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

Published online by Cambridge University Press:  17 October 2012

G. Bocharov ,
V. Chereshnev ,
I. Gainova ,
S. Bazhan ,
B. Bachmetyev ,
J. Argilaguet ,
J. Martinez  and
A. Meyerhans
G. Bocharov*
Affiliation:
Institute of Numerical Mathematics, RAS, Moscow, Russia
V. Chereshnev
Affiliation:
Institute of Immunology and Physiology, Ural Branch RAS, Ekaterinburg, Russia
I. Gainova
Affiliation:
Sobolev Institute of Mathematics, Siberian Branch RAS, Novosibirsk, Russia
S. Bazhan
Affiliation:
State Research Center of Virology and Biotechnology “Vector", Novosibirsk Region, Koltsovo, Russia
B. Bachmetyev
Affiliation:
Institute of Ecology and Genetics of Microorganisms, Ural Branch RAS, Perm, Russia
J. Argilaguet
Affiliation:
ICREA Infection Biology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
J. Martinez
Affiliation:
ICREA Infection Biology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
A. Meyerhans*
Affiliation:
ICREA Infection Biology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
*
⋆ Corresponding author. E-mail: bocharov@inm.ras.ru
⋆⋆ Corresponding author. E-mail: andreas.meyerhans@upf.edu
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Abstract

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.

Keywords

mathematical modellinghost–pathogen interactionimmune systemhuman immunodeficiency virus infection
Type
Research Article
Information
Mathematical Modelling of Natural Phenomena , Volume 7 , Issue 5: Immunology , 2012 , pp. 78 - 104
Copyright
© EDP Sciences, 2012

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References

Références

Abdool Karim, Q., Abdool Karim, S.S., Frohlich, J.A., Grobler, A.C., Baxter, C., Mansoor, L.E., Kharsany, A.B., Sibeko, S., Mlisana, K.P., Omar, Z., Gengiah, T.N., Maarschalk, S., Arulappan, N., Mlotshwa, M., Morris, L., Taylor, D.. Effectiveness and safety of tenofovir gel, an antiretroviral microbicide, for the prevention of HIV infection in women. Science, 329(5996) (2010), 1168–74. CrossRefGoogle ScholarPubMed
Adams, B.M., Banks, H.T., Davidian, M., Kwon, H.D., Tran, H.T., Wynne, S.N., Rosenberg, E.S.. HIV dynamics : Modeling, data analysis, and optimal treatment protocols. Journal of Computational and Applied Mathematics, 184 (2005), 10–49. CrossRefGoogle Scholar
Adams, B.M., Banks, H.T., Davidian, M., Rosenberg, E.S.. Estimation and prediction with HIV-treatment interruption data. Bulletin of mathematical biology, 69(2) (2007), 563–84. CrossRefGoogle ScholarPubMed
Adams, B.M., Banks, H.T., Kwon, H.D., Tran, H.T.. Dynamic multidrug therapies for hiv : optimal and sti control approaches. Mathematical biosciences and engineering, 1(2) (2004), 223–41. Google Scholar
Alizon, M., Wain-Hobson, S., Montagnier, L., Sonigo, P.. Genetic variability of the AIDS virus : nucleotide sequence analysis of two isolates from African patients. Cell, 46(1) (1986), 63–74. CrossRefGoogle Scholar
Alter, G., Heckerman, D., Schneidewind, A., Fadda, L., Kadie, C.M., Carlson, J.M., Oniangue-Ndza, C., Martin, M., Li, B., Khakoo, S. I., Carrington, M., Allen, T.M., Altfeld, M.. HIV-1 adaptation to NK-cell-mediated immune pressure. Nature, 476(7358) (2011), 96–100. CrossRefGoogle ScholarPubMed
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.
Arthos, J., Cicala, C., Martinelli, E., Macleod, K., Van Ryk, D., Wei, D., Xiao, Z., Veenstra, T.D., Conrad, T.P., Lempicki, R.A., McLaughlin, S., Pascuccio, M., Gopaul, R., McNally, J., Cruz, C.C., Censoplano, N., Chung, E., Reitano, K.N., Kottilil, S., Goode, D.J., Fauci, A.S.. 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. CrossRefGoogle Scholar
E.J. Arts, D.J. Hazuda. HIV-1 Antiretroviral Drug Therapy. Cold Spring Harbor perspectives in medicine, 2(4) (2012), p. a007161.
M.S.Ascher, Sheppard, H.W.. AIDS as immune system activation : a model for pathogenesis. Clinical and experimental immunology, 73(2) (1988), 165–7. Google Scholar
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.
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.
Autran, B., Carcelain, G., Li, T.S., Blanc, C., Mathez, D., Tubiana, R., Katlama, C., Debre, P., Leibowitch, J.. Positive effects of combined antiretroviral therapy on CD4+ T cell homeostasis and function in advanced HIV disease. Science, 277(5322) (1997), 112–6. CrossRefGoogle ScholarPubMed
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.
Baake, E.. Mutation and recombination with tight linkage. Journal of mathematical biology, 42(5) (2001), 455–88. CrossRefGoogle Scholar
Bailey, R.C., Moses, S., Parker, C.B., Agot, K., Maclean, I., Krieger, J.N., Williams, C.F. M., Campbell, R.T., Ndinya-Achola, J.O.. Male circumcision for HIV prevention in young men in Kisumu, Kenya : a randomised controlled trial. Lancet, 369(9562) (2007), 643–56. CrossRefGoogle Scholar
Banks, H.T., Davidian, M., Hu, S., Kepler, G.M., Rosenberg, E.S.. Modeling HIV Immune Response and Validation with Clinical Data. Journal of biological dynamics, 2(4) (2008), 357–85. CrossRefGoogle Scholar
Banks, H.T., Kwon, H.-D., Toivanen, J.A., Tran, H.T.. A state-dependent Riccati equation-based estimator approach for HIV feedback control. Optim. Control Appl. Meth., 27 (2006), 93–121. CrossRefGoogle Scholar
Barber, D.L., Wherry, E.J., Masopust, D., Zhu, B., Allison, J.P., Sharpe, A. H., Freeman, G.J., Ahmed, R.. Restoring function in exhausted CD8 T cells during chronic viral infection. Nature, 439(7077) (2006), 682–7. CrossRefGoogle ScholarPubMed
Barre-Sinoussi, F., Chermann, J.C., Rey, F., Nugeyre, M.T., Chamaret, S., Gruest, J., Dauguet, C., Axler-Blin, C., Vezinet-Brun, F., Rouzioux, C., Rozenbaum, W., Montagnier, L.. Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science, 220(4599) (1983), 868–71. CrossRefGoogle Scholar
Batorsky, R., Kearney, M.F., Palmer, S.E., Maldarelli, F., Rouzine, I.M., Coffin, J.M.. 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. CrossRefGoogle ScholarPubMed
Baumgartel, V., Ivanchenko, S., Dupont, A., Sergeev, M., Wiseman, P.W., Krausslich, H.G., Brauchle, C., Muller, B., Lamb, D.C.. Live-cell visualization of dynamics of HIV budding site interactions with an ESCRT component. Nature cell biology, 13(4) (2011), 469–74. CrossRefGoogle ScholarPubMed
Bello, G., Velasco-de-Castro, C.A., Bongertz, V., Rodrigues, C.A., Giacoia-Gripp, C.B., Pilotto, J.H., Grinsztejn, B., Veloso, V.G., Morgado, M.G.. Immune activation and antibody responses in non-progressing elite controller individuals infected with HIV-1. Journal of medical virology, 81(10) (2009), 1681–90. CrossRefGoogle ScholarPubMed
Bentwich, Z., Kalinkovich, A., Weisman, Z., Grossman, Z.. Immune activation in the context of HIV infection. Clinical and experimental immunology, 111(1) (1998), 1–2. CrossRefGoogle ScholarPubMed
Berntorp, E., Shapiro, A.D.. Modern haemophilia care. Lancet, 379(9824) (2012), 1447–56. CrossRefGoogle Scholar
Bocharov, G., Ford, N.J., Edwards, J., Breinig, T., Wain-Hobson, S., Meyerhans, A.. 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. CrossRefGoogle Scholar
Boily, M.C., Baggaley, R.F., Wang, L., Masse, B., White, R.G., Hayes, R.J., Alary, M.. 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. CrossRefGoogle Scholar
Bongaarts, J., Reining, P., Way, P., Conant, F.. The relationship between male circumcision and HIV infection in African populations. AIDS, 3(6) (1989), 373–7. CrossRefGoogle Scholar
Borrow, P.. Innate immunity in acute HIV-1 infection. Current opinion in HIV and AIDS, 6(5) (2011), 353–63. CrossRefGoogle ScholarPubMed
Bosinger, S.E., Li, Q., Gordon, S.N., Klatt, N.R., Duan, L., Xu, L., Francella, N., Sidahmed, A., Smith, A.J., Cramer, E.M., Zeng, M., Masopust, D., Carlis, J.V., Ran, L., Vanderford, T.H., Paiardini, M., Isett, R.B., Baldwin, D.A., Else, J.G., Staprans, S.I., Silvestri, G., Haase, A.T., Kelvin, D.J.. 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. Google Scholar
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).
