Design and evaluation of a human immunodeficiency virus type 1 RNA assay using nucleic acid sequence-based amplification technology able to quantify both group M and O viruses by using the long terminal repeat as target

Journal of Clinical Microbiology

Volumn 37, Issue 6, 1999, Pages 1813-1818

  De Baar, Michel P ^a   Van Der Schoot, Audrey M ^a   Goudsmit, Jaap ^a   Jacobs, Femke ^b   Ehren, Ron ^b   Van Der Horn, Karin H M ^a   Oudshoorn, Peter ^b   De Wolf, Frank ^a   De Ronde, Anthony ^a  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

^b Organon Teknika   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA SEQUENCE; GENE AMPLIFICATION; GENE TECHNOLOGY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; LONG TERMINAL REPEAT; NONHUMAN; PRIORITY JOURNAL; RNA ANALYSIS;

ANIMALIA; DNA VIRUSES; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; RNA VIRUSES;

EID: 0032939104     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/jcm.37.6.1813-1818.1999     Document Type: Article

References (47)

1. Alaeus, A., K. Lidman, A. Sonnerborg, and J. Albert. 1997. Subtype-specific problems with quantification of plasma HIV-1 RNA. AIDS 11:859-865.
2. Arnold, C., K. L. Barlow, S. Kaye, C. Loveday, P. Balfe, and J. P. Clewley. 1995. HIV type 1 sequence subtype G transmission from mother to infant: failure of variant sequence species to amplify in the Roche Amplicor Test. AIDS Res. Hum. Retrovir. 11:999-1001.
3. Blackburn, G. F., H. P. Shah, J. H. Kenten, J. Leland, R. A. Kamin, J. Link, J. Peterman, M. J. Powell, A. Shah, D. B. Talley, S. K. Tyagi, E. Wilkins, T.-G. Wu, and R. J. Massey. 1991. Electrochemiluminescence detection for development of immunoassays and DNA probe assays for clinical diagnostics. Clin. Chem. 37:1534-1539.
4. Boom, R., C. J. A. Sol, M. M. M. Salimans, C. L. Jansen, P. M. E. Wertheimvan Dillen, and J. van der Noordaa. 1990. Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28:495-503.
5. Collins, M. L., B. Irvine, D. Tyner, E. Fine, C. Zayati, C. Chang, T. Horn, D. Ahle, J. Detmer, L. P. Shen, J. Kolberg, S. Bushnell, M. S. Urdea, and D. D. Ho. 1997. A branched DNA signal amplification assay for quantification of nucleic acid targets below 100 molecules/ml. Nucleic Acids Res. 25:2979-2984.
6. Cornelissen, M. Unpublished data.
7. Coste, J., B. Montes, J. Reynes, M. Peeters, C. Segarra, J. P. Vendrell, E. Delaporte, and M. Segondy. 1996. Comparative evaluation of three assays for the quantitation of human immunodeficiency virus type 1 RNA in plasma. J. Med. Virol. 50:293-302.
8. Debyser, Z., E. Van Wijngaerden, K. Van Laethem, K. Beuselinck, M. Reynders, E. De Clercq, J. Desmyter, and A. M. Vandamme. 1998. Failure to quantify viral load with two of the three commercial methods in a pregnant woman harboring an HIV type 1 subtype G strain. AIDS Res. Hum. Retrovir. 14:453-459.
9. De Leys, R., B. Vanderborght, M. Vanden Haesevelde, L. Heyndrickx, A. van Geel, C. Wauters, R. Bernaerts, E. Saman, P. Nijs, B. Willems, H. Taelman, G. van der Groen, P. Piot, T. Tersmette, J. G. Huisman, and H. Van Heuverswyn. 1990. Isolation and partial characterization of an unusual human immunodeficiency retrovirus from two persons of West-Central African origin. J. Virol. 64:1207-1216.
