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Virus-Host Gene Interactions Define HIV-1 Disease Progression

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Viruses, Genes, and Cancer

Part of the book series: Current Topics in Microbiology and Immunology ((CT MICROBIOLOGY,volume 407))

Abstract

In this chapter, we will review recent research on the virology of HIV-1 transmission and the impact of the transmitted virus genotype on subsequent disease progression. In most instances of HIV-1 sexual transmission, a single genetic variant, or a very limited number of variants from the diverse viral quasi-species present in the transmitting partner establishes systemic infection. Transmission involves both stochastic and selective processes, such that in general a minority variant in the donor is transmitted. While there is clear evidence for selection, the biological properties that mediate transmission remain incompletely defined. Nevertheless, the genotype of the transmitted founder virus, which reflects prior exposure to and escape from host immune responses, clearly influences disease progression. Some escape mutations impact replicative capacity, while others effectively cloak the virus from the newly infected host’s immune response by preventing recognition. It is the balance between the impact of escape mutations on viral fitness and susceptibility to the host immunogenetics that defines HIV-1 disease progression.

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References

  • Abel K, Rocke DM, Chohan B, Fritts L, Miller CJ (2005) Temporal and anatomic relationship between virus replication and cytokine gene expression after vaginal simian immunodeficiency virus infection. J Virol 79(19):12164–12172. doi:10.1128/JVI.79.19.12164-12172.2005 79/19/12164 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Abrahams MR, Anderson JA, Giorgi EE, Seoighe C, Mlisana K, Ping LH, Athreya GS, Treurnicht FK, Keele BF, Wood N, Salazar-Gonzalez JF, Bhattacharya T, Chu H, Hoffman I, Galvin S, Mapanje C, Kazembe P, Thebus R, Fiscus S, Hide W, Cohen MS, Karim SA, Haynes BF, Shaw GM, Hahn BH, Korber BT, Swanstrom R, Williamson C (2009) Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variants. J Virol 83(8):3556–3567. doi:10.1128/JVI.02132-08 JVI.02132-08 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Alexander M, Lynch R, Mulenga J, Allen S, Derdeyn CA, Hunter E (2010) Donor and recipient envs from heterosexual human immunodeficiency virus subtype C transmission pairs require high receptor levels for entry. J Virol 84(8):4100–4104. doi:10.1128/JVI.02068-09 JVI.02068-09 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Alizon S, Fraser C (2013) Within-host and between-host evolutionary rates across the HIV-1 genome. Retrovirology 10:49. doi:10.1186/1742-4690-10-49

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Alkhatib G, Combadiere C, Broder CC, Feng Y, Kennedy PE, Murphy PM, Berger EA (1996) CC CKR5: a RANTES, MIP-1alpha, MIP-1beta receptor as a fusion cofactor for macrophage-tropic HIV-1. Science 272(5270):1955–1958

    Article  ADS  CAS  PubMed  Google Scholar 

  • Anahtar MN, Byrne EH, Doherty KE, Bowman BA, Yamamoto HS, Soumillon M, Padavattan N, Ismail N, Moodley A, Sabatini ME, Ghebremichael MS, Nusbaum C, Huttenhower C, Virgin HW, Ndung’u T, Dong KL, Walker BD, Fichorova RN, Kwon DS (2015) Cervicovaginal bacteria are a major modulator of host inflammatory responses in the female genital tract. Immunity 42(5):965–976. doi:10.1016/j.immuni.2015.04.019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Anderson JA, Ping LH, Dibben O, Jabara CB, Arney L, Kincer L, Tang Y, Hobbs M, Hoffman I, Kazembe P, Jones CD, Borrow P, Fiscus S, Cohen MS, Swanstrom R (2010) HIV-1 Populations in Semen Arise through Multiple Mechanisms. PLoS Pathog 6(8):e1001053. doi:10.1371/journal.ppat.1001053

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Arthos J, Cicala C, Martinelli E, Macleod K, Van Ryk D, Wei D, Xiao Z, Veenstra TD, Conrad TP, Lempicki RA, McLaughlin S, Pascuccio M, Gopaul R, McNally J, Cruz CC, Censoplano N, Chung E, Reitano KN, Kottilil S, Goode DJ, Fauci AS (2008) HIV-1 envelope protein binds to and signals through integrin alpha4beta7, the gut mucosal homing receptor for peripheral T cells. Nat Immunol 9(3):301–309. doi:10.1038/ni1566 ni1566 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Auvert B, Taljaard D, Lagarde E, Sobngwi-Tambekou J, Sitta R, Puren A (2005) Randomized, controlled intervention trial of male circumcision for reduction of HIV infection risk: the ANRS 1265 Trial. PLoS Med 2(11):e298. doi:10.1371/journal.pmed.0020298 05-PLME-RA-0310R1 [pii]

    Article  PubMed  PubMed Central  Google Scholar 

  • Baalwa J, Wang S, Parrish NF, Decker JM, Keele BF, Learn GH, Yue L, Ruzagira E, Ssemwanga D, Kamali A, Amornkul PN, Price MA, Kappes JC, Karita E, Kaleebu P, Sanders E, Gilmour J, Allen S, Hunter E, Montefiori DC, Haynes BF, Cormier E, Hahn BH, Shaw GM (2013) Molecular identification, cloning and characterization of transmitted/founder HIV-1 subtype A, D and A/D infectious molecular clones. Virology 436(1):33–48. doi:10.1016/j.virol.2012.10.009

    Article  CAS  PubMed  Google Scholar 

  • Bailey RC, Moses S, Parker CB, Agot K, Maclean I, Krieger JN, Williams CF, Campbell RT, Ndinya-Achola JO (2007) Male circumcision for HIV prevention in young men in Kisumu, Kenya: a randomised controlled trial. Lancet 369(9562):643–656. doi:10.1016/S0140-6736(07)60312-2 S0140-6736(07)60312-2 [pii]

    Article  PubMed  Google Scholar 

  • Barouch DH, Ghneim K, Bosche WJ, Li Y, Berkemeier B, Hull M, Bhattacharyya S, Cameron M, Liu J, Smith K, Borducchi E, Cabral C, Peter L, Brinkman A, Shetty M, Li H, Gittens C, Baker C, Wagner W, Lewis MG, Colantonio A, Kang HJ, Li W, Lifson JD, Piatak M Jr, Sekaly RP (2016) Rapid Inflammasome Activation following Mucosal SIV Infection of Rhesus Monkeys. Cell 165(3):656–667. doi:10.1016/j.cell.2016.03.021

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berger EA, Murphy PM, Farber JM (1999) Chemokine receptors as HIV-1 coreceptors: roles in viral entry, tropism, and disease. Annu Rev Immunol 17:657–700. doi:10.1146/annurev.immunol.17.1.657

    Article  CAS  PubMed  Google Scholar 

  • Bhattacharya T, Daniels M, Heckerman D, Foley B, Frahm N, Kadie C, Carlson J, Yusim K, McMahon B, Gaschen B, Mallal S, Mullins JI, Nickle DC, Herbeck J, Rousseau C, Learn GH, Miura T, Brander C, Walker B, Korber B (2007) Founder effects in the assessment of HIV polymorphisms and HLA allele associations. Science 315(5818):1583–1586. doi:10.1126/science.1131528

    Article  ADS  CAS  PubMed  Google Scholar 

  • Blaschitz C, Raffatellu M (2010) Th17 Cytokines and the Gut Mucosal Barrier. J Clin Immunol 30(2):196–203. doi:10.1007/s10875-010-9368-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boeras DI, Hraber PT, Hurlston M, Evans-Strickfaden T, Bhattachary T, Giorgi EE, Mulenga J, Karita E, Korber BT, Allen S, Hart CE, Derdeyn CA, Hunter E (2011) Role of donor genital tract HIV-1 diversity in the transmission bottleneck. Proc Natl Acad Sci USA 108(46):E156–163. doi:10.1073/pnas.1103764108

  • Borrow P, Lewicki H, Hahn BH, Shaw GM, Oldstone MB (1994) Virus-specific CD8 + cytotoxic T-lymphocyte activity associated with control of viremia in primary human immunodeficiency virus type 1 infection. J Virol 68(9):6103–6110

    CAS  PubMed  PubMed Central  Google Scholar 

  • Borrow P, Lewicki H, Wei X, Horwitz MS, Peffer N, Meyers H, Nelson JA, Gairin JE, Hahn BH, Oldstone MB, Shaw GM (1997) Antiviral pressure exerted by HIV-1-specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus. Nat Med 3(2):205–211

