journal article Open Access Apr 03, 2018

Total HIV DNA: a global marker of HIV persistence

View at Publisher Save 10.1186/s12977-018-0412-7
Topics

No keywords indexed for this article. Browse by subject →

References
79
[1]
Defective HIV-1 proviruses produce novel protein-coding RNA species in HIV-infected patients on combination antiretroviral therapy

Hiromi Imamichi, Robin L. Dewar, Joseph W. Adelsberger et al.

Proceedings of the National Academy of Sciences 2016 10.1073/pnas.1609057113
[2]
Rouzioux C, Richman D. How to best measure HIV reservoirs? Curr Opin HIV AIDS. 2013;8:170–5. 10.1097/coh.0b013e32835fc619
[3]
O’Doherty U, Swiggard WJ, Jeyakumar D, McGain D, Malim MH. A sensitive, quantitative assay for human immunodeficiency virus type 1 integration. J Virol. 2002;76:10942–50. 10.1128/jvi.76.21.10942-10950.2002
[4]
Massanella M, Richman DD. Measuring the latent reservoir in vivo. J Clin Invest. 2016;126:464–72. 10.1172/jci80567
[5]
Rouzioux C, Melard A, Avettand-Fenoel V. Quantification of total HIV1-DNA in peripheral blood mononuclear cells. Methods Mol Biol. 2014;1087:261–70. 10.1007/978-1-62703-670-2_21
[6]
Lambotte O, Boufassa F, Madec Y, Nguyen A, Goujard C, Meyer L, Rouzioux C, Venet A, Delfraissy JF. HIV controllers: a homogeneous group of HIV-1-infected patients with spontaneous control of viral replication. Clin Infect Dis. 2005;41:1053–6. 10.1086/433188
[7]
Post-Treatment HIV-1 Controllers with a Long-Term Virological Remission after the Interruption of Early Initiated Antiretroviral Therapy ANRS VISCONTI Study

Asier Sáez-Cirión, Charline Bacchus, Laurent Hocqueloux et al.

