Improved single-copy assays for quantification of persistent HIV-1 viremia in patients on suppressive antiretroviral therapy

Journal of Clinical Microbiology

Volumn 52, Issue 11, 2014, Pages 3944-3951

  Cillo, Anthony R ^a   Vagratian, David ^a   Bedison, Margaret A ^a   Anderson, Elizabeth M ^b   Kearney, Mary F ^b   Fyne, Elizabeth ^a   Koontz, Dianna ^a   Coffin, John M ^c   Piatak, Michael ^d   Mellors, John W ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c TUFTS UNIVERSITY   (United States)

^d FREDERICK NATIONAL LABORATORY FOR CANCER RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIRETROVIRUS AGENT; INTEGRASE; VIRUS RNA; OLIGONUCLEOTIDE PROBE; PRIMER DNA;

AMINO ACID SUBSTITUTION; ARTICLE; BINDING SITE; BLOOD SAMPLING; CLINICAL ARTICLE; CONTROLLED STUDY; DIAGNOSTIC EQUIPMENT; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; LIMIT OF DETECTION; NUCLEIC ACID RECOVERY; NUCLEIC ACID STRUCTURE, METABOLISM AND FUNCTION; NUCLEOTIDE SEQUENCE; PLASMA VOLUME; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RNA ANALYSIS; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; SINGLE COPY ASSAY; STRUCTURAL GENE; VALIDATION PROCESS; VIREMIA; VIRUS EXAMINATION; VIRUS GENOME; BLOOD; EVALUATION STUDY; GENETICS; HIV INFECTIONS; HUMAN IMMUNODEFICIENCY VIRUS 1; ISOLATION AND PURIFICATION; OLIGONUCLEOTIDE PROBE; PROCEDURES; SENSITIVITY AND SPECIFICITY; VIROLOGY; VIRUS LOAD;

ANTI-RETROVIRAL AGENTS; DNA PRIMERS; HIV INFECTIONS; HIV-1; HUMANS; OLIGONUCLEOTIDE PROBES; REAL-TIME POLYMERASE CHAIN REACTION; RNA, VIRAL; SENSITIVITY AND SPECIFICITY; VIRAL LOAD; VIREMIA;

EID: 84908318948     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.02060-14     Document Type: Article

References (33)

