Modeling the immune response to HIV infection

Conway, Jessica M.; Ribeiro, Ruy Miguel

doi:10.1016/j.coisb.2018.10.006

Title: Modeling the immune response to HIV infection

Journal Article · 08 November 2018 · Current Opinion in Systems Biology

DOI: https://doi.org/10.1016/j.coisb.2018.10.006 · OSTI ID:1764951

Conway, Jessica M. ^[1];

^[2]

Pennsylvania State Univ., University Park, PA (United States)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

The interplay between immune response and HIV is intensely studied via mathematical modeling, with significant insights but few direct answers. Here in this short review, we highlight advances and knowledge gaps across different aspects of immunity. In particular, we identify the innate immune response and its role in priming the adaptive response as ripe for modeling. The latter have been the focus of most modeling studies, but we also synthesize key outstanding questions regarding effector mechanisms of cellular immunity and development of broadly neutralizing antibodies. Thus far, most modeling studies aimed to infer general immune mechanisms; we foresee that significant progress will be made next by detailed quantitative fitting of models to data, and prediction of immune responses.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Los Alamos National Laboratory (LANL)

Sponsoring Organization:: National Institutes of Health (NIH); National Science Foundation (NSF); USDOE

Grant/Contract Number:: 89233218CNA000001

OSTI ID:: 1764951

Report Number(s):: LA-UR-18-27525

Journal Information:: Current Opinion in Systems Biology, Journal Name: Current Opinion in Systems Biology Vol. 12; ISSN 2452-3100

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (113)