PLOS Pathogens 2013 10.1371/journal.ppat.1003211
[8]
Canoui E, Lecuroux C, Avettand-Fenoel V, Gousset M, Rouzioux C, Saez-Cirion A, Meyer L, Boufassa F, Lambotte O. Noel N, and the ACOCSG: a subset of extreme human immunodeficiency virus (HIV) controllers is characterized by a small HIV blood reservoir and a weak T-cell activation level. Open Forum Infect Dis. 2017;4:ofx064. 10.1093/ofid/ofx064
[9]
Bertine M, Gueudin M, Melard A, Damond F, Descamps D, Matheron S, Collin F, Rouzioux C, Plantier JC, Avettand-Fenoel V. New highly sensitive real-time PCR assay for HIV-2 group A and group B DNA quantification. J Clin Microbiol. 2017;55:2850–7. 10.1128/jcm.00755-17
[10]
Avettand-Fenoel V, Hocqueloux L, Ghosn J, Cheret A, Frange P, Melard A, Viard JP, Rouzioux C. Total HIV-1 DNA, a marker of viral reservoir dynamics with clinical implications. Clin Microbiol Rev. 2016;29:859–80. 10.1128/cmr.00015-16
[11]
Hong F, Aga E, Cillo AR, Yates AL, Besson G, Fyne E, Koontz DL, Jennings C, Zheng L, Mellors JW. Novel assays for measurement of total cell-associated HIV-1 DNA and RNA. J Clin Microbiol. 2016;54:902–11. 10.1128/jcm.02904-15
[12]
Gantner P, Melard A, Damond F, Delaugerre C, Dina J, Gueudin M, Maillard A, Saune K, Rodallec A, Tuaillon E, et al. Interlaboratory quality control of total HIV-1 DNA load measurement for multicenter reservoir studies. J Med Virol. 2017;89:2047–50. 10.1002/jmv.24874
[13]
Avettand-Fenoel V, Chaix ML, Blanche S, Burgard M, Floch C, Toure K, Allemon MC, Warszawski J, Rouzioux C. LTR real-time PCR for HIV-1 DNA quantitation in blood cells for early diagnosis in infants born to seropositive mothers treated in HAART area (ANRS CO 01). J Med Virol. 2009;81:217–23. 10.1002/jmv.21390
[14]
Rouzioux C, Hubert JB, Burgard M, Deveau C, Goujard C, Bary M, Sereni D, Viard JP, Delfraissy JF, Meyer L. Early levels of HIV-1 DNA in peripheral blood mononuclear cells are predictive of disease progression independently of HIV-1 RNA levels and CD4 + T cell counts. J Infect Dis. 2005;192:46–55 (Epub 2005 May 2031). 10.1086/430610
[15]
Hocqueloux L, Avettand-Fenoel V, Jacquot S, Prazuck T, Legac E, Melard A, Niang M, Mille C, Le Moal G, Viard JP, Rouzioux C. Long-term antiretroviral therapy initiated during primary HIV-1 infection is key to achieving both low HIV reservoirs and normal T cell counts. J Antimicrob Chemother. 2013;68:1169–78. 10.1093/jac/dks533
[16]
Trypsteen W, Kiselinova M, Vandekerckhove L, De Spiegelaere W. Diagnostic utility of droplet digital PCR for HIV reservoir quantification. J Virus Erad. 2016;2:162–9. 10.1016/s2055-6640(20)30460-x
[17]
Strain MC, Lada SM, Luong T, Rought SE, Gianella S, Terry VH, Spina CA, Woelk CH, Richman DD. Highly precise measurement of HIV DNA by droplet digital PCR. PLoS ONE. 2013;8:e55943. 10.1371/journal.pone.0055943
[18]
Jones GM, Busby E, Garson JA, Grant PR, Nastouli E, Devonshire AS, Whale AS. Digital PCR dynamic range is approaching that of real-time quantitative PCR. Biomol Detect Quantif. 2016;10:31–3. 10.1016/j.bdq.2016.10.001
[19]
Kiselinova M, De Spiegelaere W, Buzon MJ, Malatinkova E, Lichterfeld M, Vandekerckhove L. Integrated and total HIV-1 DNA predict ex vivo viral outgrowth. PLoS Pathog. 2016;12:e1005472. 10.1371/journal.ppat.1005472
[20]
Bosman KJ, Nijhuis M, van Ham PM, Wensing AM, Vervisch K, Vandekerckhove L, De Spiegelaere W. Comparison of digital PCR platforms and semi-nested qPCR as a tool to determine the size of the HIV reservoir. Sci Rep. 2015;5:13811. 10.1038/srep13811
[21]
Pasternak AO, Adema KW, Bakker M, Jurriaans S, Berkhout B, Cornelissen M, Lukashov VV. Highly sensitive methods based on seminested real-time reverse transcription-PCR for quantitation of human immunodeficiency virus type 1 unspliced and multiply spliced RNA and proviral DNA. J Clin Microbiol. 2008;46:2206–11. 10.1128/jcm.00055-08
[22]
Vandergeeten C, Fromentin R, Merlini E, Bramah-Lawani M, DaFonseca S, Bakeman W, McNulty A, Ramgopal M, Michael N, Kim JH, et al. Cross-clade ultrasensitive PCR-based assays to measure HIV persistence in large cohort studies. J Virol. 2014;88:12385–96. 10.1128/jvi.00609-14
[23]
Ananworanich J, Sacdalan CP, Pinyakorn S, Chomont N, de Souza M, Luekasemsuk T, Schuetz A, Krebs SJ, Dewar R, Jagodzinski L, et al. Virological and immunological characteristics of HIV-infected individuals at the earliest stage of infection. J Virus Erad. 2016;2:43–8. 10.1016/s2055-6640(20)30688-9
