Modification of the Abbott RealTime assay for detection of HIV-1 plasma RNA viral loads less than one copy per milliliter

Journal of Virological Methods

Volumn 175, Issue 2, 2011, Pages 261-265

  Yukl, Steven A ^a,b   Li, Peilin ^a   Fujimoto, Katsuya ^a,e   Lampiris, Harry ^a,b   Lu, Chuanyi M ^a,b   Hare, C Bradley ^b,c   Deeks, Steven G ^b,c   Liegler, Teri ^b,c   Pandori, Mark ^d   Havlir, Diane V ^b,c   Wong, Joseph K ^a,b  

^a VETERANS AFFAIRS MEDICAL CENTER   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c SAN FRANCISCO GENERAL HOSPITAL   (United States)

^d Department of Public Health ^*  (United States)

^e HOKKAIDO UNIVERSITY   (Japan)

Author keywords

Abbott; HIV; Plasma RNA; Single copy; Viral load

Indexed keywords

VIRUS RNA;

ADULT; ANALYTIC METHOD; ARTICLE; BLOOD ANALYSIS; BLOOD SAMPLING; CONCENTRATION (PARAMETERS); CONFIDENCE INTERVAL; CONTROLLED STUDY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY; RNA ANALYSIS; VIRION; VIRUS DETECTION; VIRUS LOAD; VIRUS REPLICATION;

ADULT; HIV INFECTIONS; HIV-1; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; PLASMA; REPRODUCIBILITY OF RESULTS; RNA, VIRAL; SENSITIVITY AND SPECIFICITY; SPECIMEN HANDLING; VIRAL LOAD;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 79959329392     PISSN: 01660934     EISSN: 18790984     Source Type: Journal    
DOI: 10.1016/j.jviromet.2011.04.015     Document Type: Article

References (49)

