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Assays to Measure Latency, Reservoirs, and Reactivation

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HIV-1 Latency

Part of the book series: Current Topics in Microbiology and Immunology ((CT MICROBIOLOGY,volume 417))

Abstract

HIV-1 persists even in patients who are successfully treated with combination antiretroviral therapy. The major barrier to cure is a small pool of latently infected resting CD4+ T cells carrying an integrated copy of the viral genome that is not expressed while the cells remain in a resting state. Targeting this latent reservoir is a major focus of HIV-1 cure research, and the development of a rapid and scalable assay for the reservoir is a rate-limiting step in the search for a cure. The most commonly used assays are standard PCR assays targeting conserved regions of the HIV-1 genome. However, because the vast majority of HIV-1 proviruses are defective, such assays may not accurately capture changes in the minor subset of proviruses that are replication-competent and that pose a barrier to cure. On the other hand, the viral outgrowth assay that was used to initially define the latent reservoir may underestimate reservoir size because not all replication-competent proviruses are induced by a single round of T cell activation in this assay. Therefore, this assay is best regarded as a definitive minimal estimate of reservoir size. The best approach may be to measure all of the proviruses with the potential to cause viral rebound. A variety of novel assays have recently been described. Ultimately, the assay that best predicts time to viral rebound will be the most useful to the cure effort.

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References

  • Adams M, Sharmeen L, Kimpton J, Romeo JM, Garcia JV, Peterlin BM, Groudine M, Emerman M (1994) Cellular latency in human immunodeficiency virus-infected individuals with high CD4 levels can be detected by the presence of promoter-proximal transcripts. Proc Natl Acad Sci USA 91(9):3862–3866

    Article  CAS  Google Scholar 

  • Bailey JR, Sedaghat AR, Kieffer T, Brennan T, Lee PK, Wind-Rotolo M, Haggerty CM, Kamireddi AR, Liu Y, Lee J, Persaud D, Gallant JE, Cofrancesco J Jr, Quinn TC, Wilke CO, Ray SC, Siliciano JD, Nettles RE, Siliciano RF (2006) Residual human immunodeficiency virus type 1 viremia in some patients on antiretroviral therapy is dominated by a small number of invariant clones rarely found in circulating CD4+ T cells. J Virol 80(13):6441–6457

    Article  CAS  Google Scholar 

  • Baxter AE, Niessl J, Fromentin R, Richard J, Porichis F, Charlebois R, Massanella M, Brassard N, Alsahafi N, Delgado GG, Routy JP, Walker BD, Finzi A, Chomont N, Kaufmann DE (2016) Single-cell characterization of viral translation-competent reservoirs in HIV-infected individuals. Cell Host Microbe 20(3):368–380

    Article  CAS  Google Scholar 

  • Beliakova-Bethell N, Hezareh M, Wong JK, Strain MC, Lewinski MK, Richman DD, Spina CA (2017) Relative efficacy of T cell stimuli as inducers of productive HIV-1 replication in latently infected CD4 lymphocytes from patients on suppressive cART. Virology 508:127–133

    Article  CAS  Google Scholar 

  • Blankson JN, Finzi D, Pierson TC, Sabundayo BP, Chadwick K, Margolick JB, Quinn TC, Siliciano RF (2000) Biphasic decay of latently infected CD4+ T cells in acute human immunodeficiency virus type 1 infection. J Infect Dis 182(6):1636–1642

    Article  CAS  Google Scholar 

  • Bohnlein E, Lowenthal JW, Siekevitz M, Ballard DW, Franza BR, Greene WC (1988) The same inducible nuclear proteins regulates mitogen activation of both the interleukin-2 receptor-alpha gene and type 1 HIV. Cell 53(5):827–836

    Article  CAS  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  Google Scholar 

  • Bruner KM, Murray AJ, Pollack RA, Soliman MG, Laskey SB, Capoferri AA, Lai J, Strain MC, Lada SM, Hoh R, Ho YC, Richman DD, Deeks SG, Siliciano JD, Siliciano RF (2016) Defective proviruses rapidly accumulate during acute HIV-1 infection. Nat Med 22(9):1043–1049

    Article  CAS  Google Scholar 

  • Bui JK, Sobolewski MD, Keele BF, Spindler J, Musick A, Wiegand A, Luke BT, Shao W, Hughes SH, Coffin JM, Kearney MF, Mellors JW (2017) Proviruses with identical sequences comprise a large fraction of the replication-competent HIV reservoir. PLoS Pathog 13(3):E1006283

