# Introduction to HIV

0. Barré-Sinoussi F, Chermann JC, Rey F et al. [Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS).](http://www.ncbi.nlm.nih.gov/pubmed/6189183)  Science 1983; 220(4599):868-71.
0. NIH publication: [The evidence that HIV causes AIDS](http://www3.niaid.nih.gov/topics/HIVAIDS/Understanding/howHIVCausesAIDS/HIVcausesAIDS.htm)
0. AIDS Denialism: [The “evidence” against HIV as the cause of AIDS](http://www.virusmyth.net)
0. Ho DD and Bieniasz PD. [HIV-1 at 25.](http://www.ncbi.nlm.nih.gov/pubmed/18485860)  Cell. 2008; 133(4):561-5.
0. McMichael AJ, Borrow P, Tomaras GD, Goonetilleke N, Haynes BF. [The immune response during acute HIV-1 infection: clues for vaccine development.](http://www.ncbi.nlm.nih.gov/pubmed/20010788)  Nat Rev Immunol 2010; 10:11-23. Review
0. Kirchhoff F. [Immune evasion and counteraction of restriction factors by HIV-1 and other primate lentiviruses.](http://www.ncbi.nlm.nih.gov/pubmed/20638642)   Cell Host Microbe. 2010; 8(1):55-67. Review
0. Walker BD and Burton DR. [Toward an AIDS vaccine.](http://www.sciencemag.org/cgi/content/short/320/5877/760)   Science. 2008; 320(5877):760-4. Review.
0. Richman DD, Margolis DM, Delaney M, Greene WC, Hazuda D, Pomerantz RJ. [The challenge of finding a cure for HIV infection.](http://www.sciencemag.org/cgi/content/short/323/5919/1304)   Science. 2009; 323(5919):1304-7. Review.
0. Barouch DH and Korber B. [HIV-1 vaccine development after STEP.](http://www.ncbi.nlm.nih.gov/pubmed/20059334)  Annu Rev Med. 2010; 61:153-67. Review.

# Host and viral factors influencing disease progression

0. Mellors JW, Rinaldo CR Jr, Gupta P, White RM, Todd JA, Kingsley LA. [Prognosis in HIV-1 infection predicted by the quantity of virus in plasma.](http://www.ncbi.nlm.nih.gov/pubmed/8638160)  Science. 1996; 272(5265):1167-70.
0. Dean M, Carrington M, Winkler C et al. [Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene.](http://www.ncbi.nlm.nih.gov/pubmed/8791590)  Science. 1996; 273(5283):1856-62.
0. Carrington M and O'Brien SJ. [The influence of HLA genotype on AIDS.](http://www.annualreviews.org/doi/full/10.1146/annurev.med.54.101601.152346)  Annu Rev Med 2003; 54:535-551.
0. Fellay J, Shianna KV, Ge D et al. [A whole-genome association study of major determinants for host control of HIV-1.](http://www.sciencemag.org/cgi/content/abstract/1143767)  Science 2007; 317:944-947.

# HIV treatment and prevention

0. Palella FJ, Jr., Delaney KM, Moorman AC et al. [Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection.](http://www.nejm.org/doi/full/10.1056/NEJM199803263381301)  HIV Outpatient Study Investigators. N Engl J Med 1998; 338:853-860.
0. Shafer, RW.  [Assays for Antiretroviral Resistance  (HIV InSite Knowledge Base)](http://hivinsite.ucsf.edu/InSite?page=kb-00&doc=kb-02-02-03)
0. Thompson MA, Aberg JA, Cahn P, et al. [Antiretroviral treatment of adult HIV infection: 2010 recommendations of the International AIDS Society-USA panel.](http://www.ncbi.nlm.nih.gov/pubmed/20639566)   JAMA. 2010; 304(3):321-33.
0. Montaner JS, Lima VD, Barrios R et al. [Association of highly active antiretroviral therapy coverage, population viral load, and yearly new HIV diagnoses in British Columbia, Canada: a population-based study.](http://www.thelancet.com/journals/lancet/article/PIIS0140-6736%2810%2960936-1/abstract)  Lancet. 2010; Jul 16 [Epub ahead of print]
0. Rerks-Ngarm S, Pitisuttithum P, Nitayaphan S et al [Vaccination with ALVAC and AIDSVAX to Prevent HIV-1 Infection in Thailand.](http://www.nejm.org/doi/full/10.1056/NEJMoa0908492)  N Engl J Med. 2009; 361(23):2209-20.
0. Karim QA, Karim SS, Frohlich JA, et al on behalf of the CAPRISA 004 Trial Group. [Effectiveness and Safety of Tenofovir Gel, an Antiretroviral Microbicide, for the Prevention of HIV Infection in Women.](http://www.sciencemag.org/cgi/content/abstract/329/5996/1168)  Science. 2010 Jul 19 [Epub ahead of print]