Mechanisms of CD8 ⁺ T cell-mediated suppression of HIV/SIV replication McBrien, Julia Bergild; Kumar, Nitasha A.; Silvestri, Guido European Journal of Immunology, Vol. 48, Issue 6 https://doi.org/10.1002/eji.201747172	journal	March 2018
Modeling Deuterated Glucose Labeling of T-lymphocytes Ribeiro, R. Bulletin of Mathematical Biology, Vol. 64, Issue 2 https://doi.org/10.1006/bulm.2001.0282	journal	March 2002
The Disappearing CD4+T Cells in HIV Infection: a Case of Over-stimulation? Wick, David Journal of Theoretical Biology, Vol. 197, Issue 4 https://doi.org/10.1006/jtbi.1998.0891	journal	April 1999
Modeling Plasma Virus Concentration during Primary HIV Infection Stafford, Max A.; Corey, Lawrence; Cao, Yunzhen Journal of Theoretical Biology, Vol. 203, Issue 3 https://doi.org/10.1006/jtbi.2000.1076	journal	April 2000
The Dual Role of CD4 T Helper Cells in the Infection Dynamics of HIV and Their Importance for Vaccination Korthals Altes, H.; Wodarz, D.; Jansen, V. A. A. Journal of Theoretical Biology, Vol. 214, Issue 4 https://doi.org/10.1006/jtbi.2001.2483	journal	February 2002
Defining CTL-Induced Pathology: Implications for HIV Wodarz, Dominik; Krakauer, David C. Virology, Vol. 274, Issue 1 https://doi.org/10.1006/viro.2000.0399	journal	August 2000
Estimation and Prediction With HIV-Treatment Interruption Data Adams, B. M.; Banks, H. T.; Davidian, M. Bulletin of Mathematical Biology, Vol. 69, Issue 2 https://doi.org/10.1007/s11538-006-9140-6	journal	January 2007
Controlling IL-7 Injections in HIV-Infected Patients Pasin, Chloé; Dufour, François; Villain, Laura Bulletin of Mathematical Biology, Vol. 80, Issue 9 https://doi.org/10.1007/s11538-018-0465-8	journal	August 2018
HIV infection: focus on the innate immune cells Espíndola, Milena S.; Soares, Luana S.; Galvão-Lima, Leonardo J. Immunologic Research, Vol. 64, Issue 5-6 https://doi.org/10.1007/s12026-016-8862-2	journal	September 2016
Effector cytotoxic T lymphocyte numbers induced by vaccination should exceed levels in chronic infection for protection from HIV Altes, Hester Korthals; Price, David A.; Jansen, Vincent A. A. Vaccine, Vol. 20, Issue 1-2 https://doi.org/10.1016/S0264-410X(01)00318-8	journal	October 2001
Lymphocyte kinetics: the interpretation of labelling data Asquith, Becca; Debacq, Christophe; Macallan, Derek C. Trends in Immunology, Vol. 23, Issue 12 https://doi.org/10.1016/S1471-4906(02)02337-2	journal	December 2002
Mathematical models of viral latency Selinger, Christian; Katze, Michael G. Current Opinion in Virology, Vol. 3, Issue 4 https://doi.org/10.1016/j.coviro.2013.06.015	journal	August 2013
Immune impairment thresholds in HIV infection Iwami, Shingo; Nakaoka, Shinji; Takeuchi, Yasuhiro Immunology Letters, Vol. 123, Issue 2 https://doi.org/10.1016/j.imlet.2009.03.007	journal	April 2009
Mathematical modeling of viral kinetics under immune control during primary HIV-1 infection Burg, David; Rong, Libin; Neumann, Avidan U. Journal of Theoretical Biology, Vol. 259, Issue 4 https://doi.org/10.1016/j.jtbi.2009.04.010	journal	August 2009
Immune impairment in HIV infection: Existence of risky and immunodeficiency thresholds Iwami, Shingo; Miura, Tomoyuki; Nakaoka, Shinji Journal of Theoretical Biology, Vol. 260, Issue 4 https://doi.org/10.1016/j.jtbi.2009.06.023	journal	October 2009
Model with two types of CTL regulation and experiments on CTL dynamics Sergeev, R. A.; Batorsky, R. E.; Rouzine, I. M. Journal of Theoretical Biology, Vol. 263, Issue 3 https://doi.org/10.1016/j.jtbi.2009.11.003	journal	April 2010
Interpreting the effect of vaccination on steady state infection in animals challenged with Simian immunodeficiency virus Sergeev, R. A.; Batorsky, R. E.; Coffin, J. M. Journal of Theoretical Biology, Vol. 263, Issue 3 https://doi.org/10.1016/j.jtbi.2009.12.018	journal	April 2010
Paradoxical suppression of poly-specific broadly neutralizing antibodies in the presence of strain-specific neutralizing antibodies following HIV infection Ciupe, Stanca M.; De Leenheer, Patrick; Kepler, Thomas B. Journal of Theoretical Biology, Vol. 277, Issue 1 https://doi.org/10.1016/j.jtbi.2011.01.050	journal	May 2011
HIV evolution and progression of the infection to AIDS Huang, Gang; Takeuchi, Yasuhiro; Korobeinikov, Andrei Journal of Theoretical Biology, Vol. 307 https://doi.org/10.1016/j.jtbi.2012.05.013	journal	August 2012
Modeling interleukin-2-based immunotherapy in AIDS pathogenesis Joly, Marcel; Odloak, Darci Journal of Theoretical Biology, Vol. 335 https://doi.org/10.1016/j.jtbi.2013.06.019	journal	October 2013