Brass, A.L., Dykxhoorn, D.M., Benita, Y., Yan, N., Engelman, A., Xavier, R.J., Lieberman, J., Elledge, S.J.. Identification of host proteins required for HIV infection through a functional genomic screen. Science, 319(5865) (2008), 921–6. CrossRefGoogle ScholarPubMed
Brenchley, J.M., Price, D.A., Schacker, T.W., Asher, T.E., Silvestri, G., Rao, S., Kazzaz, Z., Bornstein, E., Lambotte, O., Altmann, D., Blazar, B.R., Rodriguez, B., Teixeira-Johnson, L., Landay, A., Martin, J.N., Hecht, F.M., Picker, L.J., Lederman, M.M., Deeks, S.G., Douek, D.C.. Microbial translocation is a cause of systemic immune activation in chronic HIV infection. Nature medicine, 12(12) (2006), 1365–71. CrossRefGoogle ScholarPubMed
Brenchley, J.M., Schacker, T.W., Ruff, L.E., Price, D.A., Taylor, J.H., Beilman, G.J., Nguyen, P.L., Khoruts, A., Larson, M., Haase, A.T., Douek, D.C.. 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. CrossRefGoogle ScholarPubMed
Brinchmann, J.E., Albert, J., Vartdal, F.. 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. Google ScholarPubMed
Brown, A.J.. 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. CrossRefGoogle Scholar
Brun-Vezinet, F., Rouzioux, C., Barre-Sinoussi, F., Klatzmann, D., Saimot, A.G., Rozenbaum, W., Christol, D., Gluckmann, J.C., Montagnier, L., Chermann, J.C.. Detection of IgG antibodies to lymphadenopathy-associated virus in patients with AIDS or lymphadenopathy syndrome. Lancet, 1(8389) (1984), 1253–6. CrossRefGoogle Scholar
Buchbinder, S.P., Mehrotra, D.V., Duerr, A., Fitzgerald, D.W., Mogg, R., Li, D., Gilbert, P.B., Lama, J.R., Marmor, M., Del Rio, C., McElrath, M.J., Casimiro, D.R., Gottesdiener, K.M., Chodakewitz, J.A., Corey, L., Robertson, M.N.. 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. CrossRefGoogle ScholarPubMed
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.
Capistran, M.A.. A study of latency, reactivation and apoptosis throughout HIV pathogenesis. Mathematical & Computer Modelling, 52 (2010), 1011–5. CrossRefGoogle Scholar
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.
Centlivre, M., Sala, M., Wain-Hobson, S., Berkhout, B.. In HIV-1 pathogenesis the die is cast during primary infection. AIDS, 21(1) (2007), 1–11. CrossRefGoogle ScholarPubMed
Chen, H.Y., Di Mascio, M., Perelson, A.S., Ho, D.D., Zhang, L.. 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. CrossRefGoogle Scholar
Cheng-Mayer, C., Quiroga, M., Tung, J.W., Dina, D., Levy, J.A.. 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. Google ScholarPubMed
Choudhary, S.K., Vrisekoop, N., Jansen, C.A., Otto, S.A., Schuitemaker, H., Miedema, F., Camerini, D.. 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. CrossRefGoogle ScholarPubMed
Chun, T.W., Chadwick, K., Margolick, J., Siliciano, R.F.. 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. Google ScholarPubMed
Chun, T.W., Finzi, D., Margolick, J., Chadwick, K., Schwartz, D., Siliciano, R.F.. In vivo fate of HIV-1-infected T cells : quantitative analysis of the transition to stable latency. Nature medicine, 1(12) (1995), 1284–90. CrossRefGoogle Scholar
Cicala, C., Martinelli, E., McNally, J.P., Goode, D.J., Gopaul, R., Hiatt, J., Jelicic, K., Kottilil, S., Macleod, K., O’Shea, A., Patel, N., Van Ryk, D., Wei, D., Pascuccio, M., Yi, L., McKinnon, L., Izulla, P., Kimani, J., Kaul, R., Fauci, A.S., Arthos, J.. 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. CrossRefGoogle Scholar
Ciupe, M.S., Bivort, B.L., Bortz, D.M., Nelson, P.W.. Estimating kinetic parameters from HIV primary infection data through the eyes of three different mathematical models. Mathematical biosciences, 200(1) (2006), 1–27. CrossRefGoogle ScholarPubMed
Clavel, F., Guetard, D., Brun-Vezinet, F., Chamaret, S., Rey, M.A., Santos-Ferreira, M.O., Laurent, A.G., Dauguet, C., Katlama, C., Rouzioux, C., and et al. Isolation of a new human retrovirus from West African patients with AIDS. Science, 233(4761) (1986), 343–6. CrossRefGoogle Scholar
Clayton, F., Snow, G., Reka, S., Kotler, D.P.. Selective depletion of rectal lamina propria rather than lymphoid aggregate CD4 lymphocytes in HIV infection. Clinical and experimental immunology, 107(2) (1997), 288–92. CrossRefGoogle ScholarPubMed
Cocchi, F., DeVico, A.L., Garzino-Demo, A., Cara, A., Gallo, R.C., Lusso, P.. 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. CrossRefGoogle Scholar
Coffin, J.M.. Structure, replication, and recombination of retrovirus genomes : some unifying hypotheses. The Journal of general virology, 42(1) (1979), 1–26. CrossRefGoogle ScholarPubMed
Cohen, J.. Understanding HIV latency to undo it. Science, 332(6031) (2011), 786. CrossRefGoogle Scholar
Cohen, M.S., Chen, Y.Q., McCauley, M., Gamble, T., Hosseinipour, M.C., Kumarasamy, N., Hakim, J.G., Kumwenda, J., Grinsztejn, B., Pilotto, J.H., Godbole, S.V., Mehendale, S., Chariyalertsak, S., Santos, B.R., Mayer, K.H., Hoffman, I.F., Eshleman, S.H., Piwowar-Manning, E., Wang, L., Makhema, J., Mills, L.A., de Bruyn, G., Sanne, I., Eron, J., Gallant, J., Havlir, D., Swindells, S., Ribaudo, H., Elharrar, V., Burns, D., Taha, T.E., Nielsen-Saines, K., Celentano, D., Essex, M., Fleming, T.R.. Prevention of HIV-1 infection with early antiretroviral therapy. The New England journal of medicine, 365(6) (2011), 493–505. CrossRefGoogle ScholarPubMed
Cohen Stuart, J.W., Hazebergh, M.D., Hamann, D., Otto, S.A., Borleffs, J.C., Miedema, F., Boucher, C.A., de Boer, R.J.. The dominant source of CD4+ and CD8+ T-cell activation in HIV infection is antigenic stimulation. AIDS, 25(3) (2000), 203–11. Google ScholarPubMed
Collier, A.C., Coombs, R.W., A. Schoenfeld, D., Bassett, R.L., Timpone, J., Baruch, A., Jones, M., Facey, K., Whitacre, C., McAuliffe, V.J., Friedman, H.M., Merigan, T.C., Reichman, R. C., Hooper, C., Corey, L.. 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. CrossRefGoogle Scholar
Collman, R., Hassan, N.F., Walker, R., Godfrey, B., Cutilli, J., Hastings, J.C., Friedman, H., Douglas, S.D., Nathanson, N.. 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. CrossRefGoogle Scholar
D’Souza, M.P., Harden, V.A.. Chemokines and HIV-1 second receptors. Confluence of two fields generates optimism in AIDS research. Nature medicine, 2(12) (1996), 1293–300. CrossRefGoogle Scholar
Dalgleish, A.G., Beverley, P.C., Clapham, P.R., Crawford, D.H., Greaves, M.F., Weiss, R.A.. The CD4 (T4) antigen is an essential component of the receptor for the AIDS retrovirus. Nature, 312(5996) (1984), 763–7. CrossRefGoogle ScholarPubMed
David, J., Tran, H., Banks, H.T.. HIV model analysis and estimation implementation under optimal control based treatment strategies. Int. J. Pure Appl. Math., 57 (2009), 357–92. Google Scholar
Day, C.L., Kaufmann, D.E., Kiepiela, P., Brown, J.A., Moodley, E.S., Reddy, S., Mackey, E.W., Miller, J.D., Leslie, A.J., DePierres, C., Mncube, Z., Duraiswamy, J., Zhu, B., Eichbaum, Q., Altfeld, M., Wherry, E.J., Coovadia, H.M., Goulder, P.J., Klenerman, P., Ahmed, R., Freeman, G.J., Walker, B.D.. PD-1 expression on HIV-specific T cells is associated with T-cell exhaustion and disease progression. Nature, 443(7109) (2006), 350–4. CrossRefGoogle ScholarPubMed
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.