    Article  CAS  PubMed  Google Scholar 

  • Boyd DF, Sharma A, Humes D, Cheng-Mayer C, Overbaugh J (2016) Adapting SHIVs In Vivo Selects for Envelope-Mediated Interferon-alpha Resistance. PLoS Pathog 12(7):e1005727. doi:10.1371/journal.ppat.1005727

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Brenner BG, Roger M, Routy JP, Moisi D, Ntemgwa M, Matte C, Baril JG, Thomas R, Rouleau D, Bruneau J, Leblanc R, Legault M, Tremblay C, Charest H, Wainberg MA (2007) High rates of forward transmission events after acute/early HIV-1 infection. J Infect Dis 195(7):951–959. doi:10.1086/512088 JID37441 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Brockman MA, Schneidewind A, Lahaie M, Schmidt A, Miura T, Desouza I, Ryvkin F, Derdeyn CA, Allen S, Hunter E, Mulenga J, Goepfert PA, Walker BD, Allen TM (2007) 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. J Virol 81(22):12608–12618. doi:10.1128/JVI.01369-07

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brockman MA, Brumme ZL, Brumme CJ, Miura T, Sela J, Rosato PC, Kadie CM, Carlson JM, Markle TJ, Streeck H, Kelleher AD, Markowitz M, Jessen H, Rosenberg E, Altfeld M, Harrigan PR, Heckerman D, Walker BD, Allen TM (2010) Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated for in chronic infection. J Virol 84(22):11937–11949. doi:10.1128/JVI.01086-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brodin J, Zanini F, Thebo L, Lanz C, Bratt G, Neher RA, Albert J (2016) Establishment and stability of the latent HIV-1 DNA reservoir. eLife 5. doi:10.7554/eLife.18889

  • Byrareddy SN, Kallam B, Arthos J, Cicala C, Nawaz F, Hiatt J, Kersh EN, McNicholl JM, Hanson D, Reimann KA, Brameier M, Walter L, Rogers K, Mayne AE, Dunbar P, Villinger T, Little D, Parslow TG, Santangelo PJ, Villinger F, Fauci AS, Ansari AA (2014) Targeting alpha4beta7 integrin reduces mucosal transmission of simian immunodeficiency virus and protects gut-associated lymphoid tissue from infection. Nat Med 20(12):1397–1400. doi:10.1038/nm.3715

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carlson JM, Brumme ZL, Rousseau CM, Brumme CJ, Matthews P, Kadie C, Mullins JI, Walker BD, Harrigan PR, Goulder PJ, Heckerman D (2008) Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag. PLoS Comput Biol 4(11):e1000225. doi:10.1371/journal.pcbi.1000225

    Article  ADS  MathSciNet  PubMed  PubMed Central  CAS  Google Scholar 

  • Carlson JM, Schaefer M, Monaco DC, Batorsky R, Claiborne DT, Prince J, Deymier MJ, Ende ZS, Klatt NR, DeZiel CE, Lin TH, Peng J, Seese AM, Shapiro R, Frater J, Ndung’u T, Tang J, Goepfert P, Gilmour J, Price MA, Kilembe W, Heckerman D, Goulder PJ, Allen TM, Allen S, Hunter E (2014) HIV transmission. Selection bias at the heterosexual HIV-1 transmission bottleneck. Science 345 (6193):1254031. doi:10.1126/science.1254031

  • Carlson JM, Du VY, Pfeifer N, Bansal A, Tan VY, Power K, Brumme CJ, Kreimer A, DeZiel CE, Fusi N, Schaefer M, Brockman MA, Gilmour J, Price MA, Kilembe W, Haubrich R, John M, Mallal S, Shapiro R, Frater J, Harrigan PR, Ndung’u T, Allen S, Heckerman D, Sidney J, Allen TM, Goulder PJ, Brumme ZL, Hunter E, Goepfert PA (2016) Impact of pre-adapted HIV transmission. Nat Med 22(6):606–613. doi:10.1038/nm.4100

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cartwright EK, Spicer L, Smith SA, Lee D, Fast R, Paganini S, Lawson BO, Nega M, Easley K, Schmitz JE, Bosinger SE, Paiardini M, Chahroudi A, Vanderford TH, Estes JD, Lifson JD, Derdeyn CA, Silvestri G (2016) CD8(+) Lymphocytes Are Required for Maintaining Viral Suppression in SIV-Infected Macaques Treated with Short-Term Antiretroviral Therapy. Immunity 45(3):656–668. doi:10.1016/j.immuni.2016.08.018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cecchinato V, Franchini G (2010) Th17 cells in pathogenic SIV infection of macaques. Current opinion in HIV and AIDS 5(2):141–145. doi:10.1097/COH.0b013e32833653ec

    Article  PubMed  PubMed Central  Google Scholar 

  • Choe H, Farzan M, Sun Y, Sullivan N, Rollins B, Ponath PD, Wu L, Mackay CR, LaRosa G, Newman W, Gerard N, Gerard C, Sodroski J (1996) The beta-chemokine receptors CCR3 and CCR5 facilitate infection by primary HIV-1 isolates. Cell 85(7):1135–1148

    Article  CAS  PubMed  Google Scholar 

  • Chohan B, Lang D, Sagar M, Korber B, Lavreys L, Richardson B, Overbaugh J (2005) Selection for human immunodeficiency virus type 1 envelope glycosylation variants with shorter V1-V2 loop sequences occurs during transmission of certain genetic subtypes and may impact viral RNA levels. J Virol 79(10):6528–6531. doi:10.1128/JVI.79.10.6528-6531.2005 79/10/6528 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chopera DR, Woodman Z, Mlisana K, Mlotshwa M, Martin DP, Seoighe C, Treurnicht F, de Rosa DA, Hide W, Karim SA, Gray CM, Williamson C, Team CS (2008) Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage. PLoS Pathog 4(3):e1000033. doi:10.1371/journal.ppat.1000033

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cicala C, Martinelli E, McNally JP, Goode DJ, 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 AS, Arthos J (2009) 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. Proc Natl Acad Sci U S A 106(49):20877–20882. doi:10.1073/pnas.0911796106 0911796106 [pii]

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • Claiborne DT, Prince JL, Scully E, Macharia G, Micci L, Lawson B, Kopycinski J, Deymier MJ, Vanderford TH, Nganou-Makamdop K, Ende Z, Brooks K, Tang J, Yu T, Lakhi S, Kilembe W, Silvestri G, Douek D, Goepfert PA, Price MA, Allen SA, Paiardini M, Altfeld M, Gilmour J, Hunter E (2015) Replicative fitness of transmitted HIV-1 drives acute immune activation, proviral load in memory CD4 + T cells, and disease progression. Proc Natl Acad Sci U S A 112(12):E1480–E1489. doi:10.1073/pnas.1421607112

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • Coetzer M, Nedellec R, Salkowitz J, McLaughlin S, Liu Y, Heath L, Mullins JI, Mosier DE (2008) Evolution of CCR5 use before and during coreceptor switching. J Virol 82(23):11758–11766. doi:10.1128/JVI.01141-08

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cotton LA, Kuang XT, Le AQ, Carlson JM, Chan B, Chopera DR, Brumme CJ, Markle TJ, Martin E, Shahid A, Anmole G, Mwimanzi P, Nassab P, Penney KA, Rahman MA, Milloy MJ, Schechter MT, Markowitz M, Carrington M, Walker BD, Wagner T, Buchbinder S, Fuchs J, Koblin B, Mayer KH, Harrigan PR, Brockman MA, Poon AF, Brumme ZL (2014) Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic. PLoS Genet 10(4):e1004295. doi:10.1371/journal.pgen.1004295

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Crawford H, Prado JG, Leslie A, Hue S, Honeyborne I, Reddy S, van der Stok M, Mncube Z, Brander C, Rousseau C, Mullins JI, Kaslow R, Goepfert P, Allen S, Hunter E, Mulenga J, Kiepiela P, Walker BD, Goulder PJ (2007) Compensatory mutation partially restores fitness and delays reversion of escape mutation within the immunodominant HLA-B*5703-restricted Gag epitope in chronic human immunodeficiency virus type 1 infection. J Virol 81(15):8346–8351. doi:10.1128/JVI.00465-07

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Crawford H, Lumm W, Leslie A, Schaefer M, Boeras D, Prado JG, Tang J, Farmer P, Ndung’u T, Lakhi S, Gilmour J, Goepfert P, Walker BD, Kaslow R, Mulenga J, Allen S, Goulder PJ, Hunter E (2009) Evolution of HLA-B*5703 HIV-1 escape mutations in HLA-B*5703-positive individuals and their transmission recipients. J Exp Med 206(4):909–921. doi:10.1084/jem.20081984

