficacy assessment of a cell-mediated immunity HIV-1 vaccine (the Step Study) : a double-blind, randomised, placebo-controlled, test-of-concept trial. Lancet, 372(9653) (2008), 1881–93.  
39. F.D. Bushman, N. Malani, J. Fernandes, I. D’Orso, G. Cagney, T.L. Diamond, H. Zhou, D.J. Hazuda, A.S. Espeseth, R. Konig, S. Bandyopadhyay, T. Ideker, S.P. Goff, N.J. Krogan, A.D. Frankel, J.A. Young, S.K. Chanda. Host cell factors in HIV replication : meta-analysis of genome-wide studies. PLoS pathogens, 5(5) (2009), p. e1000437.  
40. M.A. Capistran. A study of latency, reactivation and apoptosis throughout HIV pathogenesis. Mathematical & Computer Modelling, 52 (2010), 1011–5.  
41. M. Cavrois, J. Neidleman, J.F. Kreisberg, W. C. Greene. In vitro derived dendritic cells trans-infect CD4 T cells primarily with surface-bound HIV-1 virions. PLoS pathogens, 3(1) (2007), p. e4.  
42. M. Centlivre, M. Sala, S. Wain-Hobson, B. Berkhout. In HIV-1 pathogenesis the die is cast during primary infection. AIDS, 21(1) (2007), 1–11.  
43. H.Y. Chen, M. Di Mascio, A.S. Perelson, D.D. Ho, L. Zhang. Determination of virus burst size in vivo using a single-cycle SIV in rhesus macaques. Proceedings of the National Academy of Sciences of the United States of America, 104(48) (2007), 19079–84.  
44. C. Cheng-Mayer, M. Quiroga, J.W. Tung, D. Dina, J.A. Levy. Viral determinants of human immunodeficiency virus type 1 T-cell or macrophage tropism, cytopathogenicity, and CD4 antigen modulation. Journal of virology, 64(9) (1990), 4390–8.  
45. S.K. Choudhary, N. Vrisekoop, C.A. Jansen, S.A. Otto, H. Schuitemaker, F. Miedema, D. Camerini. Low immune activation despite high levels of pathogenic human immunodeficiency virus type 1 results in long-term asymptomatic disease. Journal of virology, 81(16) (2007), 8838–42.  
46. T.W. Chun, K. Chadwick, J. Margolick, R.F. Siliciano. Differential susceptibility of naive and memory CD4+ T cells to the cytopathic effects of infection with human immunodeficiency virus type 1 strain LAI. Journal of virology, 71(6) (1997), 4436–44.  
47. T.W. Chun, D. Finzi, J. Margolick, K. Chadwick, D. Schwartz, R.F. Siliciano. In vivo fate of HIV-1-infected T cells : quantitative analysis of the transition to stable latency. Nature medicine, 1(12) (1995), 1284–90.  
48. C. Cicala, E. Martinelli, J.P. McNally, D.J. Goode, R. Gopaul, J. Hiatt, K. Jelicic, S. Kottilil, K. Macleod, A. O’Shea, N. Patel, D. Van Ryk, D. Wei, M. Pascuccio, L. Yi, L. McKinnon, P. Izulla, J. Kimani, R. Kaul, A.S. Fauci, J. Arthos. The integrin alpha4beta7 forms a complex with cell-surface CD4 and defines a T-cell subset that is highly susceptible to infection by HIV-1. Proceedings of the National Academy of Sciences of the United States of America, 106(49) (2009), 20877–82.  
49. M.S. Ciupe, B.L. Bivort, D.M. Bortz, P.W. Nelson. Estimating kinetic parameters from HIV primary infection data through the eyes of three different mathematical models. Mathematical biosciences, 200(1) (2006), 1–27.  
50. F. Clavel, D. Guetard, F. Brun-Vezinet, S. Chamaret, M.A. Rey, M.O. Santos-Ferreira, A.G. Laurent, C. Dauguet, C. Katlama, C. Rouzioux, and et al. Isolation of a new human retrovirus from West African patients with AIDS. Science, 233(4761) (1986), 343–6.  
51. F. Clayton, G. Snow, S. Reka, D.P. Kotler. Selective depletion of rectal lamina propria rather than lymphoid aggregate CD4 lymphocytes in HIV infection. Clinical and experimental immunology, 107(2) (1997), 288–92.  
52. F. Cocchi, A.L. DeVico, A. Garzino-Demo, A. Cara, R.C. Gallo, P. Lusso. The V3 domain of the HIV-1 gp120 envelope glycoprotein is critical for chemokine-mediated blockade of infection. Nature medicine, 2(11) (1996), 1244–7.  
53. J.M. Coffin. Structure, replication, and recombination of retrovirus genomes : some unifying hypotheses. The Journal of general virology, 42(1) (1979), 1–26.  
54. J. Cohen. Understanding HIV latency to undo it. Science, 332(6031) (2011), 786.  
55. M.S. Cohen, Y.Q. Chen, M. McCauley, T. Gamble, M.C. Hosseinipour, N. Kumarasamy, J.G. Hakim, J. Kumwenda, B. Grinsztejn, J.H. Pilotto, S.V. Godbole, S. Mehendale, S. Chariyalertsak, B.R. Santos, K.H. Mayer, I.F. Hoffman, S.H. Eshleman, E. Piwowar-Manning, L. Wang, J. Makhema, L.A. Mills, G. de Bruyn, I. Sanne, J. Eron, J. Gallant, D. Havlir, S. Swindells, H. Ribaudo, V. Elharrar, D. Burns, T.E. Taha, K. Nielsen-Saines, D. Celentano, M. Essex, T.R. Fleming. Prevention of HIV-1 infection with early antiretroviral therapy. The New England journal of medicine, 365(6) (2011), 493–505.  
56. J.W. Cohen Stuart, M.D. Hazebergh, D. Hamann, S.A. Otto, J.C. Borleffs, F. Miedema, C.A. Boucher, R.J. de Boer. The dominant source of CD4+ and CD8+ T-cell activation in HIV infection is antigenic stimulation. AIDS, 25(3) (2000), 203–11.  
57. A.C. Collier, R.W. Coombs, D. A. Schoenfeld, R.L. Bassett, J. Timpone, A. Baruch, M. Jones, K. Facey, C. Whitacre, V.J. McAuliffe, H.M. Friedman, T.C. Merigan, R. C. Reichman, C. Hooper, L. Corey. Treatment of human immunodeficiency virus infection with saquinavir, zidovudine, and zalcitabine. AIDS Clinical Trials Group. he New England journal of medicine, 334(16) (1996), 1011–7.  
58. R. Collman, N.F. Hassan, R. Walker, B. Godfrey, J. Cutilli, J.C. Hastings, H. Friedman, S.D. Douglas, N. Nathanson. Infection of monocyte-derived macrophages with human immunodeficiency virus type 1 (HIV-1). Monocyte-tropic and lymphocyte-tropic strains of HIV-1 show distinctive patterns of replication in a panel of cell types. The Journal of experimental medicine, 170(4) (1989), 1149–63.  
59. M.P. D’Souza, V.A. Harden. Chemokines and HIV-1 second receptors. Confluence of two fields generates optimism in AIDS research. Nature medicine, 2(12) (1996), 1293–300.  
60. A.G. Dalgleish, P.C. Beverley, P.R. Clapham, D.H. Crawford, M.F. Greaves, R.A. Weiss. The CD4 (T4) antigen is an essential component of the receptor for the AIDS retrovirus. Nature, 312(5996) (1984), 763–7.  
61. J. David, H. Tran, H.T. Banks. HIV model analysis and estimation implementation under optimal control based treatment strategies. Int. J. Pure Appl. Math., 57 (2009), 357–92.  
62. C.L. Day, D.E. Kaufmann, P. Kiepiela, J.A. Brown, E.S. Moodley, S. Reddy, E.W. Mackey, J.D. Miller, A.J. Leslie, C. DePierres, Z. Mncube, J. Duraiswamy, B. Zhu, Q. Eichbaum, M. Altfeld, E.J. Wherry, H.M. Coovadia, P.J. Goulder, P. Klenerman, R. Ahmed, G.J. Freeman, B.D. Walker. PD-1 expression on HIV-specific T cells is associated with T-cell exhaustion and disease progression. Nature, 443(7109) (2006), 350–4.  
63. R.J. De Boer, R.M. Ribeiro, A.S. Perelson. Current estimates for HIV-1 production imply rapid viral clearance in lymphoid tissues. PLoS computational biology, 6(9) (2010), p. e1000906.  
64. M. De Martino, P.A. Tovo, A.E. Tozzi, P. Pezzotti, L. Galli, S. Livadiotti, D. Caselli, E. Massironi, E. Ruga, F. Fioredda. HIV-1 transmission through breast-milk : appraisal of risk according to duration of feeding. AIDS (London, England), 6(9) (1992), 991.  
65. S.G. Deeks, C.M. Kitchen, L. Liu, H. Guo, R. Gascon, A.B. Narvaez, P. Hunt, J.N. Martin, J.O. Kahn, J. Levy, M.S. McGrath, F.M. Hecht. Immune activation set point during early HIV infection predicts subsequent CD4+ T-cell changes independent of viral load. Blood, 104(4) (2004), 942–7.  
66. N.M. Dixit, A. S. Perelson. HIV dynamics with multiple infections of target cells. Proceedings of the National Academy of Sciences of the United States of America, 102(23) (2005), 8198–203.  