A multi-scale mathematical modeling framework to investigate anti-viral therapeutic opportunities in targeting HIV-1 accessory proteins Suryawanshi, Gajendra W.; Hoffmann, Alexander Journal of Theoretical Biology, Vol. 386 https://doi.org/10.1016/j.jtbi.2015.08.032	journal	December 2015
T cell and reticular network co-dependence in HIV infection Donovan, Graham M.; Lythe, Grant Journal of Theoretical Biology, Vol. 395 https://doi.org/10.1016/j.jtbi.2016.01.040	journal	April 2016
Rates of HIV immune escape and reversion: implications for vaccination Davenport, Miles P.; Loh, Liyen; Petravic, Janka Trends in Microbiology, Vol. 16, Issue 12 https://doi.org/10.1016/j.tim.2008.09.001	journal	December 2008
Model for competition from self during passive immunization, with application to broadly neutralizing antibodies for HIV Ali Tabei, S. M.; Li, Ying; Weigert, Martin Vaccine, Vol. 30, Issue 3 https://doi.org/10.1016/j.vaccine.2011.11.048	journal	January 2012
Estimating the fraction of progeny virions that must incorporate APOBEC3G for suppression of productive HIV-1 infection Thangavelu, Pulari U.; Gupta, Vipul; Dixit, Narendra M. Virology, Vol. 449 https://doi.org/10.1016/j.virol.2013.11.026	journal	January 2014
Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection Chun, Tae-Wook; Carruth, Lucy; Finzi, Diana Nature, Vol. 387, Issue 6629 https://doi.org/10.1038/387183a0	journal	May 1997
Directly measured kinetics of circulating T lymphocytes in normal and HIV-1-infected humans Hellerstein, M.; Hanley, M. B.; Cesar, D. Nature Medicine, Vol. 5, Issue 1 https://doi.org/10.1038/4772	journal	January 1999
Antibody neutralization and escape by HIV-1 Wei, Xiping; Decker, Julie M.; Wang, Shuyi Nature, Vol. 422, Issue 6929 https://doi.org/10.1038/nature01470	journal	March 2003
HIV-1 adaptation to NK-cell-mediated immune pressure Alter, Galit; Heckerman, David; Schneidewind, Arne Nature, Vol. 476, Issue 7358 https://doi.org/10.1038/nature10237	journal	August 2011
Innate immunity against HIV-1 infection Altfeld, Marcus; Gale Jr, Michael Nature Immunology, Vol. 16, Issue 6 https://doi.org/10.1038/ni.3157	journal	May 2015
A quantitative basis for antiretroviral therapy for HIV-1 infection Jilek, Benjamin L.; Zarr, Melissa; Sampah, Maame E. Nature Medicine, Vol. 18, Issue 3 https://doi.org/10.1038/nm.2649	journal	February 2012
Immune checkpoint blockade in infectious diseases Wykes, Michelle N.; Lewin, Sharon R. Nature Reviews Immunology, Vol. 18, Issue 2 https://doi.org/10.1038/nri.2017.112	journal	October 2017
Prospective Study of Acute HIV-1 Infection in Adults in East Africa and Thailand Robb, Merlin L.; Eller, Leigh A.; Kibuuka, Hannah New England Journal of Medicine, Vol. 374, Issue 22 https://doi.org/10.1056/NEJMoa1508952	journal	June 2016
Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection Frost, S. D. W.; Wrin, T.; Smith, D. M. Proceedings of the National Academy of Sciences, Vol. 102, Issue 51 https://doi.org/10.1073/pnas.0504658102	journal	December 2005
Two types of cytotoxic lymphocyte regulation explain kinetics of immune response to human immunodeficiency virus Rouzine, I. M.; Sergeev, R. A.; Glushtsov, A. I. Proceedings of the National Academy of Sciences, Vol. 103, Issue 3 https://doi.org/10.1073/pnas.0510016103	journal	January 2006
Rapid evolution of the neutralizing antibody response to HIV type 1 infection Richman, D. D.; Wrin, T.; Little, S. J. Proceedings of the National Academy of Sciences, Vol. 100, Issue 7 https://doi.org/10.1073/pnas.0630530100	journal	March 2003
In vivo CD8+ T cell control of immunodeficiency virus infection in humans and macaques Asquith, B.; McLean, A. R. Proceedings of the National Academy of Sciences, Vol. 104, Issue 15 https://doi.org/10.1073/pnas.0700666104	journal	April 2007
Post-treatment control of HIV infection Conway, Jessica M.; Perelson, Alan S. Proceedings of the National Academy of Sciences, Vol. 112, Issue 17 https://doi.org/10.1073/pnas.1419162112	journal	April 2015
Competitive exclusion by autologous antibodies can prevent broad HIV-1 antibodies from arising Luo, Shishi; Perelson, Alan S. Proceedings of the National Academy of Sciences, Vol. 112, Issue 37 https://doi.org/10.1073/pnas.1505207112	journal	August 2015
Nonlinear partial differential equations and applications: In vivo dynamics of T cell activation, proliferation, and death in HIV-1 infection: Why are CD4+ but not CD8+ T cells depleted? Ribeiro, R. M.; Mohri, H.; Ho, D. D. Proceedings of the National Academy of Sciences, Vol. 99, Issue 24 https://doi.org/10.1073/pnas.242358099	journal	November 2002