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dandekar S, George MD, Baumler AJ (2010) Th17 cells, HIV and the gut mucosal barrier. Curr Opin HIV AIDS 5(2):173–178. doi:10.1097/COH.0b013e328335eda3

    Article  PubMed  Google Scholar 

  • Dean M, Carrington M, Winkler C, Huttley GA, Smith MW, Allikmets R, Goedert JJ, Buchbinder SP, Vittinghoff E, Gomperts E, Donfield S, Vlahov D, Kaslow R, Saah A, Rinaldo C, Detels R, O’Brien SJ (1996) Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study. Science 273(5283):1856–1862

    Article  ADS  CAS  PubMed  Google Scholar 

  • Deng H, Liu R, Ellmeier W, Choe S, Unutmaz D, Burkhart M, Di Marzio P, Marmon S, Sutton RE, Hill CM, Davis CB, Peiper SC, Schall TJ, Littman DR, Landau NR (1996) Identification of a major co-receptor for primary isolates of HIV-1. Nature 381(6584):661–666. doi:10.1038/381661a0

    Article  ADS  CAS  PubMed  Google Scholar 

  • Derdeyn CA, Decker JM, Bibollet-Ruche F, Mokili JL, Muldoon M, Denham SA, Heil ML, Kasolo F, Musonda R, Hahn BH, Shaw GM, Korber BT, Allen S, Hunter E (2004) Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science 303(5666):2019–2022. doi:10.1126/science.1093137

    Article  ADS  CAS  PubMed  Google Scholar 

  • Deymier MJ, Claiborne DT, Ende Z, Ratner HK, Kilembe W, Allen S, Hunter E (2014) Particle infectivity of HIV-1 full-length genome infectious molecular clones in a subtype C heterosexual transmission pair following high fidelity amplification and unbiased cloning. Virology 468–470:454–461. doi:10.1016/j.virol.2014.08.018

    Article  PubMed  CAS  Google Scholar 

  • Deymier MJ, Ende Z, Fenton-May AE, Dilernia DA, Kilembe W, Allen SA, Borrow P, Hunter E (2015) Heterosexual Transmission of Subtype C HIV-1 Selects Consensus-Like Variants without Increased Replicative Capacity or Interferon-alpha Resistance. PLoS Pathog 11(9):e1005154. doi:10.1371/journal.ppat.1005154

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Dilernia DA, Jones L, Rodriguez S, Turk G, Rubio AE, Pampuro S, Gomez-Carrillo M, Bautista CT, Deluchi G, Benetucci J, Lasala MB, Lourtau L, Losso MH, Perez H, Cahn P, Salomon H (2008) HLA-driven convergence of HIV-1 viral subtypes B and F toward the adaptation to immune responses in human populations. PLoS ONE 3(10):e3429. doi:10.1371/journal.pone.0003429

    Article  ADS  PubMed  PubMed Central  CAS  Google Scholar 

  • Doyle T, Goujon C, Malim MH (2015) HIV-1 and interferons: who’s interfering with whom? Nat Rev Microbiol 13(7):403–413. doi:10.1038/nrmicro3449

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dragic T, Litwin V, Allaway GP, Martin SR, Huang Y, Nagashima KA, Cayanan C, Maddon PJ, Koup RA, Moore JP, Paxton WA (1996) HIV-1 entry into CD4 + cells is mediated by the chemokine receptor CC-CKR-5. Nature 381(6584):667–673. doi:10.1038/381667a0

    Article  ADS  CAS  PubMed  Google Scholar 

  • Ende Z, Deymier M, Hunter E (2017) Virologic Aspects of Mucosal Transmission. In: Mestecky J, Veazey R (eds) Mucosal Iimmunology of HIV/SIV. Bentham Science, In Press

    Google Scholar 

  • Etemad B, Gonzalez OA, White L, Laeyendecker O, Kirk GD, Mehta S, Sagar M (2014) Characterization of HIV-1 envelopes in acutely and chronically infected injection drug users. Retrovirology 11:106. doi:10.1186/s12977-014-0106-8

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Evans DT, Silvestri G (2013) Nonhuman primate models in AIDS research. Curr Opin HIV AIDS 8(4):255–261. doi:10.1097/COH.0b013e328361cee8

    Article  PubMed  PubMed Central  Google Scholar 

  • Fellay J, Shianna KV, Ge D, Colombo S, Ledergerber B, Weale M, Zhang K, Gumbs C, Castagna A, Cossarizza A, Cozzi-Lepri A, De Luca A, Easterbrook P, Francioli P, Mallal S, Martinez-Picado J, Miro JM, Obel N, Smith JP, Wyniger J, Descombes P, Antonarakis SE, Letvin NL, McMichael AJ, Haynes BF, Telenti A, Goldstein DB (2007) A whole-genome association study of major determinants for host control of HIV-1. Science 317(5840):944–947. doi:10.1126/science.1143767 1143767 [pii]

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • Feng Y, Broder CC, Kennedy PE, Berger EA (1996) HIV-1 entry cofactor: functional cDNA cloning of a seven-transmembrane. G protein-coupled receptor. Science 272(5263):872–877

    CAS  PubMed  Google Scholar 

  • Fenton-May AE, Dibben O, Emmerich T, Ding H, Pfafferott K, Aasa-Chapman MM, Pellegrino P, Williams I, Cohen MS, Gao F, Shaw GM, Hahn BH, Ochsenbauer C, Kappes JC, Borrow P (2013) Relative resistance of HIV-1 founder viruses to control by interferon-alpha. Retrovirology 10:146. doi:10.1186/1742-4690-10-146

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fideli US, Allen SA, Musonda R, Trask S, Hahn BH, Weiss H, Mulenga J, Kasolo F, Vermund SH, Aldrovandi GM (2001) Virologic and immunologic determinants of heterosexual transmission of human immunodeficiency virus type 1 in Africa. AIDS Res Hum Retroviruses 17(10):901–910. doi:10.1089/088922201750290023

    Article  PubMed  Google Scholar 

  • Fiebig EW, Wright DJ, Rawal BD, Garrett PE, Schumacher RT, Peddada L, Heldebrant C, Smith R, Conrad A, Kleinman SH, Busch MP (2003) Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection. AIDS 17(13):1871–1879. doi:10.1097/01.aids.0000076308.76477.b8

    Article  PubMed  Google Scholar 

  • Fischer W, Ganusov VV, Giorgi EE, Hraber PT, Keele BF, Leitner T, Han CS, Gleasner CD, Green L, Lo CC, Nag A, Wallstrom TC, Wang S, McMichael AJ, Haynes BF, Hahn BH, Perelson AS, Borrow P, Shaw GM, Bhattacharya T, Korber BT (2010) Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing. PLoS ONE 5(8):e12303. doi:10.1371/journal.pone.0012303

    Article  ADS  PubMed  PubMed Central  CAS  Google Scholar 

  • Forthal DN, Gabriel EE, Wang A, Landucci G, Phan TB (2012) Association of Fcgamma receptor IIIa genotype with the rate of HIV infection after gp120 vaccination. Blood 120(14):2836–2842. doi:10.1182/blood-2012-05-431361

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Foster TL, Wilson H, Iyer SS, Coss K, Doores K, Smith S, Kellam P, Finzi A, Borrow P, Hahn BH, Neil SJ (2016) Resistance of Transmitted Founder HIV-1 to IFITM-Mediated Restriction. Cell Host Microbe 20(4):429–442. doi:10.1016/j.chom.2016.08.006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fraser C, Lythgoe K, Leventhal GE, Shirreff G, Hollingsworth TD, Alizon S, Bonhoeffer S (2014) Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective. Science 343(6177):1243727. doi:10.1126/science.1243727

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Frost SD, Liu Y, Pond SL, Chappey C, Wrin T, Petropoulos CJ, Little SJ, Richman DD (2005) Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B. J Virol 79(10):6523–6527. doi:10.1128/JVI.79.10.6523-6527.2005 79/10/6523 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Galvin SR, Cohen MS (2004) The role of sexually transmitted diseases in HIV transmission. Nat Rev Microbiol 2(1):33–42. doi:10.1038/nrmicro794

