Geodesic
Human Immunodeficiency Virus Infection : from Biological Observations to Mechanistic Mathematical Modelling
G. Bocharov1 ; V. Chereshnev2 ; I. Gainova3 ; S. Bazhan4 ; B. Bachmetyev5 ; J. Argilaguet6 ; J. Martinez6 ; A. Meyerhans6
1 Institute of Numerical Mathematics, RAS, Moscow, Russia
2 Institute of Immunology and Physiology, Ural Branch RAS, Ekaterinburg, Russia
3 Sobolev Institute of Mathematics, Siberian Branch RAS, Novosibirsk, Russia
4 State Research Center of Virology and Biotechnology “Vector", Novosibirsk Region, Koltsovo, Russia
5 Institute of Ecology and Genetics of Microorganisms, Ural Branch RAS, Perm, Russia
6 ICREA Infection Biology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
Mathematical modelling of natural phenomena, Tome 7 (2012) no. 5, pp. 78-104.

Voir la notice de l'article provenant de la source EDP Sciences

HIV infection is multi-faceted and a multi-step process. The virus-induced pathogenic mechanisms are manifold and mediated through a range of positive and negative feedback regulations of immune and physiological processes engaged in virus-host interactions. The fundamental questions towards understanding the pathogenesis of HIV infection are now shifting to ‘dynamic’ categories: (i) why is the HIV-immune response equilibrium finally disrupted? (ii) can one modify the dynamic equilibrium for host benefit? (iii) can one predict the outcome of a system perturbation via antiviral drugs or drugs modulating the host immune response dynamics? Answering these questions requires a major interdisciplinary effort, and in particular, the development of novel mathematical approaches for a coherent quantitative description and prediction of intra-patient HIV evolution, the immunological responses to HIV infection, and the systems level homeostatic regulation of specific effector and regulatory lymphocyte populations in correlation with disease status. Here we summarized fundamental biological features of HIV infection and current mathematical modelling attempts to understand HIV pathogenesis.
DOI : 10.1051/mmnp/20127507

G. Bocharov 1 ; V. Chereshnev 2 ; I. Gainova 3 ; S. Bazhan 4 ; B. Bachmetyev 5 ; J. Argilaguet 6 ; J. Martinez 6 ; A. Meyerhans 6

1 Institute of Numerical Mathematics, RAS, Moscow, Russia
2 Institute of Immunology and Physiology, Ural Branch RAS, Ekaterinburg, Russia
3 Sobolev Institute of Mathematics, Siberian Branch RAS, Novosibirsk, Russia
4 State Research Center of Virology and Biotechnology “Vector", Novosibirsk Region, Koltsovo, Russia
5 Institute of Ecology and Genetics of Microorganisms, Ural Branch RAS, Perm, Russia
6 ICREA Infection Biology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain 
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G. Bocharov; V. Chereshnev; I. Gainova; S. Bazhan; B. Bachmetyev; J. Argilaguet; J. Martinez; A. Meyerhans. Human Immunodeficiency Virus Infection : from Biological Observations to Mechanistic Mathematical Modelling. Mathematical modelling of natural phenomena, Tome 7 (2012) no. 5, pp. 78-104. doi : 10.1051/mmnp/20127507. http://geodesic.mathdoc.fr/articles/10.1051/mmnp/20127507/

[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 Science 2010 1168 74

[2] B.M. Adams, H.T. Banks, M. Davidian, H.D. Kwon, H.T. Tran, S.N. Wynne, E.S. Rosenberg Journal of Computational and Applied Mathematics 2005 10 49

[3] B.M. Adams, H.T. Banks, M. Davidian, E.S. Rosenberg Bulletin of mathematical biology 2007 563 84

[4] B.M. Adams, H.T. Banks, H.D. Kwon, H.T. Tran Mathematical biosciences and engineering 2004 223 41

[5] M. Alizon, S. Wain-Hobson, L. Montagnier, P. Sonigo Cell 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 Nature 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 Nature immunology 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] H.W. Sheppard Clinical and experimental immunology 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 Science 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 Journal of mathematical biology 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 Lancet 2007 643 56

[17] H.T. Banks, M. Davidian, S. Hu, G.M. Kepler, E.S. Rosenberg Journal of biological dynamics 2008 357 85

[18] H.T. Banks, H.-D. Kwon, J.A. Toivanen, H.T. Tran Optim. Control Appl. Meth. 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 Nature 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 Science 1983 868 71