1. Boni J., Emmerich B.S., Leib S.L., Wiestler O.D., Schupbach J., Kleihues P. PCR identification of HIV-1 DNA sequences in brain tissue of patients with AIDS encephalopathy. Neurology 1993, 43:1813-1817.
2. Boni J., Shah C., Flepp M., Luthy R., Schupbach J. Detection of low copy numbers of HIV-1 proviral DNA in patient PBMCs by a high-input, sequence-capture PCR (Mega-PCR). J. Med. Virol. 2004, 72:1-9.
3. Busch M.P., Glynn S.A., Wright D.J., Hirschkorn D., Laycock M.E., McAuley J., Tu Y., Giachetti C., Gallarda J., Heitman J., Kleinman S.H. Relative sensitivities of licensed nucleic acid amplification tests for detection of viremia in early human immunodeficiency virus and hepatitis C virus infection. Transfusion 2005, 45:1853-1863.
4. Bush C.E., Di Michele L.J., Peterson W.R., Sherman D.G., Godsey J.H. Solid-phase time-resolved fluorescence detection of human immunodeficiency virus polymerase chain reaction amplification products. Anal. Biochem. 1992, 202:146-151.
5. Collins M.L., Irvine B., Tyner D., Fine E., Zayati C., Chang C., Horn T., Ahle D., Detmer J., Shen L.P., Kolberg J., Bushnell S., Urdea M.S., Ho D.D. A branched DNA signal amplification assay for quantification of nucleic acid targets below 100molecules/ml. Nucleic Acids Res. 1997, 25:2979-2984.
6. Dettenhofer M., Yu X.F. Highly purified human immunodeficiency virus type 1 reveals a virtual absence of Vif in virions. J. Virol. 1999, 73:1460-1467.
7. Dewar R.L., Highbarger C., Sarmiento M.D., Todd J.A., Vasudevachari M.B., Davey R.T., Kovacs J.A., Salzman N.P., Lane H.C., Urdea M.S. Application of branched DNA signal amplification to monitor human immunodeficiency virus type 1 burden in human plasma. J. Infect. Dis. 1994, 170:172-179.
8. Dornadula G., Zhang H., VanUitert B., Stern J., Livornese L., Ingerman M.J., Witek J., Kedanis R.J., Natkin J., DeSimone J., Pomerantz R. Residual HIV-1 RNA in blood plasma of patients taking suppressive highly active antiretroviral therapy. J. Am. Med. Assoc. 1999, 282:1627-1632.
9. Fischer M., Joos B., Niederost B., Kaiser P., Hafner R., von Wyl V., Ackermann M., Weber R., Gunthard H.F. Biphasic decay kinetics suggest progressive slowing in turnover of latently HIV-1 infected cells during antiretroviral therapy. Retrovirology 2008, 5:107.
10. Gandhi R.T., Zheng L., Bosch R.J., Chan E.S., Margolis D.M., Read S., Kallungal B., Palmer S., Medvik K., Lederman M.M., Alatrakchi N., Jacobson J.M., Wiegand A., Kearney M., Coffin J.M., Mellors J.W., Eron J.J. The effect of raltegravir intensification on low-level residual viremia in HIV-infected patients on antiretroviral therapy: a randomized controlled trial. PLoS Med. 2010, 7(8).
11. Geretti, A.M., Doyle, T., Smith, C., Garcia, A., Labbett, W., Johnson, M., Phillips, A., 2010. Association between low-level viremia below 50copies/ml and risk of virologic rebound in HIV-infected patients receiving HAART. 17th annual Conference on Retroviruses and Opportunistic Infections (CROI 2010). Abstract 505.
12. Hatano H., Delwart E.L., Norris P.J., Lee T.H., Dunn-Williams J., Hunt P.W., Hoh R., Stramer S.L., Linnen J.M., McCune J.M., Martin J.N., Busch M.P., Deeks S.G. Evidence for persistent low-level viremia in individuals who control human immunodeficiency virus in the absence of antiretroviral therapy. J. Virol. 2009, 83:329-335.
13. Hatano H., Delwart E.L., Norris P.J., Lee T.H., Neilands T.B., Kelley C.F., Hunt P.W., Hoh R., Linnen J.M., Martin J.N., Busch M.P., Deeks S.G. Evidence of persistent low-level viremia in long-term HAART-suppressed, HIV-infected individuals. AIDS 2010, 24:2535-2539.
14. Hatano, H., Hayes, T., Dahl, V., Sinclair, E., Lee, T.-H., Hunt, P., Palmer, S., Busch, M., Shacklett, B., Deeks, S., 2010b. Raltegravir intensification in antiretroviral-treated patients exhibiting a suboptimal CD4+ T cell response. 17th annual Conference on Retroviruses and Opportunistic Infections (CROI 2010). Abstract 101LB.
15. Havlir D.V., Bassett R., Levitan D., Gilbert P., Tebas P., Collier A.C., Hirsch M.S., Ignacio C., Condra J., Gunthard H.F., Richman D.D., Wong J.K. Prevalence and predictive value of intermittent viremia with combination HIV therapy. J. Am. Med. Assoc. 2001, 286:171-179.