    Article  CAS  PubMed  Google Scholar 

  • Gnanakaran S, Bhattacharya T, Daniels M, Keele BF, Hraber PT, Lapedes AS, Shen T, Gaschen B, Krishnamoorthy M, Li H, Decker JM, Salazar-Gonzalez JF, Wang S, Jiang C, Gao F, Swanstrom R, Anderson JA, Ping LH, Cohen MS, Markowitz M, Goepfert PA, Saag MS, Eron JJ, Hicks CB, Blattner WA, Tomaras GD, Asmal M, Letvin NL, Gilbert PB, Decamp AC, Magaret CA, Schief WR, Ban YE, Zhang M, Soderberg KA, Sodroski JG, Haynes BF, Shaw GM, Hahn BH, Korber B (2011) Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections. PLoS Pathog 7(9):e1002209. doi:10.1371/journal.ppat.1002209

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Goepfert PA, Lumm W, Farmer P, Matthews P, Prendergast A, Carlson JM, Derdeyn CA, Tang J, Kaslow RA, Bansal A, Yusim K, Heckerman D, Mulenga J, Allen S, Goulder PJ, Hunter E (2008) Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients. J Exp Med 205(5):1009–1017. doi:10.1084/jem.20072457

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gosmann C, Anahtar MN, Handley SA, Farcasanu M, Abu-Ali G, Bowman BA, Padavattan N, Desai C, Droit L, Moodley A, Dong M, Chen Y, Ismail N, Ndung’u T, Ghebremichael MS, Wesemann DR, Mitchell C, Dong KL, Huttenhower C, Walker BD, Virgin HW, Kwon DS (2017) Lactobacillus-Deficient Cervicovaginal Bacterial Communities Are Associated with Increased HIV Acquisition in Young South African Women. Immunity 46(1):29–37. doi:10.1016/j.immuni.2016.12.013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Goulder PJ, Phillips RE, Colbert RA, McAdam S, Ogg G, Nowak MA, Giangrande P, Luzzi G, Morgan B, Edwards A, McMichael AJ, Rowland-Jones S (1997) Late escape from an immunodominant cytotoxic T-lymphocyte response associated with progression to AIDS. Nat Med 3(2):212–217

    Article  CAS  PubMed  Google Scholar 

  • Goulder PJ, Brander C, Tang Y, Tremblay C, Colbert RA, Addo MM, Rosenberg ES, Nguyen T, Allen R, Trocha A, Altfeld M, He S, Bunce M, Funkhouser R, Pelton SI, Burchett SK, McIntosh K, Korber BT, Walker BD (2001) Evolution and transmission of stable CTL escape mutations in HIV infection. Nature 412(6844):334–338. doi:10.1038/35085576

    Article  ADS  CAS  PubMed  Google Scholar 

  • Gray RH, Li X, Kigozi G, Serwadda D, Brahmbhatt H, Wabwire-Mangen F, Nalugoda F, Kiddugavu M, Sewankambo N, Quinn TC, Reynolds SJ, Wawer MJ (2005) Increased risk of incident HIV during pregnancy in Rakai, Uganda: a prospective study. Lancet 366(9492):1182–1188. doi:10.1016/S0140-6736(05)67481-8

    Article  PubMed  Google Scholar 

  • Gray RH, Kigozi G, Serwadda D, Makumbi F, Watya S, Nalugoda F, Kiwanuka N, Moulton LH, Chaudhary MA, Chen MZ, Sewankambo NK, Wabwire-Mangen F, Bacon MC, Williams CF, Opendi P, Reynolds SJ, Laeyendecker O, Quinn TC, Wawer MJ (2007) Male circumcision for HIV prevention in men in Rakai, Uganda: a randomised trial. Lancet 369(9562):657–666. doi:10.1016/S0140-6736(07)60313-4 S0140-6736(07)60313-4 [pii]

    Article  PubMed  Google Scholar 

  • Haaland RE, Hawkins PA, Salazar-Gonzalez J, Johnson A, Tichacek A, Karita E, Manigart O, Mulenga J, Keele BF, Shaw GM, Hahn BH, Allen SA, Derdeyn CA, Hunter E (2009) Inflammatory genital infections mitigate a severe genetic bottleneck in heterosexual transmission of subtype A and C HIV-1. PLoS Pathog 5(1):e1000274. doi:10.1371/journal.ppat.1000274

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hahn BH, Shaw GM, De Cock KM, Sharp PM (2000) AIDS as a zoonosis: scientific and public health implications. Science 287(5453):607–614

    Article  ADS  CAS  PubMed  Google Scholar 

  • Hatziioannou T, Evans DT (2012) Animal models for HIV/AIDS research. Nat Rev Microbiol 10(12):852–867. doi:10.1038/nrmicro2911

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hawkins RA, Rank RG, Kelly KA (2000) Expression of mucosal homing receptor alpha4beta7 is associated with enhanced migration to the Chlamydia-infected murine genital mucosa in vivo. Infect Immun 68(10):5587–5594

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hecht FM, Hartogensis W, Bragg L, Bacchetti P, Atchison R, Grant R, Barbour J, Deeks SG (2010) HIV RNA level in early infection is predicted by viral load in the transmission source. AIDS 24(7):941–945. doi:10.1097/QAD.0b013e328337b12e

    Article  CAS  PubMed  Google Scholar 

  • Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, Macalalad AR, Berlin AM, Malboeuf CM, Ryan EM, Gnerre S, Zody MC, Erlich RL, Green LM, Berical A, Wang Y, Casali M, Streeck H, Bloom AK, Dudek T, Tully D, Newman R, Axten KL, Gladden AD, Battis L, Kemper M, Zeng Q, Shea TP, Gujja S, Zedlack C, Gasser O, Brander C, Hess C, Gunthard HF, Brumme ZL, Brumme CJ, Bazner S, Rychert J, Tinsley JP, Mayer KH, Rosenberg E, Pereyra F, Levin JZ, Young SK, Jessen H, Altfeld M, Birren BW, Walker BD, Allen TM (2012) Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog 8(3):e1002529. doi:10.1371/journal.ppat.1002529

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hladik F, McElrath MJ (2008) Setting the stage: host invasion by HIV. Nat Rev Immunol 8(6):447–457. doi:10.1038/nri2302 nri2302 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hladik F, Sakchalathorn P, Ballweber L, Lentz G, Fialkow M, Eschenbach D, McElrath MJ (2007) Initial events in establishing vaginal entry and infection by human immunodeficiency virus type-1. Immunity 26(2):257–270. doi:10.1016/j.immuni.2007.01.007 S1074-7613(07)00134-3 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hunter E (1997) Viral Entry and Receptors. In: Coffin JM, Hughes SH, Varmus HE (eds) Retroviruses. Cold Spring Harbor (NY)

    Google Scholar 

  • Iglesias MC, Almeida JR, Fastenackels S, van Bockel DJ, Hashimoto M, Venturi V, Gostick E, Urrutia A, Wooldridge L, Clement M, Gras S, Wilmann PG, Autran B, Moris A, Rossjohn J, Davenport MP, Takiguchi M, Brander C, Douek DC, Kelleher AD, Price DA, Appay V (2011) Escape from highly effective public CD8 + T-cell clonotypes by HIV. Blood 118(8):2138–2149. doi:10.1182/blood-2011-01-328781

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Isaacman-Beck J, Hermann EA, Yi Y, Ratcliffe SJ, Mulenga J, Allen S, Hunter E, Derdeyn CA, Collman RG (2009) Heterosexual transmission of human immunodeficiency virus type 1 subtype C: Macrophage tropism, alternative coreceptor use, and the molecular anatomy of CCR5 utilization. J Virol 83(16):8208–8220. doi:10.1128/JVI.00296-09 JVI.00296-09 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Iyer SS, Bibollet-Ruche F, Sherrill-Mix S, Learn GH, Plenderleith L, Smith AG, Barbian HJ, Russell RM, Gondim MV, Bahari CY, Shaw CM, Li Y, Decker T, Haynes BF, Shaw GM, Sharp PM, Borrow P, Hahn BH (2017) Resistance to type 1 interferons is a major determinant of HIV-1 transmission fitness. Proc Natl Acad Sci U S A 114(4):E590–E599. doi:10.1073/pnas.1620144114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jin X, Bauer DE, Tuttleton SE, Lewin S, Gettie A, Blanchard J, Irwin CE, Safrit JT, Mittler J, Weinberger L, Kostrikis LG, Zhang L, Perelson AS, Ho DD (1999) Dramatic rise in plasma viremia after CD8(+) T cell depletion in simian immunodeficiency virus-infected macaques. J Exp Med 189(6):991–998