[21] R. Batorsky, M.F. Kearney, S.E. Palmer, F. Maldarelli, I.M. Rouzine, J.M. Coffin Proceedings of the National Academy of Sciences of the United States of America 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 Nature cell biology 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 Journal of medical virology 2009 1681 90

[24] Z. Bentwich, A. Kalinkovich, Z. Weisman, Z. Grossman Clinical and experimental immunology 1998 1 2

[25] E. Berntorp, A.D. Shapiro Lancet 2012 1447 56

[26] G. Bocharov, N.J. Ford, J. Edwards, T. Breinig, S. Wain-Hobson, A. Meyerhans The Journal of general virology 2005 3109 18

[27] M.C. Boily, R.F. Baggaley, L. Wang, B. Masse, R.G. White, R.J. Hayes, M. Alary The Lancet infectious diseases 2009 118 29

[28] J. Bongaarts, P. Reining, P. Way, F. Conant AIDS 1989 373 7

[29] P. Borrow Current opinion in HIV and AIDS 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 The Journal of clinical investigation 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 Science 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 Nature medicine 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 The Journal of experimental medicine 2004 749 59

[35] J.E. Brinchmann, J. Albert, F. Vartdal Journal of virology 1991 2019 23

[36] A.J. Brown Proceedings of the National Academy of Sciences of the United States of America 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 Lancet 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 Lancet 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 Mathematical & Computer Modelling 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 AIDS 2007 1 11

[43] H.Y. Chen, M. Di Mascio, A.S. Perelson, D.D. Ho, L. Zhang Proceedings of the National Academy of Sciences of the United States of America 2007 19079 84

[44] C. Cheng-Mayer, M. Quiroga, J.W. Tung, D. Dina, J.A. Levy Journal of virology 1990 4390 8

[45] S.K. Choudhary, N. Vrisekoop, C.A. Jansen, S.A. Otto, H. Schuitemaker, F. Miedema, D. Camerini Journal of virology 2007 8838 42

[46] T.W. Chun, K. Chadwick, J. Margolick, R.F. Siliciano Journal of virology 1997 4436 44

[47] T.W. Chun, D. Finzi, J. Margolick, K. Chadwick, D. Schwartz, R.F. Siliciano Nature medicine 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 Proceedings of the National Academy of Sciences of the United States of America 2009 20877 82

[49] M.S. Ciupe, B.L. Bivort, D.M. Bortz, P.W. Nelson Mathematical biosciences 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 et al Science 1986 343 6

[51] F. Clayton, G. Snow, S. Reka, D.P. Kotler Clinical and experimental immunology 1997 288 92

[52] F. Cocchi, A.L. Devico, A. Garzino-Demo, A. Cara, R.C. Gallo, P. Lusso Nature medicine 1996 1244 7

[53] J.M. Coffin The Journal of general virology 1979 1 26

[54] J. Cohen Science 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 The New England journal of medicine 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 AIDS 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 he New England journal of medicine 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 The Journal of experimental medicine 1989 1149 63

[59] M.P. D’Souza, V.A. Harden Nature medicine 1996 1293 300

[60] A.G. Dalgleish, P.C. Beverley, P.R. Clapham, D.H. Crawford, M.F. Greaves, R.A. Weiss Nature 1984 763 7

[61] J. David, H. Tran, H.T. Banks Int. J. Pure Appl. Math. 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 Nature 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 AIDS (London, England) 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 Blood 2004 942 7

[66] N.M. Dixit, A. S. Perelson Proceedings of the National Academy of Sciences of the United States of America 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 Lancet 2010 2092 8

[68] D. Douek Topics in HIV medicine : a publication of the International AIDS Society, USA 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 Nature 1996 667 73

[70] J. Embretson, M. Zupancic, J.L. Ribas, A. Burke, P. Racz, K. Tenner-Racz, A.T. Haase Nature 1993 359 62

[71] A. Engelman, P. Cherepanov Nature reviews. Microbiology 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 Proceedings of the National Academy of Sciences of the United States of America 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 Nature medicine 1999 512 7

[76] C. Fraser, N.M. Ferguson, F. De Wolf, R.M. Anderson Proceedings. Biological sciences / The Royal Society 2001 2085 95