16. Havlir D.V., Strain M.C., Clerici M., Ignacio C., Trabattoni D., Ferrante P., Wong J.K. Productive infection maintains a dynamic steady state of residual viremia in human immunodeficiency virus type 1-infected persons treated with suppressive antiretroviral therapy for five years. J. Virol. 2003, 77:11212-11219.
17. Kaiser P., Joos B., Niederost B., Weber R., Gunthard H.F., Fischer M. Productive human immunodeficiency virus type 1 infection in peripheral blood predominantly takes place in CD4/CD8 double-negative T lymphocytes. J. Virol. 2007, 81:9693-9706.
18. Katzenstein D.A., Hammer S.M., Hughes M.D., Gundacker H., Jackson J.B., Fiscus S., Rasheed S., Elbeik T., Reichman R., Japour A., Merigan T.C., Hirsch M.S. The relation of virologic and immunologic markers to clinical outcomes after nucleoside therapy in HIV-infected adults with 200 to 500 CD4 cells per cubic millimeter. AIDS Clinical Trials Group Study 175 Virology Study Team. N. Engl. J. Med. 1996, 335:1091-1098.
19. Kern D., Collins M., Fultz T., Detmer J., Hamren S., Peterkin J.J., Sheridan P., Urdea M., White R., Yeghiazarian T., Todd J. An enhanced-sensitivity branched-DNA assay for quantification of human immunodeficiency virus type 1 RNA in plasma. J. Clin. Microbiol. 1996, 34:3196-3202.
20. Kumar A.M., Borodowsky I., Fernandez B., Gonzalez L., Kumar M. Human immunodeficiency virus type 1 RNA Levels in different regions of human brain: quantification using real-time reverse transcriptase-polymerase chain reaction. J. Neurovirol. 2007, 13:210-224.
21. Lelie P.N., van Drimmelen H.A., Cuypers H.T., Best S.J., Stramer S.L., Hyland C., Allain J.P., Moncharmont P., Defer C., Nubling M., Glauser A., da Silva Cardoso M., Viret J.F., Lankinen M.H., Grillner L., Wirthmuller U., Coste J., Schottstedt V., Masecar B., Dax E.M. Sensitivity of HCV RNA and HIV RNA blood screening assays. Transfusion 2002, 42:527-536.
22. Mackay I.M., Arden K.E., Nitsche A. Real-time PCR in virology. Nucleic Acids Res. 2002, 30:1292-1305.
23. Maldarelli F., Palmer S., King M.S., Wiegand A., Polis M.A., Mican J., Kovacs J.A., Davey R.T., Rock-Kress D., Dewar R., Liu S., Metcalf J.A., Rehm C., Brun S.C., Hanna G.J., Kempf D.J., Coffin J.M., Mellors J.W. ART suppresses plasma HIV-1 RNA to a stable set point predicted by pretherapy viremia. PLoS Pathog. 2007, 3:e46.
24. Mavigner M., Delobel P., Cazabat M., Dubois M., L'Faqihi-Olive F.E., Raymond S., Pasquier C., Marchou B., Massip P., Izopet J. HIV-1 residual viremia correlates with persistent T-cell activation in poor immunological responders to combination antiretroviral therapy. PLoS One 2009, 4:e7658.
25. McClure P., Curran R., Boneham S., Ball J.K. A polymerase chain reaction method for the amplification of full-length envelope genes of HIV-1 from DNA samples containing single molecules of HIV-1 provirus. J. Virol. Methods 2000, 88:73-80.
26. Mellors J.W., Rinaldo C.R., Gupta P., White R.M., Todd J.A., Kingsley L.A. Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science 1996, 272:1167-1170.
27. Nuovo G.J. In situ strand displacement amplification: an improved technique for the detection of low copy nucleic acids. Diagn. Mol. Pathol. 2000, 9:195-202.
28. O'Brien W.A., Hartigan P.M., Martin D., Esinhart J., Hill A., Benoit S., Rubin M., Simberkoff M.F., Hamilton J.D. Changes in plasma HIV-1 RNA and CD4+ lymphocyte count relative to treatment and progression to AIDS. N. Engl. J. Med. 1996, 334:426-431.
29. Ostrowski S.R., Katzenstein T.L., Pedersen B.K., Gerstoft J., Ullum H. Residual viraemia in HIV-1-infected patients with plasma viral load < or =20copies/ml is associated with increased blood levels of soluble immune activation markers. Scand. J. Immunol. 2008, 68:652-660.
30. Palmer S., Wiegand A.P., Maldarelli F., Bazmi H., Mican J.M., Polis M., Dewar R.L., Planta A., Liu S., Metcalf J.A., Mellors J.W., Coffin J.M. New real-time reverse transcriptase-initiated PCR assay with single-copy sensitivity for human immunodeficiency virus type 1 RNA in plasma. J. Clin. Microbiol. 2003, 41:4531-4536.
31. Pas S., Rossen J.W., Schoener D., Thamke D., Pettersson A., Babiel R., Schutten M. Performance evaluation of the new Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 test version 2.0 for quantification of human immunodeficiency virus type 1 RNA. J. Clin. Microbiol. 2010, 48:1195-1200.