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Joseph SB, Swanstrom R, Kashuba AD, Cohen MS (2015) Bottlenecks in HIV-1 transmission: insights from the study of founder viruses. Nat Rev Microbiol 13(7):414–425. doi:10.1038/nrmicro3471

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kamali A, Price MA, Lakhi S, Karita E, Inambao M, Sanders EJ, Anzala O, Latka MH, Bekker LG, Kaleebu P, Asiki G, Ssetaala A, Ruzagira E, Allen S, Farmer P, Hunter E, Mutua G, Makkan H, Tichacek A, Brill IK, Fast P, Stevens G, Chetty P, Amornkul PN, Gilmour J, Partnership IAHP (2015) Creating an African HIV clinical research and prevention trials network: HIV prevalence, incidence and transmission. PLoS ONE 10(1):e0116100. doi:10.1371/journal.pone.0116100

    Article  PubMed  PubMed Central  Google Scholar 

  • Kaslow RA, Carrington M, Apple R, Park L, Munoz A, Saah AJ, Goedert JJ, Winkler C, O’Brien SJ, Rinaldo C, Detels R, Blattner W, Phair J, Erlich H, Mann DL (1996) Influence of combinations of human major histocompatibility complex genes on the course of HIV-1 infection. Nat Med 2(4):405–411

    Article  CAS  PubMed  Google Scholar 

  • Kawashima Y, Pfafferott K, Frater J, Matthews P, Payne R, Addo M, Gatanaga H, Fujiwara M, Hachiya A, Koizumi H, Kuse N, Oka S, Duda A, Prendergast A, Crawford H, Leslie A, Brumme Z, Brumme C, Allen T, Brander C, Kaslow R, Tang J, Hunter E, Allen S, Mulenga J, Branch S, Roach T, John M, Mallal S, Ogwu A, Shapiro R, Prado JG, Fidler S, Weber J, Pybus OG, Klenerman P, Ndung’u T, Phillips R, Heckerman D, Harrigan PR, Walker BD, Takiguchi M, Goulder P (2009) Adaptation of HIV-1 to human leukocyte antigen class I. Nature 458(7238):641–645. doi:10.1038/nature07746

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, Salazar MG, Sun C, Grayson T, Wang S, Li H, Wei X, Jiang C, Kirchherr JL, Gao F, Anderson JA, Ping LH, Swanstrom R, Tomaras GD, Blattner WA, Goepfert PA, Kilby JM, Saag MS, Delwart EL, Busch MP, Cohen MS, Montefiori DC, Haynes BF, Gaschen B, Athreya GS, Lee HY, Wood N, Seoighe C, Perelson AS, Bhattacharya T, Korber BT, Hahn BH, Shaw GM (2008) Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci U S A 105(21):7552–7557. doi:10.1073/pnas.0802203105 0802203105 [pii]

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • Keele BF, Li H, Learn GH, Hraber P, Giorgi EE, Grayson T, Sun C, Chen Y, Yeh WW, Letvin NL, Mascola JR, Nabel GJ, Haynes BF, Bhattacharya T, Perelson AS, Korber BT, Hahn BH, Shaw GM (2009) Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1. J Exp Med 206(5):1117–1134. doi:10.1084/jem.20082831 jem.20082831 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kiepiela P, Ngumbela K, Thobakgale C, Ramduth D, Honeyborne I, Moodley E, Reddy S, de Pierres C, Mncube Z, Mkhwanazi N, Bishop K, van der Stok M, Nair K, Khan N, Crawford H, Payne R, Leslie A, Prado J, Prendergast A, Frater J, McCarthy N, Brander C, Learn GH, Nickle D, Rousseau C, Coovadia H, Mullins JI, Heckerman D, Walker BD, Goulder P (2007) CD8 + T-cell responses to different HIV proteins have discordant associations with viral load. Nat Med 13(1):46–53. doi:10.1038/nm1520 nm1520 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Kiwanuka N, Laeyendecker O, Quinn TC, Wawer MJ, Shepherd J, Robb M, Kigozi G, Kagaayi J, Serwadda D, Makumbi FE, Reynolds SJ, Gray RH (2009) HIV-1 subtypes and differences in heterosexual HIV transmission among HIV-discordant couples in Rakai. Uganda. AIDS 23(18):2479–2484. doi:10.1097/QAD.0b013e328330cc08

    Article  PubMed  Google Scholar 

  • Klatt NR, Silvestri G, Hirsch V (2012) Nonpathogenic simian immunodeficiency virus infections. Cold Spring Harb Perspect Med 2(1):a007153. doi:10.1101/cshperspect.a007153

    Article  PubMed  PubMed Central  Google Scholar 

  • Kmiec D, Iyer SS, Sturzel CM, Sauter D, Hahn BH, Kirchhoff F (2016) Vpu-Mediated Counteraction of Tetherin Is a Major Determinant of HIV-1 Interferon Resistance. mBio 7 (4). doi:10.1128/mBio.00934-16

  • Koup RA, Safrit JT, Cao Y, Andrews CA, McLeod G, Borkowsky W, Farthing C, Ho DD (1994) Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome. J Virol 68(7):4650–4655

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lee HY, Giorgi EE, Keele BF, Gaschen B, Athreya GS, Salazar-Gonzalez JF, Pham KT, Goepfert PA, Kilby JM, Saag MS, Delwart EL, Busch MP, Hahn BH, Shaw GM, Korber BT, Bhattacharya T, Perelson AS (2009) Modeling sequence evolution in acute HIV-1 infection. J Theor Biol 261(2):341–360. doi:10.1016/j.jtbi.2009.07.038 S0022-5193(09)00350-6 [pii]

    Article  MathSciNet  CAS  PubMed  PubMed Central  Google Scholar 

  • Leslie AJ, Pfafferott KJ, Chetty P, Draenert R, Addo MM, Feeney M, Tang Y, Holmes EC, Allen T, Prado JG, Altfeld M, Brander C, Dixon C, Ramduth D, Jeena P, Thomas SA, St John A, Roach TA, Kupfer B, Luzzi G, Edwards A, Taylor G, Lyall H, Tudor-Williams G, Novelli V, Martinez-Picado J, Kiepiela P, Walker BD, Goulder PJ (2004) HIV evolution: CTL escape mutation and reversion after transmission. Nat Med 10(3):282–289. doi:10.1038/nm992nm992 [pii]

    Article  CAS  PubMed  Google Scholar 

  • Li Q, Estes JD, Schlievert PM, Duan L, Brosnahan AJ, Southern PJ, Reilly CS, Peterson ML, Schultz-Darken N, Brunner KG, Nephew KR, Pambuccian S, Lifson JD, Carlis JV, Haase AT (2009) Glycerol monolaurate prevents mucosal SIV transmission. Nature 458(7241):1034–1038. doi:10.1038/nature07831 nature07831 [pii]

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu R, Paxton WA, Choe S, Ceradini D, Martin SR, Horuk R, MacDonald ME, Stuhlmann H, Koup RA, Landau NR (1996) Homozygous defect in HIV-1 coreceptor accounts for resistance of some multiply-exposed individuals to HIV-1 infection. Cell 86(3):367–377

    Article  CAS  PubMed  Google Scholar 

  • Liu J, Keele BF, Li H, Keating S, Norris PJ, Carville A, Mansfield KG, Tomaras GD, Haynes BF, Kolodkin-Gal D, Letvin NL, Hahn BH, Shaw GM, Barouch DH (2010) Low-dose mucosal simian immunodeficiency virus infection restricts early replication kinetics and transmitted virus variants in rhesus monkeys. J Virol 84(19):10406–10412. doi:10.1128/JVI.01155-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu A, Yang Y, Liu L, Meng Z, Li L, Qiu C, Xu J, Zhang X (2014) Differential compartmentalization of HIV-targeting immune cells in inner and outer foreskin tissue. PLoS ONE 9(1):e85176. doi:10.1371/journal.pone.0085176

    Article  ADS  PubMed  PubMed Central  CAS  Google Scholar 

  • Long EM, Rainwater SM, Lavreys L, Mandaliya K, Overbaugh J (2002) HIV type 1 variants transmitted to women in Kenya require the CCR5 coreceptor for entry, regardless of the genetic complexity of the infecting virus. AIDS Res Hum Retroviruses 18(8):567–576. doi:10.1089/088922202753747914