10. de Wolf, F., I. Spijkerman, P. T. Schellekens, M. Langendam, C. Kuiken, M. Bakker, M. Roos, R. Coutinho, F. Miedema, and J. Goudsmit. 1997. AIDS prognosis based on HIV-1 RNA, CD4+ T-cell count and function: markers with reciprocal predictive value over time after seroconversion. AIDS 11: 1799-1806.
11. Dyer, J. R., B. L. Gilliam, J. J. Eron, Jr., L. Grosso, M. S. Cohen, and S. A. Fiscus. 1996. Quantitation of human immunodeficiency virus type 1 RNA in cell free seminal plasma: comparison of NASBA with Amplicor reverse transcription-PCR amplification and correlation with quantitative culture. J. Virol. Methods 60:161-170.
12. Gobbers, E., K. Fransen, T. Oosterlaken, W. Janssens, L. Heyndrickx, T. Ivens, K. Vereecken, R. Schoones, P. van de Wiel, and G. van der Groen. 1997. Reactivity and amplification efficiency of the NASBA HIV-1 RNA amplification system with regard to different HIV-1 subtypes. J. Virol. Methods 66:293-301.
13. Jurriaans, S., B. Van Gemen, G. J. Weverling, D. Van Strijp, P. Nara, R. Coutinho, M. Koot, H. Schuitemaker, and J. Goudsmit. 1994. The natural history of HIV-1 infection: virus load and virus phenotype independent determinants of clinical course? Virology 204:223-233.
14. Kappes, J. C., M. S. Saag, G. M. Shaw, B. H. Hahn, P. Chopra, S. Chen, E. A. Emini, R. McFarland, L. C. Yang, M. Piatak, Jr., and J. D. Lifson. 1995. Assessment of antiretroviral therapy by plasma viral load testing: standard and ICD HIV-1 p24 antigen and viral RNA (QC-PCR) assays compared. J. Acquired Immune Defic. Syndr. Hum. Retrovirol. 10:139-149.
15. Kievits, T., B. Van Gemen, D. Van Strijp, R. Schukkink, M. Dircks, H. Adriaanse, L. Malek, R. Sooknanan, and P. Lens. 1991. NASBA isothermal enzymatic in vitro nucleic acid amplification optimized for the diagnosis of HIV-1 infection. J. Virol. Methods 35:273-286.
16. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
17. Korber, B., B. Foley, T. Leitner, F. McCutchan, B. Hahn, J. W. Mellors, G. Myers, and C. Kuiken. 1997. Human retroviruses and AIDS 1997. A compilation and analysis of nucleic acids and amino acid sequences. Theoretical Biology and Biophysics Group T-10, Los Alamos, N.Mex.
18. Korber, B. T., S. Osmanov, J. Esparza, G. Myers, and WHO Network for HIV Isolation and Characterization. 1994. The World Health Organization Global Programme on AIDS proposal for standardization of HIV sequence nomenclature. AIDS Res. Hum. Retrovir. 10:1355-1358.
19. Layne, S. P., M. J. Merges, M. Dembo, J. L. Spouge, S. R. Conley, J. P. Moore, J. L. Raina, H. Renz, H. R. Gelderblom, and P. L. Nara. 1992. Factors underlying spontaneous inactivation and susceptibility to neutralization of human immunodeficiency virus. Virology 189:695-714.
20. Loussert-Ajaka, I., D. Descamps, F. Simon, F. Brun-Vezinet, M. Ekwalanga, and S. Saragosti. 1995. Genetic diversity and HIV detection by polymerase chain reaction. Lancet 346:912-913.
21. Mellors, J. W., L. A. Kingsley, C. R. Rinaldo, Jr., J. A. Todd, B. S. Hoo, R. P. Kokka, and P. Gupta. 1995. Quantitation of HIV-1 RNA in plasma predicts outcome after seroconversion. Ann. Intern. Med. 122:573-579.
22. Mellors, J. W., C. R. Rinaldo, Jr., P. Gupta, R. M. White, J. A. Todd, and L. A. Kingsley. 1996. Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science 272:1167-1170.
23. Mulder, J., N. McKinney, C. Christopherson, J. Sninsky, L. Greenfield, and S. Kwok. 1994. Rapid and simple PCR assay for quantitation of human immunodeficiency virus type 1 RNA in plasma: application to acute retroviral infection. J. Clin. Microbiol. 32:292-300.