67. D. Donnell, J.M. Baeten, J. Kiarie, K.K. Thomas, W. Stevens, C.R. Cohen, J. McIntyre, J.R. Lingappa, C. Celum. Heterosexual HIV-1 transmission after initiation of antiretroviral therapy : a prospective cohort analysis. Lancet, 375(9731) (2010), 2092–8.  
68. D. Douek. HIV disease progression : immune activation, microbes, and a leaky gut. Topics in HIV medicine : a publication of the International AIDS Society, USA, 15(4) (2007), 114–7.  
69. T. Dragic, V. Litwin, G.P. Allaway, S.R. Martin, Y. Huang, K.A. Nagashima, C. Cayanan, P.J. Maddon, R.A. Koup, J.P. Moore, W.A. Paxton. HIV-1 entry into CD4+ cells is mediated by the chemokine receptor CC-CKR-5. Nature, 381(6584) (1996), 667–73.  
70. J. Embretson, M. Zupancic, J.L. Ribas, A. Burke, P. Racz, K. Tenner-Racz, A.T. Haase. Massive covert infection of helper T lymphocytes and macrophages by HIV during the incubation period of AIDS. Nature, 362(6418) (1993), 359–62.  
71. A. Engelman, P. Cherepanov. The structural biology of HIV-1 : mechanistic and therapeutic insights. Nature reviews. Microbiology, 10(4) (2012), 279–90.  
72. A.S. Fauci, H.C. Lane. A Preventive Vaccine Against HIV Infection. Harrison’s Principles of Internal Medicine, (2012), 18e.  
73. D. Favre, S. Lederer, B. Kanwar, Z.M. Ma, S. Proll, Z. Kasakow, J. Mold, L. Swainson, J.D. Barbour, C.R. Baskin, R. Palermo, I. Pandrea, C.J. Miller, M.G. Katze, J. M. McCune. Critical loss of the balance between Th17 and T regulatory cell populations in pathogenic SIV infection. PLoS pathogens, 5(2) (2009), p. e1000295.  
74. N.M. Ferguson, F. deWolf, A.C. Ghani, C. Fraser, C.A. Donnelly, P. Reiss, J.M. Lange, S.A. Danner, G.P. Garnett, J. Goudsmit, R.M. Anderson. Antigen-driven CD4+ T cell and HIV-1 dynamics : residual viral replication under highly active antiretroviral therapy. Proceedings of the National Academy of Sciences of the United States of America, 96(26) (1999), 15167–72.  
75. D. Finzi, J. Blankson, J.D. Siliciano, J.B. Margolick, K. Chadwick, T. Pierson, K. Smith, J. Lisziewicz, F. Lori, C. Flexner, T.C. Quinn, R.E. Chaisson, E. Rosenberg, B. Walker, S. Gange, J. Gallant, R. F. Siliciano. Latent infection of CD4+ T cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective combination therapy. Nature medicine, 5(5) (1999), 512–7.  
76. C. Fraser, N.M. Ferguson, F. de Wolf, R.M. Anderson. The role of antigenic stimulation and cytotoxic T cell activity in regulating the long-term immunopathogenesis of HIV : mechanisms and clinical implications. Proceedings. Biological sciences / The Royal Society, 268(1481) (2001), 2085–95.  
77. S.D. Frost, M.J. Dumaurier, S. Wain-Hobson, A.J. Brown. Genetic drift and within-host metapopulation dynamics of HIV-1 infection. Proceedings of the National Academy of Sciences of the United States of America, 98(12) (2001), 6975–80.  
78. R.C. Gallo, S.Z. Salahuddin, M. Popovic, G.M. Shearer, M. Kaplan, B.F. Haynes, T.J. Palker, R. Redfield, J. Oleske, B. Safai, and et al. Frequent detection and isolation of cytopathic retroviruses (HTLV-III) from patients with AIDS and at risk for AIDS. Science, 224(4648) (1984), 500–3.  
79. V.V. Ganusov, R.J. De Boern. Do most lymphocytes in humans really reside in the gut ? Trends in immunology, 28(12) (2007), 514–8.  
80. V.V. Ganusov, N. Goonetilleke, M.K. Liu, G. Ferrari, G.M. Shaw, A.J. McMichael, P. Borrow, B.T. Korber, A.S. Perelson. Fitness costs and diversity of the cytotoxic T lymphocyte (CTL) response determine the rate of CTL escape during acute and chronic phases of HIV infection. Journal of virology, 85(20) (2011), 10518–28.  
81. F. Gao, Y. Chen, D.N. Levy, J.A. Conway, T.B. Kepler, H. Hui. Unselected mutations in the human immunodeficiency virus type 1 genome are mostly nonsynonymous and often deleterious. Journal of virology, 78(5) (2004), 2426–33.  
82. E. Garcia, M. Pion, A. Pelchen-Matthews, L. Collinson, J.F. Arrighi, G. Blot, F. Leuba, J.M. Escola, N. Demaurex, M. Marsh, V. Piguet. HIV-1 trafficking to the dendritic cell-T-cell infectious synapse uses a pathway of tetraspanin sorting to the immunological synapse. Traffic, 6(6) (2005), 488–501.  
83. T.B. Geijtenbeek, D.S. Kwon, R. Torensma, S.J. van Vliet, G.C. van Duijnhoven, J. Middel, I.L. Cornelissen, H.S. Nottet, V.N. KewalRamani, D.R. Littman, C.G. Figdor, Y. van Kooyk. DC-SIGN, a dendritic cell-specific HIV-1-binding protein that enhances trans-infection of T cells. Cell, 100(5) (2000), 587–97.  
84. C. Geldmacher, J.R. Currier, E. Herrmann, A. Haule, E. Kuta, F. McCutchan, L. Njovu, S. Geis, O. Hoffmann, L. Maboko, C. Williamson, D. Birx, A. Meyerhans, J. Cox, M. Hoelscher. CD8 T-cell recognition of multiple epitopes within specific Gag regions is associated with maintenance of a low steady-state viremia in human immunodeficiency virus type 1-seropositive patients. Journal of virology, 81(5) (2007), 2440–8.  
85. H.E. Gendelman, L.M. Baca, H. Husayni, J.A. Turpin, D. Skillman, D.C. Kalter, J.M. Orenstein, D.L. Hoover, M.S. Meltzer. Macrophage-HIV interaction : viral isolation and target cell tropism. AIDS, 4(3) (1990), 221–8.  
86. J.V. Giorgi, L.E. Hultin, J.A. McKeating, T.D. Johnson, B. Owens, L.P. Jacobson, R. Shih, J. Lewis, D.J. Wiley, J.P. Phair, S.M. Wolinsky, R. Detels. Shorter survival in advanced human immunodeficiency virus type 1 infection is more closely associated with T lymphocyte activation than with plasma virus burden or virus chemokine coreceptor usage. The Journal of infectious diseases, 179(4) (1999), 859–70.  
87. D. Gisselquist, G. Upham, J.J. Potterat. Efficiency of human immunodeficiency virus transmission through injections and other medical procedures : evidence, estimates, and unfinished business. Infection control and hospital epidemiology : The official journal of the Society of Hospital Epidemiologists of America, 27(9) (2006), 944–52.  
88. M. Goodenow, T. Huet, W. Saurin, S. Kwok, J. Sninsky, S. Wain-Hobson. HIV-1 isolates are rapidly evolving quasispecies : evidence for viral mixtures and preferred nucleotide substitutions. J. Acquir. Immune Defic. Syndr., 2(4) (1989), 344–52.  
89. N. Goonetilleke, M.K. Liu, J.F. Salazar-Gonzalez, G. Ferrari, E. Giorgi, V.V. Ganusov, B.F. Keele, G.H. Learn, E.L. Turnbull, M.G. Salazar, K.J. Weinhold, S. Moore, N. Letvin, B.F. Haynes, M.S. Cohen, P. Hraber, T. Bhattacharya, P. Borrow, A.S. Perelson, B.H. Hahn, G.M. Shaw, B.T. Korber, A.J. McMichael. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. Journal of experimental medicine, 206(6) (2009), 1253–72.  
90. M.S. Gottlieb, R. Schroff, H.M. Schanker, J.D. Weisman, P.T. Fan, R.A. Wolf, A. Saxon. Pneumocystis carinii pneumonia and mucosal candidiasis in previously healthy homosexual men : evidence of a new acquired cellular immunodeficiency. The New England journal of medicine, 305(24) (1981), 1425–31.  
91. P.J. Goulder, D.I. Watkins. HIV and SIV CTL escape : implications for vaccine design. Nature reviews. Immunology, 4(8) (2004), 630–40.  
92. R.M. Grant, J.R. Lama, P.L. Anderson, V. McMahan, A.Y. Liu, L. Vargas, P. Goicochea, M. Casapia, J.V. Guanira-Carranza, M.E. Ramirez-Cardich, O. Montoya-Herrera, T. Fernandez, V.G. Veloso, S.P. Buchbinder, S. Chariyalertsak, M. Schechter, L.G. Bekker, K.H. Mayer, E.G. Kallas, K.R. Amico, K. Mulligan, L.R. Bushman, R.J. Hance, C. Ganoza, P. Defechereux, B. Postle, F. Wang, J.J. McConnell, J.H. Zheng, J. Lee, J.F. Rooney, H.S. Jaffe, A.I. Martinez, D.N. Burns, D.V. Glidden. Preexposure chemoprophylaxis for HIV prevention in men who have sex with men. The New England journal of medicine, 363(27) (2010), 2587–99.  