    Article  CAS  PubMed  Google Scholar 

  • Ma ZM, Stone M, Piatak M Jr, Schweighardt B, Haigwood NL, Montefiori D, Lifson JD, Busch MP, Miller CJ (2009) High specific infectivity of plasma virus from the pre-ramp-up and ramp-up stages of acute simian immunodeficiency virus infection. J Virol 83(7):3288–3297. doi:10.1128/JVI.02423-08 JVI.02423-08 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Margolis L, Shattock R (2006) Selective transmission of CCR5-utilizing HIV-1: the’gatekeeper’ problem resolved? Nat Rev Microbiol 4(4):312–317. doi:10.1038/nrmicro1387

    Article  CAS  PubMed  Google Scholar 

  • Martinez-Picado J, Prado JG, Fry EE, Pfafferott K, Leslie A, Chetty S, Thobakgale C, Honeyborne I, Crawford H, Matthews P, Pillay T, Rousseau C, Mullins JI, Brander C, Walker BD, Stuart DI, Kiepiela P, Goulder P (2006) Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1. J Virol 80(7):3617–3623. doi:10.1128/JVI.80.7.3617-3623.2006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Matano T, Shibata R, Siemon C, Connors M, Lane HC, Martin MA (1998) Administration of an anti-CD8 monoclonal antibody interferes with the clearance of chimeric simian/human immunodeficiency virus during primary infections of rhesus macaques. J Virol 72(1):164–169

    CAS  PubMed  PubMed Central  Google Scholar 

  • McLaren PJ, Coulonges C, Bartha I, Lenz TL, Deutsch AJ, Bashirova A, Buchbinder S, Carrington MN, Cossarizza A, Dalmau J, De Luca A, Goedert JJ, Gurdasani D, Haas DW, Herbeck JT, Johnson EO, Kirk GD, Lambotte O, Luo M, Mallal S, van Manen D, Martinez-Picado J, Meyer L, Miro JM, Mullins JI, Obel N, Poli G, Sandhu MS, Schuitemaker H, Shea PR, Theodorou I, Walker BD, Weintrob AC, Winkler CA, Wolinsky SM, Raychaudhuri S, Goldstein DB, Telenti A, de Bakker PI, Zagury JF, Fellay J (2015) Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load. Proc Natl Acad Sci U S A 112(47):14658–14663. doi:10.1073/pnas.1514867112

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • Mellors JW, Kingsley LA, Rinaldo CR Jr, Todd JA, Hoo BS, Kokka RP, Gupta P (1995) Quantitation of HIV-1 RNA in plasma predicts outcome after seroconversion. Ann Intern Med 122(8):573–579

    Article  CAS  PubMed  Google Scholar 

  • Michael NL, Chang G, Louie LG, Mascola JR, Dondero D, Birx DL, Sheppard HW (1997) The role of viral phenotype and CCR-5 gene defects in HIV-1 transmission and disease progression. Nat Med 3(3):338–340

    Article  CAS  PubMed  Google Scholar 

  • Miller WC, Rosenberg NE, Rutstein SE, Powers KA (2010) Role of acute and early HIV infection in the sexual transmission of HIV. Curr Opin HIV AIDS 5(4):277–282. doi:10.1097/COH.0b013e32833a0d3a 01222929-201007000-00004 [pii]

    Article  PubMed  PubMed Central  Google Scholar 

  • Miura T, Brockman MA, Brumme ZL, Brumme CJ, Pereyra F, Trocha A, Block BL, Schneidewind A, Allen TM, Heckerman D, Walker BD (2009) HLA-associated alterations in replication capacity of chimeric NL4-3 viruses carrying gag-protease from elite controllers of human immunodeficiency virus type 1. J Virol 83(1):140–149. doi:10.1128/JVI.01471-08

    Article  PubMed  CAS  Google Scholar 

  • Miura T, Brumme ZL, Brockman MA, Rosato P, Sela J, Brumme CJ, Pereyra F, Kaufmann DE, Trocha A, Block BL, Daar ES, Connick E, Jessen H, Kelleher AD, Rosenberg E, Markowitz M, Schafer K, Vaida F, Iwamoto A, Little S, Walker BD (2010) Impaired replication capacity of acute/early viruses in persons who become HIV controllers. J Virol 84(15):7581–7591. doi:10.1128/JVI.00286-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Monaco DC, Dilernia DA, Fiore-Gartland A, Yu T, Prince JL, Dennis KK, Qin K, Schaefer M, Claiborne DT, Kilembe W, Tang J, Price MA, Farmer P, Gilmour J, Bansal A, Allen S, Goepfert P, Hunter E (2016) Balance between transmitted HLA preadapted and nonassociated polymorphisms is a major determinant of HIV-1 disease progression. J Exp Med 213(10):2049–2063. doi:10.1084/jem.20151984

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nawaz F, Cicala C, Van Ryk D, Block KE, Jelicic K, McNally JP, Ogundare O, Pascuccio M, Patel N, Wei D, Fauci AS, Arthos J (2011) The genotype of early-transmitting HIV gp120 s promotes alphabeta-reactivity, revealing alphabetaCD4 + T cells as key targets in mucosal transmission. PLoS Pathog 7(2):e1001301. doi:10.1371/journal.ppat.1001301

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Oberle CS, Joos B, Rusert P, Campbell NK, Beauparlant D, Kuster H, Weber J, Schenkel CD, Scherrer AU, Magnus C, Kouyos R, Rieder P, Niederost B, Braun DL, Pavlovic J, Boni J, Yerly S, Klimkait T, Aubert V, Trkola A, Metzner KJ, Gunthard HF, Swiss HIVCS (2016) Tracing HIV-1 transmission: envelope traits of HIV-1 transmitter and recipient pairs. Retrovirology 13(1):62. doi:10.1186/s12977-016-0299-0

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ochsenbauer C, Edmonds TG, Ding H, Keele BF, Decker J, Salazar MG, Salazar-Gonzalez JF, Shattock R, Haynes BF, Shaw GM, Hahn BH, Kappes JC (2012) Generation of transmitted/founder HIV-1 infectious molecular clones and characterization of their replication capacity in CD4 T lymphocytes and monocyte-derived macrophages. J Virol 86(5):2715–2728. doi:10.1128/JVI.06157-11

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Paiardini M, Pandrea I, Apetrei C, Silvestri G (2009) Lessons learned from the natural hosts of HIV-related viruses. Annu Rev Med 60:485–495. doi:10.1146/annurev.med.60.041807.123753

    Article  CAS  PubMed  Google Scholar 

  • Pandrea I, Apetrei C (2010) Where the wild things are: pathogenesis of SIV infection in African nonhuman primate hosts. Curr HIV/AIDS Rep 7(1):28–36. doi:10.1007/s11904-009-0034-8

    Article  PubMed  PubMed Central  Google Scholar 

  • Pandrea I, Onanga R, Souquiere S, Mouinga-Ondeme A, Bourry O, Makuwa M, Rouquet P, Silvestri G, Simon F, Roques P, Apetrei C (2008) Paucity of CD4 + CCR5 + T cells may prevent transmission of simian immunodeficiency virus in natural nonhuman primate hosts by breast-feeding. J Virol 82(11):5501–5509. doi:10.1128/JVI.02555-07

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parrish NF, Wilen CB, Banks LB, Iyer SS, Pfaff JM, Salazar-Gonzalez JF, Salazar MG, Decker JM, Parrish EH, Berg A, Hopper J, Hora B, Kumar A, Mahlokozera T, Yuan S, Coleman C, Vermeulen M, Ding H, Ochsenbauer C, Tilton JC, Permar SR, Kappes JC, Betts MR, Busch MP, Gao F, Montefiori D, Haynes BF, Shaw GM, Hahn BH, Doms RW (2012) Transmitted/founder and chronic subtype C HIV-1 use CD4 and CCR5 receptors with equal efficiency and are not inhibited by blocking the integrin alpha4beta7. PLoS Pathog 8(5):e1002686. doi:10.1371/journal.ppat.1002686

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parrish NF, Gao F, Li H, Giorgi EE, Barbian HJ, Parrish EH, Zajic L, Iyer SS, Decker JM, Kumar A, Hora B, Berg A, Cai F, Hopper J, Denny TN, Ding H, Ochsenbauer C, Kappes JC, Galimidi RP, West AP Jr, Bjorkman PJ, Wilen CB, Doms RW, O’Brien M, Bhardwaj N, Borrow P, Haynes BF, Muldoon M, Theiler JP, Korber B, Shaw GM, Hahn BH (2013) Phenotypic properties of transmitted founder HIV-1. Proc Natl Acad Sci U S A 110(17):6626–6633. doi:10.1073/pnas.1304288110