24. Nkengasong, J. N., M. Kalou, C. Maurice, C. Bile, M.-Y. Borget, S. Koblavi, E. Boateng, M. Sassan-Morokro, E. Anatole-Ehounou, P. Ghys, A. E. Greenberg, and S. Z. Wiktor. 1998. Comparison of NucliSens and Amplicor Monitor assays for quantification of human immunodeficiency virus type 1 (HIV-1) RNA in plasma of persons with HIV-1 subtype A infection in Abidjan, Côte d'Ivoire. J. Clin. Microbiol. 36:2495-2498.
25. Nolte, F. S., J. Boysza, C. Thurmond, W. S. Clark, and J. L. Lennox. 1998. Clinical comparison of an enhanced-sensitivity branched-DNA assay and reverse transcription-PCR for quantitation of human immunodeficiency virus type 1 RNA in plasma. J. Clin. Microbiol. 36:716-720.
26. O'Brien, W. A., P. M. Hartigan, D. Martin, J. Esinhart, A. Hill, S. Benoit, M. Rubin, M. S. Simberkoff, and J. D. Hamilton. 1996. Changes in plasma HIV-1 RNA and CD4+ lymphocyte counts and the risk of progression to AIDS. Veterans Affairs Cooperative Study Group on AIDS. N. Engl. J. Med. 334:426-431.
27. Pachl, C., J. A. Todd, D. G. Kern, P. J. Sheridan, S. J. Fong, M. Stempien, B. Hoo, D. Besemer, T. Yeghiazarian, B. Irvine, J. Kolberg, R. Kokka, P. Neuwald, and M. S. Urdea. 1995. Rapid and precise quantification of HIV-1 RNA in plasma using a branched DNA signal amplification assay. J. Acquired Immune Defic. Syndr. Hum. Retrovirol. 8:446-454.
28. Perelson, A. S., P. Essunger, Y. Cao, M. Vesanen, A. Hurley, K. Saksela, M. Markowitz, and D. D. Ho. 1997. Decay characteristics of HIV-1-infected compartments during combination therapy. Nature 387:188-191.
29. Respess, R. A., A. Butcher, H. Wang, T. Chaowanachan, N. Young, N. Shaffer, T. D. Mastro, B. Biryahwaho, R. Downing, A. Tanuri, M. Schechter, R. Pascu, L. Zekeng, L. Kaptué, L. Gürtler, J. Eberle, D. Ellenberger, C. Fridlund, M. Rayfield, and S. Kwok. 1997. Detection of genetically diverse human immunodeficiency virus type 1 group M and O isolates by PCR. J. Clin. Microbiol. 35:1284-1286.
30. Revets, H., D. Marissens, S. De Wit, P. Lacor, N. Clumeck, S. Lauwers, and G. Zissis. 1996. Comparative evaluation of NASBA HIV-1 RNA QT, AMPLICOR-HIV Monitor, and QUANTIPLEX HIV RNA assay, three methods for quantification of human immunodeficiency virus type 1 RNA in plasma. J. Clin. Microbiol. 34:1058-1064.
31. Saag, M. S., M. Holodniy, D. R. Kuritzkes, W. A. O'Brien, R. Coombs, M. E. Poscher, D. M. Jacobsen, G. M. Shaw, D. D. Richman, and P. A. Volberding. 1996. HIV viral load markers in clinical practice. Nat. Med. 2:625-629.
32. Schuurman, R., D. Descamps, G. J. Weverling, S. Kaye, J. Tijnagel, I. Williams, R. van Leeuwen, R. Tedder, C. A. B. Boucher, F. Brun-Vezinet, and C. Loveday. 1996. Multicenter comparison of three commercial methods for quantification of human immunodeficiency virus type 1 RNA in plasma. J. Clin. Microbiol. 34:3016-3022.
33. Simon, F., P. Mauclere, P. Roques, I. Loussert-Ajaka, M. C. Muller-Trutwin, S. Saragosti, M. C. Georges-Courbot, F. Barre-Sinoussi, and F. Brun-Vezinet. 1998. Identification of a new human immunodeficiency virus type 1 distinct from group M and group O. Nat. Med. 4:1032-1037.
34. Spijkerman, I. J., M. Prins, J. Goudsmit, P. J. Veugelers, R. A. Coutinho, F. Miedema, and F. de Wolf. 1997. Early and late HIV-1 RNA level and its association with other markers and disease progression in long-term AIDS-free homosexual men. AIDS 11:1383-1388.