93. R.H. Gray, M.J. Wawer, R. Brookmeyer, N.K. Sewankambo, D. Serwadda, F. Wabwire-Mangen, T. Lutalo, X. Li, T. vanCott, T.C. Quinn. Probability of HIV-1 transmission per coital act in monogamous, heterosexual, HIV-1-discordant couples in Rakai, Uganda. Lancet, 357(9263) (2001), 1149–53.  
94. F. Groot, T.M. van Capel, J. Schuitemaker, B. Berkhout, E.C. de Jong. Differential susceptibility of naive, central memory and effector memory T cells to dendritic cell-mediated HIV-1 transmission. Retrovirology, 3 (2006), 52.  
95. Z. Grossman. Mathematical modeling of thymopoiesis in HIV infection : real data, virtual data, and data interpretation. Clin. Immunol., 107(3) (2003), 137–9.  
96. Z. Grossman, M.B. Feinberg, W.E. Paul. Multiple modes of cellular activation and virus transmission in HIV infection : a role for chronically and latently infected cells in sustaining viral replication. Proceedings of the National Academy of Sciences of the United States of America, 95(11) (1998), 6314–9.  
97. Z. Grossman, M. Meier-Schellersheim, W.E. Paul, L.J. Picker. Pathogenesis of HIV infection : what the virus spares is as important as what it destroys. Nature medicine, 12(3) (2006), 289–95.  
98. Z. Grossman, M. Meier-Schellersheim, A. E. Sousa, R. M. Victorino, and W.E. Paul. CD4+ T-cell depletion in HIV infection : are we closer to understanding the cause ? Nature medicine, 8(4) (2002), 319–23.  
99. Z. Grossman, B. Min, M. Meier-Schellersheim, W. E. Paul. Concomitant regulation of T-cell activation and homeostasis. Nature reviews. Immunology, 4(5) (2004), 387–95.  
100. Z. Grossman, W.E. Paul. The impact of HIV on naive T-cell homeostasis. Nature medicine, 6(9) (2000), 976–7.  
101. Z. Grossman, L. J. Picker. Pathogenic mechanisms in simian immunodeficiency virus infection. CCurrent opinion in HIV and AIDS, 3(3) (2008), 380–6.  
102. L.A. Guay, P. Musoke, T. Fleming, D. Bagenda, M. Allen, C. Nakabiito, J. Sherman, P. Bakaki, C. Ducar, M. Deseyve, L. Emel, M. Mirochnick, M. G. Fowler, L. Mofenson, P. Miotti, K. Dransfield, D. Bray, F. Mmiro, J.B. Jackson. Intrapartum and neonatal single-dose nevirapine compared with zidovudine for prevention of mother-to-child transmission of HIV-1 in Kampala, Uganda : HIVNET 012 randomised trial. Lancet, 354(9181), (1999), 795–802.  
103. M. Guyader, M. Emerman, P. Sonigo, F. Clavel, L. Montagnier, M. Alizon. Genome organization and transactivation of the human immunodeficiency virus type 2. Nature, 326(6114) (1987), 662–9.  
104. A.T. Haase. Population biology of HIV-1 infection : viral and CD4+ T cell demographics and dynamics in lymphatic tissues. Annual review of immunology, 17 (1999), 625–56.  
105. A.T. Haase. Targeting early infection to prevent HIV-1 mucosal transmission. Nature, 464(7286) (2010), 217–23.  
106. M. Hadjiandreou, R. Conejeros, V.S. Vassiliadis. Towards a long-term model construction for the dynamic simulation of HIV infection. Mathematical biosciences and engineering, 4(3) (2007), 489–504.  
107. M. Hadjiandreou, R. Conejeros, J. Wilson. HIV treatment planning on a case-by-case basis. International Journal of Biological and Life Sciences, 7 (2011), 148–57.  
108. B.H. Hahn, G.M. Shaw, M.E. Taylor, R.R. Redfield, P.D. Markham, S.Z. Salahuddin, F. Wong-Staal, R.C. Gallo, E.S. Parks, W.P. Parks. Genetic variation in HTLV-III/LAV over time in patients with AIDS or at risk for AIDS. Science, 232(4757) (1986), 1548–53.  
109. R.S. Harris, K.N. Bishop, A.M. Sheehy, H.M. Craig, S.K. Petersen-Mahrt, I.N. Watt, M.S. Neuberger, M.H. Malim. DNA deamination mediates innate immunity to retroviral infection. Cell, 113(6) (2003), 803–9.  
110. B.F. Haynes, P.B. Gilbert, M.J. McElrath, S. Zolla-Pazner, G.D. Tomaras, S.M. Alam, D.T. Evans, D.C. Montefiori, C. Karnasuta, R. Sutthent, H.X. Liao, A.L. DeVico, G.K. Lewis, C. Williams, A. Pinter, Y. Fong, H. Janes, A. DeCamp, Y. Huang, M. Rao, E. Billings, N. Karasavvas, M.L. Robb, V. Ngauy, M.S. de Souza, R. Paris, G. Ferrari, R.T. Bailer, K.A. Soderberg, C. Andrews, P.W. Berman, N. Frahm, S.C. De Rosa, MD. Alpert, N. L. Yates, X. Shen, R.A. Koup, P. Pitisuttithum, J. Kaewkungwal, S. Nitayaphan, S. Rerks-Ngarm, N.L. Michael, J.H. Kim. Immune-correlates analysis of an HIV-1 vaccine efficacy trial. The New England journal of medicine, 366(14) (2012), 1275–86.  
111. M.D. Hazenberg, S.A. Otto, J.W. Cohen Stuart, M.C. Verschuren, J.C. Borleffs, C.A. Boucher, R.A. Coutinho, J.M. Lange, T.F. Rinke de Wit, A. Tsegaye, J.J. van Dongen, D. Hamann, R.J. de Boer, F. Miedema. Increased cell division but not thymic dysfunction rapidly affects the T-cell receptor excision circle content of the naive T cell population in HIV-1 infection. Nature medicine, 6(9) (2000), 1036–42.  
112. M.D. Hazenberg, S. A. Otto, B.H. van Benthem, M.T. Roos, R.A. Coutinho, J.M. Lange, D. Hamann, M. Prins, F. Miedema. Persistent immune activation in HIV-1 infection is associated with progression to AIDS. AIDS, 17(13) (2003), 1881–8.  
113. M.D. Hazenberg, J.W. Stuart, S.A. Otto, J.C. Borleffs, C.A. Boucher, R.J. de Boer, F. Miedema, D. Hamann. T-cell division in human immunodeficiency virus (HIV)-1 infection is mainly due to immune activation : a longitudinal analysis in patients before and during highly active antiretroviral therapy (HAART). Blood, 95(1) (2000), 249–55.  
114. S.L. Heath, J.G. Tew, J.G. Tew, A.K. Szakal, G.F. Burton. Follicular dendritic cells and human immunodeficiency virus infectivity. Nature, 377(6551) (1995), 740–4.  
115. M. Hellerstein, M.B. Hanley, D. Cesar, S. Siler, C. Papageorgopoulos, E. Wieder, D. Schmidt, R. Hoh, R. Neese, D. Macallan, S. Deeks, J.M. McCune. Directly measured kinetics of circulating T lymphocytes in normal and HIV-1-infected humans. Nature medicine, 5(1) (1999), 83–9.  
116. J.T. Herbeck, M. Rolland, Y. Liu, S. McLaughlin, J. McNevin, H. Zhao, K. Wong, J.N. Stoddard, D. Raugi, S. Sorensen, I. Genowati, B. Birditt, A. McKay, K. Diem, B.S. Maust, W. Deng, A.C. Collier, J.D. Stekler, M.J. McElrath, J.I. Mullins. Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes. Journal of virology, 85(15) (2011), 7523–34.  
117. E.A. Hernandez-Vargas, D. Mehta, R.H. Middleton. Towards Modelling HIV Long Term Behavior. Preprints of the 18th IFAC World Congress, (2011), 581–6.  
118. D.D. Ho, A.U. Neumann, A.S. Perelson, W. Chen, J.M. Leonard, M. Markowitz. Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature, 373(6510) (1995), 123–6.  
119. I.B. Hogue, S.H. Bajaria, B.A. Fallert, S. Qin, T.A. Reinhart, D.E. Kirschner. The dual role of dendritic cells in the immune response to human immunodeficiency virus type 1 infection. The Journal of general virology, 89 (2008), 2228–39.  
120. T. Hraba, J. Dolezal. A mathematical model and CD4+ lymphocyte dynamics in HIV infection. Emerging infectious diseases, 2(4) (1996), 299–305.  
121. K. Hrecka, C. Hao, M. Gierszewska, S.K. Swanson, M. Kesik-Brodacka, S. Srivastava, L. Florens, M.P. Washburn, J. Skowronski. Vpx relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein. Nature, 474(7353) (2011), 658–61.  
122. K.J. Huang, D.P. Wooley. 2005. A new cell-based assay for measuring the forward mutation rate of HIV-1. Journal of virological methods124:95-104.  
123. K. Huang, D. Wooley. A new cell-based assay for measuring the forward mutation rate of HIV-1. Journal of virological methods, 124(1-2) (2005), 95–104.  
124. S.S. Hwang, T.J. Boyle, H.K. Lyerly, B.R. Cullen. Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1. Science, 253(5015) (1991), 71–4.  
125. N. Izquierdo-Useros, M. Lorizate, F.X. Contreras, M.T. Rodriguez-Plata, B. Glass, I. Erkizia, J.G. Prado, J. Casas, G. Fabrias, H.G. Krausslich, J. Martinez-Picado. Sialyllactose in Viral Membrane Gangliosides Is a Novel Molecular Recognition Pattern for Mature Dendritic Cell Capture of HIV-1. PLoS biology, 10(4) (2012), p. e1001315.  
126. B. Jacquelin, V. Mayau, B. Targat, A.S. Liovat, D. Kunkel, G. Petitjean, M. A. Dillies, P. Roques, C. Butor, G. Silvestri, L.D. Giavedoni, P. Lebon, F. Barre-Sinoussi, A. Benecke, M.C. Muller-Trutwin. Nonpathogenic SIV infection of African green monkeys induces a strong but rapidly controlled type I IFN response. The Journal of clinical investigation, 119(12) (2009), 3544–55.  
127. S. Jager, P. Cimermancic, N. Gulbahce, J.R. Johnson, K.E. McGovern, S.C. Clarke, M. Shales, G. Mercenne, L. Pache, K. Li, H. Hernandez, G.M. Jang, S.L. Roth, E. Akiva, J. Marlett, M. Stephens, I. D’Orso, J. Fernandes, M. Fahey, C. Mahon, A.J. O’Donoghue, A. Todorovic, J.H. Morris, D.A. Maltby, T. Alber, G. Cagney, F.D. Bushman, J.A. Young, S.K. Chanda, W.I. Sundquist, T. Kortemme, R.D. Hernandez, C.S. Craik, A. Burlingame, A. Sali, A.D. Frankel, N.J. Krogan. Global landscape of HIV-human protein complexes. Nature, 481(7381) (2012), 365–70.  
128. A.E. Jetzt, H. Yu, G.J. Klarmann, Y. Ron, B.D. Preston, J.P. Dougherty. High rate of recombination throughout the human immunodeficiency virus type 1 genome. Journal of virology, 74(3) (2000), 1234–40.  
129. M.I. Johnston, A.S. Fauci. An HIV vaccine-evolving concepts. The New England journal of medicine, 356(20) (2007), 2073–81.  
130. L. Josefsson, M.S. King, B. Makitalo, J. Brannstrom, W. Shao, F. Maldarelli, M.F. Kearney, W. S. Hu, J. Chen, H. Gaines, J.W. Mellors, J. Albert, J.M. Coffin, S.E. Palmer. Majority of CD4+ T cells from peripheral blood of HIV-1-infected individuals contain only one HIV DNA molecule. Proceedings of the National Academy of Sciences of the United States of America, 2011.  
131. A. Jung, R. Maier, J.P. Vartanian, G. Bocharov, V. Jung, U. Fischer, E. Meese, S. Wain-Hobson, A. Meyerhans. Recombination : Multiply infected spleen cells in HIV patients. Nature, 418(6894) (2002), 144.  
132. U.D. Kadolsky, B. Asquith. Quantifying the impact of human immunodeficiency virus-1 escape from cytotoxic T-lymphocytes. PLoS computational biology, 6(11) (2010), p. e1000981.  
133. A. Kamina, R.W. Makuch, H. Zhao. A stochastic modeling of early HIV-1 population dynamics. Mathematical biosciences, 170(2) (2001), 187–98.  
134. P.D. Katsikis, Y.M. Mueller, F.Villinger. The cytokine network of acute HIV infection : a promising target for vaccines and therapy to reduce viral set-point ? PLoS pathogens, 7(8) (2011), p. e1002055.  
135. B.H. Keele, E.E. Giorgi, J.F. Salazar-Gonzalez, J.M. Decker, K.T. Pham, M.G. Salazar, C. Sun, T. Grayson, S. Wang, H. Li, X. Wei, C. Jiang, J.L. Kirchherr, F. Gao, J. A. Anderson, L.H. Ping, R. Swanstrom, G.D. Tomaras, W.A. Blattner, P.A. Goepfert, J.M. Kilby, M.S. Saag, E.L. Delwart, M.P. Busch, M.S. Cohen, D.C. Montefiori, B.F. Haynes, B. Gaschen, G.S. Athreya, H.Y. Lee, N. Wood, C. Seoighe, A.S. Perelson, T. Bhattacharya, B.T. Korber, B.H. Hahn, G.M. Shaw. Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proceedings of the National Academy of Sciences of the United States of America, 105(21) (2008), 7552–7.  
136. P. Kiepiela, A.J. Leslie, I. Honeyborne, D. Ramduth, C. Thobakgale, S. Chetty, P. Rathnavalu, C. Moore, K.J. Pfafferott, L. Hilton. Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA. Nature, 432(7018) (2004), 769–75.  
137. F. Kirchhoff. Immune evasion and counteraction of restriction factors by HIV-1 and other primate lentiviruses. Cell host & microbe, 8(1) (2010), 55–67.  
138. M.M. Kitahata, S.J. Gange, A.G. Abraham, B. Merriman, M.S. Saag, A.C. Justice, R.S. Hogg, S.G. Deeks, J.J. Eron, J.T. Brooks. Effect of early versus deferred antiretroviral therapy for HIV on survival. New England Journal of Medicine, 360(18) (2009), 1815–26.  
139. D. Klatzmann, F. Barre-Sinoussi, M.T. Nugeyre, C. Danquet, E. Vilmer, C. Griscelli, F. Brun-Veziret, C. Rouzioux, J.C. Gluckman, J.C. Chermann, and et al. Selective tropism of lymphadenopathy associated virus (LAV) for helper-inducer T lymphocytes. Science, 225(4657) (1984), 59–63.  
140. R. Konig, Y. Zhou, D. Elleder, T.L. Diamond, G.M. Bonamy, J.T. Irelan, C.Y. Chiang, B.P. Tu, P.D. De Jesus, C.E. Lilley, S. Seidel, A.M. Opaluch, J.S. Caldwell, M.D. Weitzman, K.L. Kuhen, S. Bandyopadhyay, T. Ideker, A.P. Orth, L.J. Miraglia, F.D. Bushman, J.A. Young, S.K. Chanda. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell, 135(1) (2008), 49–60.  
141. L.G. Kostrikis, G. Touloumi, R. Karanicolas, N. Pantazis, C. Anastassopoulou, A. Karafoulidou, J.J. Goedert, A. Hatzakis. Quantitation of human immunodeficiency virus type 1 DNA forms with the second template switch in peripheral blood cells predicts disease progression independently of plasma RNA load. Journal of virology, 76(20) (2002), 10099–108.  
142. I.N. Koulinska, E. Villamor, B. Chaplin, G. Msamanga, W. Fawzi, B. Renjifo, M. Essex. Transmission of cell-free and cell-associated HIV-1 through breast-feeding. AIDS, 41(1) (2006), 93.  
143. R.D. Kouyos, C.L. Althaus, S. Bonhoeffer. Stochastic or deterministic : what is the effective population size of HIV-1 ?. Trends in microbiology, 14(12) (2006), 507–11.  
144. Y. Koyanagi, S. Miles, R.T. Mitsuyasu, J.E. Merrill, H.V. Vinters, I.S. Chen. Dual infection of the central nervous system by AIDS viruses with distinct cellular tropisms. Science, 236(4803) (1987), 819–22.  
145. H.B Kramer, K.J. Lavender, L. Qin, A.R. Stacey, M.K. Liu, K. di Gleria, A. Simmons, N. Gasper-Smith, B.F. Haynes, A.J. McMichael, P. Borrow, B.M. Kessler. Elevation of intact and proteolytic fragments of acute phase proteins constitutes the earliest systemic antiviral response in HIV-1 infection. PLoS pathogens, 6(5) (2010), p. e1000893.  
146. D. Kwa, J. Vingerhoed, B. Boeser-Nunnink, S. Broersen, H. Schuitemaker. Cytopathic effects of non-syncytium-inducing and syncytium-inducing human immunodeficiency virus type 1 variants on different CD4(+)-T-cell subsets are determined only by coreceptor expression. Journal of virology, 75(21) (2001), 10455–9.  
147. P.D. Kwong, J.R. Mascola, G.J. Nabel. Rational Design of Vaccines to Elicit Broadly Neutralizing Antibodies to HIV-1. Cold Spring Harbor perspectives in medicine, 1(1) (2011), p. a007278.  
148. N. Laguette, B. Sobhian, N. Casartelli, M. Ringeard, C. Chable-Bessia, E. Segeral, A. Yatim, S. Emiliani, O. Schwartz, M. Benkirane. SAMHD1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by Vpx. Nature, 474(7353) (2011), 654–7.  
149. D. Lecossier, F. Bouchonnet, F. Clavel, A.J. Hance. Hypermutation of HIV-1 DNA in the absence of the Vif protein. Science, 300(5622) (2003), 1112.  
150. S. Lederer, D. Favre, K.A. Walters, S. Proll, B. Kanwar, Z. Kasakow, C.R. Baskin, R. Palermo, J.M. McCune, M.G. Katze. Transcriptional profiling in pathogenic and non-pathogenic SIV infections reveals significant distinctions in kinetics and tissue compartmentalization. PLoS pathogens, 5(2) (2009), p. e1000296.  