Early establishment of a pool of latently infected, resting CD4+ T cells during primary HIV-1 infection Chun, T. -W.; Engel, D.; Berrey, M. M. Proceedings of the National Academy of Sciences, Vol. 95, Issue 15 https://doi.org/10.1073/pnas.95.15.8869	journal	July 1998
Anti-viral drug treatment along with immune activator IL-2: a control-based mathematical approach for HIV infection Chatterjee, Amar Nath; Roy, Priti Kumar International Journal of Control, Vol. 85, Issue 2 https://doi.org/10.1080/00207179.2011.643414	journal	February 2012
Turnover of CD4 ⁺ and CD8 ⁺ T Lymphocytes in HIV-1 Infection as Measured by Ki-67 Antigen Sachsenberg, Nicolas; Perelson, Alan S.; Yerly, Sabine The Journal of Experimental Medicine, Vol. 187, Issue 8 https://doi.org/10.1084/jem.187.8.1295	journal	April 1998
Dramatic Rise in Plasma Viremia after CD8 ⁺ T Cell Depletion in Simian Immunodeficiency Virus–infected Macaques Jin, Xia; Bauer, Daniel E.; Tuttleton, Sarah E. The Journal of Experimental Medicine, Vol. 189, Issue 6 https://doi.org/10.1084/jem.189.6.991	journal	March 1999
Increased Turnover of T Lymphocytes in HIV-1 Infection and Its Reduction by Antiretroviral Therapy Mohri, Hiroshi; Perelson, Alan S.; Tung, Keith The Journal of Experimental Medicine, Vol. 194, Issue 9 https://doi.org/10.1084/jem.194.9.1277	journal	October 2001
Innate Immune Activation in Primary HIV‐1 Infection Chang, J. Judy; Altfeld, Marcus The Journal of Infectious Diseases, Vol. 202, Issue S2 https://doi.org/10.1086/655657	journal	October 2010
Relative Significance of Different Pathways of Immune Reconstitution in HIV Type 1 Infection as Estimated by Mathematical Modeling Kaufmann, Gilbert R.; Zaunders, John; Murray, John AIDS Research and Human Retroviruses, Vol. 17, Issue 2 https://doi.org/10.1089/08892220150217238	journal	January 2001
Therapeutic Vaccine Against HIV, Viral Variability, Cytotoxic T Lymphocyte Epitopes, and Genetics of Patients Fleury, Herve; Tumiotto, Camille; Bellecave, Pantxika AIDS Research and Human Retroviruses, Vol. 34, Issue 1 https://doi.org/10.1089/aid.2017.0175	journal	January 2018
Proof-of-Principle for Immune Control of Global HIV-1 Reactivation In Vivo Smith, Nicola M. G.; Mlcochova, Petra; Watters, Sarah A. Clinical Infectious Diseases, Vol. 61, Issue 1 https://doi.org/10.1093/cid/civ219	journal	March 2015
Exploring the benefits of antibody immune response in HIV-1 infection using a discrete model Showa, S. P.; Nyabadza, F.; Hove-Musekwa, S. D. Mathematical Medicine and Biology, Vol. 33, Issue 2 https://doi.org/10.1093/imammb/dqv014	journal	April 2015
Humoral and Innate Antiviral Immunity as Tools to Clear Persistent HIV Infection Ferrari, Guido; Pollara, Justin; Tomaras, Georgia D. The Journal of Infectious Diseases, Vol. 215, Issue suppl_3 https://doi.org/10.1093/infdis/jiw555	journal	March 2017
Risks and benefits of structured antiretroviral drug therapy interruptions in HIV-1 infection Bonhoeffer, Sebastian; Rembiszewski, Michal; Ortiz, Gabriel M. AIDS, Vol. 14, Issue 15 https://doi.org/10.1097/00002030-200010200-00012	journal	January 2000
Depletion of naive CD4 T cells by CXCR4-using HIV-1 variants occurs mainly through increased T-cell death and activation Hazenberg, Mette D.; Otto, Sigrid A.; Hamann, Dörte AIDS, Vol. 17, Issue 10 https://doi.org/10.1097/00002030-200307040-00001	journal	January 2003
Model of HIV-1 Disease Progression Based on Virus-Induced Lymph Node Homing and Homing-Induced Apoptosis of CD4+ Lymphocytes Kirschner, Denise; Webb, G. F.; Cloyd, Miles Journal of Acquired Immune Deficiency Syndromes, Vol. 24, Issue 4 https://doi.org/10.1097/00042560-200008010-00010	journal	January 2000
Model of HIV-1 Disease Progression Based on Virus-Induced Lymph Node Homing and Homing-Induced Apoptosis of CD4+ Lymphocytes Kirschner, Denise; Webb, G. F.; Cloyd, Miles JAIDS Journal of Acquired Immune Deficiency Syndromes, Vol. 24, Issue 4 https://doi.org/10.1097/00126334-200008010-00010	journal	January 2000
Dynamic models of viral replication and latency Mohammadi, Pejman; Ciuffi, Angela; Beerenwinkel, Niko Current Opinion in HIV and AIDS, Vol. 10, Issue 2 https://doi.org/10.1097/COH.0000000000000136	journal	January 2015
Therapeutic HIV-1 vaccine: time for immunomodulation and combinatorial strategies Seddiki, Nabila; Lévy, Yves Current Opinion in HIV and AIDS, Vol. 13, Issue 2 https://doi.org/10.1097/COH.0000000000000444	journal	January 2018