De Martino, M., Tovo, P.A., Tozzi, A.E., Pezzotti, P., Galli, L., Livadiotti, S., Caselli, D., Massironi, E., Ruga, E., Fioredda, F.. HIV-1 transmission through breast-milk : appraisal of risk according to duration of feeding. AIDS (London, England), 6(9) (1992), 991. CrossRefGoogle ScholarPubMed
Deeks, S.G., Kitchen, C.M., Liu, L., Guo, H., Gascon, R., Narvaez, A.B., Hunt, P., Martin, J.N., Kahn, J.O., Levy, J., McGrath, M.S., Hecht, F.M.. Immune activation set point during early HIV infection predicts subsequent CD4+ T-cell changes independent of viral load. Blood, 104(4) (2004), 942–7. CrossRefGoogle Scholar
Dixit, N.M., Perelson, A. S.. 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. CrossRefGoogle Scholar
Donnell, D., Baeten, J.M., Kiarie, J., Thomas, K.K., Stevens, W., Cohen, C.R., McIntyre, J., Lingappa, J.R., Celum, C.. Heterosexual HIV-1 transmission after initiation of antiretroviral therapy : a prospective cohort analysis. Lancet, 375(9731) (2010), 2092–8. CrossRefGoogle ScholarPubMed
Douek, D.. 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. Google Scholar
Dragic, T., Litwin, V., Allaway, G.P., Martin, S.R., Huang, Y., Nagashima, K.A., Cayanan, C., Maddon, P.J., Koup, R.A., Moore, J.P., Paxton, W.A.. HIV-1 entry into CD4+ cells is mediated by the chemokine receptor CC-CKR-5. Nature, 381(6584) (1996), 667–73. CrossRefGoogle ScholarPubMed
Embretson, J., Zupancic, M., Ribas, J.L., Burke, A., Racz, P., Tenner-Racz, K., Haase, A.T.. Massive covert infection of helper T lymphocytes and macrophages by HIV during the incubation period of AIDS. Nature, 362(6418) (1993), 359–62. CrossRefGoogle Scholar
Engelman, A., Cherepanov, P.. The structural biology of HIV-1 : mechanistic and therapeutic insights. Nature reviews. Microbiology, 10(4) (2012), 279–90. CrossRefGoogle ScholarPubMed
A.S. Fauci, H.C. Lane. A Preventive Vaccine Against HIV Infection. Harrison’s Principles of Internal Medicine, (2012), 18e.
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.
Ferguson, N.M., deWolf, F., Ghani, A.C., Fraser, C., Donnelly, C.A., Reiss, P., Lange, J.M., Danner, S.A., Garnett, G.P., Goudsmit, J., Anderson, R.M.. 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. CrossRefGoogle ScholarPubMed
Finzi, D., Blankson, J., Siliciano, J.D., Margolick, J.B., Chadwick, K., Pierson, T., Smith, K., Lisziewicz, J., Lori, F., Flexner, C., Quinn, T.C., Chaisson, R.E., Rosenberg, E., Walker, B., Gange, S., Gallant, J., Siliciano, R. F.. 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. Google ScholarPubMed
Fraser, C., Ferguson, N.M., de Wolf, F., Anderson, R.M.. 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. CrossRefGoogle ScholarPubMed
Frost, S.D., Dumaurier, M.J., Wain-Hobson, S., Brown, A.J.. 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. CrossRefGoogle ScholarPubMed
Gallo, R.C., Salahuddin, S.Z., Popovic, M., Shearer, G.M., Kaplan, M., Haynes, B.F., Palker, T.J., Redfield, R., Oleske, J., Safai, B., 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. CrossRefGoogle Scholar
Ganusov, V.V., De Boern, R.J.. Do most lymphocytes in humans really reside in the gut ? Trends in immunology, 28(12) (2007), 514–8. CrossRefGoogle Scholar
Ganusov, V.V., Goonetilleke, N., Liu, M.K., Ferrari, G., Shaw, G.M., McMichael, A.J., Borrow, P., Korber, B.T., Perelson, A.S.. 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. CrossRefGoogle ScholarPubMed
Gao, F., Chen, Y., Levy, D.N., Conway, J.A., Kepler, T.B., Hui, H.. Unselected mutations in the human immunodeficiency virus type 1 genome are mostly nonsynonymous and often deleterious. Journal of virology, 78(5) (2004), 2426–33. CrossRefGoogle ScholarPubMed
Garcia, E., Pion, M., Pelchen-Matthews, A., Collinson, L., Arrighi, J.F., Blot, G., Leuba, F., Escola, J.M., Demaurex, N., Marsh, M., Piguet, V.. 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. CrossRefGoogle ScholarPubMed
Geijtenbeek, T.B., Kwon, D.S., Torensma, R., van Vliet, S.J., van Duijnhoven, G.C., Middel, J., Cornelissen, I.L., Nottet, H.S., KewalRamani, V.N., Littman, D.R., Figdor, C.G., van Kooyk, Y.. DC-SIGN, a dendritic cell-specific HIV-1-binding protein that enhances trans-infection of T cells. Cell, 100(5) (2000), 587–97. CrossRefGoogle ScholarPubMed
Geldmacher, C., Currier, J.R., Herrmann, E., Haule, A., Kuta, E., McCutchan, F., Njovu, L., Geis, S., Hoffmann, O., Maboko, L., Williamson, C., Birx, D., Meyerhans, A., Cox, J., Hoelscher, M.. 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. CrossRefGoogle ScholarPubMed
Gendelman, H.E., Baca, L.M., Husayni, H., Turpin, J.A., Skillman, D., Kalter, D.C., Orenstein, J.M., Hoover, D.L., Meltzer, M.S.. Macrophage-HIV interaction : viral isolation and target cell tropism. AIDS, 4(3) (1990), 221–8. CrossRefGoogle Scholar
Giorgi, J.V., Hultin, L.E., McKeating, J.A., Johnson, T.D., Owens, B., Jacobson, L.P., Shih, R., Lewis, J., Wiley, D.J., Phair, J.P., Wolinsky, S.M., Detels, R.. 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. CrossRefGoogle ScholarPubMed
Gisselquist, D., Upham, G., Potterat, J.J.. 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. CrossRefGoogle Scholar
Goodenow, M., Huet, T., Saurin, W., Kwok, S., Sninsky, J., Wain-Hobson, S.. 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. Google ScholarPubMed
Goonetilleke, N., Liu, M.K., Salazar-Gonzalez, J.F., Ferrari, G., Giorgi, E., Ganusov, V.V., Keele, B.F., Learn, G.H., Turnbull, E.L., Salazar, M.G., Weinhold, K.J., Moore, S., Letvin, N., Haynes, B.F., Cohen, M.S., Hraber, P., Bhattacharya, T., Borrow, P., Perelson, A.S., Hahn, B.H., Shaw, G.M., Korber, B.T., McMichael, A.J.. 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. CrossRefGoogle Scholar
Gottlieb, M.S., Schroff, R., Schanker, H.M., Weisman, J.D., Fan, P.T., Wolf, R.A., Saxon, A.. 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. CrossRefGoogle ScholarPubMed
Goulder, P.J., Watkins, D.I.. HIV and SIV CTL escape : implications for vaccine design. Nature reviews. Immunology, 4(8) (2004), 630–40. CrossRefGoogle ScholarPubMed
Grant, R.M., Lama, J.R., Anderson, P.L., McMahan, V., Liu, A.Y., Vargas, L., Goicochea, P., Casapia, M., Guanira-Carranza, J.V., Ramirez-Cardich, M.E., Montoya-Herrera, O., Fernandez, T., Veloso, V.G., Buchbinder, S.P., Chariyalertsak, S., Schechter, M., Bekker, L.G., Mayer, K.H., Kallas, E.G., Amico, K.R., Mulligan, K., Bushman, L.R., Hance, R.J., Ganoza, C., Defechereux, P., Postle, B., Wang, F., McConnell, J.J., Zheng, J.H., Lee, J., Rooney, J.F., Jaffe, H.S., Martinez, A.I., Burns, D.N., Glidden, D.V.. Preexposure chemoprophylaxis for HIV prevention in men who have sex with men. The New England journal of medicine, 363(27) (2010), 2587–99. CrossRefGoogle ScholarPubMed
Gray, R.H., Wawer, M.J., Brookmeyer, R., Sewankambo, N.K., Serwadda, D., Wabwire-Mangen, F., Lutalo, T., Li, X., vanCott, T., Quinn, T.C.. Probability of HIV-1 transmission per coital act in monogamous, heterosexual, HIV-1-discordant couples in Rakai, Uganda. Lancet, 357(9263) (2001), 1149–53. CrossRefGoogle ScholarPubMed
Groot, F., van Capel, T.M., Schuitemaker, J., Berkhout, B., de Jong, E.C.. Differential susceptibility of naive, central memory and effector memory T cells to dendritic cell-mediated HIV-1 transmission. Retrovirology, 3 (2006), 52. CrossRefGoogle ScholarPubMed
Grossman, Z.. Mathematical modeling of thymopoiesis in HIV infection : real data, virtual data, and data interpretation. Clin. Immunol., 107(3) (2003), 137–9. CrossRefGoogle ScholarPubMed
Grossman, Z., Feinberg, M.B., Paul, W.E.. 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. CrossRefGoogle ScholarPubMed