    Article  Google Scholar 

  • Bukrinsky MI, Stanwick TL, Dempsey MP, Stevenson M (1991) Quiescent T lymphocytes as an inducible virus reservoir in HIV-1 infection. Science (New York, N.Y.) 254(5030):423–427

    Article  CAS  Google Scholar 

  • Bullen CK, Laird GM, Durand CM, Siliciano, JD, Siliciano RF (2014) New ex vivo approaches distinguish effective and ineffective single agents for reversing HIV-1 latency in vivo. Nat Med

    Google Scholar 

  • Calantone N, Wu F, Klase Z, Deleage C, Perkins M, Matsuda K, Thompson EA, Ortiz AM, Vinton CL, Ourmanov I, Lore K, Douek DC, Estes JD, Hirsch VM, Brenchley JM (2014) Tissue myeloid cells in SIV-infected primates acquire viral DNA through phagocytosis of infected T cells. Immunity 41(3):493–502

    Article  CAS  Google Scholar 

  • Chun TW, Finzi D, Margolick J, Chadwick K, Schwartz D, Siliciano RF (1995) In vivo fate of HIV-1-infected T cells: quantitative analysis of the transition to stable latency. Nat Med 1(12):1284–1290

    Article  CAS  Google Scholar 

  • Chun TW, Carruth L, Finzi D, Shen X, Digiuseppe JA, Taylor H, Hermankova M, Chadwick K, Margolick J, Quinn TC, Kuo YH, Brookmeyer R, Zeiger MA, Barditch-Crovo P, Siliciano RF (1997a) Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection. Nature 387(6629):183–188

    Article  CAS  Google Scholar 

  • Chun TW, Stuyver L, Mizell SB, Ehler LA, Mican JA, Baseler M, Lloyd AL, Nowak MA, Fauci AS (1997b) Presence of an inducible HIV-1 latent reservoir during highly active antiretroviral therapy. Proc Natl Acad Sci USA 94(24):13193–13197

    Article  CAS  Google Scholar 

  • Cillo AR, Sobolewski MD, Bosch RJ, Fyne E, Piatak M Jr, Coffin JM, Mellors JW (2014) Quantification of HIV-1 latency reversal in resting CD4+ T cells from patients on suppressive antiretroviral therapy. Proc Natl Acad Sci USA 111(19):7078–7083

    Article  CAS  Google Scholar 

  • Crooks AM, Bateson R, Cope AB, Dahl NP, Griggs MK, Kuruc JD, Gay CL, Eron JJ, Margolis DM, Bosch RJ, Archin NM (2015) Precise quantitation of the latent HIV-1 reservoir: implications for eradication strategies. J Infect Dis

    Google Scholar 

  • Davey RT Jr, Bhat N, Yoder C, Chun TW, Metcalf JA, Dewar R, Natarajan V, Lempicki RA, Adelsberger JW, Miller KD, Kovacs JA, Polis MA, Walker RE, Falloon J, Masur H, Gee D, Baseler M, Dimitrov DS, Fauci AS, Lane HC (1999) HIV-1 and T cell dynamics after interruption of highly active antiretroviral therapy (HAART) in patients with a history of sustained viral suppression. Proc Natl Acad Sci USA 96(26):15109–15114

    Article  CAS  Google Scholar 

  • Deeks SG, Lewin SR, Ross AL, Ananworanich J, Benkirane M, Cannon P, Chomont N, Douek D, Lifson JD, Lo YR, Kuritzkes D, Margolis D, Mellors J, Persaud D, Tucker JD, Barre-Sinoussi F, International Aids Society Towards A Cure Working Group, Alter G, Auerbach J, Autran B, Barouch DH, Behrens G, Cavazzana M, Chen Z, Cohen EA, Corbelli GM, Eholie S, Eyal N, Fidler S, Garcia L, Grossman C, Henderson G, Henrich TJ, Jefferys R, Kiem HP, Mccune J, Moodley K, Newman PA, Nijhuis M, Nsubuga MS, Ott M, Palmer S, Richman D, Saez-Cirion A, Sharp M, Siliciano J, Silvestri G, Singh J, Spire B, Taylor J, Tolstrup M, Valente S, Van Lunzen J, Walensky R, Wilson I, Zack J (2016) International AIDS society global scientific strategy: towards an HIV cure 2016. Nat Med 22(8):839–850

    Article  CAS  Google Scholar 

  • Deleage C, Wietgrefe SW, Del Prete G, Morcock DR, Hao XP, Piatak M Jr, Bess J, Anderson JL, Perkey KE, Reilly C, Mccune JM, Haase AT, Lifson JD, Schacker TW, Estes JD (2016) Defining HIV and SIV reservoirs in lymphoid tissues. Pathog Immun 1(1):68–106

