The Use of Transcription-based Amplification Systems in the Diagnosis of HIV-1 Infections

  • Deborah Y. Kwoh
  • Thomas R. Gingeras
Part of the Applied Virology Research book series (AVIR, volume 3)


The advances in nucleic acid sequencing and detection by hybridization have opened new approaches to the diagnosis of human pathogens. While nucleic acid hybridization made detection of target sequences highly specific and/or relatively rapid in comparison to standardized immunological or culture-based assays, the methodology was slow in being adapted to clinical settings for two major reasons. First, the most sensitive nucleic acid hybridization techniques requires the use of radiolabeled probes making everyday utilization and waste management problematic. Secondly, even using radioactivity, nucleic acid hybridization is unable to detect targets below approximately 104 molecules (Chou and Merigan, 1982). This limitation in sensitivity poses a major stumbling block for the use of probes especially in viral diagnostics since several clinically important viruses such as human T-cell lymphoma/leukemia virus type 1 and 2 (HTLV-1 and 2), cytomegalovirus (CMV) and especially human immunodeficiency virus type 1 (HIV-1) frequently are present clinical samples well below the level of sensitivity achievable by most nucleic acid-based hybridization assays (Landry, 1990). A major breakthrough in the utility of nucleic acid hybridization as a diagnostic tool occurred with the introduction of in vitro nucleic acid target amplification. The development of the polymerase chain reaction (PCR) in 1985 (Saiki et al.,1985) permitted the amplification of target nucleic acid sequences over a million-fold, thereby allowing a single copy of a target molecule to be detected in a clinical sample. The only other diagnostic tool comparable in sensitivity is the in vitro propagation by culturing of the pathogen.


Hepatitis Delta Virus Polymerase Chain Reaction Protocol Nucleic Acid Hybridization Polymerase Chain Reaction Technology Promoter Binding Site 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Abbott, J. M., Poiesz, B. J., Byrne, B. C., Kwok, S., Sninsky, J. J. and Ehrlich, G. D. (1988) J. Infect. Dis. 158, 1158–1169.PubMedCrossRefGoogle Scholar
  2. Barany, F. (1991a) Proc. Natl. Acad. Sci. U.S.A. 88, 189–193.PubMedCrossRefGoogle Scholar
  3. Barany, F. (1991b) PCR Method.Applic. 1, 5–16.CrossRefGoogle Scholar
  4. Barringer, K. J., Orgel, L., Wahl, G. and Gingeras, T. R. (1990) Gene 89, 117–122.PubMedCrossRefGoogle Scholar
  5. Becker-André, M. and Hahlbrock, K. (1989) Nucl. Acids Res. 17, 9437–9446.PubMedCrossRefGoogle Scholar
  6. Bhagavati, S., Ehrlich, G., Kula, R. W., Kwok, S., Sninsky, J., Udani, V. and Poeisz, B. J. (1988) N. Engl. J. Med. 318, 1141–1147.PubMedCrossRefGoogle Scholar
  7. Boucher, C. A. B., Tersmette, M., Lange, J. M. A., Kellam, P., deGoede, R. E. Y., Mulder, J. W., Darby, G., Goudsmit, J. and Larder, B. A. (1990) Lancet 336, 585–590.PubMedCrossRefGoogle Scholar
  8. Buchbinder, A., Josephs, S. F., Ablashi, D., Salahuddin, S. Z., Klotman, M. E., Manak, M., Krueger, G. R., Wong-Staal, F. and Gallo, R. C. (1988) J. Virol. Meth. 21, 191–197.CrossRefGoogle Scholar
  9. Chelly, J., Kaplan, J.-C., Maire, P., Gautron, S. and Kahn, A. (1988) Nature 333, 858–860.PubMedCrossRefGoogle Scholar
  10. Chou, S. and Merigan, T. C. (1982) N. Engl. J. Med. 308, 921–925.CrossRefGoogle Scholar
  11. Cimino, G. D., Metchette, K. C., Hearst, J. E. and Isaacs, S. T. (1991) Nucl. Acids Res. 19, 99–107.PubMedCrossRefGoogle Scholar
  12. Davis, G. R., Blumeyer, K., DiMichele, L. J., Whitfield, K. M., Chappelle, H., Riggs, N., Ghosh, S. S., Kao, P., Fahy, E., Kwoh, D. Y., Guatelli, J. C., Spector, S. A., Richman, D. D. and Gingeras, T. R. (1990) J. Infect. Dis. 162, 13–20.PubMedCrossRefGoogle Scholar
  13. de la Salle, C., Bass, M. J., Laustriat, D., Guy, B., Bordes, E., Wiesel, M. L., Grunebaum, L., Lutz, P., Partisani, M., Lang, J. M. et al. (1991) Ann. Hematol. 62, 165–168.PubMedCrossRefGoogle Scholar
  14. Demmler, G. J., Buffone, G. J., Schimbor, C. M. and May, R. A. (1988) J. Infect. Dis. 158, 1177–1184.PubMedCrossRefGoogle Scholar
  15. Duggan, D. B., Ehrlich, G. D., Davey, F. P., Kwok, S., Sninsky, J., Goldberg, J., Baltrucki, L. and Poiesz, B. J. (1988) Blood 71, 1027–1032.PubMedGoogle Scholar
  16. Duncan, B. K., (1991) In The Enzymes (P. Boyer, ed.), pp. 565–586, Academic Press, Inc., New York.Google Scholar
  17. Erlich, H. A., ed. (1989). In PCR Technology: Principles and Applications for DNA Amplification, Stockton Press, New York.Google Scholar
  18. Erlich, H. A., Gelfand, D. H. and Saiki, R. K. (1988) Nature 331, 461–472.CrossRefGoogle Scholar
  19. Fahy, E., Kwoh, D. Y. and Gingeras, T. R. (1991) PCR Method. Applic. 1, 25–33.CrossRefGoogle Scholar
  20. Farzadegan, H., Polis, M. A., Wolinsky, S. M., Rinaldo, C. R. J., Sninsky, J. J., Kwok, S., Griffith, R. L., Kaslow, R. A., Phair, J. P., Polk, E. B. and Saah, A. J. (1988) Ann. Intern. Med. 108, 785–790.PubMedCrossRefGoogle Scholar
  21. Gama, R. E., Hughes, R. J., Bruce, C. B. and Stanway, G. (1988) Nucl. Acids Res. 16, 9346.PubMedCrossRefGoogle Scholar
  22. Gaudette, M. F. and Crain, W. R. (1991) Nucl. Acids Res. 19, 1879–1884.PubMedCrossRefGoogle Scholar
  23. Gelfand, D. H. and White, T. J., (1990) In PCR Protocols: A Guide to Methods and Applications (M. Innis, D. Gelfand, J. Sninsky and T. White, eds.), pp. 129–141, Academic Press, New York.Google Scholar
  24. Gibbs, R. A., Chamberlain, J. S. and Caskey, C. T., (1989) In PCR Technology: Principles and Applications for DNA Amplification (H. Erlich, ed.), pp. 171–191, Stockton Press, New York.Google Scholar
  25. Gilliland, G., Perrin, S. and Bunn, H. F., (1990a) In PCR Protocols: A Guide to Methods and Applications (M. Innis, D. Gelfand, J. Sninsky and T. White, eds.), pp. 60–69, Academic Press, Inc., San Diego, CA.Google Scholar
  26. Gilliland, G., Perrin, S., Blanchard, K. and Bunn, H. F. (1990b) Proc. Natl. Acad. Sci. U.S.A. 87, 2725–2729.PubMedCrossRefGoogle Scholar
  27. Gingeras, T. R. and Kwoh, D. Y. (1991) In Diagnostic Nucleic Acid Probe Technology (C. Dangler and B. Osburn eds.) Hanser Publishers, New York.Google Scholar
  28. Gingeras, T. R., Prodanovich, P., Latimer, T., Guatelli, J. C., Richman, D. D. and Barringer, K. J. (1991) J. Infect. Dis. 164 Google Scholar
  29. Gingeras, T. R., Richman, D. D., Kwoh, D. Y. and Guatelli, J. C. (1990a) Veterinary Microbiology 24, 235–251.PubMedCrossRefGoogle Scholar
  30. Gingeras, T. R., Whitfield, K. M. and Kwoh, D. Y. (1990b) Annales du Biologie Clinique 48, 498–501.Google Scholar
  31. Guatelli, J. C., Whitfield, K. M., Kwoh, D. Y., Barringer, K. J., Richman, D. D. and Gingeras, T. R. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 1874–1878.PubMedCrossRefGoogle Scholar
  32. Gyllensten, U. and Erlich, H. A. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 7652–7656.PubMedCrossRefGoogle Scholar
  33. Hart, C., Schochetman, G., Spira, T., Lifson, A., Moore, J., Galphin, J., Sninsky, J. and Ou, C. Y. (1988) Lancet 2, 596–599.PubMedCrossRefGoogle Scholar
  34. Hemmilä, I., Dakuba, S., Mukkala, V.-M., Sitari, H. A. and Lövgren, T. (1984) Anal. Biochem. 137, 335–343.PubMedCrossRefGoogle Scholar
  35. Hewlett, I., Y., L., Epstein, J., Hawthorne, C. A., Ruta, M. and Allain, J. P. (1990) J. AIDS 3, 714–720.Google Scholar
  36. Imagawa, D. T., Lee, M. H., Wolinsky, S. M., Sano, K., Morales, F., Kwok, S., Sninsky, J.J., Nishanian, P.G., Giorgi, J., Fahey, J.L., Dudley, J., Visscher, B.R. and Detels, R. (1989) N. Engl. J. Med. 320, 1458–1462.PubMedCrossRefGoogle Scholar
  37. Innis, M. A. and Gelfand, D. H., (1990). In PCR Protocols: A Guide to Methods and Applications, (M. Innis, D. Gelfand, J. Sninsky and T. White, eds.). