Free Access
Math. Model. Nat. Phenom.
Volume 7, Number 5, 2012
Page(s) 78 - 104
Published online 17 October 2012
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [Google Scholar]
  9. E.J. Arts, D.J. Hazuda. HIV-1 Antiretroviral Drug Therapy. Cold Spring Harbor perspectives in medicine, 2(4) (2012), p. a007161. [Google Scholar]
  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. [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  15. E. Baake. Mutation and recombination with tight linkage. Journal of mathematical biology, 42(5) (2001), 455–88. [CrossRef] [MathSciNet] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  25. E. Berntorp, A.D. Shapiro. Modern haemophilia care. Lancet, 379(9824) (2012), 1447–56. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  29. P. Borrow. Innate immunity in acute HIV-1 infection. Current opinion in HIV and AIDS, 6(5) (2011), 353–63. [CrossRef] [PubMed] [Google Scholar]
  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. [PubMed] [Google Scholar]
  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). [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  40. M.A. Capistran. A study of latency, reactivation and apoptosis throughout HIV pathogenesis. Mathematical & Computer Modelling, 52 (2010), 1011–5. [CrossRef] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  53. J.M. Coffin. Structure, replication, and recombination of retrovirus genomes : some unifying hypotheses. The Journal of general virology, 42(1) (1979), 1–26. [CrossRef] [PubMed] [Google Scholar]
  54. J. Cohen. Understanding HIV latency to undo it. Science, 332(6031) (2011), 786. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  71. A. Engelman, P. Cherepanov. The structural biology of HIV-1 : mechanistic and therapeutic insights. Nature reviews. Microbiology, 10(4) (2012), 279–90. [CrossRef] [PubMed] [Google Scholar]
  72. A.S. Fauci, H.C. Lane. A Preventive Vaccine Against HIV Infection. Harrison’s Principles of Internal Medicine, (2012), 18e. [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [PubMed] [Google Scholar]
  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. [CrossRef] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  91. P.J. Goulder, D.I. Watkins. HIV and SIV CTL escape : implications for vaccine design. Nature reviews. Immunology, 4(8) (2004), 630–40. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  95. Z. Grossman. Mathematical modeling of thymopoiesis in HIV infection : real data, virtual data, and data interpretation. Clin. Immunol., 107(3) (2003), 137–9. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  100. Z. Grossman, W.E. Paul. The impact of HIV on naive T-cell homeostasis. Nature medicine, 6(9) (2000), 976–7. [CrossRef] [PubMed] [Google Scholar]
  101. Z. Grossman, L. J. Picker. Pathogenic mechanisms in simian immunodeficiency virus infection. CCurrent opinion in HIV and AIDS, 3(3) (2008), 380–6. [CrossRef] [Google Scholar]
  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. [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  105. A.T. Haase. Targeting early infection to prevent HIV-1 mucosal transmission. Nature, 464(7286) (2010), 217–23. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  120. T. Hraba, J. Dolezal. A mathematical model and CD4+ lymphocyte dynamics in HIV infection. Emerging infectious diseases, 2(4) (1996), 299–305. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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 methods 124:95-104. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  129. M.I. Johnston, A.S. Fauci. An HIV vaccine-evolving concepts. The New England journal of medicine, 356(20) (2007), 2073–81. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  133. A. Kamina, R.W. Makuch, H. Zhao. A stochastic modeling of early HIV-1 population dynamics. Mathematical biosciences, 170(2) (2001), 187–98. [CrossRef] [MathSciNet] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [PubMed] [Google Scholar]
  164. D.M. Margolis. Histone deacetylase inhibitors and HIV latency. Current opinion in HIV and AIDS, 6(1) (2011), 25–9. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  167. J.L. Marx. Circumcision may protect against the AIDS virus. Science, 245(4917) (1989), 470–1. [CrossRef] [PubMed] [Google Scholar]
  168. J.R. Mascola, D.C. Montefiori. The role of antibodies in HIV vaccines. Annual review of immunology, 28 (2010), 413–44. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [PubMed] [Google Scholar]
  175. S. Moir, A.S. Fauci. B cells in HIV infection and disease. Nature reviews. Immunology, 9(4) (2009), 235–45. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  179. R.A. Neher, T. Leitner. Recombination rate and selection strength in HIV intra-patient evolution. PLoS computational biology, 6(1) (2010), p. e1000660. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  183. M.A. Nowak, R.M. May. Virus Dynamics. Mathematical Pronciples of Immunology and Virology Oxford University Press, Oxford, 2000. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  187. G. Pantaleo, A.S. Fauci. Immunopathogenesis of HIV infection. Annual review of microbiology, 50 (1996), 825–54. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  194. D.M. Phillips. The role of cell-to-cell transmission in HIV infection. AIDS, 8(6) (1994), 719–31. [CrossRef] [PubMed] [Google Scholar]
  195. M. Piatak Jr., 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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  204. J.D. Roberts, K. Bebenek, T.A. Kunkel. The accuracy of reverse transcriptase from HIV-1. Science, 242(4882) (1988), 1171–3. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [Google Scholar]
  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. [CrossRef] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  213. Q. Sattentau. Avoiding the void : cell-to-cell spread of human viruses. Nature reviews. Microbiology, 6(11) (2008), 815–26. [Google Scholar]
  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. [CrossRef] [Google Scholar]
  215. T. Schaller, C. Goujon, M.H. Malim. AIDS/HIV. HIV interplay with SAMHD1. Science, 335(6074) (2012), 1313–4. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  222. Y. Senturia, A. Ades, C. Peckham, C. Giaquinto, N. Baumslag. Breast-feeding and HIV infection. Lancet, 2 (1987). [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  227. H.W. Sheppard, M.S. Ascher, J.F. Krowka. Viral burden and HIV disease. Nature, 364(6435) (1993), 291–2. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  232. B. Siewe, A. Landay. Key Concepts in the Early Immunology of HIV-1 Infection. Current infectious disease reports, 14(1) (2012), 102–9. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [PubMed] [Google Scholar]
  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. [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  238. H. Soudeyns, G. Pantaleo. The moving target : mechanisms of HIV persistence during primary infection. Immunology today, 20(10) (1999), 446–50. [CrossRef] [PubMed] [Google Scholar]
  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. [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [PubMed] [Google Scholar]
  255. D. Verotta. Models and estimation methods for clinical HIV-1 data. Journal of Computational and Applied Mathematics, 184 (2005), 275–300. [CrossRef] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  258. S. Wain-Hobson. Viral burden in AIDS. Nature, 366(6450) (1993), 22. [CrossRef] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [MathSciNet] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  263. E.J. Wherry. T cell exhaustion. Nature immunology, 12(6) (2011), 492–9. [Google Scholar]
  264. WHO, posting date. Progress report 2011 : Global HIV/AIDS response. [Online.] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  270. Y. Yuan, L.J. Allen. Stochastic models for virus and immune system dynamics. Mathematical biosciences, 234(2) (2011), 84–94. [CrossRef] [MathSciNet] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]
  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. [Google Scholar]
  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. [CrossRef] [PubMed] [Google Scholar]

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