Grossman, Z., Meier-Schellersheim, M., Paul, W.E., Picker, L.J.. Pathogenesis of HIV infection : what the virus spares is as important as what it destroys. Nature medicine, 12(3) (2006), 289–95. CrossRefGoogle ScholarPubMed
Grossman, Z., Meier-Schellersheim, M., Sousa, A. E., Victorino, R. M., and Paul, W.E.. CD4+ T-cell depletion in HIV infection : are we closer to understanding the cause ? Nature medicine, 8(4) (2002), 319–23. CrossRefGoogle ScholarPubMed
Grossman, Z., Min, B., Meier-Schellersheim, M., Paul, W. E.. Concomitant regulation of T-cell activation and homeostasis. Nature reviews. Immunology, 4(5) (2004), 387–95. CrossRefGoogle ScholarPubMed
Grossman, Z., Paul, W.E.. The impact of HIV on naive T-cell homeostasis. Nature medicine, 6(9) (2000), 976–7. CrossRefGoogle Scholar
Grossman, Z., Picker, L. J.. Pathogenic mechanisms in simian immunodeficiency virus infection. CCurrent opinion in HIV and AIDS, 3(3) (2008), 380–6. CrossRefGoogle ScholarPubMed
Guay, L.A., Musoke, P., Fleming, T., Bagenda, D., Allen, M., Nakabiito, C., Sherman, J., Bakaki, P., Ducar, C., Deseyve, M., Emel, L., Mirochnick, M., G. Fowler, M., Mofenson, L., Miotti, P., Dransfield, K., Bray, D., Mmiro, F., Jackson, J.B.. 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. CrossRefGoogle ScholarPubMed
Guyader, M., Emerman, M., Sonigo, P., Clavel, F., Montagnier, L., Alizon, M.. Genome organization and transactivation of the human immunodeficiency virus type 2. Nature, 326(6114) (1987), 662–9. CrossRefGoogle ScholarPubMed
Haase, A.T.. 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. CrossRefGoogle Scholar
Haase, A.T.. Targeting early infection to prevent HIV-1 mucosal transmission. Nature, 464(7286) (2010), 217–23. CrossRefGoogle ScholarPubMed
Hadjiandreou, M., Conejeros, R., Vassiliadis, V.S.. Towards a long-term model construction for the dynamic simulation of HIV infection. Mathematical biosciences and engineering, 4(3) (2007), 489–504. CrossRefGoogle Scholar
Hadjiandreou, M., Conejeros, R., Wilson, J.. HIV treatment planning on a case-by-case basis. International Journal of Biological and Life Sciences, 7 (2011), 148–57. Google Scholar
Hahn, B.H., Shaw, G.M., Taylor, M.E., Redfield, R.R., Markham, P.D., Salahuddin, S.Z., Wong-Staal, F., Gallo, R.C., Parks, E.S., Parks, W.P.. Genetic variation in HTLV-III/LAV over time in patients with AIDS or at risk for AIDS. Science, 232(4757) (1986), 1548–53. CrossRefGoogle ScholarPubMed
Harris, R.S., Bishop, K.N., Sheehy, A.M., Craig, H.M., Petersen-Mahrt, S.K., Watt, I.N., Neuberger, M.S., Malim, M.H.. DNA deamination mediates innate immunity to retroviral infection. Cell, 113(6) (2003), 803–9. CrossRefGoogle ScholarPubMed
Haynes, B.F., Gilbert, P.B., McElrath, M.J., Zolla-Pazner, S., Tomaras, G.D., Alam, S.M., Evans, D.T., Montefiori, D.C., Karnasuta, C., Sutthent, R., Liao, H.X., DeVico, A.L., Lewis, G.K., Williams, C., Pinter, A., Fong, Y., Janes, H., DeCamp, A., Huang, Y., Rao, M., Billings, E., Karasavvas, N., Robb, M.L., Ngauy, V., de Souza, M.S., Paris, R., Ferrari, G., Bailer, R.T., Soderberg, K.A., Andrews, C., Berman, P.W., Frahm, N., De Rosa, S.C., Alpert, MD., Yates, N. L., Shen, X., Koup, R.A., Pitisuttithum, P., Kaewkungwal, J., Nitayaphan, S., Rerks-Ngarm, S., Michael, N.L., Kim, J.H.. Immune-correlates analysis of an HIV-1 vaccine efficacy trial. The New England journal of medicine, 366(14) (2012), 1275–86. CrossRefGoogle Scholar
Hazenberg, M.D., Otto, S.A., Cohen Stuart, J.W., Verschuren, M.C., Borleffs, J.C., Boucher, C.A., Coutinho, R.A., Lange, J.M., Rinke de Wit, T.F., Tsegaye, A., van Dongen, J.J., Hamann, D., de Boer, R.J., Miedema, F.. 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. Google Scholar
Hazenberg, M.D., Otto, S. A., van Benthem, B.H., Roos, M.T., Coutinho, R.A., Lange, J.M., Hamann, D., Prins, M., Miedema, F.. Persistent immune activation in HIV-1 infection is associated with progression to AIDS. AIDS, 17(13) (2003), 1881–8. CrossRefGoogle ScholarPubMed
Hazenberg, M.D., Stuart, J.W., Otto, S.A., Borleffs, J.C., Boucher, C.A., de Boer, R.J., Miedema, F., Hamann, D.. 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. Google Scholar
Heath, S.L., Tew, J.G., Tew, J.G., Szakal, A.K., Burton, G.F.. Follicular dendritic cells and human immunodeficiency virus infectivity. Nature, 377(6551) (1995), 740–4. CrossRefGoogle Scholar
Hellerstein, M., Hanley, M.B., Cesar, D., Siler, S., Papageorgopoulos, C., Wieder, E., Schmidt, D., Hoh, R., Neese, R., Macallan, D., Deeks, S., McCune, J.M.. Directly measured kinetics of circulating T lymphocytes in normal and HIV-1-infected humans. Nature medicine, 5(1) (1999), 83–9. CrossRefGoogle ScholarPubMed
Herbeck, J.T., Rolland, M., Liu, Y., McLaughlin, S., McNevin, J., Zhao, H., Wong, K., Stoddard, J.N., Raugi, D., Sorensen, S., Genowati, I., Birditt, B., McKay, A., Diem, K., Maust, B.S., Deng, W., Collier, A.C., Stekler, J.D., McElrath, M.J., Mullins, J.I.. Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes. Journal of virology, 85(15) (2011), 7523–34. CrossRefGoogle ScholarPubMed
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.
Ho, D.D., Neumann, A.U., Perelson, A.S., Chen, W., Leonard, J.M., Markowitz, M.. Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature, 373(6510) (1995), 123–6. CrossRefGoogle ScholarPubMed
Hogue, I.B., Bajaria, S.H., Fallert, B.A., Qin, S., Reinhart, T.A., Kirschner, D.E.. 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. CrossRefGoogle ScholarPubMed
Hraba, T., Dolezal, J.. A mathematical model and CD4+ lymphocyte dynamics in HIV infection. Emerging infectious diseases, 2(4) (1996), 299–305. CrossRefGoogle ScholarPubMed
Hrecka, K., Hao, C., Gierszewska, M., Swanson, S.K., Kesik-Brodacka, M., Srivastava, S., Florens, L., Washburn, M.P., Skowronski, J.. Vpx relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein. Nature, 474(7353) (2011), 658–61. CrossRefGoogle ScholarPubMed
Huang, K.J., Wooley, D.P.. 2005. A new cell-based assay for measuring the forward mutation rate of HIV-1. Journal of virological methods 124:95-104. CrossRefGoogle ScholarPubMed
Huang, K., Wooley, D.. A new cell-based assay for measuring the forward mutation rate of HIV-1. Journal of virological methods, 124(1-2) (2005), 95–104. CrossRefGoogle ScholarPubMed
Hwang, S.S., Boyle, T.J., Lyerly, H.K., Cullen, B.R.. Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1. Science, 253(5015) (1991), 71–4. CrossRefGoogle ScholarPubMed
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.
Jacquelin, B., Mayau, V., Targat, B., Liovat, A.S., Kunkel, D., Petitjean, G., Dillies, M. A., Roques, P., Butor, C., Silvestri, G., Giavedoni, L.D., Lebon, P., Barre-Sinoussi, F., Benecke, A., Muller-Trutwin, M.C.. 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
Jager, S., Cimermancic, P., Gulbahce, N., Johnson, J.R., McGovern, K.E., Clarke, S.C., Shales, M., Mercenne, G., Pache, L., Li, K., Hernandez, H., Jang, G.M., Roth, S.L., Akiva, E., Marlett, J., Stephens, M., D’Orso, I., Fernandes, J., Fahey, M., Mahon, C., O’Donoghue, A.J., Todorovic, A., Morris, J.H., Maltby, D.A., Alber, T., Cagney, G., Bushman, F.D., Young, J.A., Chanda, S.K., Sundquist, W.I., Kortemme, T., Hernandez, R.D., Craik, C.S., Burlingame, A., Sali, A., Frankel, A.D., Krogan, N.J.. Global landscape of HIV-human protein complexes. Nature, 481(7381) (2012), 365–70. Google Scholar
Jetzt, A.E., Yu, H., Klarmann, G.J., Ron, Y., Preston, B.D., Dougherty, J.P.. High rate of recombination throughout the human immunodeficiency virus type 1 genome. Journal of virology, 74(3) (2000), 1234–40. CrossRefGoogle ScholarPubMed
Johnston, M.I., Fauci, A.S.. An HIV vaccine-evolving concepts. The New England journal of medicine, 356(20) (2007), 2073–81. CrossRefGoogle ScholarPubMed
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.