151. H.Y. Lee, A.S. Perelson, S.C. Park, T. Leitner. Dynamic correlation between intrahost HIV-1 quasispecies evolution and disease progression. PLoS computational biology, 4(12) (2008), p. e1000240.  
152. M.C. Levesque, M.A. Moody, K.K. Hwang, D.J. Marshall, J.F. Whitesides, J.D. Amos, T.C. Gurley, S. Allgood, B.B. Haynes, N.A. Vandergrift, S. Plonk, D.C. Parker, M.S. Cohen, G.D. Tomaras, P.A. Goepfert, G.M. Shaw, J.E. Schmitz, J.J. Eron, N.J. Shaheen, C.B. Hicks, H.X. Liao, M. Markowitz, G. Kelsoe, D.M. Margolis, B.F. Haynes. Polyclonal B cell differentiation and loss of gastrointestinal tract germinal centers in the earliest stages of HIV-1 infection. PLoS Med., 6(7) (2009), p. e1000107.  
153. D.N. Levy, G.M. Aldrovandi, O. Kutsch, G.M. Shaw. Dynamics of HIV-1 recombination in its natural target cells. Proceedings of the National Academy of Sciences of the United States of America, 101(12) (2004), 4204–9.  
154. J.A. Levy, A.D. Hoffman, S.M. Kramer, J.A. Landis, J.M. Shimabukuro, L.S. Oshiro. Isolation of lymphocytopathic retroviruses from San Francisco patients with AIDS. Science, 225(4664) (1984), 840–2.  
155. S.G. Lim, A. Condez, C.A. Lee, M.A. Johnson, C. Elia, L.W. Poulter. Loss of mucosal CD4 lymphocytes is an early feature of HIV infection. Clinical and experimental immunology, 92(3) (1993), 448–54.  
156. P.F. Lindholm, K. Annen, G. Ramsey. Approaches to minimize infection risk in blood banking and transfusion practice. Infectious disorders drug targets, 11(1) (2011), 45–56.  
157. F. Lori, A. Malykh, A. Cara, D. Sun, J.N. Weinstein, J. Lisziewicz, R.C. Gallo. Hydroxyurea as an inhibitor of human immunodeficiency virus-type 1 replication. Science, 266(5186) (1994), 801–5.  
158. J.N. Mandl, A.P. Barry, T.H. Vanderford, N. Kozyr, R. Chavan, S. Klucking, F.J. Barrat, R.L. Coffman, S.I. Staprans, M.B. Feinberg. Divergent TLR7 and TLR9 signaling and type I interferon production distinguish pathogenic and nonpathogenic AIDS virus infections. Nature medicine, 14(10) (2008), 1077–87.  
159. L. Manganaro, M. Lusic, M.I. Gutierrez, A. Cereseto, G. Del Sal, M. Giacca. Concerted action of cellular JNK and Pin1 restricts HIV-1 genome integration to activated CD4+ T lymphocytes. Nature medicine, 16(3) (2010), 329–33.  
160. B. Mangeat, P. Turelli, G. Caron, M. Friedli, L. Perrin, D. Trono. Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts. Nature, 424(6944) (2003), 99–103.  
161. L.M. Mansky. Forward mutation rate of human immunodeficiency virus type 1 in a T lymphoid cell line. AIDS research and human retroviruses, 12(4) (1996), 307–14.  
162. L.M. Mansky. The mutation rate of human immunodeficiency virus type 1 is influenced by the vpr gene. Virology, 222(2) (1996), 391–400.  
163. L.M. Mansky, H.M. Temin. Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. Journal of virology, 69(8) (1995), 5087–94.  
164. D.M. Margolis. Histone deacetylase inhibitors and HIV latency. Current opinion in HIV and AIDS, 6(1) (2011), 25–9.  
165. R. Mariani, D. Chen, B. Schrofelbauer, F. Navarro, R. Konig, B. Bollman, C. Munk, H. Nymark-McMahon, N.R. Landau. Species-specific exclusion of APOBEC3G from HIV-1 virions by Vif. Cell, 114(1) (2003), 21–31.  
166. N. Martin, Q. Sattentau. Cell-to-cell HIV-1 spread and its implications for immune evasion. Current opinion in HIV and AIDS, 4(2) (2009), 143–9.  
167. J.L. Marx. Circumcision may protect against the AIDS virus. Science, 245(4917) (1989), 470–1.  
168. J.R. Mascola, D.C. Montefiori. The role of antibodies in HIV vaccines. Annual review of immunology, 28 (2010), 413–44.  
169. A.J. McMichael, P. Borrow, G.D. Tomaras, N. Goonetilleke, B.F. Haynes. The immune response during acute HIV-1 infection : clues for vaccine development. Nature reviews. Immunology, 10(1) (2010), 11–23.  
170. S. Mehandru, M.A. Poles, K. Tenner-Racz, A. Horowitz, A. Hurley, C. Hogan, D. Boden, P. Racz, M. Markowitz. Primary HIV-1 infection is associated with preferential depletion of CD4+ T lymphocytes from effector sites in the gastrointestinal tract. The Journal of experimental medicine, 200(6) (2004), 761–70.  
171. J.W. Mellors, A. Munoz, J.V. Giorgi, J.B. Margolick, C.J. Tassoni, P. Gupta, L.A. Kingsley, J.A. Todd, A.J. Saah, R. Detels, J.P. Phair, C.R. Rinaldo, Jr. Plasma viral load and CD4+ lymphocytes as prognostic markers of HIV-1 infection. Annals of internal medicine, 126(12) (1997), 946–54.  
172. J.W. Mellors, C. R. Rinaldo, Jr., P. Gupta, R.M. White, J. A. Todd, L. A. Kingsley. Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science, 272(5265) (1996), 1167–70.  
173. A. Meyerhans, R. Cheynier, J. Albert, M. Seth, S. Kwok, J. Sninsky, L. Morfeldt-Manson, B. Asjo, S. Wain-Hobson. Temporal fluctuations in HIV quasispecies in vivo are not reflected by sequential HIV isolations. Cell, 58(5) (1989), 901–10.  
174. A. Meyerhans, J.P. Vartanian, C. Hultgren, U. Plikat, A. Karlsson, L. Wang, S. Eriksson, S. Wain-Hobson. Restriction and enhancement of human immunodeficiency virus type 1 replication by modulation of intracellular deoxynucleoside triphosphate pools. Journal of virology, 68(1) (1994), 535–40.  
175. S. Moir, A.S. Fauci. B cells in HIV infection and disease. Nature reviews. Immunology, 9(4) (2009), 235–45.  
176. V. Muller, A. F. Maree, R. J. De Boer. Small variations in multiple parameters account for wide variations in HIV-1 set-points : a novel modelling approach. Proceedings. Biological sciences / The Royal Society, 268(1464) (2001), 235–42.  
177. F. Nawaz, C. Cicala, D. Van Ryk, K.E. Block, K. Jelicic, J.P. McNally, O. Ogundare, M. Pascuccio, N. Patel, D. Wei, A.S. Fauci, J. Arthos. The genotype of early-transmitting HIV gp120s promotes alpha (4) beta(7)-reactivity, revealing alpha (4) beta(7) +/CD4+ T cells as key targets in mucosal transmission. PLoS pathogens, 7(2) (2011), p. e1001301.  
178. R. Nduati, G. John, D. Mbori-Ngacha, B. Richardson, J. Overbaugh, A. Mwatha, J. Ndinya-Achola, J. Bwayo, F.E. Onyango, J. Hughes, J. Kreiss. Effect of breastfeeding and formula feeding on transmission of HIV-1 : a randomized clinical trial. JAMA : The Journal of the American Medical Association, 283(9) (2000), 1167–74.  
179. R.A. Neher, T. Leitner. Recombination rate and selection strength in HIV intra-patient evolution. PLoS computational biology, 6(1) (2010), p. e1000660.  
180. S.J. Neil, V. Sandrin, W.I. Sundquist, P.D. Bieniasz. An interferon-alpha-induced tethering mechanism inhibits HIV-1 and Ebola virus particle release but is counteracted by the HIV-1 Vpu protein. Cell host & microbe, 2(3) (2007), 193–203.  
181. S.J. Neil, T. Zang, P.D. Bieniasz. Tetherin inhibits retrovirus release and is antagonized by HIV-1 Vpu. Nature, 451(7177) (2008), 425–30.  
182. D.G. Nguyen, K.C. Wolff, H. Yin, J.S. Caldwell, K.L. Kuhen. “UnPAKing" human immunodeficiency virus (HIV) replication : using small interfering RNA screening to identify novel cofactors and elucidate the role of group I PAKs in HIV infection. Journal of virology, 80(1) (2006), 130–7.  
183. M.A. Nowak, R.M. May. Virus Dynamics. Mathematical Pronciples of Immunology and Virology Oxford University Press, Oxford, 2000.  
184. A. Okoye, M. Meier-Schellersheim, J.M. Brenchley, S.I. Hagen, J.M. Walker, M. Rohankhedkar, R. Lum, J.B. Edgar, S.L. Planer, A. Legasse, A.W. Sylwester, M. Piatak, Jr., J.D. Lifson, V.C. Maino, D.L. Sodora, D.C. Douek, M.K. Axthelm, Z. Grossman, L.J. Picker. Progressive CD4+ central memory T cell decline results in CD4+ effector memory insufficiency and overt disease in chronic SIV infection. The Journal of experimental medicine, 204(9) (2007), 2171–85.  