35. Todd, J., C. Pachl, R. White, T. Yeghiazarian, P. Johnson, B. Taylor, M. Holodniy, D. Kern, S. Hamren, D. Chernoff, and M. Urdea. 1995 Performance characteristics for the quantitation of plasma HIV-1 RNA using branched DNA signal amplification technology. J. Acquired Immune Defic. Syndr. Hum. Retrovirol. 10(Suppl.):S35-S44.
36. Urdea, M. S., J. C. Wilber, T. Yeghiazarian, J. A. Todd, D. G. Kern, S. J. Fong, D. Besemer, B. Hoo, P. J. Sheridan, R. Kokka, P. Neuwald, and C. Pachl. 1993. Direct and quantitative detection of HIV-1 RNA in human plasma with a branched DNA signal amplification assay. AIDS 7(Suppl.): S11-S14.
37. Vandamme, A. M., J. C. Schmit, S. Van Dooren, K. Van Laethem, E. Gobbers, W. Kok, P. Goubau, M. Witvrouw, W. Peetermans, E. De Clercq, and J. Desmyter. 1996. Quantification of HIV-1 RNA in plasma: comparable results with the NASBA HIV-1 RNA QT and the AMPLICOR HIV monitor test. J. Acquired Immune Defic. Syndr. Hum. Retrovirol. 13:127-139.
38. Vandamme, A. M., S. Van Dooren, W. Kok, P. Goubau, K. Fransen, T. Kievits, J. C. Schmit, E. De Clercq, and J. Desmyter. 1995. Detection of HIV-1 RNA in plasma and serum samples using the NASBA amplification system compared to RNA-PCR. J. Virol. Methods 52:121-132.
39. Van de Peer, Y., and R. De Wachter. 1994. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Appl. Biosci. 10:569-570.
40. Van Gemen, B., T. Kievits, P. Nara, H. G. Huisman, S. Jurriaans, J. Goudsmit, and P. Lens. 1993. Qualitative and quantitative detection of HIV-1 RNA by nucleic acid sequence-based amplification. AIDS 7(Suppl.): S107-S110.
41. Van Gemen, B., T. Kievits, R. Schukkink, D. Van Strijp, L. T. Malek, R. Sooknanan, H. G. Huisman, and P. Lens. 1993. Quantification of HIV-1 RNA in plasma using NASBA during HIV-1 primary infection. J. Virol. Methods 43:177-187.
42. Van Gemen, B., R. van Beuningen, A. Nabbe, D. Van Strijp, S. Jurriaans, P. Lens, and T. Kievits. 1994. A one-tube quantitative HIV-1 RNA NASBA nucleic acid amplification assay using electrochemiluminescent (ECL) labelled probes. J. Virol. Methods 49:157-167.
43. Wei, X., S. K. Ghosh, M. E. Taylor, V. A. Johnson, E. A. Emini, P. Deutsch, J. D. Lifson, S. Bonhoeffer, M. A. Nowak, B. H. Hahn, M. S. Saag, and G. M. Shaw. 1995. Viral dynamics in human immunodeficiency virus type 1 infection. Nature 373-117-122.
44. Weverling, G. J., J. M. A. Lange, S. Jurriaans, J. M. Prins, V. V. Lukashov, D. W. Notermans, M. Roos, H. Schuitemaker, R. M. W. Hoetelmans, S. A. Danner, J. Goudsmit, and F. de Wolf. 1998. Alternative multidrug regimen provides improved suppression of HIV-1 replication over triple therapy. AIDS 12:F117-F122.
45. WHO Network for HIV Isolation and Characterization. 1994. HIV type 1 variation in World Health Organization-sponsored vaccine evaluation sites: genetic screening, sequence analysis and preliminary biological characterization of selected viral strains. AIDS Res. Hum. Retrovir. 11:1327-1343.
46. Wilber, J. C. 1997. Branched DNA for quantification of viral load. Immunol. Investig. 26:9-13.
47. Zaaijer, H. L., W. Kok, J. H. ten Veen, H. W. Reesink, H. Foolen, I. N. Winkel, J. G. Huisman, H. T. Cuypers, T. Kievits, and P. N. Lelie. 1995. Detection of HIV-1 RNA in plasma by isothermal amplification (NASBA) irrespective of the stage of HIV-1 infection. J. Virol. Methods 52:175-181.