[77] S.D. Frost, M.J. Dumaurier, S. Wain-Hobson, A.J. Brown Proceedings of the National Academy of Sciences of the United States of America 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 Frequent detection and isolation of cytopathic retroviruses (HTLV-III) from patients with AIDS and at risk for AIDS Science 1984 500 3

[79] V.V. Ganusov, R.J. De Boern Trends in immunology 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 Journal of virology 2011 10518 28

[81] F. Gao, Y. Chen, D.N. Levy, J.A. Conway, T.B. Kepler, H. Hui Journal of virology 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 Traffic 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 Cell 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 Journal of virology 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 AIDS 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 The Journal of infectious diseases 1999 859 70

[87] D. Gisselquist, G. Upham, J.J. Potterat Infection control and hospital epidemiology : The official journal of the Society of Hospital Epidemiologists of America 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. 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 Journal of experimental medicine 2009 1253 72

[90] M.S. Gottlieb, R. Schroff, H.M. Schanker, J.D. Weisman, P.T. Fan, R.A. Wolf, A. Saxon The New England journal of medicine 1981 1425 31

[91] P.J. Goulder, D.I. Watkins Nature reviews. Immunology 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 The New England journal of medicine 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 Lancet 2001 1149 53

[94] F. Groot, T.M. Van Capel, J. Schuitemaker, B. Berkhout, E.C. De Jong Retrovirology 2006 52

[95] Z. Grossman Clin. Immunol. 2003 137 9

[96] Z. Grossman, M.B. Feinberg, W.E. Paul Proceedings of the National Academy of Sciences of the United States of America 1998 6314 9

[97] Z. Grossman, M. Meier-Schellersheim, W.E. Paul, L.J. Picker Nature medicine 2006 289 95

[98] Z. Grossman, M. Meier-Schellersheim, A. E. Sousa, R. M. Victorino, W.E. Paul Nature medicine 2002 319 23

[99] Z. Grossman, B. Min, M. Meier-Schellersheim, W. E. Paul Nature reviews. Immunology 2004 387 95

[100] Z. Grossman, W.E. Paul Nature medicine 2000 976 7

[101] Z. Grossman, L. J. Picker CCurrent opinion in HIV and AIDS 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 Lancet 1999 795 802

[103] M. Guyader, M. Emerman, P. Sonigo, F. Clavel, L. Montagnier, M. Alizon Nature 1987 662 9

[104] A.T. Haase Annual review of immunology 1999 625 56

[105] A.T. Haase Nature 2010 217 23

[106] M. Hadjiandreou, R. Conejeros, V.S. Vassiliadis Mathematical biosciences and engineering 2007 489 504

[107] M. Hadjiandreou, R. Conejeros, J. Wilson International Journal of Biological and Life Sciences 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 Science 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 Cell 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 The New England journal of medicine 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 Nature medicine 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 AIDS 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 Blood 2000 249 55

[114] S.L. Heath, J.G. Tew, J.G. Tew, A.K. Szakal, G.F. Burton Nature 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 Nature medicine 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 Journal of virology 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 Nature 1995 123 6

[119] I.B. Hogue, S.H. Bajaria, B.A. Fallert, S. Qin, T.A. Reinhart, D.E. Kirschner The Journal of general virology 2008 2228 39

[120] T. Hraba, J. Dolezal Emerging infectious diseases 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 Nature 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 methods 95 104

[123] K. Huang, D. Wooley Journal of virological methods 2005 95 104

[124] S.S. Hwang, T.J. Boyle, H.K. Lyerly, B.R. Cullen Science 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 The Journal of clinical investigation 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 Nature 2012 365 70

[128] A.E. Jetzt, H. Yu, G.J. Klarmann, Y. Ron, B.D. Preston, J.P. Dougherty Journal of virology 2000 1234 40

[129] M.I. Johnston, A.S. Fauci The New England journal of medicine 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 Nature 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 Mathematical biosciences 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 Proceedings of the National Academy of Sciences of the United States of America 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 Nature 2004 769 75

[137] F. Kirchhoff Cell host & microbe 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 New England Journal of Medicine 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 Science 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 Cell 2008 49 60

[141] L.G. Kostrikis, G. Touloumi, R. Karanicolas, N. Pantazis, C. Anastassopoulou, A. Karafoulidou, J.J. Goedert, A. Hatzakis Journal of virology 2002 10099 108

[142] I.N. Koulinska, E. Villamor, B. Chaplin, G. Msamanga, W. Fawzi, B. Renjifo, M. Essex AIDS 2006 93

[143] R.D. Kouyos, C.L. Althaus, S. Bonhoeffer Trends in microbiology 2006 507 11

[144] Y. Koyanagi, S. Miles, R.T. Mitsuyasu, J.E. Merrill, H.V. Vinters, I.S. Chen Science 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 Journal of virology 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 Nature 2011 654 7

[149] D. Lecossier, F. Bouchonnet, F. Clavel, A.J. Hance Science 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 Proceedings of the National Academy of Sciences of the United States of America 2004 4204 9

[154] J.A. Levy, A.D. Hoffman, S.M. Kramer, J.A. Landis, J.M. Shimabukuro, L.S. Oshiro Science 1984 840 2

[155] S.G. Lim, A. Condez, C.A. Lee, M.A. Johnson, C. Elia, L.W. Poulter Clinical and experimental immunology 1993 448 54

[156] P.F. Lindholm, K. Annen, G. Ramsey Infectious disorders drug targets 2011 45 56

[157] F. Lori, A. Malykh, A. Cara, D. Sun, J.N. Weinstein, J. Lisziewicz, R.C. Gallo Science 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 Nature medicine 2008 1077 87

[159] L. Manganaro, M. Lusic, M.I. Gutierrez, A. Cereseto, G. Del Sal, M. Giacca Nature medicine 2010 329 33

[160] B. Mangeat, P. Turelli, G. Caron, M. Friedli, L. Perrin, D. Trono Nature 2003 99 103

[161] L.M. Mansky AIDS research and human retroviruses 1996 307 14

[162] L.M. Mansky Virology 1996 391 400

[163] L.M. Mansky, H.M. Temin Journal of virology 1995 5087 94

[164] D.M. Margolis Current opinion in HIV and AIDS 2011 25 9

[165] R. Mariani, D. Chen, B. Schrofelbauer, F. Navarro, R. Konig, B. Bollman, C. Munk, H. Nymark-Mcmahon, N.R. Landau Cell 2003 21 31

[166] N. Martin, Q. Sattentau Current opinion in HIV and AIDS 2009 143 9

[167] J.L. Marx Science 1989 470 1

[168] J.R. Mascola, D.C. Montefiori Annual review of immunology 2010 413 44

[169] A.J. Mcmichael, P. Borrow, G.D. Tomaras, N. Goonetilleke, B.F. Haynes Nature reviews. Immunology 2010 11 23

[170] S. Mehandru, M.A. Poles, K. Tenner-Racz, A. Horowitz, A. Hurley, C. Hogan, D. Boden, P. Racz, M. Markowitz The Journal of experimental medicine 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 Annals of internal medicine 1997 946 54

[172] J.W. Mellors, C. R. Rinaldo, P. Gupta, R.M. White, J. A. Todd, L. A. Kingsley Science 1996 1167 70

[173] A. Meyerhans, R. Cheynier, J. Albert, M. Seth, S. Kwok, J. Sninsky, L. Morfeldt-Manson, B. Asjo, S. Wain-Hobson Cell 1989 901 10

[174] A. Meyerhans, J.P. Vartanian, C. Hultgren, U. Plikat, A. Karlsson, L. Wang, S. Eriksson, S. Wain-Hobson Journal of virology 1994 535 40

[175] S. Moir, A.S. Fauci Nature reviews. Immunology 2009 235 45

[176] V. Muller, A. F. Maree, R. J. De Boer Proceedings. Biological sciences / The Royal Society 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 JAMA : The Journal of the American Medical Association 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 Cell host & microbe 2007 193 203

[181] S.J. Neil, T. Zang, P.D. Bieniasz Nature 2008 425 30

[182] D.G. Nguyen, K.C. Wolff, H. Yin, J.S. Caldwell, K.L. Kuhen Journal of virology 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, J.D. Lifson, V.C. Maino, D.L. Sodora, D.C. Douek, M.K. Axthelm, Z. Grossman, L.J. Picker The Journal of experimental medicine 2007 2171 85

[185] A. Onafuwa, W. An, N.D. Robson, A. Telesnitsky Journal of virology 2003 4577 87

[186] P. Paci, F. Martini, M. Bernaschi, G. D’Offizi, F. Castiglione BMC infectious diseases 2011 56