185. A. Onafuwa, W. An, N.D. Robson, A. Telesnitsky. Human immunodeficiency virus type 1 genetic recombination is more frequent than that of Moloney murine leukemia virus despite similar template switching rates. Journal of virology, 77(8) (2003), 4577–87.  
186. P. Paci, F. Martini, M. Bernaschi, G. D’Offizi, F. Castiglione. Timely HAART initiation may pave the way for a better viral control. BMC infectious diseases, 11 (2011), 56.  
187. G. Pantaleo, A.S. Fauci. Immunopathogenesis of HIV infection. Annual review of microbiology, 50 (1996), 825–54.  
188. G. Pantaleo, C. Graziosi, J.F. Demarest, L. Butini, M. Montroni, C.H. Fox, J.M. Orenstein, D.P. Kotler, A.S. Fauci. HIV infection is active and progressive in lymphoid tissue during the clinically latent stage of disease. Nature, 362(6418) (1993), 355–8.  
189. A.S. Perelson, P. Essunger, Y. Cao, M. Vesanen, A. Hurley, K. Saksela, M. Markowitz, D.D. Ho. Decay characteristics of HIV-1-infected compartments during combination therapy. Nature, 387(6629) (1997), 188–91.  
190. A.S. Perelson, P. W. Nelson. Mathematical Analysis of HIV-1 Dynamics in Vivo. SIAM review. Society for Industrial and Applied Mathematics, 41 (1999), 3–44.  
191. A.S. Perelson, A.U. Neumann, M. Markowitz, J.M. Leonard, D.D. Ho. HIV-1 dynamics in vivo : virion clearance rate, infected cell life-span, and viral generation time. Science, 271(5255) (1996), 1582–6.  
192. F. Pereyra, X. Jia, P.J. McLaren, A. Telenti, P.I.W. de Bakker, B.D. Walker, S. Ripke, C.J. Brumme, S.L. Pulit, M. Carrington. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science (New York, NY), 330(6010) (2010), 1551.  
193. D. Perrin, H.J. Ruskin, M. Crane. Model refinement through high-performance computing : an agent-based HIV example. Immunome research, 6 Suppl 1 (2010), p. S3.  
194. D.M. Phillips. The role of cell-to-cell transmission in HIV infection. AIDS, 8(6) (1994), 719–31.  
195. M. PiatakJr., M.S. Saag, L.C. Yang, S.J. Clark, J.C. Kappes, K.C. Luk, B.H. Hahn, G.M. Shaw, J.D. Lifson. High levels of HIV-1 in plasma during all stages of infection determined by competitive PCR. Science, 259(5102) (1993), 1749–54.  
196. L.J. Picker, S.I. Hagen, R. Lum, E.F. Reed-Inderbitzin, L.M. Daly, A.W. Sylwester, J.M. Walker, D.C. Siess, M. Piatak, Jr., C. Wang, D.B. Allison, V.C. Maino, J.D. Lifson, T. Kodama, M. K. Axthelm. Insufficient production and tissue delivery of CD4+ memory T cells in rapidly progressive simian immunodeficiency virus infection. The Journal of experimental medicine, 200(10) (2004), 1299–314.  
197. M.M. Popovic, M.G. Sarngadharan, E. Read, R.C. Gallo. Detection, isolation, and continuous production of cytopathic retroviruses (HTLV-III) from patients with AIDS and pre-AIDS. Science, 224(4648) (1984), 497–500.  
198. K.A. Powers, A.C. Ghani, W.C. Miller, I.F. Hoffman, A.E. Pettifor, G. Kamanga, F.E. Martinson, M.S. Cohen. The role of acute and early HIV infection in the spread of HIV and implications for transmission prevention strategies in Lilongwe, Malawi : a modelling study. Lancet, 378(9787) (2011), 256–68.  
199. I. Puigdomenech, M. Massanella, C. Cabrera, B. Clotet, J. Blanco. On the steps of cell-to-cell HIV transmission between CD4 T cells. Retrovirology, 6 (2009), 89.  
200. P. Racz, K. Tenner-Racz, C. Kahl, A.C. Feller, P. Kern, M. Dietrich. Spectrum of morphologic changes of lymph nodes from patients with AIDS or AIDS-related complexes. Progress in allergy, 37 (1986), 81–181.  
201. S. Rato, S. Maia, P.M. Brito, L. Resende, C.F. Pereira, C. Moita, R.P. Freitas, J. Moniz-Pereira, N. Hacohen, L.F. Moita, J. Goncalves. Novel HIV-1 knockdown targets identified by an enriched kinases/phosphatases shRNA library using a long-term iterative screen in Jurkat T-cells. PLoS One, 5(2) (2010), p. e9276.  
202. S. Rerks-Ngarm, P. Pitisuttithum, S. Nitayaphan, J. Kaewkungwal, J. Chiu, R. Paris, N. Premsri, C. Namwat, M. de Souza, E. Adams, M. Benenson, S. Gurunathan, J. Tartaglia, J.G. McNeil, D.P. Francis, D. Stablein, D.L. Birx, S. Chunsuttiwat, C. Khamboonruang, P. Thongcharoen, M.L. Robb, N.L. Michael, P. Kunasol, J.H. Kim. Vaccination with ALVAC and AIDSVAX to prevent HIV-1 infection in Thailand. The New England journal of medicine, 361(23) (2009), 2209–20.  
203. T.D. Rhodes, O. Nikolaitchik, J. Chen, D. Powell, W.S. Hu. Genetic recombination of human immunodeficiency virus type 1 in one round of viral replication : effects of genetic distance, target cells, accessory genes, and lack of high negative interference in crossover events. Journal of virology, 79(3) (2005), 1666–77.  
204. J.D. Roberts, K. Bebenek, T.A. Kunkel. The accuracy of reverse transcriptase from HIV-1. Science, 242(4882) (1988), 1171–3.  
205. L. Roberts, J. A. Passmore, C. Williamson, F. Little, L.M. Bebell, K. Mlisana, W. A. Burgers, F. van Loggerenberg, G. Walzl, J.F. Djoba Siawaya, Q. Abdool Karim, S.S. Karim. Plasma cytokine levels during acute HIV-1 infection predict HIV disease progression. AIDS, 24(6) (2010), 819–31.  
206. E.S. Rosenberg, M. Davidian, H.T. Banks. Using mathematical modeling and control to develop structured treatment interruption strategies for HIV infection. Drug and alcohol dependence, 88 Suppl 2 (2007), S41–51.  
207. M. Rotger, J. Dalmau, A. Rauch, P. McLaren, S.E. Bosinger, R. Martinez, N.G. Sandler, A. Roque, J. Liebner, M. Battegay, E. Bernasconi, P. Descombes, I. Erkizia, J. Fellay, B. Hirschel, J.M. Miro, E. Palou, M. Hoffmann, M. Massanella, J. Blanco, M. Woods, H.F. Gunthard, P. de Bakker, D.C. Douek, G. Silvestri, J. Martinez-Picado, A. Telenti. Comparative transcriptomics of extreme phenotypes of human HIV-1 infection and SIV infection in sooty mangabey and rhesus macaque. The Journal of clinical investigation, 121(6) (2011), 2391–400.  
208. I.M. Rouzine, J.M. Coffin. Linkage disequilibrium test implies a large effective population number for HIV in vivo. Proceedings of the National Academy of Sciences of the United States of America, 96(19) (1999), 10758–63.  
209. I.M. Rouzine, K. Murali-Krishna, R. Ahmed. Generals die in friendly fire, or modelling immune response to HIV. Journal of Computational and Applied Mathematic, 184 (2005), 258–74.  
210. I.M. Rouzine, A. Rodrigo, J. M. Coffin. Transition between stochastic evolution and deterministic evolution in the presence of selection : general theory and application to virology. Microbiology and molecular biology reviews, 65(1) (2001), 151–85.  
211. D. Rudnicka, J. Feldmann, F. Porrot, S. Wietgrefe, S. Guadagnini, M. C. Prevost, J. Estaquier, A.T. Haase, N. Sol-Foulon, O. Schwartz. Simultaneous cell-to-cell transmission of human immunodeficiency virus to multiple targets through polysynapses. Journal of virology, 83(12) (2009), 6234–46.  
212. M.G. Sarngadharan, M. Popovic, L. Bruch, J. Schupbach, R.C. Gallo. Antibodies reactive with human T-lymphotropic retroviruses (HTLV-III) in the serum of patients with AIDS. Science, 224(4648) (1984), 506–8.  
213. Q. Sattentau. Avoiding the void : cell-to-cell spread of human viruses. Nature reviews. Microbiology, 6(11) (2008), 815–26.  
214. P.E. Sax, L. R. Baden. When to start antiretroviral therapy — ready when you are ?. New England Journal of Medicine, 360(18) (2009), 1897–9.  