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • Pilcher CD, Joaki G, Hoffman IF, Martinson FE, Mapanje C, Stewart PW, Powers KA, Galvin S, Chilongozi D, Gama S, Price MA, Fiscus SA, Cohen MS (2007) Amplified transmission of HIV-1: comparison of HIV-1 concentrations in semen and blood during acute and chronic infection. AIDS 21(13):1723–1730. doi:10.1097/QAD.0b013e3281532c82

    Article  PubMed  Google Scholar 

  • Powers KA, Poole C, Pettifor AE, Cohen MS (2008) Rethinking the heterosexual infectivity of HIV-1: a systematic review and meta-analysis. Lancet Infect Dis 8(9):553–563. doi:10.1016/S1473-3099(08)70156-7

    Article  PubMed  PubMed Central  Google Scholar 

  • Prince JL, Claiborne DT, Carlson JM, Schaefer M, Yu T, Lahki S, Prentice HA, Yue L, Vishwanathan SA, Kilembe W, Goepfert P, Price MA, Gilmour J, Mulenga J, Farmer P, Derdeyn CA, Tang J, Heckerman D, Kaslow RA, Allen SA, Hunter E (2012) Role of transmitted Gag CTL polymorphisms in defining replicative capacity and early HIV-1 pathogenesis. PLoS Pathog 8(11):e1003041. doi:10.1371/journal.ppat.1003041

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Quinn TC, Wawer MJ, Sewankambo N, Serwadda D, Li C, Wabwire-Mangen F, Meehan MO, Lutalo T, Gray RH (2000) Viral load and heterosexual transmission of human immunodeficiency virus type 1. Rakai Project Study Group. N Engl J Med 342(13):921–929. doi:10.1056/NEJM200003303421303

    Article  CAS  PubMed  Google Scholar 

  • Redd AD, Collinson-Streng AN, Chatziandreou N, Mullis CE, Laeyendecker O, Martens C, Ricklefs S, Kiwanuka N, Nyein PH, Lutalo T, Grabowski MK, Kong X, Manucci J, Sewankambo N, Wawer MJ, Gray RH, Porcella SF, Fauci AS, Sagar M, Serwadda D, Quinn TC (2012) Previously transmitted HIV-1 strains are preferentially selected during subsequent sexual transmissions. J Infect Dis 206(9):1433–1442. doi:10.1093/infdis/jis503

    Article  PubMed  PubMed Central  Google Scholar 

  • Regoes RR, Bonhoeffer S (2005) The HIV coreceptor switch: a population dynamical perspective. Trends Microbiol 13(6):269–277. doi:10.1016/j.tim.2005.04.005

    Article  CAS  PubMed  Google Scholar 

  • Richardson SI, Gray ES, Mkhize NN, Sheward DJ, Lambson BE, Wibmer CK, Masson L, Werner L, Garrett N, Passmore JA, Karim QA, Karim SS, Williamson C, Moore PL, Morris L (2015) South African HIV-1 subtype C transmitted variants with a specific V2 motif show higher dependence on alpha4beta7 for replication. Retrovirology 12:54. doi:10.1186/s12977-015-0183-3

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Roberts HE, Hurst J, Robinson N, Brown H, Flanagan P, Vass L, Fidler S, Weber J, Babiker A, Phillips RE, McLean AR, Frater J, investigators St (2015) Structured observations reveal slow HIV-1 CTL escape. PLoS genetics 11 (2):e1004914. doi:10.1371/journal.pgen.1004914

  • Sagar M, Lavreys L, Baeten JM, Richardson BA, Mandaliya K, Ndinya-Achola JO, Kreiss JK, Overbaugh J (2004) Identification of modifiable factors that affect the genetic diversity of the transmitted HIV-1 population. AIDS 18(4):615–619. 00002030-200403050-00005 [pii]

    Article  PubMed  Google Scholar 

  • Sagar M, Laeyendecker O, Lee S, Gamiel J, Wawer MJ, Gray RH, Serwadda D, Sewankambo NK, Shepherd JC, Toma J, Huang W, Quinn TC (2009) Selection of HIV variants with signature genotypic characteristics during heterosexual transmission. J Infect Dis 199(4):580–589. doi:10.1086/596557

    Article  PubMed  Google Scholar 

  • Salazar-Gonzalez JF, Bailes E, Pham KT, Salazar MG, Guffey MB, Keele BF, Derdeyn CA, Farmer P, Hunter E, Allen S, Manigart O, Mulenga J, Anderson JA, Swanstrom R, Haynes BF, Athreya GS, Korber BT, Sharp PM, Shaw GM, Hahn BH (2008) Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing. J Virol 82(8):3952–3970. doi:10.1128/JVI.02660-07 JVI.02660-07 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Salazar-Gonzalez JF, Salazar MG, Keele BF, Learn GH, Giorgi EE, Li H, Decker JM, Wang S, Baalwa J, Kraus MH, Parrish NF, Shaw KS, Guffey MB, Bar KJ, Davis KL, Ochsenbauer-Jambor C, Kappes JC, Saag MS, Cohen MS, Mulenga J, Derdeyn CA, Allen S, Hunter E, Markowitz M, Hraber P, Perelson AS, Bhattacharya T, Haynes BF, Korber BT, Hahn BH, Shaw GM (2009) Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. J Exp Med 206(6):1273–1289. doi:10.1084/jem.20090378 jem.20090378 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Samson M, Libert F, Doranz BJ, Rucker J, Liesnard C, Farber CM, Saragosti S, Lapoumeroulie C, Cognaux J, Forceille C, Muyldermans G, Verhofstede C, Burtonboy G, Georges M, Imai T, Rana S, Yi Y, Smyth RJ, Collman RG, Doms RW, Vassart G, Parmentier M (1996) Resistance to HIV-1 infection in caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature 382(6593):722–725. doi:10.1038/382722a0

    Article  ADS  CAS  PubMed  Google Scholar 

  • Sandler NG, Bosinger SE, Estes JD, Zhu RT, Tharp GK, Boritz E, Levin D, Wijeyesinghe S, Makamdop KN, del Prete GQ, Hill BJ, Timmer JK, Reiss E, Yarden G, Darko S, Contijoch E, Todd JP, Silvestri G, Nason M, Norgren RB Jr, Keele BF, Rao S, Langer JA, Lifson JD, Schreiber G, Douek DC (2014) Type I interferon responses in rhesus macaques prevent SIV infection and slow disease progression. Nature 511(7511):601–605. doi:10.1038/nature13554

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • Schmitz JE, Kuroda MJ, Santra S, Sasseville VG, Simon MA, Lifton MA, Racz P, Tenner-Racz K, Dalesandro M, Scallon BJ, Ghrayeb J, Forman MA, Montefiori DC, Rieber EP, Letvin NL, Reimann KA (1999) Control of viremia in simian immunodeficiency virus infection by CD8 + lymphocytes. Science 283(5403):857–860

    Article  ADS  CAS  PubMed  Google Scholar 

  • Schneidewind A, Brockman MA, Yang R, Adam RI, Li B, Le Gall S, Rinaldo CR, Craggs SL, Allgaier RL, Power KA, Kuntzen T, Tung CS, LaBute MX, Mueller SM, Harrer T, McMichael AJ, Goulder PJ, Aiken C, Brander C, Kelleher AD, Allen TM (2007) 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. J Virol 81(22):12382–12393. doi:10.1128/JVI.01543-07

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schneidewind A, Brumme ZL, Brumme CJ, Power KA, Reyor LL, O’Sullivan K, Gladden A, Hempel U, Kuntzen T, Wang YE, Oniangue-Ndza C, Jessen H, Markowitz M, Rosenberg ES, Sekaly RP, Kelleher AD, Walker BD, Allen TM (2009) Transmission and long-term stability of compensated CD8 escape mutations. J Virol 83(8):3993–3997. doi:10.1128/JVI.01108-08

    Article  CAS  PubMed  Google Scholar 

  • Selhorst P, Combrinck C, Ndabambi N, Ismail SD, Abrahams MR, Lacerda M, Samsunder N, Garrett N, Abdool Karim Q, Abdool Karim SS, Williamson C (2017a) Replication Capacity of Viruses from Acute Infection Drives HIV-1 Disease Progression. J Virol 91 (8). doi:10.1128/JVI.01806-16

  • Selhorst P, Masson L, Ismail SD, Samsunder N, Garrett N, Mansoor LE, Abdool Karim Q, Abdool Karim SS, Passmore JS, Williamson C (2017b) Cervicovaginal Inflammation Facilitates Acquisition of Less Infectious HIV Variants. Clin Infect Dis 64(1):79–82. doi:10.1093/cid/ciw663