Therapeutic vaccination for HIV: hopes and challenges Stephenson, Kathryn E. Current Opinion in HIV and AIDS, Vol. 13, Issue 5 https://doi.org/10.1097/COH.0000000000000491	journal	January 2018
The role of antigenic stimulation and cytotoxic T cell activity in regulating the long–term immunopathogenesis of HIV: mechanisms and clinical implications Frazer, Christophe; Ferguson, Neil M.; Wolf, Frank de Proceedings of the Royal Society of London. Series B: Biological Sciences, Vol. 268, Issue 1481 https://doi.org/10.1098/rspb.2001.1777	journal	October 2001
Estimating average cellular turnover from 5–bromo–2'–deoxyuridine (BrdU) measurements De Boer, Rob J.; Mohri, Hiroshi; Ho, David D. Proceedings of the Royal Society of London. Series B: Biological Sciences, Vol. 270, Issue 1517 https://doi.org/10.1098/rspb.2002.2316	journal	April 2003
The race between initial T–helper expansion and virus growth upon HIV infection influences polyclonality of the response and viral set–point Altes, H. Korthals; Ribeiro, R. M.; de Boer, R. J. Proceedings of the Royal Society of London. Series B: Biological Sciences, Vol. 270, Issue 1522 https://doi.org/10.1098/rspb.2003.2377	journal	July 2003
Integrating genealogical and dynamical modelling to infer escape and reversion rates in HIV epitopes Palmer, Duncan; Frater, John; Phillips, Rodney Proceedings of the Royal Society B: Biological Sciences, Vol. 280, Issue 1762 https://doi.org/10.1098/rspb.2013.0696	journal	July 2013
The challenges of modelling antibody repertoire dynamics in HIV infection Luo, Shishi; Perelson, Alan S. Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 370, Issue 1676 https://doi.org/10.1098/rstb.2014.0247	journal	September 2015
The dual role of dendritic cells in the immune response to human immunodeficiency virus type 1 infection Hogue, Ian B.; Bajaria, Seema H.; Fallert, Beth A. Journal of General Virology, Vol. 89, Issue 9 https://doi.org/10.1099/vir.0.83600-0	journal	September 2008
Identification and specificity of broadly neutralizing antibodies against HIV McCoy, Laura E.; Burton, Dennis R. Immunological Reviews, Vol. 275, Issue 1 https://doi.org/10.1111/imr.12484	journal	January 2017
The dynamics of simian immunodeficiency virus after depletion of CD8+ cells Cardozo, Erwing Fabian; Apetrei, Cristian; Pandrea, Ivona Immunological Reviews, Vol. 285, Issue 1 https://doi.org/10.1111/imr.12691	journal	August 2018
Current best estimates for the average lifespans of mouse and human leukocytes: reviewing two decades of deuterium-labeling experiments Borghans, José A. M.; Tesselaar, Kiki; de Boer, Rob J. Immunological Reviews, Vol. 285, Issue 1 https://doi.org/10.1111/imr.12693	journal	August 2018
Antigenic diversity thresholds and the development of AIDS Nowak, M.; Anderson, R.; McLean, A. Science, Vol. 254, Issue 5034 https://doi.org/10.1126/science.1683006	journal	November 1991
Reduction of HIV Concentration During Acute Infection: Independence from a Specific Immune Response Phillips, A. N. Science, Vol. 271, Issue 5248 https://doi.org/10.1126/science.271.5248.497	journal	January 1996
Notwithstanding Circumstantial Alibis, Cytotoxic T Cells Can Be Major Killers of HIV-1-Infected Cells Gadhamsetty, Saikrishna; Coorens, Tim; de Boer, Rob J. Journal of Virology, Vol. 90, Issue 16 https://doi.org/10.1128/JVI.00306-16	journal	May 2016
Predicting the Impact of CD8+ T Cell Polyfunctionality on HIV Disease Progression Graw, F.; Regoes, R. R. Journal of Virology, Vol. 88, Issue 17 https://doi.org/10.1128/JVI.00647-14	journal	June 2014
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 Ganusov, V. V.; Goonetilleke, N.; Liu, M. K. P. Journal of Virology, Vol. 85, Issue 20 https://doi.org/10.1128/JVI.00655-11	journal	August 2011
Estimating the Effectiveness of Simian Immunodeficiency Virus-Specific CD8+ T Cells from the Dynamics of Viral Immune Escape Mandl, Judith N.; Regoes, Roland R.; Garber, David A. Journal of Virology, Vol. 81, Issue 21 https://doi.org/10.1128/JVI.00946-07	journal	August 2007
Cytotoxic T-Lymphocyte Escape Mutations Identified by HLA Association Favor Those Which Escape and Revert Rapidly Fryer, Helen R.; Frater, John; Duda, Anna Journal of Virology, Vol. 86, Issue 16 https://doi.org/10.1128/JVI.07020-11	journal	June 2012
Rapid Viral Escape at an Immunodominant Simian-Human Immunodeficiency Virus Cytotoxic T-Lymphocyte Epitope Exacts a Dramatic Fitness Cost Fernandez, Caroline S.; Stratov, Ivan; De Rose, Robert Journal of Virology, Vol. 79, Issue 9 https://doi.org/10.1128/JVI.79.9.5721-5731.2005	journal	May 2005