    Article  Google Scholar 

  • Descours B, Petitjean G, Lopez-Zaragoza JL, Bruel T, Raffel R, Psomas C, Reynes J, Lacabaratz C, Levy Y, Schwartz O, Lelievre JD, Benkirane M (2017) CD32a is a marker of a CD4 T-cell HIV reservoir harbouring replication-competent proviruses. Nature 543(7646):564–567

    Article  CAS  Google Scholar 

  • Dinoso JB, Kim SY, Wiegand AM, Palmer SE, Gange SJ, Cranmer L, O’shea A, Callender M, Spivak A, Brennan T, Kearney MF, Proschan MA, Mican JM, Rehm CA, Coffin JM, Mellors JW, Siliciano RF, Maldarelli F (2009a) Treatment intensification does not reduce residual HIV-1 viremia in patients on highly active antiretroviral therapy. Proc Natl Acad Sci USA 106(23):9403–9408

    Article  CAS  Google Scholar 

  • Dinoso JB, Rabi SA, Blankson JN, Gama L, Mankowski JL, Siliciano RF, Zink MC, Clements JE (2009b) A simian immunodeficiency virus-infected macaque model to study viral reservoirs that persist during highly active antiretroviral therapy. J Virol 83(18):9247–9257

    Article  CAS  Google Scholar 

  • Dornadula G, Zhang H, Vanuitert B, Stern J, Livornese L Jr, Ingerman MJ, Witek J, Kedanis RJ, Natkin J, Desimone J, Pomerantz RJ (1999) Residual HIV-1 RNA in blood plasma of patients taking suppressive highly active antiretroviral therapy. JAMA, J Am Med Assoc 282(17):1627–1632

    Article  CAS  Google Scholar 

  • Duh EJ, Maury WJ, Folks TM, Fauci AS, Rabson AB (1989) Tumor necrosis factor alpha activates human immunodeficiency virus type 1 through induction of nuclear factor binding to the NF-kappa B sites in the long terminal repeat. Proc Natl Acad Sci USA 86(15):5974–5978

    Article  CAS  Google Scholar 

  • Eisele E, Siliciano RF (2012) Redefining the viral reservoirs that prevent HIV-1 eradication. Immunity 37(3):377–388

    Article  CAS  Google Scholar 

  • Eriksson S, Graf EH, Dahl V, Strain MC, Yukl SA, Lysenko ES, Bosch RJ, Lai J, Chioma S, Emad F, Abdel-Mohsen M, Hoh R, Hecht F, Hunt P, Somsouk M, Wong J, Johnston R, Siliciano RF, Richman DD, O’doherty U, Palmer S, Deeks SG, Siliciano JD (2013) Comparative analysis of measures of viral reservoirs in HIV-1 eradication studies. PLoS Pathog 9(2):E1003174

    Article  CAS  Google Scholar 

  • Finzi D, Hermankova M, Pierson T, Carruth LM, Buck C, Chaisson RE, Quinn TC, Chadwick K, Margolick J, Brookmeyer R, Gallant J, Markowitz M, Ho DD, Richman DD, Siliciano RF (1997) Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy. Science (New York, N.Y.) 278(5341):1295–1300

    Article  CAS  Google Scholar 

  • Finzi D, Blankson J, Siliciano JD, Margolick JB, Chadwick K, Pierson T, Smith K, Lisziewicz J, Lori F, Flexner C, Quinn TC, Chaisson RE, Rosenberg E, Walker B, Gange S, Gallant J, Siliciano RF (1999) Latent infection of CD4+ T cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective combination therapy. Nat Med 5(5):512–517

    Article  CAS  Google Scholar 

  • Gama L, Abreu CM, Shirk EN, Price SL, Li M, Laird GM, Pate KA, Wietgrefe SW, O’connor SL, Pianowski L, Haase AT, Van Lint C, Siliciano RF, Clements JE, Lra-Siv Study Group (2017) Reactivation of simian immunodeficiency virus reservoirs in the brain of virally suppressed macaques. AIDS (London, England) 31(1):5–14

    Article  CAS  Google Scholar 

  • Gandhi RT, Zheng L, Bosch RJ, Chan ES, Margolis DM, Read S, Kallungal B, Palmer S, Medvik K, Lederman MM, Alatrakchi N, Jacobson JM, Wiegand A, Kearney M, Coffin JM, Mellors JW, Eron JJ, Aids Clinical Trials Group A5244 Team (2010) The effect of raltegravir intensification on low-level residual viremia in HIV-infected patients on antiretroviral therapy: a randomized controlled trial. PLOS Med 7(8):E1000321

    Google Scholar 

  • Grau-Exposito J, Serra-Peinado C, Miguel L, Navarro J, Curran A, Burgos J, Ocana I, Ribera E, Torrella A, Planas B, Badia R, Castellvi J, Falco V, Crespo M, Buzon MJ (2017) A novel single-cell fish-flow assay identifies effector memory Cd4+ T Cells as a major niche for HIV-1 transcription in HIV-infected patients. Mbio 8(4). doi:10.1128/Mbio.00876-17

  • Gulick RM, Mellors JW, Havlir D, Eron JJ, Gonzalez C, Mcmahon D, Richman DD, Valentine FT, Jonas L, Meibohm A, Emini EA, Chodakewitz JA (1997) Treatment with indinavir, zidovudine, and lamivudine in adults with human immunodeficiency virus infection and prior antiretroviral therapy. N Engl J Med 337(11):734–739

    Article  CAS  Google Scholar 

  • Hammer SM, Squires KE, Hughes MD, Grimes JM, Demeter LM, Currier JS, Eron JJ Jr, Feinberg JE, Balfour HH Jr, Deyton LR, Chodakewitz JA, Fischl MA (1997) A controlled trial of two nucleoside analogues plus indinavir in persons with human immunodeficiency virus infection and CD4 cell counts of 200 per cubic millimeter or less. AIDS Clinical Trials Group 320 Study Team. N Engl J Med 337(11):725–733

    Article  CAS  Google Scholar 

  • Henrich TJ, Hu Z, Li JZ, Sciaranghella G, Busch MP, Keating SM, Gallien S, Lin NH, Giguel FF, Lavoie L, Ho VT, Armand P, Soiffer RJ, Sagar M, Lacasce AS, Kuritzkes DR (2013) Long-term reduction in peripheral blood HIV type 1 reservoirs following reduced-intensity conditioning allogeneic stem cell transplantation. J Infect Dis 207(11):1694–1702

    Article  CAS  Google Scholar 

  • Henrich TJ, Hanhauser E, Marty FM, Sirignano MN, Keating S, Lee TH, Robles YP, Davis BT, Li JZ, Heisey A, Hill AL, Busch MP, Armand P, Soiffer RJ, Altfeld M, Kuritzkes DR (2014) Antiretroviral-free HIV-1 remission and viral rebound after allogeneic stem cell transplantation: report of 2 cases. Ann Intern Med 161(5):319–327

    Article  Google Scholar 

  • Hermankova M, Ray SC, Ruff C, Powell-Davis M, Ingersoll R, D’aquila RT, Quinn TC, Siliciano JD, Siliciano RF, Persaud D (2001) HIV-1 drug resistance profiles in children and adults with viral load of< 50 copies/ml receiving combination therapy. JAMA, J Am Med Assoc 286(2):196–207

    Article  CAS  Google Scholar 

  • Hermankova M, Siliciano JD, Zhou Y, Monie D, Chadwick K, Margolick JB, Quinn TC, Siliciano RF (2003) Analysis of human immunodeficiency virus type 1 gene expression in latently infected resting CD4+ T lymphocytes in vivo. J Virol 77(13):7383–7392

    Article  CAS  Google Scholar 

  • Hill AL, Rosenbloom DI, Fu F, Nowak MA, Siliciano RF (2014) Predicting the outcomes of treatment to eradicate the latent reservoir for HIV-1. Proc Natl Acad Sci USA

    Google Scholar 

  • Ho DD, Neumann AU, Perelson AS, Chen W, Leonard JM, Markowitz M (1995) Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature 373(6510):123–126

    Article  CAS  Google Scholar 

  • Ho YC, Shan L, Hosmane NN, Wang J, Laskey SB, Rosenbloom DI, Lai J, Blankson JN, Siliciano JD, Siliciano RF (2013) Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure. Cell 155(3):540–551

    Article  CAS  Google Scholar 

  • Honeycutt JB, Wahl A, Baker C, Spagnuolo RA, Foster J, Zakharova O, Wietgrefe S, Caro-Vegas C, Madden V, Sharpe G, Haase AT, Eron JJ, Garcia JV (2016) Macrophages sustain HIV replication in vivo independently of T cells. J Clin Invest

    Google Scholar 

  • Hosmane NN, Kwon KJ, Bruner KM, Capoferri AA, Beg S, Rosenbloom DI, Keele BF, Ho YC, Siliciano JD, Siliciano RF (2017) Proliferation of latently infected CD4+ T cells carrying replication-competent HIV-1: Potential role in latent reservoir dynamics. J Exp Med 214(4):959–972

    Article  CAS  Google Scholar 

  • Imamichi H, Dewar RL, Adelsberger JW, Rehm CA, O’doherty U, Paxinos EE, Fauci AS, Lane HC (2016) Defective HIV-1 proviruses produce novel protein-coding RNA species in HIV-infected patients on combination antiretroviral therapy. Proc Natl Acad Sci USA

    Google Scholar 

  • Kieffer TL, Finucane MM, Nettles RE, Quinn TC, Broman KW, Ray SC, Persaud D, Siliciano RF (2004) Genotypic analysis of HIV-1 drug resistance at the limit of detection: virus production without evolution in treated adults with undetectable HIV loads. J Infect Dis 189(8):1452–1465

    Article  CAS  Google Scholar 

  • Kinoshita S, Chen BK, Kaneshima H, Nolan GP (1998) Host control of HIV-1 parasitism in T cells by the nuclear factor of activated T cells. Cell 95(5):595–604

    Article  CAS  Google Scholar 

  • Laird GM, Eisele EE, Rabi SA, Lai J, Chioma S, Blankson JN, Siliciano JD, Siliciano RF (2013) Rapid quantification of the latent reservoir for HIV-1 using a viral outgrowth assay. PLoS Pathog 9(5):E1003398

    Article  CAS  Google Scholar 

  • Laird GM, Rosenbloom DI, Lai J, Siliciano RF, Siliciano JD (2016) Measuring the frequency of latent HIV-1 in resting Cd4(+) T cells using a limiting dilution coculture assay. Methods Mol Biol (Clifton, N.J.) 1354:239–253

    Google Scholar 

  • Lee GQ, Orlova-Fink N, Einkauf K, Chowdhury FZ, Sun X, Harrington S, Kuo HH, Hua S, Chen HR, Ouyang Z, Reddy K, Dong K, Ndung’u T, Walker BD, Rosenberg ES, Yu XG, Lichterfeld M (2017) Clonal expansion of genome-intact HIV-1 in functionally polarized Th1 CD4+ T cells. J Clin Investig 127(7):2689–2696

    Article  Google Scholar 

  • Lin X, Irwin D, Kanazawa S, Huang L, Romeo J, Yen TS, Peterlin BM (2003) Transcriptional profiles of latent human immunodeficiency virus in infected individuals: effects of Tat on the host and reservoir. J Virol 77(15):8227–8236

    Article  CAS  Google Scholar 

  • Liszewski MK, Yu JJ, O’doherty U (2009) Detecting HIV-1 integration by repetitive-sampling Alu-gag PCR. Methods (San Diego, Calif.) 47(4):254–260

    Google Scholar 

  • Lorenzi JC, Cohen YZ, Cohn LB, Kreider EF, Barton JP, Learn GH, Oliveira T, Lavine CL, Horwitz JA, Settler A, Jankovic M, Seaman MS, Chakraborty AK, Hahn BH, Caskey M, Nussenzweig MC (2016) Paired quantitative and qualitative assessment of the replication-competent HIV-1 reservoir and comparison with integrated proviral DNA. Proc Natl Acad Sci USA 113(49):E7908–E7916

    Article  CAS  Google Scholar 

  • Luzuriaga K, Gay H, Ziemniak C, Sanborn KB, Somasundaran M, Rainwater-Lovett K, Mellors JW, Rosenbloom D, Persaud D (2015) Viremic relapse after HIV-1 remission in a perinatally infected child. N Engl J Med 372(8):786–788

    Article  CAS  Google Scholar 

  • Maldarelli F, Palmer S, King MS, Wiegand A, Polis MA, Mican J, Kovacs JA, Davey RT, Rock-Kress D, Dewar R, Liu S, Metcalf JA, Rehm C, Brun SC, Hanna GJ, Kempf DJ, Coffin JM, Mellors JW (2007) ART suppresses plasma HIV-1 RNA to a stable set point predicted by pretherapy viremia. PLoS Pathog 3(4):E46

    Article  Google Scholar 

  • Massanella M, Richman DD (2016) Measuring the latent reservoir in vivo. J Clin Investig 126(2):464–472

    Article  Google Scholar 

  • Nabel G, Baltimore D (1987) An inducible transcription factor activates expression of human immunodeficiency virus in T cells. Nature 326(6114):711–713

    Article  CAS  Google Scholar 

  • Nettles RE, Kieffer TL, Kwon P, Monie D, Han Y, Parsons T, Cofrancesco J Jr, Gallant JE, Quinn TC, Jackson B, Flexner C, Carson K, Ray S, Persaud D, Siliciano RF (2005) Intermittent HIV-1 viremia (Blips) and drug resistance in patients receiving HAART. JAMA, J Am Med Assoc 293(7):817–829