# Molecular epidemiology of HIV/AIDS and it's origins

0. Taylor BS, Sobieszczyk ME, McCutchan FE, Hammer SM. [The challenge of HIV-1 subtype diversity.](http://www.ncbi.nlm.nih.gov/pubmed/18403767)  N Engl J Med. 2008; 358(15):1590-602.
0. Korber B, Muldoon M, Theiler J, et al. [Timing the ancestor of the HIV-1 pandemic strains.](http://www.sciencemag.org/cgi/content/abstract/288/5472/1789)   Science 2000; 288(5472):1789-96.
0. Worobey M, Gemmel M, Teuwen DE et al. [Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.](http://www.nature.com/nature/journal/v455/n7213/abs/nature07390.html)  Nature 2008; 455(7213):661-4.

# CD8 T-cell responses to HIV

0. Walker BD, Chakrabarti S, Moss B et al. [HIV-specific cytotoxic T lymphocytes in seropositive individuals.](http://www.ncbi.nlm.nih.gov/pubmed/3496541)  Nature 1987; 328(6128):345-8.
0. Borrow P, Lewicki H, Hahn BH, Shaw GM, Oldstone MB. [Virus-specific CD8+ cytotoxic T-lymphocyte activity associated with control of viremia in primary human immunodeficiency virus type 1 infection.](http://www.ncbi.nlm.nih.gov/pubmed/8057491)  J Virol 1994; 68:6103-6110
0. Safrit JT, Andrews CA, Zhu T, Ho DD, Koup RA. [Characterization of human immunodeficiency virus type 1-specific cytotoxic T lymphocyte clones isolated during acute seroconversion: recognition of autologous virus sequences within a conserved immunodominant epitope.](http://www.ncbi.nlm.nih.gov/pubmed/8294860)  J Exp Med 1994; 179(2):463-72.
0. Schmitz JE, Kuroda MJ, Santra S, et al. [Control of viremia in simian immunodeficiency virus infection by CD8+ lymphocytes.](http://www.ncbi.nlm.nih.gov/pubmed/9933172)  Science 1999; 283:857-860.

# HIV evolution and CTL immune escape

0. Shankarappa R, Margolick JB, Gange SJ, et al. [Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection.](http://www.ncbi.nlm.nih.gov/pubmed/10559367)  J Virol 1999; 73:10489-10502.
0. Kelleher AD, Long C, Holmes EC, et al. [Clustered mutations in HIV-1 gag are consistently required for escape from HLA-B27-restricted cytotoxic T lymphocyte responses.](http://www.ncbi.nlm.nih.gov/pubmed/11157057)  J Exp Med 2001; 193:375-386
0. Goulder PJ, Watkins DI. [HIV and SIV CTL escape: implications for vaccine design.](http://www.ncbi.nlm.nih.gov/pubmed/15286729)  Nat Rev Immunol 2004; 4:630-640.
0. Draenert R, Allen TM, Liu Y, et al. [Constraints on HIV-1 evolution and immunodominance revealed in monozygotic adult twins infected with the same virus.](http://www.ncbi.nlm.nih.gov/pubmed/16533886)  J Exp Med 2006; 203:529-539.
0. Leslie AJ, Pfafferott KJ, Chetty P, et al. [HIV evolution: CTL escape mutation and reversion after transmission.](http://www.nature.com/nm/journal/v10/n3/abs/nm992.html)  Nat Med 2004; 10:282-289
0. Moore CB, John M, James IR, Christiansen FT, Witt CS, Mallal SA. [Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level.](http://www.ncbi.nlm.nih.gov/pubmed/12029127)  Science 2002; 296:1439-1443.
0. Bhattacharya T, Daniels M, Heckerman D, Foley B, Frahm N, Kadie C, et al. [Founder effects in the assessment of HIV polymorphisms and HLA allele associations.](http://www.sciencemag.org/cgi/content/short/sci;315/5818/1583)  Science 2007; 315:1583-1586.
0. Brumme ZL, John M, Carlson JM, Brumme CJ, Chan D, Brockman MA, et al. [HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef Proteins.](http://www.ncbi.nlm.nih.gov/pubmed/19690614)  PloS ONE 2009; 4:e6687.
0. Kawashima Y, Pfafferott K, Frater J, Matthews P, Payne R, Addo M, et al. [Adaptation of HIV-1 to human leukocyte antigen class I.](http://www.ncbi.nlm.nih.gov/pubmed/19242411)  Nature 2009; 458:641-645.