Naïve and Memory Cell Turnover as Drivers of CCR5-to-CXCR4 Tropism Switch in Human Immunodeficiency Virus Type 1: Implications for Therapy Ribeiro, Ruy M.; Hazenberg, Mette D.; Perelson, Alan S. Journal of Virology, Vol. 80, Issue 2 https://doi.org/10.1128/JVI.80.2.802-809.2006	journal	January 2006
Naive T-Cell Dynamics in Human Immunodeficiency Virus Type 1 Infection: Effects of Highly Active Antiretroviral Therapy Provide Insights into the Mechanisms of Naive T-Cell Depletion Di Mascio, M.; Sereti, I.; Matthews, L. T. Journal of Virology, Vol. 80, Issue 6 https://doi.org/10.1128/JVI.80.6.2665-2674.2006	journal	February 2006
Control of Human Viral Infections by Natural Killer Cells Jost, Stephanie; Altfeld, Marcus Annual Review of Immunology, Vol. 31, Issue 1 https://doi.org/10.1146/annurev-immunol-032712-100001	journal	March 2013
Broadly Neutralizing Antibodies to HIV and Their Role in Vaccine Design Burton, Dennis R.; Hangartner, Lars Annual Review of Immunology, Vol. 34, Issue 1 https://doi.org/10.1146/annurev-immunol-041015-055515	journal	May 2016
The APOBEC3 Cytidine Deaminases: An Innate Defensive Network Opposing Exogenous Retroviruses and Endogenous Retroelements Chiu, Ya-Lin; Greene, Warner C. Annual Review of Immunology, Vol. 26, Issue 1 https://doi.org/10.1146/annurev.immunol.26.021607.090350	journal	April 2008
HIV-Specific Antibody Responses in HIV-Infected Patients: From a Monoclonal to a Polyclonal View Gallerano, Daniela; Cabauatan, Clarissa R.; Sibanda, Elopy N. International Archives of Allergy and Immunology, Vol. 167, Issue 4 https://doi.org/10.1159/000438484	journal	January 2015
HIV-1 proviral landscapes distinguish posttreatment controllers from noncontrollers Sharaf, Radwa; Lee, Guinevere Q.; Sun, Xiaoming Journal of Clinical Investigation, Vol. 128, Issue 9 https://doi.org/10.1172/JCI120549	journal	August 2018
Closing the gap between T-cell life span estimates from stable isotope-labeling studies in mice and humans Westera, Liset; Drylewicz, Julia; den Braber, Ineke Blood, Vol. 122, Issue 13 https://doi.org/10.1182/blood-2013-03-488411	journal	September 2013
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) Hazenberg, Mette D.; Stuart, James W. T. Cohen; Otto, Sigrid A. Blood, Vol. 95, Issue 1 https://doi.org/10.1182/blood.V95.1.249	journal	January 2000
Innate immunity against HIV: a priority target for HIV prevention research Borrow, Persephone; Shattock, Robin J.; Vyakarnam, Annapurna Retrovirology, Vol. 7, Issue 1 https://doi.org/10.1186/1742-4690-7-84	journal	October 2010
Inefficient Cytotoxic T Lymphocyte–Mediated Killing of HIV-1–Infected Cells In Vivo Asquith, Becca; Edwards, Charles T. T.; Lipsitch, Marc PLoS Biology, Vol. 4, Issue 4 https://doi.org/10.1371/journal.pbio.0040090	journal	March 2006
Estimating Costs and Benefits of CTL Escape Mutations in SIV/HIV Infection Ganusov, Vitaly V.; De Boer, Rob J. PLoS Computational Biology, Vol. 2, Issue 3 https://doi.org/10.1371/journal.pcbi.0020024	journal	March 2006
Dynamics of Immune Escape during HIV/SIV Infection Althaus, Christian L.; De Boer, Rob J. PLoS Computational Biology, Vol. 4, Issue 7 https://doi.org/10.1371/journal.pcbi.1000103	journal	July 2008
Modeling Latently Infected Cell Activation: Viral and Latent Reservoir Persistence, and Viral Blips in HIV-infected Patients on Potent Therapy Rong, Libin; Perelson, Alan S. PLoS Computational Biology, Vol. 5, Issue 10 https://doi.org/10.1371/journal.pcbi.1000533	journal	October 2009
Estimating the Stoichiometry of HIV Neutralization Magnus, Carsten; Regoes, Roland R. PLoS Computational Biology, Vol. 6, Issue 3 https://doi.org/10.1371/journal.pcbi.1000713	journal	March 2010
Quantification of the Relative Importance of CTL, B Cell, NK Cell, and Target Cell Limitation in the Control of Primary SIV-Infection Elemans, Marjet; Thiébaut, Rodolphe; Kaur, Amitinder PLoS Computational Biology, Vol. 7, Issue 3 https://doi.org/10.1371/journal.pcbi.1001103	journal	March 2011
The Route of HIV Escape from Immune Response Targeting Multiple Sites Is Determined by the Cost-Benefit Tradeoff of Escape Mutations Batorsky, Rebecca; Sergeev, Rinat A.; Rouzine, Igor M. PLoS Computational Biology, Vol. 10, Issue 10 https://doi.org/10.1371/journal.pcbi.1003878	journal	October 2014
Reconciling Estimates of Cell Proliferation from Stable Isotope Labeling Experiments Ahmed, Raya; Westera, Liset; Drylewicz, Julia PLOS Computational Biology, Vol. 11, Issue 10 https://doi.org/10.1371/journal.pcbi.1004355	journal	October 2015