Jung, A., Maier, R., Vartanian, J.P., Bocharov, G., Jung, V., Fischer, U., Meese, E., Wain-Hobson, S., Meyerhans, A.. Recombination : Multiply infected spleen cells in HIV patients. Nature, 418(6894) (2002), 144. CrossRefGoogle ScholarPubMed
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.
Kamina, A., Makuch, R.W., Zhao, H.. A stochastic modeling of early HIV-1 population dynamics. Mathematical biosciences, 170(2) (2001), 187–98. CrossRefGoogle ScholarPubMed
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.
Keele, B.H., Giorgi, E.E., Salazar-Gonzalez, J.F., Decker, J.M., Pham, K.T., Salazar, M.G., Sun, C., Grayson, T., Wang, S., Li, H., Wei, X., Jiang, C., Kirchherr, J.L., Gao, F., Anderson, J. A., Ping, L.H., Swanstrom, R., Tomaras, G.D., Blattner, W.A., Goepfert, P.A., Kilby, J.M., Saag, M.S., Delwart, E.L., Busch, M.P., Cohen, M.S., Montefiori, D.C., Haynes, B.F., Gaschen, B., Athreya, G.S., Lee, H.Y., Wood, N., Seoighe, C., Perelson, A.S., Bhattacharya, T., Korber, B.T., Hahn, B.H., Shaw, G.M.. 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. CrossRefGoogle Scholar
Kiepiela, P., Leslie, A.J., Honeyborne, I., Ramduth, D., Thobakgale, C., Chetty, S., Rathnavalu, P., Moore, C., Pfafferott, K.J., Hilton, L.. Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA. Nature, 432(7018) (2004), 769–75. CrossRefGoogle Scholar
Kirchhoff, F.. Immune evasion and counteraction of restriction factors by HIV-1 and other primate lentiviruses. Cell host & microbe, 8(1) (2010), 55–67. CrossRefGoogle ScholarPubMed
Kitahata, M.M., Gange, S.J., Abraham, A.G., Merriman, B., Saag, M.S., Justice, A.C., Hogg, R.S., Deeks, S.G., Eron, J.J., Brooks, J.T.. Effect of early versus deferred antiretroviral therapy for HIV on survival. New England Journal of Medicine, 360(18) (2009), 1815–26. CrossRefGoogle ScholarPubMed
Klatzmann, D., Barre-Sinoussi, F., Nugeyre, M.T., Danquet, C., Vilmer, E., Griscelli, C., Brun-Veziret, F., Rouzioux, C., Gluckman, J.C., Chermann, J.C., and et al. Selective tropism of lymphadenopathy associated virus (LAV) for helper-inducer T lymphocytes. Science, 225(4657) (1984), 59–63. CrossRefGoogle ScholarPubMed
Konig, R., Zhou, Y., Elleder, D., Diamond, T.L., Bonamy, G.M., Irelan, J.T., Chiang, C.Y., Tu, B.P., De Jesus, P.D., Lilley, C.E., Seidel, S., Opaluch, A.M., Caldwell, J.S., Weitzman, M.D., Kuhen, K.L., Bandyopadhyay, S., Ideker, T., Orth, A.P., Miraglia, L.J., Bushman, F.D., Young, J.A., Chanda, S.K.. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell, 135(1) (2008), 49–60. CrossRefGoogle Scholar
Kostrikis, L.G., Touloumi, G., Karanicolas, R., Pantazis, N., Anastassopoulou, C., Karafoulidou, A., Goedert, J.J., Hatzakis, A.. 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. CrossRefGoogle Scholar
Koulinska, I.N., Villamor, E., Chaplin, B., Msamanga, G., Fawzi, W., Renjifo, B., Essex, M.. Transmission of cell-free and cell-associated HIV-1 through breast-feeding. AIDS, 41(1) (2006), 93. Google ScholarPubMed
Kouyos, R.D., Althaus, C.L., Bonhoeffer, S.. Stochastic or deterministic : what is the effective population size of HIV-1 ?. Trends in microbiology, 14(12) (2006), 507–11. CrossRefGoogle ScholarPubMed
Koyanagi, Y., Miles, S., Mitsuyasu, R.T., Merrill, J.E., Vinters, H.V., Chen, I.S.. Dual infection of the central nervous system by AIDS viruses with distinct cellular tropisms. Science, 236(4803) (1987), 819–22. CrossRefGoogle ScholarPubMed
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.
Kwa, D., Vingerhoed, J., Boeser-Nunnink, B., Broersen, S., Schuitemaker, H.. 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. CrossRefGoogle ScholarPubMed
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.
Laguette, N., Sobhian, B., Casartelli, N., Ringeard, M., Chable-Bessia, C., Segeral, E., Yatim, A., Emiliani, S., Schwartz, O., Benkirane, M.. SAMHD1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by Vpx. Nature, 474(7353) (2011), 654–7. CrossRefGoogle Scholar
Lecossier, D., Bouchonnet, F., Clavel, F., Hance, A.J.. Hypermutation of HIV-1 DNA in the absence of the Vif protein. Science, 300(5622) (2003), 1112. CrossRefGoogle Scholar
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.
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.
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.
Levy, D.N., Aldrovandi, G.M., Kutsch, O., Shaw, G.M.. 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. CrossRefGoogle ScholarPubMed
Levy, J.A., Hoffman, A.D., Kramer, S.M., Landis, J.A., Shimabukuro, J.M., Oshiro, L.S.. Isolation of lymphocytopathic retroviruses from San Francisco patients with AIDS. Science, 225(4664) (1984), 840–2. CrossRefGoogle ScholarPubMed
Lim, S.G., Condez, A., Lee, C.A., Johnson, M.A., Elia, C., Poulter, L.W.. Loss of mucosal CD4 lymphocytes is an early feature of HIV infection. Clinical and experimental immunology, 92(3) (1993), 448–54. CrossRefGoogle ScholarPubMed
Lindholm, P.F., Annen, K., Ramsey, G.. Approaches to minimize infection risk in blood banking and transfusion practice. Infectious disorders drug targets, 11(1) (2011), 45–56. CrossRefGoogle Scholar
Lori, F., Malykh, A., Cara, A., Sun, D., Weinstein, J.N., Lisziewicz, J., Gallo, R.C.. Hydroxyurea as an inhibitor of human immunodeficiency virus-type 1 replication. Science, 266(5186) (1994), 801–5. CrossRefGoogle ScholarPubMed
Mandl, J.N., Barry, A.P., Vanderford, T.H., Kozyr, N., Chavan, R., Klucking, S., Barrat, F.J., Coffman, R.L., Staprans, S.I., Feinberg, M.B.. Divergent TLR7 and TLR9 signaling and type I interferon production distinguish pathogenic and nonpathogenic AIDS virus infections. Nature medicine, 14(10) (2008), 1077–87. CrossRefGoogle ScholarPubMed
Manganaro, L., Lusic, M., Gutierrez, M.I., Cereseto, A., Del Sal, G., Giacca, M.. Concerted action of cellular JNK and Pin1 restricts HIV-1 genome integration to activated CD4+ T lymphocytes. Nature medicine, 16(3) (2010), 329–33. CrossRefGoogle Scholar
Mangeat, B., Turelli, P., Caron, G., Friedli, M., Perrin, L., Trono, D.. Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts. Nature, 424(6944) (2003), 99–103. CrossRefGoogle ScholarPubMed
Mansky, L.M.. 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. CrossRefGoogle Scholar
Mansky, L.M.. The mutation rate of human immunodeficiency virus type 1 is influenced by the vpr gene. Virology, 222(2) (1996), 391–400. CrossRefGoogle Scholar
Mansky, L.M., Temin, H.M.. 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. Google ScholarPubMed
Margolis, D.M.. Histone deacetylase inhibitors and HIV latency. Current opinion in HIV and AIDS, 6(1) (2011), 25–9. CrossRefGoogle ScholarPubMed
Mariani, R., Chen, D., Schrofelbauer, B., Navarro, F., Konig, R., Bollman, B., Munk, C., Nymark-McMahon, H., Landau, N.R.. Species-specific exclusion of APOBEC3G from HIV-1 virions by Vif. Cell, 114(1) (2003), 21–31. CrossRefGoogle ScholarPubMed
Martin, N., Sattentau, Q.. Cell-to-cell HIV-1 spread and its implications for immune evasion. Current opinion in HIV and AIDS, 4(2) (2009), 143–9. CrossRefGoogle ScholarPubMed
Marx, J.L.. Circumcision may protect against the AIDS virus. Science, 245(4917) (1989), 470–1. CrossRefGoogle ScholarPubMed
Mascola, J.R., Montefiori, D.C.. The role of antibodies in HIV vaccines. Annual review of immunology, 28 (2010), 413–44. CrossRefGoogle ScholarPubMed
McMichael, A.J., Borrow, P., Tomaras, G.D., Goonetilleke, N., Haynes, B.F.. The immune response during acute HIV-1 infection : clues for vaccine development. Nature reviews. Immunology, 10(1) (2010), 11–23. CrossRefGoogle ScholarPubMed
Mehandru, S., Poles, M.A., Tenner-Racz, K., Horowitz, A., Hurley, A., Hogan, C., Boden, D., Racz, P., Markowitz, M.. 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. CrossRefGoogle ScholarPubMed
Mellors, J.W., Munoz, A., Giorgi, J.V., Margolick, J.B., Tassoni, C.J., Gupta, P., Kingsley, L.A., Todd, J.A., Saah, A.J., Detels, R., Phair, J.P., Rinaldo, C.R. Jr. Plasma viral load and CD4+ lymphocytes as prognostic markers of HIV-1 infection. Annals of internal medicine, 126(12) (1997), 946–54. CrossRefGoogle ScholarPubMed
Mellors, J.W., Rinaldo, C. R. Jr., Gupta, P., White, R.M., Todd, J. A., Kingsley, L. A.. Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science, 272(5265) (1996), 1167–70. CrossRefGoogle Scholar
Meyerhans, A., Cheynier, R., Albert, J., Seth, M., Kwok, S., Sninsky, J., Morfeldt-Manson, L., Asjo, B., Wain-Hobson, S.. Temporal fluctuations in HIV quasispecies in vivo are not reflected by sequential HIV isolations. Cell, 58(5) (1989), 901–10. CrossRefGoogle Scholar
Meyerhans, A., Vartanian, J.P., Hultgren, C., Plikat, U., Karlsson, A., Wang, L., Eriksson, S., Wain-Hobson, S.. 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. Google ScholarPubMed
Moir, S., Fauci, A.S.. B cells in HIV infection and disease. Nature reviews. Immunology, 9(4) (2009), 235–45. CrossRefGoogle ScholarPubMed
Muller, V., Maree, A. F., De Boer, R. J.. 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. CrossRefGoogle Scholar
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.