    Article  PubMed  Google Scholar 

  • Shaw GM, Hunter E (2012) HIV transmission. Cold Spring Harb Perspect Med 2 (11). doi:10.1101/cshperspect.a006965

  • Stieh DJ, Maric D, Kelley ZL, Anderson MR, Hattaway HZ, Beilfuss BA, Rothwangl KB, Veazey RS, Hope TJ (2014) Vaginal challenge with an SIV-based dual reporter system reveals that infection can occur throughout the upper and lower female reproductive tract. PLoS Pathog 10(10):e1004440. doi:10.1371/journal.ppat.1004440

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Stieh DJ, Matias E, Xu H, Fought AJ, Blanchard JL, Marx PA, Veazey RS, Hope TJ (2016) Th17 Cells Are Preferentially Infected Very Early after Vaginal Transmission of SIV in Macaques. Cell Host Microbe 19(4):529–540. doi:10.1016/j.chom.2016.03.005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trask SA, Derdeyn CA, Fideli U, Chen Y, Meleth S, Kasolo F, Musonda R, Hunter E, Gao F, Allen S, Hahn BH (2002) Molecular epidemiology of human immunodeficiency virus type 1 transmission in a heterosexual cohort of discordant couples in Zambia. J Virol 76(1):397–405

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • UNAIDS (2016) Global AIDS Update 2016

    Google Scholar 

  • Veazey RS, Pilch-Cooper HA, Hope TJ, Alter G, Carias AM, Sips M, Wang X, Rodriguez B, Sieg SF, Reich A, Wilkinson P, Cameron MJ, Lederman MM (2016) Prevention of SHIV transmission by topical IFN-beta treatment. Mucosal Immunol 9(6):1528–1536. doi:10.1038/mi.2015.146

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Walker BD, Yu XG (2013) Unravelling the mechanisms of durable control of HIV-1. Nat Rev Immunol 13(7):487–498. doi:10.1038/nri3478

    Article  CAS  PubMed  Google Scholar 

  • Wawer MJ, Gray RH, Sewankambo NK, Serwadda D, Li X, Laeyendecker O, Kiwanuka N, Kigozi G, Kiddugavu M, Lutalo T, Nalugoda F, Wabwire-Mangen F, Meehan MP, Quinn TC (2005) Rates of HIV-1 transmission per coital act, by stage of HIV-1 infection, in Rakai. Uganda. J Infect Dis 191(9):1403–1409. doi:10.1086/429411 JID33445 [pii]

    Article  PubMed  Google Scholar 

  • Wilen CB, Parrish NF, Pfaff JM, Decker JM, Henning EA, Haim H, Petersen JE, Wojcechowskyj JA, Sodroski J, Haynes BF, Montefiori DC, Tilton JC, Shaw GM, Hahn BH, Doms RW (2011) Phenotypic and immunologic comparison of clade B transmitted/founder and chronic HIV-1 envelope glycoproteins. J Virol 85(17):8514–8527. doi:10.1128/JVI.00736-11

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wilen CB, Tilton JC, Doms RW (2012) HIV: Cell Binding and Entry. Cold Spring Harbor Perspectives in Medicine 2(8):a006866. doi:10.1101/cshperspect.a006866

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wolfs TF, Zwart G, Bakker M, Goudsmit J (1992) HIV-1 genomic RNA diversification following sexual and parenteral virus transmission. Virology 189(1):103–110

    Article  CAS  PubMed  Google Scholar 

  • Wolinsky SM, Wike CM, Korber BT, Hutto C, Parks WP, Rosenblum LL, Kunstman KJ, Furtado MR, Munoz JL (1992) Selective transmission of human immunodeficiency virus type-1 variants from mothers to infants. Science 255(5048):1134–1137

    Article  ADS  CAS  PubMed  Google Scholar 

  • Wright JK, Brumme ZL, Carlson JM, Heckerman D, Kadie CM, Brumme CJ, Wang B, Losina E, Miura T, Chonco F, van der Stok M, Mncube Z, Bishop K, Goulder PJ, Walker BD, Brockman MA, Ndung’u T (2010) Gag-protease-mediated replication capacity in HIV-1 subtype C chronic infection: associations with HLA type and clinical parameters. J Virol 84(20):10820–10831. doi:10.1128/JVI.01084-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wright JK, Novitsky V, Brockman MA, Brumme ZL, Brumme CJ, Carlson JM, Heckerman D, Wang B, Losina E, Leshwedi M, van der Stok M, Maphumulo L, Mkhwanazi N, Chonco F, Goulder PJ, Essex M, Walker BD, Ndung’u T (2011) Influence of Gag-protease-mediated replication capacity on disease progression in individuals recently infected with HIV-1 subtype C. J Virol 85(8):3996–4006. doi:10.1128/JVI.02520-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yokomaku Y, Miura H, Tomiyama H, Kawana-Tachikawa A, Takiguchi M, Kojima A, Nagai Y, Iwamoto A, Matsuda Z, Ariyoshi K (2004) Impaired processing and presentation of cytotoxic-T-lymphocyte (CTL) epitopes are major escape mechanisms from CTL immune pressure in human immunodeficiency virus type 1 infection. J Virol 78(3):1324–1332

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yue L, Prentice HA, Farmer P, Song W, He D, Lakhi S, Goepfert P, Gilmour J, Allen S, Tang J, Kaslow RA, Hunter E (2013) Cumulative impact of host and viral factors on HIV-1 viral-load control during early infection. J Virol 87(2):708–715. doi:10.1128/JVI.02118-12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yue L, Pfafferott KJ, Baalwa J, Conrod K, Dong CC, Chui C, Rong R, Claiborne DT, Prince JL, Tang J, Ribeiro RM, Cormier E, Hahn BH, Perelson AS, Shaw GM, Karita E, Gilmour J, Goepfert P, Derdeyn CA, Allen SA, Borrow P, Hunter E (2015) Transmitted virus fitness and host T cell responses collectively define divergent infection outcomes in two HIV-1 recipients. PLoS Pathog 11(1):e1004565. doi:10.1371/journal.ppat.1004565

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang LQ, MacKenzie P, Cleland A, Holmes EC, Brown AJ, Simmonds P (1993) Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection. J Virol 67(6):3345–3356

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu T, Mo H, Wang N, Nam DS, Cao Y, Koup RA, Ho DD (1993) Genotypic and phenotypic characterization of HIV-1 patients with primary infection. Science 261(5125):1179–1181

    Article  ADS  CAS  PubMed  Google Scholar 

  • Zhu T, Wang N, Carr A, Nam DS, Moor-Jankowski R, Cooper DA, Ho DD (1996) Genetic characterization of human immunodeficiency virus type 1 in blood and genital secretions: evidence for viral compartmentalization and selection during sexual transmission. J Virol 70(5):3098–3107

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zimmerman PA, Buckler-White A, Alkhatib G, Spalding T, Kubofcik J, Combadiere C, Weissman D, Cohen O, Rubbert A, Lam G, Vaccarezza M, Kennedy PE, Kumaraswami V, Giorgi JV, Detels R, Hunter J, Chopek M, Berger EA, Fauci AS, Nutman TB, Murphy PM (1997) Inherited resistance to HIV-1 conferred by an inactivating mutation in CC chemokine receptor 5: studies in populations with contrasting clinical phenotypes, defined racial background, and quantified risk. Mol Med 3(1):23–36

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road, Atlanta, GA, 30329, USA

    Daniela C. Monaco, Zachary Ende & Eric Hunter

  2. Department of Pathology and Laboratory Medicine, Emory University, 954 Gatewood Road, Atlanta, GA, 30329, USA

    Eric Hunter

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  1. Daniela C. Monaco
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  2. Zachary Ende
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  3. Eric Hunter
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  1. Emory Vaccine Center, Emory University, Atlanta, GA, USA

    Eric Hunter

  2. Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria

    Klaus Bister

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Dedication: This chapter is dedicated to Peter K. Vogt in honor of his 50 years as an editor of Current Topics of Microbiology and Immunology, his continued contributions to science and 45 years of mentorship and friendship.

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Monaco, D.C., Ende, Z., Hunter, E. (2017). Virus-Host Gene Interactions Define HIV-1 Disease Progression. In: Hunter, E., Bister, K. (eds) Viruses, Genes, and Cancer. Current Topics in Microbiology and Immunology, vol 407. Springer, Cham. https://doi.org/10.1007/82_2017_33

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