Broad CTL Response in Early HIV Infection Drives Multiple Concurrent CTL Escapes Leviyang, Sivan; Ganusov, Vitaly V. PLOS Computational Biology, Vol. 11, Issue 10 https://doi.org/10.1371/journal.pcbi.1004492	journal	October 2015
Modeling the Slow CD4+ T Cell Decline in HIV-Infected Individuals Wang, Sunpeng; Hottz, Patricia; Schechter, Mauro PLOS Computational Biology, Vol. 11, Issue 12 https://doi.org/10.1371/journal.pcbi.1004665	journal	December 2015
Investigating the Consequences of Interference between Multiple CD8+ T Cell Escape Mutations in Early HIV Infection Garcia, Victor; Feldman, Marcus W.; Regoes, Roland R. PLOS Computational Biology, Vol. 12, Issue 2 https://doi.org/10.1371/journal.pcbi.1004721	journal	February 2016
Structured Observations Reveal Slow HIV-1 CTL Escape Roberts, Hannah E.; Hurst, Jacob; Robinson, Nicola PLOS Genetics, Vol. 11, Issue 2 https://doi.org/10.1371/journal.pgen.1004914	journal	February 2015
Host-Pathogen Coevolution and the Emergence of Broadly Neutralizing Antibodies in Chronic Infections Nourmohammad, Armita; Otwinowski, Jakub; Plotkin, Joshua B. PLOS Genetics, Vol. 12, Issue 7 https://doi.org/10.1371/journal.pgen.1006171	journal	July 2016
Timing of Immune Escape Linked to Success or Failure of Vaccination Reece, Jeanette C.; Loh, Liyen; Alcantara, Sheilajen PLoS ONE, Vol. 5, Issue 9 https://doi.org/10.1371/journal.pone.0012774	journal	September 2010
Vaccination-Induced Noncytolytic Effects in the Acute Phase of SHIV Infection Petravic, Janka; Davenport, Miles P. PLoS ONE, Vol. 5, Issue 11 https://doi.org/10.1371/journal.pone.0015083	journal	November 2010
Biologically-Directed Modeling Reflects Cytolytic Clearance of SIV-Infected Cells In Vivo in Macaques Wick, W. David; Yang, Otto O. PLoS ONE, Vol. 7, Issue 9 https://doi.org/10.1371/journal.pone.0044778	journal	September 2012
APOBEC3G-Augmented Stem Cell Therapy to Modulate HIV Replication: A Computational Study Hosseini, Iraj; Mac Gabhann, Feilim PLoS ONE, Vol. 8, Issue 5 https://doi.org/10.1371/journal.pone.0063984	journal	May 2013
Vaccination and Timing Influence SIV Immune Escape Viral Dynamics In Vivo Loh, Liyen; Petravic, Janka; Batten, C. Jane PLoS Pathogens, Vol. 4, Issue 1 https://doi.org/10.1371/journal.ppat.0040012	journal	January 2008
CD8+ T Cell Control of HIV—A Known Unknown Davenport, Miles P.; Petravic, Janka PLoS Pathogens, Vol. 6, Issue 1 https://doi.org/10.1371/journal.ppat.1000728	journal	January 2010
CD8+ Lymphocytes Control Viral Replication in SIVmac239-Infected Rhesus Macaques without Decreasing the Lifespan of Productively Infected Cells Klatt, Nichole R.; Shudo, Emi; Ortiz, Alex M. PLoS Pathogens, Vol. 6, Issue 1 https://doi.org/10.1371/journal.ppat.1000747	journal	January 2010
In Vivo CD8+ T-Cell Suppression of SIV Viremia Is Not Mediated by CTL Clearance of Productively Infected Cells Wong, Joseph K.; Strain, Matthew C.; Porrata, Rodin PLoS Pathogens, Vol. 6, Issue 1 https://doi.org/10.1371/journal.ppat.1000748	journal	January 2010
Post-Treatment HIV-1 Controllers with a Long-Term Virological Remission after the Interruption of Early Initiated Antiretroviral Therapy ANRS VISCONTI Study Sáez-Cirión, Asier; Bacchus, Charline; Hocqueloux, Laurent PLoS Pathogens, Vol. 9, Issue 3 https://doi.org/10.1371/journal.ppat.1003211	journal	March 2013
Optimal Combinations of Broadly Neutralizing Antibodies for Prevention and Treatment of HIV-1 Clade C Infection Wagh, Kshitij; Bhattacharya, Tanmoy; Williamson, Carolyn PLOS Pathogens, Vol. 12, Issue 3 https://doi.org/10.1371/journal.ppat.1005520	journal	March 2016
Predicting HIV-1 transmission and antibody neutralization efficacy in vivo from stoichiometric parameters Brandenberg, Oliver F.; Magnus, Carsten; Rusert, Peter PLOS Pathogens, Vol. 13, Issue 5 https://doi.org/10.1371/journal.ppat.1006313	journal	May 2017
HIV-1 adaptation to NK cell-mediated immune pressure Elemans, Marjet; Boelen, Lies; Rasmussen, Michael PLOS Pathogens, Vol. 13, Issue 6 https://doi.org/10.1371/journal.ppat.1006361	journal	June 2017
Pneumocystis Pneumonia—Los Angeles Gottlieb, Michael S. American Journal of Public Health, Vol. 96, Issue 6 https://doi.org/10.2105/AJPH.96.6.980	journal	June 2006
The Effect of Interference on the CD8+ T Cell Escape Rates in HIV Garcia, Victor; Regoes, Roland Robert Frontiers in Immunology, Vol. 5 https://doi.org/10.3389/fimmu.2014.00661	journal	January 2015
Kinetics of HIV-Specific CTL Responses Plays a Minimal Role in Determining HIV Escape Dynamics Yang, Yiding; Ganusov, Vitaly V. Frontiers in Immunology, Vol. 9 https://doi.org/10.3389/fimmu.2018.00140	journal	February 2018

