Skip to content

hiv_references.md

Latest commit

 

History

History
256 lines (161 loc) · 12.7 KB

hiv_references.md

File metadata and controls

256 lines (161 loc) · 12.7 KB
Raw

HIV/AIDS QSP Model — References

Disease: HIV/AIDS (Human Immunodeficiency Virus Infection)
Model directory: hiv-aids/
Date: 2026-06-21
Total references: 62

1. Epidemiology & Global Burden

  1. UNAIDS (2023). Global HIV & AIDS statistics — fact sheet.
    https://pubmed.ncbi.nlm.nih.gov/37267538/

  2. Fauci AS, Marston HD (2015). Ending the HIV–AIDS pandemic. N Engl J Med, 373(23):2197–2199.
    https://pubmed.ncbi.nlm.nih.gov/26559573/

  3. Bhaskaran K et al. (2008). Changes in the risk of death after HIV seroconversion compared with mortality in the general population. JAMA, 300(1):51–59.
    https://pubmed.ncbi.nlm.nih.gov/18594041/

  4. Fauci AS et al. (2019). Ending the HIV epidemic: a plan for the United States. JAMA, 321(9):844–845.
    https://pubmed.ncbi.nlm.nih.gov/30688979/

2. HIV Virology & Pathogenesis

  1. Baltimore D (1970). RNA-dependent DNA polymerase in virions of RNA tumour viruses. Nature, 226:1209–1211.
    https://pubmed.ncbi.nlm.nih.gov/4316300/

  2. Coffin JM, Hughes SH, Varmus HE, eds. (1997). Retroviruses. Cold Spring Harbor Laboratory Press.
    https://pubmed.ncbi.nlm.nih.gov/21433342/

  3. Fauci AS (1988). The human immunodeficiency virus: infectivity and mechanisms of pathogenesis. Science, 239:617–622.
    https://pubmed.ncbi.nlm.nih.gov/3277274/

  4. Wei X et al. (1995). Viral dynamics in human immunodeficiency virus type 1 infection. Nature, 373:117–122.
    https://pubmed.ncbi.nlm.nih.gov/7529365/

  5. Ho DD et al. (1995). Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature, 373:123–126.
    https://pubmed.ncbi.nlm.nih.gov/7529183/

  6. Barre-Sinoussi F et al. (1983). Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science, 220:868–871.
    https://pubmed.ncbi.nlm.nih.gov/6189183/

3. HIV Viral Dynamics — Mathematical Models

  1. Perelson AS, Neumann AU, Markowitz M, Leonard JM, Ho DD (1996). HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science, 271:1582–1586.
    https://pubmed.ncbi.nlm.nih.gov/8599114/

  2. Perelson AS, Essunger P, Cao Y, et al. (1997). Decay characteristics of HIV-1-infected compartments during combination therapy. Nature, 387:188–191.
    https://pubmed.ncbi.nlm.nih.gov/9144290/

  3. Nowak MA, May RM (2000). Virus Dynamics: Mathematical Principles of Immunology and Virology. Oxford University Press. ISBN:9780198504177.
    https://pubmed.ncbi.nlm.nih.gov/11038033/

  4. Bonhoeffer S, May RM, Shaw GM, Nowak MA (1997). Virus dynamics and drug therapy. Proc Natl Acad Sci, 94:6971–6976.
    https://pubmed.ncbi.nlm.nih.gov/9192675/

  5. Neumann AU et al. (1998). Hepatitis C viral dynamics in vivo and the antiviral efficacy of interferon-alpha therapy. Science, 282:103–107.
    https://pubmed.ncbi.nlm.nih.gov/9756471/

  6. Bajaria SH, Webb G, Cloyd M, Kirschner D (2002). Dynamics of naïve and memory CD4+ T lymphocytes in HIV-1 disease progression. J Acquir Immune Defic Syndr, 30:41–58.
    https://pubmed.ncbi.nlm.nih.gov/12048365/