Nduati, R., John, G., Mbori-Ngacha, D., Richardson, B., Overbaugh, J., Mwatha, A., Ndinya-Achola, J., Bwayo, J., Onyango, F.E., Hughes, J., Kreiss, J.. 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. CrossRefGoogle ScholarPubMed
R.A. Neher, T. Leitner. Recombination rate and selection strength in HIV intra-patient evolution. PLoS computational biology, 6(1) (2010), p. e1000660.
Neil, S.J., Sandrin, V., Sundquist, W.I., Bieniasz, P.D.. 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. CrossRefGoogle ScholarPubMed
Neil, S.J., Zang, T., Bieniasz, P.D.. Tetherin inhibits retrovirus release and is antagonized by HIV-1 Vpu. Nature, 451(7177) (2008), 425–30. CrossRefGoogle ScholarPubMed
Nguyen, D.G., Wolff, K.C., Yin, H., Caldwell, J.S., Kuhen, K.L.. “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. CrossRefGoogle Scholar
M.A. Nowak, R.M. May. Virus Dynamics. Mathematical Pronciples of Immunology and Virology Oxford University Press, Oxford, 2000.
Okoye, A., Meier-Schellersheim, M., Brenchley, J.M., Hagen, S.I., Walker, J.M., Rohankhedkar, M., Lum, R., Edgar, J.B., Planer, S.L., Legasse, A., Sylwester, A.W., Piatak, M. Jr., Lifson, J.D., Maino, V.C., Sodora, D.L., Douek, D.C., Axthelm, M.K., Grossman, Z., Picker, L.J.. 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. CrossRefGoogle ScholarPubMed
Onafuwa, A., An, W., Robson, N.D., Telesnitsky, A.. 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. CrossRefGoogle ScholarPubMed
Paci, P., Martini, F., Bernaschi, M., D’Offizi, G., Castiglione, F.. Timely HAART initiation may pave the way for a better viral control. BMC infectious diseases, 11 (2011), 56. CrossRefGoogle ScholarPubMed
Pantaleo, G., Fauci, A.S.. Immunopathogenesis of HIV infection. Annual review of microbiology, 50 (1996), 825–54. CrossRefGoogle ScholarPubMed
Pantaleo, G., Graziosi, C., Demarest, J.F., Butini, L., Montroni, M., Fox, C.H., Orenstein, J.M., Kotler, D.P., Fauci, A.S.. HIV infection is active and progressive in lymphoid tissue during the clinically latent stage of disease. Nature, 362(6418) (1993), 355–8. CrossRefGoogle ScholarPubMed
Perelson, A.S., Essunger, P., Cao, Y., Vesanen, M., Hurley, A., Saksela, K., Markowitz, M., Ho, D.D.. Decay characteristics of HIV-1-infected compartments during combination therapy. Nature, 387(6629) (1997), 188–91. CrossRefGoogle ScholarPubMed
Perelson, A.S., Nelson, P. W.. Mathematical Analysis of HIV-1 Dynamics in Vivo. SIAM review. Society for Industrial and Applied Mathematics, 41 (1999), 3–44. Google Scholar
Perelson, A.S., Neumann, A.U., Markowitz, M., Leonard, J.M., Ho, D.D.. HIV-1 dynamics in vivo : virion clearance rate, infected cell life-span, and viral generation time. Science, 271(5255) (1996), 1582–6. CrossRefGoogle Scholar
Pereyra, F., Jia, X., McLaren, P.J., Telenti, A., de Bakker, P.I.W., Walker, B.D., Ripke, S., Brumme, C.J., Pulit, S.L., Carrington, M.. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science (New York, NY), 330(6010) (2010), 1551. Google ScholarPubMed
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.
Phillips, D.M.. The role of cell-to-cell transmission in HIV infection. AIDS, 8(6) (1994), 719–31. CrossRefGoogle ScholarPubMed
Piatak, M. Jr., Saag, M.S., Yang, L.C., Clark, S.J., Kappes, J.C., Luk, K.C., Hahn, B.H., Shaw, G.M., Lifson, J.D.. High levels of HIV-1 in plasma during all stages of infection determined by competitive PCR. Science, 259(5102) (1993), 1749–54. CrossRefGoogle ScholarPubMed
Picker, L.J., Hagen, S.I., Lum, R., Reed-Inderbitzin, E.F., Daly, L.M., Sylwester, A.W., Walker, J.M., Siess, D.C., Piatak, M. Jr., Wang, C., Allison, D.B., Maino, V.C., Lifson, J.D., Kodama, T., Axthelm, M. K.. 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. CrossRefGoogle ScholarPubMed
Popovic, M.M., Sarngadharan, M.G., Read, E., Gallo, R.C.. Detection, isolation, and continuous production of cytopathic retroviruses (HTLV-III) from patients with AIDS and pre-AIDS. Science, 224(4648) (1984), 497–500. CrossRefGoogle ScholarPubMed
Powers, K.A., Ghani, A.C., Miller, W.C., Hoffman, I.F., Pettifor, A.E., Kamanga, G., Martinson, F.E., Cohen, M.S.. 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. CrossRefGoogle ScholarPubMed
Puigdomenech, I., Massanella, M., Cabrera, C., Clotet, B., Blanco, J.. On the steps of cell-to-cell HIV transmission between CD4 T cells. Retrovirology, 6 (2009), 89. CrossRefGoogle ScholarPubMed
Racz, P., Tenner-Racz, K., Kahl, C., Feller, A.C., Kern, P., Dietrich, M.. Spectrum of morphologic changes of lymph nodes from patients with AIDS or AIDS-related complexes. Progress in allergy, 37 (1986), 81–181. Google ScholarPubMed
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.