[24]
Khoury G, Anderson JL, Fromentin R, Hartogenesis W, Smith MZ, Bacchetti P, Hecht FM, Chomont N, Cameron PU, Deeks SG, Lewin SR. Persistence of integrated HIV DNA in CXCR3 + CCR6 + memory CD4 + T cells in HIV-infected individuals on antiretroviral therapy. AIDS. 2016;30:1511–20. 10.1097/qad.0000000000001029
[25]
Boritz EA, Darko S, Swaszek L, Wolf G, Wells D, Wu X, Henry AR, Laboune F, Hu J, Ambrozak D, et al. Multiple origins of virus persistence during natural control of HIV infection. Cell. 2016;166:1004–15. 10.1016/j.cell.2016.06.039
[26]
Eriksson S, Graf E, Dahl V, Strain MC, Yukl S, Lysenko E, Bosch RJ, Lai J, Chioma S, Emad F, et al. Comparative analysis of measures of viral reservoirs in HIV-1 eradication studies. PLoS Pathog. 2013;9:e1003174. 10.1371/journal.ppat.1003174
[27]
Avettand-Fenoel V, Boufassa F, Galimand J, Meyer L, Rouzioux C. HIV-1 DNA for the measurement of the HIV reservoir is predictive of disease progression in seroconverters whatever the mode of result expression is. J Clin Virol. 2008;42:399–404. 10.1016/j.jcv.2008.03.013
[28]
Goujard C, Bonarek M, Meyer L, Bonnet F, Chaix ML, Deveau C, Sinet M, Galimand J, Delfraissy JF, Venet A, et al. CD4 cell count and HIV DNA level are independent predictors of disease progression after primary HIV type 1 infection in untreated patients. Clin Infect Dis. 2006;42:709–15. 10.1086/500213
[29]
Descours B, Avettand-Fenoel V, Blanc C, Samri A, Melard A, Supervie V, Theodorou I, Carcelain G, Rouzioux C, Autran B, Group AACS. Immune responses driven by protective human leukocyte antigen alleles from long-term nonprogressors are associated with low HIV reservoir in central memory CD4 T cells. Clin Infect Dis. 2012;54:1495–503. 10.1093/cid/cis188
[30]
Fletcher CV, Staskus K, Wietgrefe SW, Rothenberger M, Reilly C, Chipman JG, Beilman GJ, Khoruts A, Thorkelson A, Schmidt TE, et al. Persistent HIV-1 replication is associated with lower antiretroviral drug concentrations in lymphatic tissues. Proc Natl Acad Sci USA. 2014;111:2307–12. 10.1073/pnas.1318249111
[31]
Avettand-Fenoel V, Prazuck T, Hocqueloux L, Melard A, Michau C, Kerdraon R, Agoute E, Rouzioux C. HIV-DNA in rectal cells is well correlated with HIV-DNA in blood in different groups of patients, including long-term non-progressors. Aids. 2008;22:1880–2. 10.1097/qad.0b013e32830fbdbc
[32]
Hey-Nguyen WJ, Xu Y, Pearson CF, Bailey M, Suzuki K, Tantau R, Obeid S, Milner B, Field A, Carr A, et al. Quantification of residual germinal center activity and HIV-1 DNA and RNA levels using fine needle biopsies of lymph nodes during antiretroviral therapy. AIDS Res Hum Retroviruses. 2017;33:648–57. 10.1089/aid.2016.0171
[33]
Fukazawa Y, Lum R, Okoye AA, Park H, Matsuda K, Bae JY, Hagen SI, Shoemaker R, Deleage C, Lucero C, et al. B cell follicle sanctuary permits persistent productive simian immunodeficiency virus infection in elite controllers. Nat Med. 2015;21:132–9. 10.1038/nm.3781
[34]
Laanani M, Ghosn J, Essat A, Melard A, Seng R, Gousset M, Panjo H, Mortier E, Girard PM, Goujard C, et al. Impact of the timing of initiation of antiretroviral therapy during primary HIV-1 infection on the decay of cell-associated HIV-DNA. Clin Infect Dis. 2015;60:1715–21. 10.1093/cid/civ171
[35]
Ananworanich J, Chomont N, Eller LA, Kroon E, Tovanabutra S, Bose M, Nau M, Fletcher JL, Tipsuk S, Vandergeeten C, et al. HIV DNA set point is rapidly established in acute HIV infection and dramatically reduced by early ART. EBioMedicine. 2016;11:68–72. 10.1016/j.ebiom.2016.07.024
[36]
Boulle C, Rouet F, Fassinou P, Msellati P, Debeaudrap P, Chaix ML, Rouzioux C, Avettand-Fenoel V. HIV-1 DNA concentrations and evolution among African HIV-1-infected children under antiretroviral treatment (ANRS 1244/1278). J Antimicrob Chemother. 2014;69:3047–50. 10.1093/jac/dku274
[37]
Avettand-Fenoel V, Bouteloup V, Melard A, Fagard C, Chaix ML, Leclercq P, Chene G, Viard JP, Rouzioux C. Higher HIV-1 DNA associated with lower gains in CD4 cell count among patients with advanced therapeutic failure receiving optimized treatment (ANRS 123–ETOILE). J Antimicrob Chemother. 2010;65:2212–4. 10.1093/jac/dkq282
[38]
Jumare J, Sunshine S, Ahmed H, El-Kamary SS, Magder L, Hungerford L, Burdo T, Eyzaguirre LM, Umlauf A, Cherner M, et al. Peripheral blood lymphocyte HIV DNA levels correlate with HIV associated neurocognitive disorders in Nigeria. J Neurovirol. 2017;23:474–82. 10.1007/s13365-017-0520-5
[39]
Valcour VG, Shiramizu BT, Sithinamsuwan P, Nidhinandana S, Ratto-Kim S, Ananworanich J, Siangphoe U, Kim JH, de Souza M, Degruttola V, et al. HIV DNA and cognition in a Thai longitudinal HAART initiation cohort: the SEARCH 001 Cohort Study. Neurology. 2009;72:992–8. 10.1212/01.wnl.0000344404.12759.83
[40]
Noel N, Pena R, David A, Avettand-Fenoel V, Erkizia I, Jimenez E, Lecuroux C, Rouzioux C, Boufassa F, Pancino G, et al. Long-term Spontaneous control of HIV-1 relates to low frequency of infected cells and inefficient viral reactivation. J Virol. 2016;90:6148–58. 10.1128/jvi.00419-16
[41]
Hatano H, Jain V, Hunt PW, Lee TH, Sinclair E, Do TD, Hoh R, Martin JN, McCune JM, Hecht F, et al. Cell-based measures of viral persistence are associated with immune activation and programmed cell death protein 1 (PD-1)-expressing CD4 + T cells. J Infect Dis. 2013;208:50–6. 10.1093/infdis/jis630
[42]
Cockerham LR, Siliciano JD, Sinclair E, O’Doherty U, Palmer S, Yukl SA, Strain MC, Chomont N, Hecht FM, Siliciano RF, et al. CD4 + and CD8 + T cell activation are associated with HIV DNA in resting CD4 + T cells. PLoS ONE. 2014;9:e110731. 10.1371/journal.pone.0110731
[43]
Minga AK, Anglaret X, d’ Aquin Toni T, Chaix ML, Dohoun L, Abo Y, Coulibaly A, Duvignac J, Gabillard D, Rouet F, Rouzioux C. HIV-1 DNA in peripheral blood mononuclear cells is strongly associated with HIV-1 disease progression in recently infected West African adults. J Acquir Immune Defic Syndr. 2008;48:350–4. 10.1097/qai.0b013e3181775e55
[44]
Hatzakis AE, Touloumi G, Pantazis N, Anastassopoulou CG, Katsarou O, Karafoulidou A, Goedert JJ, Kostrikis LG. Cellular HIV-1 DNA load predicts HIV-RNA rebound and the outcome of highly active antiretroviral therapy. AIDS. 2004;18:2261–7. 10.1097/00002030-200411190-00006
[45]
Tsiara CG, Nikolopoulos GK, Bagos PG, Goujard C, Katzenstein TL, Minga AK, Rouzioux C, Hatzakis A. Impact of HIV type 1 DNA levels on spontaneous disease progression: a meta-analysis. AIDS Res Hum Retrovir. 2012;28:366–73. 10.1089/aid.2011.0032
[46]
Yukl SA, Shergill AK, Ho T, Killian M, Girling V, Epling L, Li P, Wong LK, Crouch P, Deeks SG, et al. The distribution of HIV DNA and RNA in cell subsets differs in gut and blood of HIV-positive patients on ART: implications for viral persistence. J Infect Dis. 2013;208:1212–20. 10.1093/infdis/jit308
[47]
Hatano H, Somsouk M, Sinclair E, Harvill K, Gilman L, Cohen M, Hoh R, Hunt PW, Martin JN, Wong JK, et al. Comparison of HIV DNA and RNA in gut-associated lymphoid tissue of HIV-infected controllers and noncontrollers. AIDS. 2013;27:2255–60. 10.1097/qad.0b013e328362692f
[48]
Canaud G, Dejucq-Rainsford N, Avettand-Fenoel V, Viard JP, Anglicheau D, Bienaime F, Muorah M, Galmiche L, Gribouval O, Noel LH, et al. The kidney as a reservoir for HIV-1 after renal transplantation. J Am Soc Nephrol. 2014;25:407–19. 10.1681/asn.2013050564
[49]
Damouche A, Lazure T, Avettand-Fenoel V, Huot N, Dejucq-Rainsford N, Satie AP, Melard A, David L, Gommet C, Ghosn J, et al. Adipose tissue is a neglected viral reservoir and an inflammatory site during chronic HIV and SIV infection. PLoS Pathog. 2015;11:e1005153. 10.1371/journal.ppat.1005153
[50]
Ghosn J, Leruez-Ville M, Blanche J, Delobelle A, Beaudoux C, Mascard L, Lecuyer H, Canestri A, Landman R, Zucman D, et al. HIV-1 DNA levels in peripheral blood mononuclear cells and cannabis use are associated with intermittent HIV shedding in semen of men who have sex with men on successful antiretroviral regimens. Clin Infect Dis. 2014;58:1763–70. 10.1093/cid/ciu187

Showing 50 of 79 references

Cited By
53
IP-10 is highly involved in HIV infection

Jie Lei, Xiaowan Yin · 2019

Cytokine
Metrics
53
Citations
79
References
Details
Published
Apr 03, 2018
Vol/Issue
15(1)
License
View
Cite This Article
Christine Rouzioux, Véronique Avettand-Fenoel (2018). Total HIV DNA: a global marker of HIV persistence. Retrovirology, 15(1). https://doi.org/10.1186/s12977-018-0412-7