    Article  CAS  Google Scholar 

  • O’doherty U, Swiggard WJ, Jeyakumar D, Mcgain D, Malim MH (2002) A sensitive, quantitative assay for human immunodeficiency virus type 1 integration. J Virol 76(21):10942–10950

    Article  Google Scholar 

  • Palmer S, Wiegand AP, Maldarelli F, Bazmi H, Mican JM, Polis M, Dewar RL, Planta A, Liu S, Metcalf JA, Mellors JW, Coffin JM (2003) New real-time reverse transcriptase-initiated PCR assay with single-copy sensitivity for human immunodeficiency virus type 1 RNA in plasma. J Clin Microbiol 41(10):4531–4536

    Article  CAS  Google Scholar 

  • Passaes CP, Bruel T, Decalf J, David A, Angin M, Monceaux V, Muller-Trutwin M, Noel N, Bourdic K, Lambotte O, Albert ML, Duffy D, Schwartz O, Saez-Cirion A, Anrs Rhiviera Consortium (2017) Ultrasensitive HIV-1 P24 assay detects single infected cells and differences in reservoir induction by latency reversal agents. J Virol 91(6). doi:10.1128/Jvi.02296-16. Print Mar 15 2017

  • Pearson R, Kim YK, Hokello J, Lassen K, Friedman J, Tyagi M, Karn J (2008) Epigenetic silencing of human immunodeficiency virus (HIV) transcription by formation of restrictive chromatin structures at the viral long terminal repeat drives the progressive entry of HIV into latency. J Virol 82(24):12291–12303

    Article  CAS  Google Scholar 

  • Perelson AS, Essunger P, Cao Y, Vesanen M, Hurley A, Saksela K, Markowitz M, Ho DD (1997) Decay characteristics of HIV-1-infected compartments during combination therapy. Nature 387(6629):188–191

    Article  CAS  Google Scholar 

  • Perng GC, Jones C (2010) Towards an understanding of the herpes simplex virus type 1 latency-reactivation cycle. Interdisc Perspect Infect Dis 2010:262415

    Google Scholar 

  • Persaud D, Siberry GK, Ahonkhai A, Kajdas J, Monie D, Hutton N, Watson DC, Quinn TC, Ray SC, Siliciano RF (2004) Continued production of drug-sensitive human immunodeficiency virus type 1 in children on combination antiretroviral therapy who have undetectable viral loads. J Virol 78(2):968–979

    Article  CAS  Google Scholar 

  • Persaud D, Gay H, Ziemniak C, Chen YH, Piatak M Jr, Chun TW, Strain M, Richman D, Luzuriaga K (2013) Absence of detectable HIV-1 viremia after treatment cessation in an infant. N Engl J Med 369(19):1828–1835

    Article  CAS  Google Scholar 

  • Piatak M Jr, Saag MS, Yang LC, Clark SJ, Kappes JC, Luk KC, Hahn BH, Shaw GM, Lifson JD (1993) High levels of HIV-1 in plasma during all stages of infection determined by competitive PCR. Science (New York, N.Y.) 259(5102):1749–1754

    Article  CAS  Google Scholar 

  • Pollack RA, Jones RB, Pertea M, Bruner KM, Martin AR, Thomas AS, Capoferri AA, Beg SA, Huang SH, Karandish S, Hao H, Halper-Stromberg E, Yong PC, Kovacs C, Benko E, Siliciano RF, Ho YC (2017) Defective HIV-1 Proviruses Are Expressed and Can Be Recognized by Cytotoxic T Lymphocytes, which Shape the Proviral Landscape. Cell Host Microbe 21(4):494–506. E4

    Article  Google Scholar 

  • Procopio FA, Fromentin R, Kulpa DA, Brehm JH, Bebin AG, Strain MC, Richman DD, O’doherty U, Palmer S, Hecht FM, Hoh R, Barnard RJ, Miller MD, Hazuda DJ, Deeks SG, Sekaly RP, Chomont N (2015) A novel assay to measure the magnitude of the inducible viral reservoir in HIV-infected individuals. Ebiomedicine 2(8):872–881

    Article  Google Scholar 

  • Rice AP, Herrmann CH (2003) Regulation of TAK/P-TEFb in CD4+ T lymphocytes and macrophages. Curr HIV Res 1(4):395–404

    Article  CAS  Google Scholar 

  • Richman DD, Wrin T, Little SJ, Petropoulos CJ (2003) Rapid evolution of the neutralizing antibody response to HIV type 1 infection. Proc Natl Acad Sci USA 100(7):4144–4149