215. T. Schaller, C. Goujon, M.H. Malim. AIDS/HIV. HIV interplay with SAMHD1. Science, 335(6074) (2012), 1313–4.  
216. J.F. Scheid, H. Mouquet, N. Feldhahn, M.S. Seaman, K. Velinzon, J. Pietzsch, R.G. Ott, R.M. Anthony, H. Zebroski, A. Hurley, A. Phogat, B. Chakrabarti, Y. Li, M. Connors, F. Pereyra, B.D. Walker, H. Wardemann, D. Ho, R.T. Wyatt, J.R. Mascola, J.V. Ravetch, M.C. Nussenzweig. Broad diversity of neutralizing antibodies isolated from memory B cells in HIV-infected individuals. Nature, 458(7238) (2009), 636–40.  
217. M. Schindler, J. Munch, O. Kutsch, H. Li, M.L. Santiago, F. Bibollet-Ruche, M.C. Muller-Trutwin, F.J. Novembre, M. Peeters, V. Courgnaud, E. Bailes, P. Roques, D.L. Sodora, G. Silvestri, P.M. Sharp, B.H. Hahn, F. Kirchhoff. Nef-mediated suppression of T cell activation was lost in a lentiviral lineage that gave rise to HIV-1. Cell, 125(6) (2006), 1055–67.  
218. T. Schneider, H.U. Jahn, W. Schmidt, E.O. Riecken, M. Zeitz, R. Ullrich. Loss of CD4 T lymphocytes in patients infected with human immunodeficiency virus type 1 is more pronounced in the duodenal mucosa than in the peripheral blood. Berlin Diarrhea/Wasting Syndrome Study Group. Gut, 37(4) (1995), 524–9.  
219. H. Schuitemaker, N.A. Kootstra, R.E. de Goede, F. de Wolf, F. Miedema, M. Tersmette. Monocytotropic human immunodeficiency virus type 1 (HIV-1) variants detectable in all stages of HIV-1 infection lack T-cell line tropism and syncytium-inducing ability in primary T-cell culture. Journal of virology, 65(1) (1991), 356–63.  
220. A. Schultz, S. Sopper, U. Sauermann, A. Meyerhans, R. Suspene. Stable multi-infection of splenocytes during SIV infection — the basis for continuous recombination. Retrovirology, 9(1) (2012), 31.  
221. S. Schwartz, B.K. Felber, E.M. Fenyo, G.N. Pavlakis. Rapidly and slowly replicating human immunodeficiency virus type 1 isolates can be distinguished according to target-cell tropism in T-cell and monocyte cell lines. Proceedings of the National Academy of Sciences of the United States of America, 86(18) (1989), 7200–3.  
222. Y. Senturia, A. Ades, C. Peckham, C. Giaquinto, N. Baumslag. Breast-feeding and HIV infection. Lancet, 2 (1987).  
223. L. Shan, K. Deng, N.S. Shroff, C.M. Durand, S.A. Rabi, H.C. Yang, H. Zhang, J.B. Margolick, J.N. Blankson, R.F. Siliciano. Stimulation of HIV-1-specific cytolytic T lymphocytes facilitates elimination of latent viral reservoir after virus reactivation. Immunity, 36(3) (2012), 491–501.  
224. R. Shankarappa, J.B. Margolick, S.J. Gange, A.G. Rodrigo, D. Upchurch, H. Farzadegan, P. Gupta, C.R. Rinaldo, G.H. Learn, X. He, X.L. Huang, J.I. Mullins. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. Journal of virology, 73(12) (1999), 10489–502.  
225. A.M. Sheehy, N.C. Gaddis, J.D. Choi, M.H. Malim. Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein. Nature, 418(6898) (2002), 646–50.  
226. A.M. Sheehy, N.C. Gaddis, M.H. Malim. The antiretroviral enzyme APOBEC3G is degraded by the proteasome in response to HIV-1 Vif. Nature medicine, 9(11) (2003), 1404–7.  
227. H.W. Sheppard, M.S. Ascher, J.F. Krowka. Viral burden and HIV disease. Nature, 364(6435) (1993), 291–2.  
228. N.M. Sherer, M. J. Lehmann, L. F. Jimenez-Soto, C. Horensavitz, M. Pypaert, W. Mothes. Retroviruses can establish filopodial bridges for efficient cell-to-cell transmission. Nature cell biology, 9(3) (2007), 310–5.  
229. T. Shioda, J. A. Levy, C. Cheng-Mayer. Macrophage and T cell-line tropisms of HIV-1 are determined by specific regions of the envelope gp120 gene. Nature, 349(6305) (1991), 167–9.  
230. K. Shirakawa, A. Takaori-Kondo, M. Yokoyama, T. Izumi, M. Matsui, K. Io, T. Sato, H. Sato, T. Uchiyama. Phosphorylation of APOBEC3G by protein kinase A regulates its interaction with HIV-1 Vif. Nature structural & molecular biology, 15(11) (2008), 1184–91.  
231. D. Shriner, A.G. Rodrigo, D.C. Nickle, J.I. Mullins. Pervasive genomic recombination of HIV-1 in vivo. Genetics, 167(4) (2004), 1573–83.  
232. B. Siewe, A. Landay. Key Concepts in the Early Immunology of HIV-1 Infection. Current infectious disease reports, 14(1) (2012), 102–9.  
233. A. Sigal, J.T. Kim, A.B. Balazs, E. Dekel, A. Mayo, R. Milo, D. Baltimore. Cell-to-cell spread of HIV permits ongoing replication despite antiretroviral therapy. Nature, 477(7362) (2011), 95–8.  
234. J.D. Siliciano, J. Kajdas, D. Finzi, T.C. Quinn, K. Chadwick, J.B. Margolick, C. Kovacs, S.J. Gange, R.F. Siliciano. Long-term follow-up studies confirm the stability of the latent reservoir for HIV-1 in resting CD4+ T cells. Nature medicine, 9(6) (2003), 727–8.  
235. G. Silvestri, M.B. Feinberg. Turnover of lymphocytes and conceptual paradigms in HIV infection. The Journal of clinical investigation, 112(6) (2003), 821–4.  
236. P. Simmonds, P. Balfe, J.F. Peutherer, C.A. Ludlam, J.O. Bishop, A.J. Brown. Human immunodeficiency virus-infected individuals contain provirus in small numbers of peripheral mononuclear cells and at low copy numbers. Journal of virology, 64(2) (1990), 864–72.  
237. M. Sips, G. Sciaranghella, T. Diefenbach, A. S. Dugast, C.T. Berger, Q. Liu, D. Kwon, M. Ghebremichael, J.D. Estes, M. Carrington, J.N. Martin, S.G. Deeks, P.W. Hunt, G. Alter. Altered distribution of mucosal NK cells during HIV infection. Mucosal immunology, 5(1) (2012), 30–40.  
238. H. Soudeyns, G. Pantaleo. The moving target : mechanisms of HIV persistence during primary infection. Immunology today, 20(10) (1999), 446–50.  
239. A.E. Sousa, J. Carneiro, M. Meier-Schellersheim, Z. Grossman, R.M. Victorino. CD4 T cell depletion is linked directly to immune activation in the pathogenesis of HIV-1 and HIV-2 but only indirectly to the viral load. J. Immunol., 169(6) (2002), 3400–6.  
240. A.R. Stacey, P.J. Norris, L. Qin, E.A. Haygreen, E. Taylor, J. Heitman, M. Lebedeva, A. DeCamp, D. Li, D. Grove, S.G. Self, P. Borrow. Induction of a striking systemic cytokine cascade prior to peak viremia in acute human immunodeficiency virus type 1 infection, in contrast to more modest and delayed responses in acute hepatitis B and C virus infections. Journal of virology, 83(8) (2009), 3719–33.  
241. M.A. Stafford, L. Corey, Y. Cao, E.S. Daar, D.D. Ho, A.S. Perelson. Modeling plasma virus concentration during primary HIV infection. Journal of theoretical biology, 203(3) (2000), 285–301.  
242. J.A. Sterne, M. May, D. Costagliola, F. de Wolf, A.N. Phillips, R. Harris, M.J. Funk, R.B. Geskus, J. Gill, F. Dabis, J.M. Miro, A.C. Justice, B. Ledergerber, G. Fatkenheuer, R.S. Hogg, A.D. Monforte, M. Saag, C. Smith, S. Staszewski, M. Egger, S.R. Cole. Timing of initiation of antiretroviral therapy in AIDS-free HIV-1-infected patients : a collaborative analysis of 18 HIV cohort studies. Lancet, 373(9672) (2009), 1352–63.  
243. C.A. Stoddart, R.A. Reyes. Models of HIV-1 disease : A review of current status. Drug Discovery Today : Disease Models, 3 (2006), 113–119.  
244. M.C. Strain, H.F. Gunthard, D.V. Havlir, C.C. Ignacio, D.M. Smith, A.J. Leigh-Brown, T.R. Macaranas, R.Y. Lam, O.A. Daly, M. Fischer, M. Opravil, H. Levine, L. Bacheler, C.A. Spina, D.D. Richman, J.K. Wong. Heterogeneous clearance rates of long-lived lymphocytes infected with HIV : intrinsic stability predicts lifelong persistence. Proceedings of the National Academy of Sciences of the United States of America, 100(8) (2003), 4819–24.  
245. H. Streeck, J.S. Jolin, Y. Qi, B. Yassine-Diab, R.C. Johnson, D.S. Kwon, M.M. Addo, C. Brumme, J.P. Routy, S. Little, H.K. Jessen, A.D. Kelleher, F.M. Hecht, R.P. Sekaly, E.S. Rosenberg, B.D. Walker, M. Carrington, M. Altfeld. Human immunodeficiency virus type 1-specific CD8+ T-cell responses during primary infection are major determinants of the viral set point and loss of CD4+ T cells. Journal of virology, 83(15) (2009), 7641–8.  