[187] G. Pantaleo, A.S. Fauci Annual review of microbiology 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 Nature 1993 355 8

[189] A.S. Perelson, P. Essunger, Y. Cao, M. Vesanen, A. Hurley, K. Saksela, M. Markowitz, D.D. Ho Nature 1997 188 91

[190] A.S. Perelson, P. W. Nelson SIAM review. Society for Industrial and Applied Mathematics 1999 3 44

[191] A.S. Perelson, A.U. Neumann, M. Markowitz, J.M. Leonard, D.D. Ho Science 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 Science 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 AIDS 1994 719 31

[195] M. Piatak, M.S. Saag, L.C. Yang, S.J. Clark, J.C. Kappes, K.C. Luk, B.H. Hahn, G.M. Shaw, J.D. Lifson Science 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, C. Wang, D.B. Allison, V.C. Maino, J.D. Lifson, T. Kodama, M. K. Axthelm The Journal of experimental medicine 2004 1299 314

[197] M.M. Popovic, M.G. Sarngadharan, E. Read, R.C. Gallo Science 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 Lancet 2011 256 68

[199] I. Puigdomenech, M. Massanella, C. Cabrera, B. Clotet, J. Blanco Retrovirology 2009 89

[200] P. Racz, K. Tenner-Racz, C. Kahl, A.C. Feller, P. Kern, M. Dietrich Progress in allergy 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 The New England journal of medicine 2009 2209 20

[203] T.D. Rhodes, O. Nikolaitchik, J. Chen, D. Powell, W.S. Hu Journal of virology 2005 1666 77

[204] J.D. Roberts, K. Bebenek, T.A. Kunkel Science 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 AIDS 2010 819 31

[206] E.S. Rosenberg, M. Davidian, H.T. Banks Drug and alcohol dependence 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 The Journal of clinical investigation 2011 2391 400

[208] I.M. Rouzine, J.M. Coffin Proceedings of the National Academy of Sciences of the United States of America 1999 10758 63

[209] I.M. Rouzine, K. Murali-Krishna, R. Ahmed Journal of Computational and Applied Mathematic 2005 258 74

[210] I.M. Rouzine, A. Rodrigo, J. M. Coffin Microbiology and molecular biology reviews 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 Journal of virology 2009 6234 46

[212] M.G. Sarngadharan, M. Popovic, L. Bruch, J. Schupbach, R.C. Gallo Science 1984 506 8

[213] Q. Sattentau Nature reviews. Microbiology 2008 815 26

[214] P.E. Sax, L. R. Baden New England Journal of Medicine 2009 1897 9

[215] T. Schaller, C. Goujon, M.H. Malim Science 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 Nature 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 Cell 2006 1055 67

[218] T. Schneider, H.U. Jahn, W. Schmidt, E.O. Riecken, M. Zeitz, R. Ullrich Gut 1995 524 9

[219] H. Schuitemaker, N.A. Kootstra, R.E. De Goede, F. De Wolf, F. Miedema, M. Tersmette Journal of virology 1991 356 63

[220] A. Schultz, S. Sopper, U. Sauermann, A. Meyerhans, R. Suspene Retrovirology 2012 31

[221] S. Schwartz, B.K. Felber, E.M. Fenyo, G.N. Pavlakis Proceedings of the National Academy of Sciences of the United States of America 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 Immunity 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 Journal of virology 1999 10489 502

[225] A.M. Sheehy, N.C. Gaddis, J.D. Choi, M.H. Malim Nature 2002 646 50

[226] A.M. Sheehy, N.C. Gaddis, M.H. Malim Nature medicine 2003 1404 7

[227] H.W. Sheppard, M.S. Ascher, J.F. Krowka Nature 1993 291 2

[228] N.M. Sherer, M. J. Lehmann, L. F. Jimenez-Soto, C. Horensavitz, M. Pypaert, W. Mothes Nature cell biology 2007 310 5

[229] T. Shioda, J. A. Levy, C. Cheng-Mayer Nature 1991 167 9

[230] K. Shirakawa, A. Takaori-Kondo, M. Yokoyama, T. Izumi, M. Matsui, K. Io, T. Sato, H. Sato, T. Uchiyama Nature structural & molecular biology 2008 1184 91