    Article  CAS  Google Scholar 

  • Rosenbloom DI, Elliott O, Hill AL, Henrich TJ, Siliciano JM, Siliciano RF (2015) Designing and interpreting limiting dilution assays: general principles and applications to the latent reservoir for human immunodeficiency virus-1. Open Forum Infect Dis 2(4):Ofv123

    Google Scholar 

  • Rothenberger MK, Keele BF, Wietgrefe SW, Fletcher CV, Beilman GJ, Chipman JG, Khoruts A, Estes JD, Anderson J, Callisto SP, Schmidt TE, Thorkelson A, Reilly C, Perkey K, Reimann TG, Utay NS, Nganou Makamdop K, Stevenson M, Douek DC, Haase AT, Schacker TW (2015) Large number of rebounding/founder HIV variants emerge from multifocal infection in lymphatic tissues after treatment interruption. Proc Natl Acad Sci USA 112(10):E1126–E1134

    Article  CAS  Google Scholar 

  • Sanyal A, Mailliard RB, Rinaldo CR, Ratner D, Ding M, Chen Y, Zerbato JM, Giacobbi NS, Venkatachari NJ, Patterson BK, Chargin A, Sluis-Cremer N, Gupta P (2017) Novel assay reveals a large, inducible, replication-competent HIV-1 reservoir in resting CD4+ T cells. Nat Med 23(7):885–889

    Article  CAS  Google Scholar 

  • Shan L, Rabi SA, Laird GM, Eisele E, Zhang H, Margolick JB, Siliciano RF (2013) A novel PCR assay for quantification of HIV-1 RNA. J Virol

    Google Scholar 

  • Shan L, Deng K, Xing S, Capoferri A, Gao H, Durand CM, Rabi SA, Laird GM, Kim M, Hosmane NN, Yang HC, Zhang H, Margolick JB, Ke R, Siliciano JD, Siliciano RF (2017) Unique features of effector to memory transition render CD4+ T cells permissive for latent HIV-1 infection. Immunity. In Press

    Google Scholar 

  • Shen A, Zink MC, Mankowski JL, Chadwick K, Margolick JB, Carruth LM, Li M, Clements JE, Siliciano RF (2003) Resting CD4+ T lymphocytes but not thymocytes provide a latent viral reservoir in a simian immunodeficiency virus-Macaca nemestrina model of human immunodeficiency virus type 1-infected patients on highly active antiretroviral therapy. J Virol 77(8):4938–4949

    Article  CAS  Google Scholar 

  • Siliciano JD, Kajdas J, Finzi D, Quinn TC, Chadwick K, Margolick JB, Kovacs C, Gange SJ, Siliciano RF (2003) Long-term follow-up studies confirm the stability of the latent reservoir for HIV-1 in resting CD4+ T cells. Nat Med 9(6):727–728

    Article  CAS  Google Scholar 

  • Siliciano JD, Siliciano RF (2005) Enhanced culture assay for detection and quantitation of latently infected, resting CD4+ T-cells carrying replication-competent virus in HIV-1-infected individuals. Methods Mol Biol (Clifton, N.J.) 304:3–15

    Google Scholar 

  • Speck SH, Ganem D (2010) Viral latency and its regulation: lessons from the gamma-herpesviruses. Cell Host Microbe 8(1):100–115

    Article  CAS  Google Scholar 

  • Strain MC, Gunthard HF, Havlir DV, Ignacio CC, Smith DM, Leigh-Brown AJ, Macaranas TR, Lam RY, Daly OA, Fischer M, Opravil M, Levine H, Bacheler L, Spina CA, Richman DD, Wong JK (2003) Heterogeneous clearance rates of long-lived lymphocytes infected with HIV: intrinsic stability predicts lifelong persistence. Proc Natl Acad Sci USA 100(8):4819–4824

    Article  CAS  Google Scholar 

  • Strain MC, Richman DD (2013) New assays for monitoring residual HIV burden in effectively treated individuals. Curr Opin HIV AIDS 8(2):106–110

    Article  CAS  Google Scholar 

  • Tobin NH, Learn GH, Holte SE, Wang Y, Melvin AJ, Mckernan JL, Pawluk DM, Mohan KM, Lewis PF, Mullins JI, Frenkel LM (2005) Evidence that low-level viremias during effective highly active antiretroviral therapy result from two processes: expression of archival virus and replication of virus. J Virol 79(15):9625–9634

    Article  CAS  Google Scholar 

  • Treatment Action Group (2017, June 12), 2017-Last Update, Research toward a cure