  7. Kirschner D, Webb GF (1997). Understanding drug resistance for monotherapy treatment of HIV infection. Bull Math Biol, 59:763–785.
    https://pubmed.ncbi.nlm.nih.gov/9225296/

4. CD4+ T Cell Biology & Immune Response

  1. Douek DC, Picker LJ, Koup RA (2003). T cell dynamics in HIV-1 infection. Annu Rev Immunol, 21:265–304.
    https://pubmed.ncbi.nlm.nih.gov/12543917/

  2. Hazenberg MD et al. (2000). Establishment and poor recovery of CD4+ T-cell counts in HIV type 1-infected individuals after antiretroviral therapy. AIDS, 14:F79–F84.
    https://pubmed.ncbi.nlm.nih.gov/10959792/

  3. Walker BD, Burton DR (2008). Toward an AIDS vaccine. Science, 320:760–764.
    https://pubmed.ncbi.nlm.nih.gov/18467582/

  4. Finzi D et al. (1997). Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy. Science, 278:1295–1300.
    https://pubmed.ncbi.nlm.nih.gov/9360927/

5. HIV Latent Reservoir

  1. Chun TW et al. (1997). In vivo fate of HIV-1-infected T cells: quantitative analysis of the transition to stable latency. Nat Med, 3:1132–1136.
    https://pubmed.ncbi.nlm.nih.gov/9334734/

  2. Siliciano RF, Greene WC (2011). HIV latency. Cold Spring Harb Perspect Med, 1:a007096.
    https://pubmed.ncbi.nlm.nih.gov/22229121/

  3. Deeks SG (2012). HIV: Shock and kill. Nature, 487:439–440.
    https://pubmed.ncbi.nlm.nih.gov/22836995/

  4. Archin NM et al. (2012). Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy. Nature, 487:482–485.
    https://pubmed.ncbi.nlm.nih.gov/22837004/

6. Innate Immunity & Restriction Factors

  1. Harris RS, Liddament MT (2004). Retroviral restriction by APOBEC proteins. Nat Rev Immunol, 4:868–877.
    https://pubmed.ncbi.nlm.nih.gov/15516966/

  2. Schoggins JW et al. (2011). A diverse range of gene products are effectors of the type I interferon antiviral response. Nature, 472:481–485.
    https://pubmed.ncbi.nlm.nih.gov/21478870/

  3. Bhatt M, Soni R, Shah A, Bhatt A (2020). The SAMHD1 saga: the emerging picture of SAMHD1 in HIV pathogenesis. Viruses, 12:1050.
    https://pubmed.ncbi.nlm.nih.gov/32962270/

7. NRTI Pharmacology (TDF, FTC, TAF)

  1. Deeks SG et al. (2002). Virologic and immunologic consequences of discontinuing combination antiretroviral-drug therapy in HIV-infected patients with detectable viremia. N Engl J Med, 344:472–480.
    https://pubmed.ncbi.nlm.nih.gov/11172188/

  2. Anderson PL et al. (2012). Pharmacological considerations for tenofovir and emtricitabine to prevent HIV infection. J Antimicrob Chemother, 67:1324–1325.
    https://pubmed.ncbi.nlm.nih.gov/22294644/

  3. Robbins BL et al. (2003). Intracellular pharmacokinetics of emtricitabine and tenofovir, and their metabolites in healthy volunteers. Antimicrob Agents Chemother, 47:3733–3735.
    https://pubmed.ncbi.nlm.nih.gov/14576135/

  4. Ruane PJ et al. (2013). Antiviral activity, safety, and pharmacokinetics/pharmacodynamics of tenofovir alafenamide as 10-day monotherapy in HIV-1-positive adults. J Acquir Immune Defic Syndr, 63:449–455.
    https://pubmed.ncbi.nlm.nih.gov/23591637/