Rerks-Ngarm, S., Pitisuttithum, P., Nitayaphan, S., Kaewkungwal, J., Chiu, J., Paris, R., Premsri, N., Namwat, C., de Souza, M., Adams, E., Benenson, M., Gurunathan, S., Tartaglia, J., McNeil, J.G., Francis, D.P., Stablein, D., Birx, D.L., Chunsuttiwat, S., Khamboonruang, C., Thongcharoen, P., Robb, M.L., Michael, N.L., Kunasol, P., Kim, J.H.. Vaccination with ALVAC and AIDSVAX to prevent HIV-1 infection in Thailand. The New England journal of medicine, 361(23) (2009), 2209–20. CrossRefGoogle ScholarPubMed
Rhodes, T.D., Nikolaitchik, O., Chen, J., Powell, D., Hu, W.S.. 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. CrossRefGoogle ScholarPubMed
Roberts, J.D., Bebenek, K., Kunkel, T.A.. The accuracy of reverse transcriptase from HIV-1. Science, 242(4882) (1988), 1171–3. CrossRefGoogle ScholarPubMed
Roberts, L., A. Passmore, J., Williamson, C., Little, F., Bebell, L.M., Mlisana, K., Burgers, W. A., van Loggerenberg, F., Walzl, G., Djoba Siawaya, J.F., Abdool Karim, Q., Karim, S.S.. Plasma cytokine levels during acute HIV-1 infection predict HIV disease progression. AIDS, 24(6) (2010), 819–31. CrossRefGoogle ScholarPubMed
Rosenberg, E.S., Davidian, M., Banks, H.T.. Using mathematical modeling and control to develop structured treatment interruption strategies for HIV infection. Drug and alcohol dependence, 88 Suppl 2 (2007), S41–51. CrossRefGoogle ScholarPubMed
Rotger, M., Dalmau, J., Rauch, A., McLaren, P., Bosinger, S.E., Martinez, R., Sandler, N.G., Roque, A., Liebner, J., Battegay, M., Bernasconi, E., Descombes, P., Erkizia, I., Fellay, J., Hirschel, B., Miro, J.M., Palou, E., Hoffmann, M., Massanella, M., Blanco, J., Woods, M., Gunthard, H.F., de Bakker, P., Douek, D.C., Silvestri, G., Martinez-Picado, J., Telenti, A.. 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. CrossRefGoogle Scholar
Rouzine, I.M., Coffin, J.M.. 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. CrossRefGoogle Scholar
Rouzine, I.M., Murali-Krishna, K., Ahmed, R.. Generals die in friendly fire, or modelling immune response to HIV. Journal of Computational and Applied Mathematic, 184 (2005), 258–74. CrossRefGoogle Scholar
Rouzine, I.M., Rodrigo, A., Coffin, J. M.. 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. CrossRefGoogle ScholarPubMed
Rudnicka, D., Feldmann, J., Porrot, F., Wietgrefe, S., Guadagnini, S., Prevost, M. C., Estaquier, J., Haase, A.T., Sol-Foulon, N., Schwartz, O.. Simultaneous cell-to-cell transmission of human immunodeficiency virus to multiple targets through polysynapses. Journal of virology, 83(12) (2009), 6234–46. CrossRefGoogle ScholarPubMed
Sarngadharan, M.G., Popovic, M., Bruch, L., Schupbach, J., Gallo, R.C.. Antibodies reactive with human T-lymphotropic retroviruses (HTLV-III) in the serum of patients with AIDS. Science, 224(4648) (1984), 506–8. CrossRefGoogle Scholar
Sattentau, Q.. Avoiding the void : cell-to-cell spread of human viruses. Nature reviews. Microbiology, 6(11) (2008), 815–26. CrossRefGoogle ScholarPubMed
Sax, P.E., Baden, L. R.. When to start antiretroviral therapy — ready when you are ?. New England Journal of Medicine, 360(18) (2009), 1897–9. CrossRefGoogle Scholar
Schaller, T., Goujon, C., Malim, M.H.. AIDS/HIV. HIV interplay with SAMHD1. Science, 335(6074) (2012), 1313–4. CrossRefGoogle ScholarPubMed
Scheid, J.F., Mouquet, H., Feldhahn, N., Seaman, M.S., Velinzon, K., Pietzsch, J., Ott, R.G., Anthony, R.M., Zebroski, H., Hurley, A., Phogat, A., Chakrabarti, B., Li, Y., Connors, M., Pereyra, F., Walker, B.D., Wardemann, H., Ho, D., Wyatt, R.T., Mascola, J.R., Ravetch, J.V., Nussenzweig, M.C.. Broad diversity of neutralizing antibodies isolated from memory B cells in HIV-infected individuals. Nature, 458(7238) (2009), 636–40. CrossRefGoogle Scholar
Schindler, M., Munch, J., Kutsch, O., Li, H., Santiago, M.L., Bibollet-Ruche, F., Muller-Trutwin, M.C., Novembre, F.J., Peeters, M., Courgnaud, V., Bailes, E., Roques, P., Sodora, D.L., Silvestri, G., Sharp, P.M., Hahn, B.H., Kirchhoff, F.. 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. CrossRefGoogle Scholar
Schneider, T., Jahn, H.U., Schmidt, W., Riecken, E.O., Zeitz, M., Ullrich, R.. 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. CrossRefGoogle ScholarPubMed
Schuitemaker, H., Kootstra, N.A., de Goede, R.E., de Wolf, F., Miedema, F., Tersmette, M.. 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. Google ScholarPubMed
Schultz, A., Sopper, S., Sauermann, U., Meyerhans, A., Suspene, R.. Stable multi-infection of splenocytes during SIV infection — the basis for continuous recombination. Retrovirology, 9(1) (2012), 31. CrossRefGoogle ScholarPubMed
Schwartz, S., Felber, B.K., Fenyo, E.M., Pavlakis, G.N.. 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. CrossRefGoogle ScholarPubMed
Y. Senturia, A. Ades, C. Peckham, C. Giaquinto, N. Baumslag. Breast-feeding and HIV infection. Lancet, 2 (1987).
Shan, L., Deng, K., Shroff, N.S., Durand, C.M., Rabi, S.A., Yang, H.C., Zhang, H., Margolick, J.B., Blankson, J.N., Siliciano, R.F.. Stimulation of HIV-1-specific cytolytic T lymphocytes facilitates elimination of latent viral reservoir after virus reactivation. Immunity, 36(3) (2012), 491–501. CrossRefGoogle ScholarPubMed
Shankarappa, R., Margolick, J.B., Gange, S.J., Rodrigo, A.G., Upchurch, D., Farzadegan, H., Gupta, P., Rinaldo, C.R., Learn, G.H., He, X., Huang, X.L., Mullins, J.I.. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. Journal of virology, 73(12) (1999), 10489–502. Google ScholarPubMed
Sheehy, A.M., Gaddis, N.C., Choi, J.D., Malim, M.H.. Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein. Nature, 418(6898) (2002), 646–50. CrossRefGoogle Scholar
Sheehy, A.M., Gaddis, N.C., Malim, M.H.. The antiretroviral enzyme APOBEC3G is degraded by the proteasome in response to HIV-1 Vif. Nature medicine, 9(11) (2003), 1404–7. CrossRefGoogle Scholar
Sheppard, H.W., Ascher, M.S., Krowka, J.F.. Viral burden and HIV disease. Nature, 364(6435) (1993), 291–2. CrossRefGoogle Scholar
Sherer, N.M., Lehmann, M. J., Jimenez-Soto, L. F., Horensavitz, C., Pypaert, M., Mothes, W.. Retroviruses can establish filopodial bridges for efficient cell-to-cell transmission. Nature cell biology, 9(3) (2007), 310–5. CrossRefGoogle Scholar
Shioda, T., Levy, J. A., Cheng-Mayer, C.. 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. CrossRefGoogle Scholar
Shirakawa, K., Takaori-Kondo, A., Yokoyama, M., Izumi, T., Matsui, M., Io, K., Sato, T., Sato, H., Uchiyama, T.. Phosphorylation of APOBEC3G by protein kinase A regulates its interaction with HIV-1 Vif. Nature structural & molecular biology, 15(11) (2008), 1184–91. CrossRefGoogle Scholar
Shriner, D., Rodrigo, A.G., Nickle, D.C., Mullins, J.I.. Pervasive genomic recombination of HIV-1 in vivo. Genetics, 167(4) (2004), 1573–83. CrossRefGoogle ScholarPubMed
Siewe, B., Landay, A.. Key Concepts in the Early Immunology of HIV-1 Infection. Current infectious disease reports, 14(1) (2012), 102–9. CrossRefGoogle ScholarPubMed
Sigal, A., Kim, J.T., Balazs, A.B., Dekel, E., Mayo, A., Milo, R., Baltimore, D.. Cell-to-cell spread of HIV permits ongoing replication despite antiretroviral therapy. Nature, 477(7362) (2011), 95–8. CrossRefGoogle ScholarPubMed
Siliciano, J.D., Kajdas, J., Finzi, D., Quinn, T.C., Chadwick, K., Margolick, J.B., Kovacs, C., Gange, S.J., Siliciano, R.F.. 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. CrossRefGoogle ScholarPubMed
Silvestri, G., Feinberg, M.B.. Turnover of lymphocytes and conceptual paradigms in HIV infection. The Journal of clinical investigation, 112(6) (2003), 821–4. CrossRefGoogle ScholarPubMed
Simmonds, P., Balfe, P., Peutherer, J.F., Ludlam, C.A., Bishop, J.O., Brown, A.J.. 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. Google Scholar
Sips, M., Sciaranghella, G., Diefenbach, T., Dugast, A. S., Berger, C.T., Liu, Q., Kwon, D., Ghebremichael, M., Estes, J.D., Carrington, M., Martin, J.N., Deeks, S.G., Hunt, P.W., Alter, G.. Altered distribution of mucosal NK cells during HIV infection. Mucosal immunology, 5(1) (2012), 30–40. CrossRefGoogle ScholarPubMed
Soudeyns, H., Pantaleo, G.. The moving target : mechanisms of HIV persistence during primary infection. Immunology today, 20(10) (1999), 446–50. CrossRefGoogle Scholar