# Impact of CTL escape on HIV fitness

0. Zhang WH, Hockley DJ, Nermut MV, Jones IM. [Functional consequences of mutations in HIV-1 Gag p55 selected by CTL pressure.](http://www.ncbi.nlm.nih.gov/pubmed/8030265)  Virology. 1994; 203(1):101-5.
0. Nietfield W, Bauer M, Fevrier M, et al. [Sequence constraints and recognition by CTL of an HLA-B27-restricted HIV-1 gag epitope.](http://www.ncbi.nlm.nih.gov/pubmed/7868892)  J Immunol. 1995; 154(5):2189-97.
0. Schneidewind A, Brockman MA, Yang R et al. [Escape from the dominant HLA-B27-restricted cytotoxic T-lymphocyte response in Gag is associated with a dramatic reduction in human immunodeficiency virus type 1 replication.](http://www.ncbi.nlm.nih.gov/pubmed/17804494)  J Virol 2007; 81:12382-12393.
0. Brockman MA, Schneidewind A, Lahaie M et al. [Escape and compensation from early HLA-B57-mediated cytotoxic T-lymphocyte pressure on human immunodeficiency virus type 1 Gag alter capsid interactions with cyclophilin A.](http://www.ncbi.nlm.nih.gov/pubmed/17728232)  J Virol 2007; 81:12608-12618.
0. Ariën KK, Vanham G, Arts EJ. [Is HIV-1 evolving to a less virulent form in humans?](http://www.ncbi.nlm.nih.gov/pubmed/17203103)  Nat Rev Microbiol. 2007; 5(2):141-51. Review
0. Troyer RM, McNevin J, Liu Y et al. [Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response.](http://www.ncbi.nlm.nih.gov/pubmed/19343217)  PLoS Pathog. 2009; 5(4):e1000365.
0. Chopera DR, Woodman Z, Mlisana K et al; CAPRISA 002 Study Team. [Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage.](http://www.ncbi.nlm.nih.gov/pubmed/18369479)  PLoS Pathog. 2008; 4(3):e1000033.
0. Goepfert PA, Lumm W, Farmer P et al.  [Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients.](http://www.ncbi.nlm.nih.gov/pubmed/18426987)  J Exp Med. 2008; 205(5):1009-17.