Cited By (3)

Immunological Paradigms, Mechanisms, and Models: Conceptual Understanding Is a Prerequisite to Effective Modeling Grossman, Zvi Frontiers in Immunology, Vol. 10 https://doi.org/10.3389/fimmu.2019.02522	journal	November 2019
Modeling HIV Dynamics Under Combination Therapy with Inducers and Antibodies Yan, Chao; Wang, Wendi Bulletin of Mathematical Biology, Vol. 81, Issue 7 https://doi.org/10.1007/s11538-019-00621-0	journal	June 2019
Immunological Paradigms, Mechanisms, and Models: Conceptual Understanding Is a Prerequisite to Effective Modeling Grossman, Zvi Frontiers in Immunology, Vol. 10 https://doi.org/10.3389/fimmu.2019.02522	journal	November 2019

Similar Records

Immunization of cows with HIV envelope trimers generates broadly neutralizing antibodies to the V2-apex from the ultralong CDRH3 repertoire

Journal Article · 2024 · PLoS Pathogens · OSTI ID:2582882

Altman, Pilar; Ozorowski, Gabriel; Stanfield, Robyn; +20 more

Modeling the Effects of Morphine-Altered Virus Specific Antibody Responses on HIV/SIV Dynamics

Journal Article · 2019 · Scientific Reports · OSTI ID:1619505

Mutua, Jones M.; Perelson, Alan S.; Kumar, Anil; +1 more

Immunization of neonatal mice with LAMP/p55 HIV gag DNA elicits robust immune responses that last to adulthood

Journal Article · 2010 · Virology · OSTI ID:21417250

Ordonhez Rigato, Paula; Maciel, Milton; Goldoni, Adriana Leticia; +6 more

Related Subjects

60 APPLIED LIFE SCIENCES
Biological Science

Title: Modeling the immune response to HIV infection

Citation Formats

References (113)

Cited By (3)

Similar Records

Related Subjects