1. Fiebig EW, Wright DJ, Rawal BD, Garret PE, Schumacher RT, Peddada L, Heldebrandt 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 17:1871-1879. http://dx.doi.org/10.1097/00002030-200309050-00005.
2. Mellors JW, Rinaldo CR, Jr, Gupta P, White RM, Todd JA, Kingsley LA. 1996. Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science 272: 1167-1170. http://dx.doi.org/10.1126/science.272.5265.1167.
3. Mellors JW, Muñoz A, Giorgi JV, Margolick JB, Tassoni CJ, Gupta P, Kingsley LA, Todd JA, Saah AJ, Detels R, Phair JP, Rinaldo, CR, Jr. 1997. Plasma viral load and CD4+ lymphocytes as prognostic markers of HIV-1 infection. Ann. Intern. Med. 126:946-954. http://dx.doi.org/10.7326/0003-4819-126-12-199706150-00003.
4. 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: 123-126. http://dx.doi.org/10.1038/373123a0.
5. Perelson AS, Neumann AU, Markowitz M, Leonard JM, Ho DD. 1996. HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science 271:1582-1586. http://dx.doi.org/10.1126/science.271.5255.1582.
6. 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 387:188-191. http://dx.doi.org/10.1038/387188a0.
7. 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 282:1626-1632.
8. 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. 41:4531- 4536. http://dx.doi.org/10.1128/JCM.41.10.4531-4536.2003.
9. 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 pre-therapy viremia. PLoS Pathog. 3:e46. http://dx.doi.org/10.1371/journal.ppat.0030046.
10. Palmer S, Maldarelli F, Wiegand A, Bernstein B, Hanna GJ, Brun SC, Kempf DJ, Mellors JW, Coffin JM, King MS. 2008. Low-level viremia persists for at least 7 years in patients on suppressive antiretroviral therapy. Proc. Natl. Acad. Sci. U. S. A. 105:3879-3884. http://dx.doi.org/10.1073/pnas.0800050105.
11. Anderson JA, Archin NM, Ince W, Parker D, Wiegand A, Coffin JM, Kuruc J, Eron J, Swanstrom R, Margolis DM. 2011. Clonal sequences recovered from plasma from patients with residual HIV-1 viremia and on intensified antiretroviral therapy are identical to replicating viral RNAs recovered from circulating resting CD4+ T cells. J. Virol. 85:5220-5223. http://dx.doi.org/10.1128/JVI.00284-11.
12. Dinoso JB, Kim SY, Wiegand AM, Palmer SE, Gange JS, 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. 2009. Treatment intensification does not reduce residual HIV-1 viremia in patients on highly active antiretroviral therapy. Proc. Natl. Acad. Sci. U. S. A. 106:9403-9408. http://dx.doi.org/10.1073/pnas.0903107106.
13. McMahon D, Jones J, Wiegand A, Gange SJ, Kearney M, Palmer S, McNulty S, Metcalf JA, Acosta E, Rehm C, Coffin JM, Mellors JW, Maldarelli F. 2010. Short-course raltegravir intensification does not reduce persistent low-level viremia in patients with HIV-1 suppression during receipt of combination antiretroviral therapy. Clin. Infect. Dis. 50: 912-919. http://dx.doi.org/10.1086/650749.
14. 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:e1000321. http://dx.doi.org/10.1371/journal.pmed.1000321.
15. Li JZ, Gallien S, Ribaudo H, Heisey A, Bangsberg DR, Kuritzkes DR. 2014. Incomplete adherence to antiretroviral therapy is associated with higher levels of residual HIV-1 viremia. AIDS 28:181-186. http://dx.doi.org/10.1097/QAD.0000000000000123.
16. Archin NM, Liberty AL, Kashuba AD, Choudhary SK, Kuruc JD, Crooks AM, Parker DC, Anderson EM, Kearney MF, Strain MC, Richman DD, Hudgens MG, Bosch RJ, Coffin JM, Eron JJ, Hazuda DJ, Margolis DM. 2012. Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy. Nature 487:482-485. http://dx.doi.org/10.1038/nature11286.
17. Gandhi RT, Bosch RJ, Aga E, Bedison MA, Bastow B, Schmitz JL, Siliciano JD, Siliciano RF, Eron JJ, Mellors JW, ACTG A5173 Team. 2013. Residual plasma viremia and infectious HIV-1 recovery from resting memory CD4 cells in patients on antiretroviral therapy: results from ACTG A5173. Antivir. Ther. 18: 607- 613. http://dx.doi.org/10.3851/IMP2543.
18. Venneti S, Bonneh-Barkay D, Lopresti BJ, Bissel SJ, Wang G, Mathis CA, Piatak M, Jr, Lifson JD, Nyaundi JO, Murphey-Corb M, Wiley CA. 2008. Longitudinal in vivo positron emission tomography imaging of infected and activated brain macrophages in a macaque model of human immunodeficiency virus encephalitis correlates with central and peripheral markers of encephalitis and areas of synaptic degeneration. Am. J. Pathol. 172:1603-1616. http://dx.doi.org/10.2353/ajpath.2008.070967.
19. Schaefer-Klien J, Givol I, Barsov EV, Whitcomb JM, Van Brocklin M, Foster DN, Federspiel MJ, Hughes SH. 1998. The EV-O-derived cell line DF-1 supports the efficient replication of avian leukosis-sarcoma viruses and vectors. Virology 248:305-311. http://dx.doi.org/10.1006/viro.1998.9291.
20. Hughes SH. 2004. The RCAS vector system. Folia Biol. (Praha) 50:107-119.
21. Wain-Hobson S, Vartanian JP, Henry M, Chenciner N, Cheynier R, Delassus S, Martins LP, Sala M, Nugeyre MT, Guétard D, Klatzmann D, Gluckman JC, Willy Rozenbaum, Françoise Barré-Sinoussi, Montagnier L. 1991. LAV revisited: origins of the early HIV-1 isolated from Institut Pasteur. Science 252:961-965. http://dx.doi.org/10.1126/science.2035026.
22. Cillo AR, Krishnan A, Mitsuyasu RT, McMahon DK, Li S, Rossi JJ, Zaia JA, Mellors JW. 2013. Plasma viremia and cellular HIV-1 DNA persist despite autologous hematopoietic stem cell transplantation for HIV-related lymphoma. J. Acquir. Immune Defic. Syndr. 63:438-441. http://dx.doi.org/10.1097/QAI.0b013e31828e6163.
23. Core Team R. 2014. A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/.
24. Charif D, Lobry JR. 2007. Seqin{R} 1.0-2: a contributed packaged to the {R} project for statistical computing devoted to biological sequences retrieval and analysis. p 207-232. In Bastolla U, Porto M, Roman HE, VendruscoloM (ed), Structural approaches to sequence evolution: molecules, networks and populations, Springer Verlag, New York, NY.
25. Pages H, Aboyoun P, Gentleman R, DebRoy S. 2014. Biostrings: string objects representing biological sequences, and matching algorithms. R package version 2.32.1. R Foundation for Statistical Computing, Vienna, Austria.
26. Bembom O. 2014. seqLogo: sequence logos for DNA sequence alignments. R package version 1.30.0. R Foundation for Statistical Computing, Vienna, Austria.
27. Paradis E, Claude J, Strimmer K. 2004. APE: analysis of phylogenetics and evolution in R language. Bioinformatics 20:289-290. http://dx.doi.org/10.1093/bioinformatics/btg412.
28. Wickham H. 2009. ggplot2: elegant graphics for data analysis. Springer, New York, NY.
29. Wickham H. 2014. scales: scale functions for graphics. R package, version 0.2.4. R Foundation for Statistical Computing, Vienna, Austria. http://CRAN.R-project.org/package scales.
30. Mansky LM, Temin HM. 1995. Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J. Virol. 69:5087-5094.
31. Rouet F, Chiax ML, Nerrient E, Hgo-Giang-Huong N, Plantier JC, Burgard M, Peeters M, Damond F, Ekouevi DK, Msellati P, Ferradini L, Rukobo S, Maréchal V, Schvachsa N, Wakrim L, Rafalimanana C, Rakotoambinina B, Viard JP, Seigneurin JM, Rouzioux C. 2007. Impact of HIV-1 genetic diversity on plasma HIV-1 RNA quantification: usefulness of the Agence Nationale de Recherches sur le SIDA second-generation long terminal repeat-based real-time reverse transcriptase polymerase chain reaction test. J. Acquir. Immune Defic. Syndr. 45:380-388. http://dx.doi.org/10.1097/QAI.0b013e3180640cf5.
32. 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:e1003174. http://dx.doi.org/10.1371/journal.ppat.1003174.
33. Archin NM, Vaidya NK, Kuruc JD, Liberty AL, Weigand A, Kearney MF, Cohen MS, Coffin JM, Bosch RJ, Gay CL, Eron JJ, Margolis DM, Perelson AS. 2012. Immediate antiviral therapy appears to restrict resting CD4+ cell HIV-1 infection without accelerating the decay of latent infection. Proc. Natl. Acad. Sci. U. S. A. 109:9523-9526. http://dx.doi.org/10.1073/pnas.1120248109.