Sousa, A.E., Carneiro, J., Meier-Schellersheim, M., Grossman, Z., Victorino, R.M.. 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. CrossRefGoogle ScholarPubMed
Stacey, A.R., Norris, P.J., Qin, L., Haygreen, E.A., Taylor, E., Heitman, J., Lebedeva, M., DeCamp, A., Li, D., Grove, D., Self, S.G., Borrow, P.. 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. CrossRefGoogle ScholarPubMed
Stafford, M.A., Corey, L., Cao, Y., Daar, E.S., Ho, D.D., Perelson, A.S.. Modeling plasma virus concentration during primary HIV infection. Journal of theoretical biology, 203(3) (2000), 285–301. CrossRefGoogle Scholar
Sterne, J.A., May, M., Costagliola, D., de Wolf, F., Phillips, A.N., Harris, R., Funk, M.J., Geskus, R.B., Gill, J., Dabis, F., Miro, J.M., Justice, A.C., Ledergerber, B., Fatkenheuer, G., Hogg, R.S., Monforte, A.D., Saag, M., Smith, C., Staszewski, S., Egger, M., Cole, S.R.. 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. Google ScholarPubMed
Stoddart, C.A., Reyes, R.A.. Models of HIV-1 disease : A review of current status. Drug Discovery Today : Disease Models, 3 (2006), 113–119. Google Scholar
Strain, M.C., Gunthard, H.F., Havlir, D.V., Ignacio, C.C., Smith, D.M., Leigh-Brown, A.J., Macaranas, T.R., Lam, R.Y., Daly, O.A., Fischer, M., Opravil, M., Levine, H., Bacheler, L., Spina, C.A., Richman, D.D., Wong, J.K.. 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. CrossRefGoogle ScholarPubMed
Streeck, H., Jolin, J.S., Qi, Y., Yassine-Diab, B., Johnson, R.C., Kwon, D.S., Addo, M.M., Brumme, C., Routy, J.P., Little, S., Jessen, H.K., Kelleher, A.D., Hecht, F.M., Sekaly, R.P., Rosenberg, E.S., Walker, B.D., Carrington, M., Altfeld, M.. 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. CrossRefGoogle ScholarPubMed
Stremlau, M.C., Owens, C.M., Perron, M.J., Kiessling, M., Autissier, P., Sodroski, J.. The cytoplasmic body component TRIM5alpha restricts HIV-1 infection in Old World monkeys. Nature, 427(6977) (2004), 848–53. CrossRefGoogle ScholarPubMed
Sturt, A.S., Halpern, M.S., Sullivan, B., Maldonado, Y.A.. 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. CrossRefGoogle Scholar
Thobakgale, C.F., Fadda, L., Lane, K., Toth, I., Pereyra, F., Bazner, S., Ndung’u, T., Walker, B.D., Rosenberg, E.S., Alter, G., Carrington, M., Allen, T.M., Altfeld, M.. 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. CrossRefGoogle ScholarPubMed
Tomaras, G.D., Yates, N.L., Liu, P., Qin, L., Fouda, G.G., Chavez, L.L., Decamp, A.C., Parks, R.J., Ashley, V.C., Lucas, J.T., Cohen, M., Eron, J., Hicks, C.B., Liao, H.X., Self, S.G., Landucci, G., Forthal, D.N., Weinhold, K.J., Keele, B.F., Hahn, B.H., Greenberg, M.L., Morris, L., Karim, S.S., Blattner, W.A., Montefiori, D.C., Shaw, G.M., Perelson, A.S., Haynes, B.F.. 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. CrossRefGoogle ScholarPubMed
Tsunetsugu-Yokota, Y., Akagawa, K., Kimoto, H., Suzuki, K., Iwasaki, M., Yasuda, S., Hausser, G., Hultgren, C., Meyerhans, A., Takemori, T.. 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. Google ScholarPubMed
Van Damme, N., Goff, D., Katsura, C., Jorgenson, R.L., Mitchell, R., Johnson, M.C., Stephens, E.B., Guatelli, J.. 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. CrossRefGoogle ScholarPubMed
Van Montfort, T., Thomas, A.A., Pollakis, G., Paxton, W.A.. 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. CrossRefGoogle ScholarPubMed
Varela-Rohena, A., Molloy, P. E., Dunn, S.M., Li, Y., Suhoski, M.M., Carroll, R.G., Milicic, A., Mahon, T., Sutton, D.H., Laugel, B., Moysey, R., Cameron, B.J., Vuidepot, A., Purbhoo, M.A., Cole, D.K., Phillips, R.E., June, C.H., Jakobsen, B.K., Sewell, A.K., Riley, J.L.. Control of HIV-1 immune escape by CD8 T cells expressing enhanced T-cell receptor. Nature medicine, 14(12) (2008), 1390–5. CrossRefGoogle Scholar
Vartanian, J.P., Meyerhans, A., Asjo, B., Wain-Hobson, S.. Selection, recombination, and G- - - -A hypermutation of human immunodeficiency virus type 1 genomes. Journal of virology, 65(4) (1991), 1779–88. Google Scholar
Verotta, D.. Models and estimation methods for clinical HIV-1 data. Journal of Computational and Applied Mathematics, 184 (2005), 275–300. CrossRefGoogle Scholar
Vijay, N.N., Vasantika, R., Ajmani, R., Perelson, A.S., Dixit, N.M.. Recombination increases human immunodeficiency virus fitness, but not necessarily diversity. The Journal of general virology, 89 (2008), 1467–77. CrossRefGoogle Scholar
Wagner, N., Lohler, J., Kunkel, E.J., Ley, K., Leung, E., Krissansen, G., Rajewsky, K., Muller, W.. Critical role for beta7 integrins in formation of the gut-associated lymphoid tissue. Nature, 382(6589) (1996), 366–70. CrossRefGoogle ScholarPubMed
Wain-Hobson, S.. Viral burden in AIDS. Nature, 366(6450) (1993), 22. CrossRefGoogle Scholar
Wain-Hobson, S., Sonigo, P., Danos, O., Cole, S., Alizon, M.. Nucleotide sequence of the AIDS virus, LAV. Cell, 40(1) (1985), 9–17. CrossRefGoogle ScholarPubMed
Wasserstein-Robbins, F.. 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. CrossRefGoogle ScholarPubMed
Wei, X., Ghosh, S. K., Taylor, M.E., Johnson, V.A., Emini, E. A., Deutsch, P., Lifson, J.D., Bonhoeffer, S., Nowak, M.A., Hahn, B.H., and et al. Viral dynamics in human immunodeficiency virus type 1 infection. Nature, 373(6510) (1995), 117–22. CrossRefGoogle Scholar
Wendelsdorf, K., Dean, G., Hu, S., Nordone, S., Banks, H.T.. Host immune responses that promote initial HIV spread. Journal of theoretical biology, 289 (2011), 17–35. CrossRefGoogle ScholarPubMed
Wherry, E.J.. T cell exhaustion. Nature immunology, 12(6) (2011), 492–9. CrossRefGoogle ScholarPubMed
WHO, posting date. Progress report 2011 : Global HIV/AIDS response. [Online.]
Wick, D., Self, S. G.. Early HIV infection in vivo : branching-process model for studying timing of immune responses and drug therapy. Mathematical biosciences, 165(2) (2000), 115–34. CrossRefGoogle Scholar
Wiley, R.D., Gummuluru, S.. 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. CrossRefGoogle Scholar
Wong-Staal, F., Shaw, G.M., Hahn, B.H., Salahuddin, S.Z., Popovic, M., Markham, P., Redfield, R., Gallo, R.C.. Genomic diversity of human T-lymphotropic virus type III (HTLV-III). Science, 229(4715) (1985), 759–62. CrossRefGoogle Scholar
Yamamoto, T., Price, D.A., Casazza, J.P., Ferrari, G., Nason, M., Chattopadhyay, P.K., Roederer, M., Gostick, E., Katsikis, P.D., Douek, D.C., Haubrich, R., Petrovas, C., Koup, R.A.. 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. CrossRefGoogle Scholar
Yeung, M.L., Houzet, L., Yedavalli, V.S., Jeang, K.T.. 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. CrossRefGoogle ScholarPubMed
Yuan, Y., Allen, L.J.. Stochastic models for virus and immune system dynamics. Mathematical biosciences, 234(2) (2011), 84–94. CrossRefGoogle ScholarPubMed
Zaitseva, M., Blauvelt, A., Lee, S., Lapham, C.K., Klaus-Kovtun, V., Mostowski, H., Manischewitz, J., Golding, H.. 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. CrossRefGoogle Scholar
Zeng, M., Paiardini, M., Engram, J.C., Beilman, G.J., Chipman, J.G., Schacker, T.W., Silvestri, G., Haase, A.T.. Critical role of CD4 T cells in maintaining lymphoid tissue structure for immune cell homeostasis and reconstitution. Blood, 120(9) (2012), 1856–67. CrossRefGoogle ScholarPubMed
Zhang, H., Yang, B., Pomerantz, R. J., Zhang, C., Arunachalam, S.C., Gao, L.. The cytidine deaminase CEM15 induces hypermutation in newly synthesized HIV-1 DNA. Nature, 424(6944) (2003), 94–8. CrossRefGoogle ScholarPubMed
Zhang, L., Dailey, P.J., Gettie, A., Blanchard, J., Ho, D.D.. The liver is a major organ for clearing simian immunodeficiency virus in rhesus monkeys. Journal of virology, 76(10) (2002), 5271–3. CrossRefGoogle ScholarPubMed
Zhou, H., Xu, M., Huang, Q., Gates, A.T., Zhang, X.D., Castle, J.C., Stec, E., Ferrer, M., Strulovici, B., Hazuda, D.J., Espeseth, A.S.. Genome-scale RNAi screen for host factors required for HIV replication. Cell host & microbe, 4(5) (2008), 495–504. CrossRefGoogle ScholarPubMed
Zhuang, J., Jetzt, A.E., Sun, G., Yu, H., Klarmann, G., Ron, Y., Preston, B.D., Dougherty, J.P.. Human immunodeficiency virus type 1 recombination : rate, fidelity, and putative hot spots. Journal of virology, 76(22) (2002), 11273–82. CrossRefGoogle ScholarPubMed