246. M.C. Stremlau, C.M. Owens, M.J. Perron, M. Kiessling, P. Autissier, J. Sodroski. The cytoplasmic body component TRIM5alpha restricts HIV-1 infection in Old World monkeys. Nature, 427(6977) (2004), 848–53.  
247. A.S. Sturt, M.S. Halpern, B. Sullivan, Y.A. Maldonado. Timing of Antiretroviral Therapy Initiation and its Impact on Disease Progression in Perinatal Human Immunodeficiency Virus-1 Infection. The Pediatric Infectious Disease Journal, 31(1) (2012), 53.  
248. C.F. Thobakgale, L. Fadda, K. Lane, I. Toth, F. Pereyra, S. Bazner, T. Ndung’u, B.D. Walker, E.S. Rosenberg, G. Alter, M. Carrington, T.M. Allen, M. Altfeld. Frequent and Strong Antibody-Mediated Natural Killer Cell Activation in Response to HIV-1 Env in Individuals with Chronic HIV-1 Infection. Journal of virology, 86(12) (2012), 6986–93.  
249. G.D. Tomaras, N.L. Yates, P. Liu, L. Qin, G.G. Fouda, L.L. Chavez, A.C. Decamp, R.J. Parks, V.C. Ashley, J.T. Lucas, M. Cohen, J. Eron, C.B. Hicks, H.X. Liao, S.G. Self, G. Landucci, D.N. Forthal, K.J. Weinhold, B.F. Keele, B.H. Hahn, M.L. Greenberg, L. Morris, S.S. Karim, W.A. Blattner, D.C. Montefiori, G.M. Shaw, A.S. Perelson, B.F. Haynes. Initial B-cell responses to transmitted human immunodeficiency virus type 1 : virion-binding immunoglobulin M (IgM) and IgG antibodies followed by plasma anti-gp41 antibodies with ineffective control of initial viremia. Journal of virology, 82(24) (2008), 12449–63.  
250. Y. Tsunetsugu-Yokota, K. Akagawa, H. Kimoto, K. Suzuki, M. Iwasaki, S. Yasuda, G. Hausser, C. Hultgren, A. Meyerhans, T. Takemori. Monocyte-derived cultured dendritic cells are susceptible to human immunodeficiency virus infection and transmit virus to resting T cells in the process of nominal antigen presentation. Journal of virology, 69(7) (1995), 4544–7.  
251. N. Van Damme, D. Goff, C. Katsura, R.L. Jorgenson, R. Mitchell, M.C. Johnson, E.B. Stephens, J. Guatelli. The interferon-induced protein BST-2 restricts HIV-1 release and is downregulated from the cell surface by the viral Vpu protein. Cell host & microbe, 3(4) (2008), 245–52.  
252. T. Van Montfort, A.A. Thomas, G. Pollakis, W.A. Paxton. Dendritic cells preferentially transfer CXCR4-using human immunodeficiency virus type 1 variants to CD4+ T lymphocytes in trans. Journal of virology, 82(16) (2008), 7886–96.  
253. A. Varela-Rohena, P. E. Molloy, S.M. Dunn, Y. Li, M.M. Suhoski, R.G. Carroll, A. Milicic, T. Mahon, D.H. Sutton, B. Laugel, R. Moysey, B.J. Cameron, A. Vuidepot, M.A. Purbhoo, D.K. Cole, R.E. Phillips, C.H. June, B.K. Jakobsen, A.K. Sewell, J.L. Riley. Control of HIV-1 immune escape by CD8 T cells expressing enhanced T-cell receptor. Nature medicine, 14(12) (2008), 1390–5.  
254. J.P. Vartanian, A. Meyerhans, B. Asjo, S. Wain-Hobson. Selection, recombination, and G- - - -A hypermutation of human immunodeficiency virus type 1 genomes. Journal of virology, 65(4) (1991), 1779–88.  
255. D. Verotta. Models and estimation methods for clinical HIV-1 data. Journal of Computational and Applied Mathematics, 184 (2005), 275–300.  
256. N.N. Vijay, R. Vasantika, R. Ajmani, A.S. Perelson, N.M. Dixit. Recombination increases human immunodeficiency virus fitness, but not necessarily diversity. The Journal of general virology, 89 (2008), 1467–77.  
257. N. Wagner, J. Lohler, E.J. Kunkel, K. Ley, E. Leung, G. Krissansen, K. Rajewsky, W. Muller. Critical role for beta7 integrins in formation of the gut-associated lymphoid tissue. Nature, 382(6589) (1996), 366–70.  
258. S. Wain-Hobson. Viral burden in AIDS. Nature, 366(6450) (1993), 22.  
259. S. Wain-Hobson, P. Sonigo, O. Danos, S. Cole, M. Alizon. Nucleotide sequence of the AIDS virus, LAV. Cell, 40(1) (1985), 9–17.  
260. F. Wasserstein-Robbins. A mathematical model of HIV infection : Simulating T4, T8, macrophages, antibody, and virus via specific anti-HIV response in the presence of adaptation and tropism. Bulletin of mathematical biology, 72(5) (2010), 1208–53.  
261. X. Wei, S. K. Ghosh, M.E. Taylor, V.A. Johnson, E. A. Emini, P. Deutsch, J.D. Lifson, S. Bonhoeffer, M.A. Nowak, B.H. Hahn, and et al. Viral dynamics in human immunodeficiency virus type 1 infection. Nature, 373(6510) (1995), 117–22.  
262. K. Wendelsdorf, G. Dean, S. Hu, S. Nordone, H.T. Banks. Host immune responses that promote initial HIV spread. Journal of theoretical biology, 289 (2011), 17–35.  
263. E.J. Wherry. T cell exhaustion. Nature immunology, 12(6) (2011), 492–9.  
264. WHO, posting date. Progress report 2011 : Global HIV/AIDS response. [Online.]  
265. D. Wick, S. G. Self. Early HIV infection in vivo : branching-process model for studying timing of immune responses and drug therapy. Mathematical biosciences, 165(2) (2000), 115–34.  
266. R.D. Wiley, S. Gummuluru. Immature dendritic cell-derived exosomes can mediate HIV-1 trans infection. Proceedings of the National Academy of Sciences of the United States of America, 103(3) (2006), 738–43.  
267. F. Wong-Staal, G.M. Shaw, B.H. Hahn, S.Z. Salahuddin, M. Popovic, P. Markham, R. Redfield, R.C. Gallo. Genomic diversity of human T-lymphotropic virus type III (HTLV-III). Science, 229(4715) (1985), 759–62.  
268. T. Yamamoto, D.A. Price, J.P. Casazza, G. Ferrari, M. Nason, P.K. Chattopadhyay, M. Roederer, E. Gostick, P.D. Katsikis, D.C. Douek, R. Haubrich, C. Petrovas, R.A. Koup. Surface expression patterns of negative regulatory molecules identify determinants of virus-specific CD8+ T-cell exhaustion in HIV infection. Blood, 117(18) (2011), 4805–15.  
269. M.L. Yeung, L. Houzet, V.S. Yedavalli, K.T. Jeang. A genome-wide short hairpin RNA screening of jurkat T-cells for human proteins contributing to productive HIV-1 replication. The Journal of biological chemistry, 284(29) (2009), 19463–73.  
270. Y. Yuan, L.J. Allen. Stochastic models for virus and immune system dynamics. Mathematical biosciences, 234(2) (2011), 84–94.  
271. M. Zaitseva, A. Blauvelt, S. Lee, C.K. Lapham, V. Klaus-Kovtun, H. Mostowski, J. Manischewitz, H. Golding. Expression and function of CCR5 and CXCR4 on human Langerhans cells and macrophages : implications for HIV primary infection. Nature medicine, 3(12) (1997), 1369–75.  
272. M. Zeng, M. Paiardini, J.C. Engram, G.J. Beilman, J.G. Chipman, T.W. Schacker, G. Silvestri, A.T. Haase. Critical role of CD4 T cells in maintaining lymphoid tissue structure for immune cell homeostasis and reconstitution. Blood, 120(9) (2012), 1856–67.  
273. H. Zhang, B. Yang, R. J. Pomerantz, C. Zhang, S.C. Arunachalam, L. Gao. The cytidine deaminase CEM15 induces hypermutation in newly synthesized HIV-1 DNA. Nature, 424(6944) (2003), 94–8.  
274. L. Zhang, P.J. Dailey, A. Gettie, J. Blanchard, D.D. Ho. The liver is a major organ for clearing simian immunodeficiency virus in rhesus monkeys. Journal of virology, 76(10) (2002), 5271–3.  
275. H. Zhou, M. Xu, Q. Huang, A.T. Gates, X.D. Zhang, J.C. Castle, E. Stec, M. Ferrer, B. Strulovici, D.J. Hazuda, A.S. Espeseth. Genome-scale RNAi screen for host factors required for HIV replication. Cell host & microbe, 4(5) (2008), 495–504.  
276. J. Zhuang, A.E. Jetzt, G. Sun, H. Yu, G. Klarmann, Y. Ron, B.D. Preston, J.P. Dougherty. Human immunodeficiency virus type 1 recombination : rate, fidelity, and putative hot spots. Journal of virology, 76(22) (2002), 11273–82.