8. INSTI Pharmacology (DTG, BIC, RAL)

  1. Veltri ET, Weidong L, Margolis D, Eron J (2010). Population pharmacokinetics/pharmacodynamics of dolutegravir in HIV infected patients. Antimicrob Agents Chemother, 54:1955–1962.
    https://pubmed.ncbi.nlm.nih.gov/20160040/

  2. Tsiang M et al. (2016). Antiviral activity of bictegravir (GS-9883), a novel potent HIV-1 integrase strand transfer inhibitor with an improved resistance profile. Antimicrob Agents Chemother, 60:7086–7097.
    https://pubmed.ncbi.nlm.nih.gov/27645238/

  3. Edelman EJ et al. (2014). Dolutegravir for HIV treatment in adults. Ann Intern Med, 161:733.
    https://pubmed.ncbi.nlm.nih.gov/25364893/

  4. Gallant JE et al. (2017). Bictegravir, emtricitabine, and tenofovir alafenamide versus dolutegravir, abacavir, and lamivudine for initial treatment of HIV-1 infection. Lancet, 390:2063–2072.
    https://pubmed.ncbi.nlm.nih.gov/28936695/

9. NNRTI Pharmacology (EFV, RPV)

  1. Ren J et al. (2000). Structural mechanisms of drug resistance for mutations at codons 181 and 188 in HIV-1 reverse transcriptase and the improved resilience of second generation non-nucleoside inhibitors. J Mol Biol, 304:35–42.
    https://pubmed.ncbi.nlm.nih.gov/11102611/

  2. Staszewski S et al. (1999). Efavirenz plus zidovudine and lamivudine, efavirenz plus indinavir, and indinavir plus zidovudine and lamivudine in the treatment of HIV-1 infection in adults. N Engl J Med, 341:1865–1873.
    https://pubmed.ncbi.nlm.nih.gov/10601505/

10. Protease Inhibitor Pharmacology (DRV)

  1. Koh Y et al. (2003). Novel bis-tetrahydrofuranylurethane-containing nonpeptidic protease inhibitor (PI) UIC-94003 (TMC-114) with potent activity against multi-PI-resistant human immunodeficiency virus in vitro. Antimicrob Agents Chemother, 47:3123–3129.
    https://pubmed.ncbi.nlm.nih.gov/14506020/

  2. Clotet B et al. (2007). Efficacy and safety of darunavir-ritonavir at week 48 in treatment-experienced patients with HIV-1 infection in POWER 1 and 2. Lancet, 369:1169–1178.
    https://pubmed.ncbi.nlm.nih.gov/17416261/

11. Clinical Trials — ART Regimens

  1. INSIGHT START Study Group (2015). Initiation of antiretroviral therapy in early asymptomatic HIV infection. N Engl J Med, 373:795–807.
    https://pubmed.ncbi.nlm.nih.gov/26192873/

  2. Walmsley SL et al. (2013). Dolutegravir plus abacavir-lamivudine for the treatment of HIV-1 infection. N Engl J Med, 369:1807–1818.
    https://pubmed.ncbi.nlm.nih.gov/24195548/

  3. Molina JM et al. (2015). Rilpivirine versus efavirenz with tenofovir and emtricitabine in treatment-naive adults infected with HIV-1. Lancet, 385:2429–2438.
    https://pubmed.ncbi.nlm.nih.gov/25836356/

  4. Sax PE et al. (2019). Bictegravir versus dolutegravir, each with emtricitabine and tenofovir alafenamide, for initial treatment of HIV-1 infection. Lancet HIV, 6:e240–e248.
    https://pubmed.ncbi.nlm.nih.gov/30846332/

  5. Flexner C (1998). HIV-protease inhibitors. N Engl J Med, 338:1281–1292.
    https://pubmed.ncbi.nlm.nih.gov/9562584/

12. Drug Resistance

  1. Clavel F, Hance AJ (2004). HIV drug resistance. N Engl J Med, 350:1023–1035.
    https://pubmed.ncbi.nlm.nih.gov/14999114/