32. Richman D.D., Margolis D.M., Delaney M., Greene W.C., Hazuda D., Pomerantz R.J. The challenge of finding a cure for HIV infection. Science 2009, 323:1304-1307.
33. Ruiz L., Romeu J., Clotet B., Balague M., Cabrera C., Sirera G., Ibanez A., Martinez-Picado J., Raventos A., Tural C., Segura A., Foz M. Quantitative HIV-1 RNA as a marker of clinical stability and survival in a cohort of 302 patients with a mean CD4 cell count of 300×10(6)/l. AIDS 1996, 10:F39-F44.
34. Saag M.S., Holodniy M., Kuritzkes D.R., O'Brien W.A., Coombs R., Poscher M.E., Jacobsen D.M., Shaw G.M., Richman D.D., Volberding P.A. HIV viral load markers in clinical practice. Nat. Med. 1996, 2:625-629.
35. Saha B.K., Tian B., Bucy R.P. Quantitation of HIV-1 by real-time PCR with a unique fluorogenic probe. J. Virol. Methods 2001, 93:33-42.
36. Schockmel G.A., Yerly S., Perrin L. Detection of low HIV-1 RNA levels in plasma. J Acquir. Immune Defic. Syndr. Hum. Retrovirol. 1997, 14:179-183.
37. Simmonds P., Balfe P., Peutherer J.F. Human immunodeficiency virus-infected individuals contain provirus in small numbers of peripheral mononuclear cell and at low-copy numbers. J. Virol. 1990, 64:864-872.
38. Spann W., Pachmann K., Zabnienska H., Pielmeier A., Emmerich B. In situ amplification of single copy gene segments in individual cells by the polymerase chain reaction. Infection 1991, 19:242-244.
39. Sun R., Ku J., Jayakar H., Kuo J.C., Brambilla D., Herman S., Rosenstraus M., Spadoro J. Ultrasensitive reverse transcription-PCR assay for quantitation of human immunodeficiency virus type 1 RNA in plasma. J. Clin. Microbiol. 1998, 36:2964-2969.
40. Swanson P., Huang S., Abravaya K., de Mendoza C., Soriano V., Devare S.G., Hackett J. Evaluation of performance across the dynamic range of the Abbott RealTime HIV-1 assay as compared to VERSANT HIV-1 RNA 3.0 and AMPLICOR HIV-1 MONITOR v1.5 using serial dilutions of 39 group M and O viruses. J. Virol. Methods 2007, 141:49-57.
41. Tang N., Huang S., Salituro J., Mak W.B., Cloherty G., Johanson J., Li Y.H., Schneider G., Robinson J., Hackett J., Swanson P., Abravaya K. A RealTime HIV-1 viral load assay for automated quantitation of HIV-1 RNA in genetically diverse group M subtypes A-H, group O and group N samples. J. Virol. Methods 2007, 146:236-245.
42. Trono D., Van Lint C., Rouzioux C., Verdin E., Barre-Sinoussi F., Chun T.W., Chomont N. HIV persistence and the prospect of long-term drug-free remissions for HIV-infected individuals. Science 2010, 329:174-180.
43. van Gemen B., Kievits T., Schukkink R., van Strijp D., Malek L.T., Sooknanan R., Huisman H.G., Lens P. Quantification of HIV-1 RNA in plasma using NASBA during HIV-1 primary infection. J. Virol. Methods 1993, 43:177-187.
44. Wieland U., Suhr H., Salzberger B., Eggers H.J., Braun R.W., Kuhn J.E. Quantification of HIV-1 proviral DNA and analysis of genomic diversity by polymerase chain reaction and temperature gradient gel electrophoresis. J. Virol. Methods 1996, 57:127-139.
45. Yourno J. Direct polymerase chain reaction for detection of human immunodeficiency virus in blood spot residues on filter paper after elution of antibodies: an adjunct to serological surveys for estimating vertical transmission rates among human immunodeficiency virus antibody-positive newborns. J. Clin. Microbiol. 1993, 31:1364-1367.
46. Yourno J., Conroy J. A novel polymerase chain reaction method for detection of human immunodeficiency virus in dried blood spots on filter paper. J. Clin. Microbiol. 1992, 30:2887-2892.
47. Yukl S.A., Gianella S., Sinclair E., Epling L., Li Q., Duan L., Choi A.L., Girling V., Ho T., Li P., Fujimoto K., Lampiris H., Hare C.B., Pandori M., Haase A.T., Gunthard H.F., Fischer M., Shergill A.K., McQuaid K., Havlir D.V., Wong J.K. Differences in HIV burden and immune activation within the gut of HIV-positive patients receiving suppressive antiretroviral therapy. J. Infect. Dis. 2010, 202:1553-1561.
48. Zazzi M., Romano L., Brasini A., Valensin P.E. Nested polymerase chain reaction for detection of human immunodeficiency virus type 1 DNA in clinical specimens. J. Med. Virol. 1992, 38:172-174.
49. Zazzi M., Romano L., Brasini A., Valensin P.E. Simultaneous amplification of multiple HIV-1 DNA sequences from clinical specimens by using nested-primer polymerase chain reaction. AIDS Res. Hum. Retrov. 1993, 9:315-320.