    Google Scholar 

  • Van Lint C, Emiliani S, Ott M, Verdin E (1996) Transcriptional activation and chromatin remodeling of the HIV-1 promoter in response to histone acetylation. Embo J 15(5):1112–1120

    Article  Google Scholar 

  • Wei DG, Chiang V, Fyne E, Balakrishnan M, Barnes T, Graupe M, Hesselgesser J, Irrinki A, Murry JP, Stepan G, Stray KM, Tsai A, Yu H, Spindler J, Kearney M, Spina CA, Mcmahon D, Lalezari J, Sloan D, Mellors J, Geleziunas R, Cihlar T (2014) Histone deacetylase inhibitor romidepsin induces HIV expression in CD4 T cells from patients on suppressive antiretroviral therapy at concentrations achieved by clinical dosing. PLoS Pathog 10(4):E1004071

    Article  Google Scholar 

  • Wei X, Ghosh SK, Taylor ME, Johnson VA, Emini EA, Deutsch P, Lifson JD, Bonhoeffer S, Nowak MA, Hahn BH (1995) Viral dynamics in human immunodeficiency virus type 1 infection. Nature 373(6510):117–122

    Article  CAS  Google Scholar 

  • Wei X, Decker JM, Wang S, Hui H, Kappes JC, Wu X, Salazar-Gonzalez JF, Salazar MG, Kilby JM, Saag MS, Komarova NL, Nowak MA, Hahn BH, Kwong PD, Shaw GM (2003) Antibody neutralization and escape by HIV-1. Nature 422(6929):307–312

    Article  CAS  Google Scholar 

  • Wong JK, Hezareh M, Gunthard HF, Havlir DV, Ignacio CC, Spina CA, Richman DD (1997) Recovery of replication-competent HIV despite prolonged suppression of plasma viremia. Science (New York, N.Y.) 278(5341):1291–1295

    Article  CAS  Google Scholar 

  • Wu G, Swanson M, Talla A, Graham D, Strizki J, Gorman D, Barnard RJ, Blair W, Sogaard OS, Tolstrup M, Ostergaard L, Rasmussen TA, Sekaly RP, Archin NM, Margolis DM, Hazuda DJ, Howell BJ (2017) HDAC inhibition induces HIV-1 protein and enables immune-based clearance following latency reversal. JCI Insight 2(16). doi:10.1172/Jci.Insight.92901

  • Yu JJ, Wu TL, Liszewski MK, Dai J, Swiggard WJ, Baytop C, Frank I, Levine BL, Yang W, Theodosopoulos T, O’doherty U (2008) A more precise HIV integration assay designed to detect small differences finds lower levels of integrated DNA in HAART treated patients. Virology 379(1):78–86

    Article  CAS  Google Scholar 

  • Zack JA, Arrigo SJ, Weitsman SR, Go AS, Haislip A, Chen IS (1990) HIV-1 entry into quiescent primary lymphocytes: molecular analysis reveals a labile, latent viral structure. Cell 61(2):213–222

    Article  CAS  Google Scholar 

  • Zhu Y, Pe’ery T, Peng J, Ramanathan Y, Marshall N, Marshall T, Amendt B, Mathews MB, Price DH (1997) Transcription elongation factor P-TEFb is required for HIV-1 tat transactivation in vitro. Genes Dev 11(20):2622–2632

    Article  CAS  Google Scholar 

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Acknowledgements

This work was supported by the NIH Martin Delaney I4C, Beat-HIV and DARE Collaboratories, by the Johns Hopkins Center for AIDS Research (P30AI094189), by NIH grant 43222, and by the Howard Hughes Medical Institute and the Bill and Melinda Gates Foundation.

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Authors and Affiliations

  1. Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA

    Janet D. Siliciano

  2. Johns Hopkins University School of Medicine, Howard Hughes Medical Institute, Baltimore, MD, 21205, USA

    Robert F. Siliciano

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  1. Janet D. Siliciano
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  2. Robert F. Siliciano
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Correspondence to Robert F. Siliciano .

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Editors and Affiliations

  1. School of Medicine, Emory University, Atlanta, GA, USA

    Guido Silvestri

  2. The Brigham and Women’s Hospital and the Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA

    Mathias Lichterfeld

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Siliciano, J.D., Siliciano, R.F. (2017). Assays to Measure Latency, Reservoirs, and Reactivation. In: Silvestri, G., Lichterfeld, M. (eds) HIV-1 Latency. Current Topics in Microbiology and Immunology, vol 417. Springer, Cham. https://doi.org/10.1007/82_2017_75

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