# T-cell receptors and CTL function

0. Kalams SA, Johnson RP, Trocha AK et al. [Longitudinal analysis of T cell receptor (TCR) gene usage by human immunodeficiency virus 1 envelope-specific cytotoxic T lymphocyte clones reveals a limited TCR repertoire.](http://www.ncbi.nlm.nih.gov/pubmed/8145043)   J Exp Med. 1994; 179(4):1261-71.
0. Meyer-Olson D, Brady KW, Bartman MT et al.  [Fluctuations of functionally distinct CD8+ T-cell clonotypes demonstrate flexibility of the HIV-specific TCR repertoire.](http://www.ncbi.nlm.nih.gov/pubmed/16322475)  Blood. 2006; 107(6):2373-83.
0. Yu XG, Lichterfeld M, Chetty S et al. [Mutually exclusive T-cell receptor induction and differential susceptibility to human immunodeficiency virus type 1 mutational escape associated with a two-amino-acid difference between HLA class I subtypes.](http://www.ncbi.nlm.nih.gov/pubmed/17121793)  J Virol. 2007; 81(4):1619-31.
0. Turnbull EL, Lopes AR, Jones NA et al. [HIV-1 epitope-specific CD8+ T cell responses strongly associated with delayed disease progression cross-recognize epitope variants efficiently.](http://www.ncbi.nlm.nih.gov/pubmed/16670322)  J Immunol. 2006; 176(10):6130-46.
0. Yang OO, Church J, Kitchen CM et al. [Genetic and stochastic influences on the interaction of human immunodeficiency virus type 1 and cytotoxic T lymphocytes in identical twins.](http://www.ncbi.nlm.nih.gov/pubmed/16306608)   J Virol. 2005; 79(24):15368-75.
0. Price DA, Asher TE, Wilson NA et al. [Public clonotype usage identifies protective Gag-specific CD8+ T cell responses in SIV infection.](http://www.ncbi.nlm.nih.gov/pubmed/19349463)  J Exp Med. 2009; 206(4):923-36.
0. Meyer-Olson D, Simons BC, Conrad JA et al. [Clonal expansion and TCR-independent differentiation shape the HIV-specific CD8+ effector-memory T-cell repertoire in vivo.](http://www.ncbi.nlm.nih.gov/pubmed/20424187)  Blood. 2010; 116(3):396-405.
0. Geldmacher C, Metzler IS, Tovanabutra S et al.  [Minor viral and host genetic polymorphisms can dramatically impact the biologic outcome of an epitope-specific CD8 T-cell response.](http://www.ncbi.nlm.nih.gov/pubmed/19542300)  Blood. 2009; 114(8):1553-62.
0. Klenerman P, Rowland-Jones S, McAdam S et al. [Cytotoxic T-cell activity antagonized by naturally occurring HIV-1 Gag variants.](http://www.ncbi.nlm.nih.gov/pubmed/7515165)  Nature. 1994; 369(6479):403-7.

# T-cell cloning
0. Marcela V. Maus, Anna K. Thomas, Debra G.B. Leonard. [Ex vivo expansion of polyclonal and antigen-specific cytotoxic T lymphocytes by artificial APCs expressing ligands for the T-cell receptor, CD28 and 4-1BB](http://www.nature.com/nbt/journal/v20/n2/abs/nbt0202-143.html)  Nature 2002.

# New directions in vaccines and theraputics

0. Varela-Rohena A, Molloy PE, Dunn SM et al. [Control of HIV-1 immune escape by CD8 T cells expressing enhanced T-cell receptor.](http://www.ncbi.nlm.nih.gov/pubmed/18997777)  Nat Med. 2008; 14(12):1390-5.
0. Schaubert KL, Price DA, Salkowitz JR et al. [Generation of robust CD8(+) T-cell responses against subdominant epitopes in conserved regions of HIV-1 by repertoire mining with mimotopes.](http://www.ncbi.nlm.nih.gov/pubmed/20432235)  Eur J Immunol. 2010; 40(7):1950-1962.
0. Honda M, Wang R, Kong WP et al.  [Different vaccine vectors delivering the same antigen elicit CD8+ T cell responses with distinct clonotype and epitope specificity.](http://www.ncbi.nlm.nih.gov/pubmed/19620307)  J Immunol. 2009; 183(4):2425-34.
0. Cheong C, Choi JH, Vitale L et al. [Improved cellular and humoral immune responses in vivo following targeting of HIV Gag to dendritic cells within human anti-human DEC205 monoclonal antibody.](http://www.ncbi.nlm.nih.gov/pubmed/20668230)  Blood. 2010 Jul 28. [Epub ahead of print]
0. Barouch DH, O'Brien KL, Simmons NL et al.  [Mosaic HIV-1 vaccines expand the breadth and depth of cellular immune responses in rhesus monkeys.](http://www.ncbi.nlm.nih.gov/pubmed/20173752)   Nat Med. 2010; 16(3):319-23.