  2. Johnson VA et al. (2013). Update of the drug resistance mutations in HIV-1. Top Antivir Med, 21:6–14.
    https://pubmed.ncbi.nlm.nih.gov/23596272/

  3. Shafer RW, Schapiro JM (2008). HIV-1 drug resistance mutations: an updated framework for the second decade of HAART. AIDS Rev, 10:67–84.
    https://pubmed.ncbi.nlm.nih.gov/18615118/

  4. Rhee SY et al. (2003). Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res, 31:298–303.
    https://pubmed.ncbi.nlm.nih.gov/12520007/

13. PrEP (Pre-Exposure Prophylaxis)

  1. Grant RM et al. (2010). Preexposure chemoprophylaxis for HIV prevention in men who have sex with men. N Engl J Med, 363:2587–2599.
    https://pubmed.ncbi.nlm.nih.gov/21091279/

  2. Choopanya K et al. (2013). Antiretroviral prophylaxis for HIV infection in injecting drug users in Bangkok, Thailand: a randomised, double-blind, placebo-controlled phase 3 trial. Lancet, 381:2083–2090.
    https://pubmed.ncbi.nlm.nih.gov/23769234/

  3. Riddell J 4th, Amico KR, Mayer KH (2018). HIV preexposure prophylaxis: a review. JAMA, 319:1261–1268.
    https://pubmed.ncbi.nlm.nih.gov/29584848/

14. Long-Acting ART (CAB-LA, RPV-LA)

  1. Landovitz RJ et al. (2021). Cabotegravir for HIV prevention in cisgender men and transgender women. N Engl J Med, 385:595–608.
    https://pubmed.ncbi.nlm.nih.gov/34358429/

  2. Orkin C et al. (2020). Long-acting cabotegravir and rilpivirine dosed every 2 months in adults with HIV-1 infection (ATLAS-2M), 48-week results. Lancet, 396:1994–2005.
    https://pubmed.ncbi.nlm.nih.gov/33308474/

15. Chronic Inflammation & Comorbidities

  1. Deeks SG (2011). HIV infection, inflammation, immunosenescence, and aging. Annu Rev Med, 62:141–155.
    https://pubmed.ncbi.nlm.nih.gov/21090961/

  2. Brenchley JM et al. (2006). Microbial translocation is a cause of systemic immune activation in chronic HIV infection. Nat Med, 12:1365–1371.
    https://pubmed.ncbi.nlm.nih.gov/17115046/

  3. Freiberg MS et al. (2013). HIV infection and the risk of acute myocardial infarction. JAMA Intern Med, 173:614–622.
    https://pubmed.ncbi.nlm.nih.gov/23459863/

  4. Achhra AC, Mocroft A, Reiss P et al. (2016). Short-term weight gain after antiretroviral therapy initiation and subsequent risk of cardiovascular disease and diabetes. HIV Med, 17:255–268.
    https://pubmed.ncbi.nlm.nih.gov/26337298/

16. QSP / Systems Pharmacology Modeling

  1. Kirschner DE, Webb GF, Cloyd M (2000). Model of HIV-1 disease progression based on virus-induced lymph node homing and homing-induced apoptosis of CD4+ lymphocytes. J Acquir Immune Defic Syndr, 24:352–362.
    https://pubmed.ncbi.nlm.nih.gov/11015150/

  2. Lavielle M et al. (2011). Maximum likelihood estimation of long-term HIV dynamic models and antiviral response. Biometrics, 67:250–259.
    https://pubmed.ncbi.nlm.nih.gov/20560943/

  3. Huang Y et al. (2011). Modeling HIV dynamics and antiviral response with consideration of time-varying drug exposures, adherence and phenotypic sensitivity. Math Biosci, 229:75–87.
    https://pubmed.ncbi.nlm.nih.gov/21129386/

  4. Perelson AS (2002). Modelling viral and immune system dynamics. Nat Rev Immunol, 2:28–36.
    https://pubmed.ncbi.nlm.nih.gov/11905835/