[231] D. Shriner, A.G. Rodrigo, D.C. Nickle, J.I. Mullins Genetics 2004 1573 83

[232] B. Siewe, A. Landay Current infectious disease reports 2012 102 9

[233] A. Sigal, J.T. Kim, A.B. Balazs, E. Dekel, A. Mayo, R. Milo, D. Baltimore Nature 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 Nature medicine 2003 727 8

[235] G. Silvestri, M.B. Feinberg The Journal of clinical investigation 2003 821 4

[236] P. Simmonds, P. Balfe, J.F. Peutherer, C.A. Ludlam, J.O. Bishop, A.J. Brown Journal of virology 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 Mucosal immunology 2012 30 40

[238] H. Soudeyns, G. Pantaleo Immunology today 1999 446 50

[239] A.E. Sousa, J. Carneiro, M. Meier-Schellersheim, Z. Grossman, R.M. Victorino J. Immunol. 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 Journal of virology 2009 3719 33

[241] M.A. Stafford, L. Corey, Y. Cao, E.S. Daar, D.D. Ho, A.S. Perelson Journal of theoretical biology 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 Lancet 2009 1352 63

[243] C.A. Stoddart, R.A. Reyes Drug Discovery Today : Disease Models 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 Proceedings of the National Academy of Sciences of the United States of America 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 Journal of virology 2009 7641 8

[246] M.C. Stremlau, C.M. Owens, M.J. Perron, M. Kiessling, P. Autissier, J. Sodroski Nature 2004 848 53

[247] A.S. Sturt, M.S. Halpern, B. Sullivan, Y.A. Maldonado The Pediatric Infectious Disease Journal 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 Journal of virology 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 Journal of virology 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 Journal of virology 1995 4544 7

[251] N. Van Damme, D. Goff, C. Katsura, R.L. Jorgenson, R. Mitchell, M.C. Johnson, E.B. Stephens, J. Guatelli Cell host & microbe 2008 245 52

[252] T. Van Montfort, A.A. Thomas, G. Pollakis, W.A. Paxton Journal of virology 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 Nature medicine 2008 1390 5

[254] J.P. Vartanian, A. Meyerhans, B. Asjo, S. Wain-Hobson Journal of virology 1991 1779 88

[255] D. Verotta Journal of Computational and Applied Mathematics 2005 275 300

[256] N.N. Vijay, R. Vasantika, R. Ajmani, A.S. Perelson, N.M. Dixit The Journal of general virology 2008 1467 77

[257] N. Wagner, J. Lohler, E.J. Kunkel, K. Ley, E. Leung, G. Krissansen, K. Rajewsky, W. Muller Nature 1996 366 70

[258] S. Wain-Hobson Nature 1993 22

[259] S. Wain-Hobson, P. Sonigo, O. Danos, S. Cole, M. Alizon Cell 1985 9 17

[260] F. Wasserstein-Robbins Bulletin of mathematical biology 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 Nature 1995 117 22

[262] K. Wendelsdorf, G. Dean, S. Hu, S. Nordone, H.T. Banks Journal of theoretical biology 2011 17 35

[263] E.J. Wherry Nature immunology 2011 492 9

[264] WHO, posting date. Progress report 2011 : Global HIV/AIDS response. [Online.]

[265] D. Wick, S. G. Self Mathematical biosciences 2000 115 34

[266] R.D. Wiley, S. Gummuluru Proceedings of the National Academy of Sciences of the United States of America 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 Science 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 Blood 2011 4805 15

[269] M.L. Yeung, L. Houzet, V.S. Yedavalli, K.T. Jeang The Journal of biological chemistry 2009 19463 73

[270] Y. Yuan, L.J. Allen Mathematical biosciences 2011 84 94

[271] M. Zaitseva, A. Blauvelt, S. Lee, C.K. Lapham, V. Klaus-Kovtun, H. Mostowski, J. Manischewitz, H. Golding Nature medicine 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 Blood 2012 1856 67

[273] H. Zhang, B. Yang, R. J. Pomerantz, C. Zhang, S.C. Arunachalam, L. Gao Nature 2003 94 8

[274] L. Zhang, P.J. Dailey, A. Gettie, J. Blanchard, D.D. Ho Journal of virology 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 Cell host & microbe 2008 495 504

[276] J. Zhuang, A.E. Jetzt, G. Sun, H. Yu, G. Klarmann, Y. Ron, B.D. Preston, J.P. Dougherty Journal of virology 2002 11273 82

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