A More Precise HIV Integration Assay Designed to Detect Small Differences Finds Lower Levels of Integrated DNA in HAART Treated Patients

Overview

Journal Virology

Specialty Microbiology

Date 2008 Jul 25

PMID 18649912

Citations 56

Authors

Jianqing J Yu

Te Lang Wu

Megan K Liszewski

Jihong Dai

William J Swiggard

Clifford Baytop

Ian Frank

Bruce L Levine

Wei Yang

Theodore Theodosopoulos

Una ODoherty

Affiliations

Soon will be listed here.

Abstract

Many studies report the level of total viral DNA in HIV-infected patients, but few studies report the level of integrated DNA. It is important to measure integrated DNA in HIV-infected patients because the information could shed light on the effectiveness of antiretroviral therapy, especially intensified therapy, when viral loads may remain undetectable. In order to develop an integration assay for patient samples, we enhanced the sensitivity of our prior integration assay. To do this, we exploited a technique that we developed, called repetitive sampling, and optimized reaction conditions for rare event detection, rather than large dynamic range. We also designed our primers to match more conserved regions of HIV. The result is a new, sensitive, quantitative assay that allows us to measure integrated DNA in HIV-infected patients. When we applied our integration assay to patient PBMCs, we found that the use of HAART is associated with reduced levels of integrated DNA.

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References

Chun T, Engel D, Berrey M, Shea T, Corey L, Fauci A . Early establishment of a pool of latently infected, resting CD4(+) T cells during primary HIV-1 infection. Proc Natl Acad Sci U S A. 1998; 95(15):8869-73. PMC: 21169. DOI: 10.1073/pnas.95.15.8869. View

Ibanez A, Puig T, Elias J, Clotet B, Ruiz L, Martinez M . Quantification of integrated and total HIV-1 DNA after long-term highly active antiretroviral therapy in HIV-1-infected patients. AIDS. 1999; 13(9):1045-9. DOI: 10.1097/00002030-199906180-00007. View

Rouzioux C, Hubert J, Burgard M, Deveau C, Goujard C, Bary M . 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(1):46-55. DOI: 10.1086/430610. View

Wu Y, Marsh J . Gene transcription in HIV infection. Microbes Infect. 2003; 5(11):1023-7. DOI: 10.1016/s1286-4579(03)00187-4. View

ODoherty U, Swiggard W, Jeyakumar D, McGain D, Malim M . A sensitive, quantitative assay for human immunodeficiency virus type 1 integration. J Virol. 2002; 76(21):10942-50. PMC: 136638. DOI: 10.1128/jvi.76.21.10942-10950.2002. View

Debiaggi M, Zara F, Pistorio A, Bruno R, Sacchi P, Patruno S . Quantification of HIV-1 proviral DNA in patients with undetectable plasma viremia over long-term highly active antiretroviral therapy. Int J Infect Dis. 2001; 4(4):187-93. DOI: 10.1016/s1201-9712(00)90107-3. View

Ngo-Giang-Huong N, Deveau C, da Silva I, Pellegrin I, Venet A, Harzic M . Proviral HIV-1 DNA in subjects followed since primary HIV-1 infection who suppress plasma viral load after one year of highly active antiretroviral therapy. AIDS. 2001; 15(6):665-73. DOI: 10.1097/00002030-200104130-00001. View

Lehrman G, Hogue I, Palmer S, Jennings C, Spina C, Wiegand A . Depletion of latent HIV-1 infection in vivo: a proof-of-concept study. Lancet. 2005; 366(9485):549-55. PMC: 1894952. DOI: 10.1016/S0140-6736(05)67098-5. View

Wu Y, Marsh J . Early transcription from nonintegrated DNA in human immunodeficiency virus infection. J Virol. 2003; 77(19):10376-82. PMC: 228496. DOI: 10.1128/jvi.77.19.10376-10382.2003. View

10.

Coffin J . HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science. 1995; 267(5197):483-9. DOI: 10.1126/science.7824947. View

11.

Blumenthal R, Walter A, COVELL D, Eidelman O . pH-dependent fusion of vesicular stomatitis virus with Vero cells. Measurement by dequenching of octadecyl rhodamine fluorescence. J Biol Chem. 1987; 262(28):13614-9. View

12.

Viard J, Burgard M, Hubert J, Aaron L, Rabian C, Pertuiset N . Impact of 5 years of maximally successful highly active antiretroviral therapy on CD4 cell count and HIV-1 DNA level. AIDS. 2004; 18(1):45-9. DOI: 10.1097/00002030-200401020-00005. View

13.

Lassen K, Han Y, Zhou Y, Siliciano J, Siliciano R . The multifactorial nature of HIV-1 latency. Trends Mol Med. 2004; 10(11):525-31. DOI: 10.1016/j.molmed.2004.09.006. View

14.

Chun T, Stuyver L, Mizell S, Ehler L, Mican J, Baseler M . Presence of an inducible HIV-1 latent reservoir during highly active antiretroviral therapy. Proc Natl Acad Sci U S A. 1997; 94(24):13193-7. PMC: 24285. DOI: 10.1073/pnas.94.24.13193. View

15.

Swiggard W, Baytop C, Yu J, Dai J, Li C, Schretzenmair R . Human immunodeficiency virus type 1 can establish latent infection in resting CD4+ T cells in the absence of activating stimuli. J Virol. 2005; 79(22):14179-88. PMC: 1280214. DOI: 10.1128/JVI.79.22.14179-14188.2005. View

16.

Lillo F, Grasso M, Lodini S, Bellotti M, Colucci G . Few modifications of the Cobas Amplicor HIV Monitor 1.5 test allow reliable quantitation of HIV-1 proviral load in peripheral blood mononuclear cells. J Virol Methods. 2004; 120(2):201-5. DOI: 10.1016/j.jviromet.2004.05.008. View

17.

Fouchier R, Meyer B, Simon J, Fischer U, Malim M . HIV-1 infection of non-dividing cells: evidence that the amino-terminal basic region of the viral matrix protein is important for Gag processing but not for post-entry nuclear import. EMBO J. 1997; 16(15):4531-9. PMC: 1170079. DOI: 10.1093/emboj/16.15.4531. View

18.

Nakajima N, Lu R, Engelman A . Human immunodeficiency virus type 1 replication in the absence of integrase-mediated dna recombination: definition of permissive and nonpermissive T-cell lines. J Virol. 2001; 75(17):7944-55. PMC: 115038. DOI: 10.1128/jvi.75.17.7944-7955.2001. View

19.

Douek D, Brenchley J, Betts M, Ambrozak D, Hill B, Okamoto Y . HIV preferentially infects HIV-specific CD4+ T cells. Nature. 2002; 417(6884):95-8. DOI: 10.1038/417095a. View

20.

Burgard M, Izopet J, Dumon B, Tamalet C, Descamps D, Ruffault A . HIV RNA and HIV DNA in peripheral blood mononuclear cells are consistent markers for estimating viral load in patients undergoing long-term potent treatment. AIDS Res Hum Retroviruses. 2001; 16(18):1939-47. DOI: 10.1089/088922200750054666. View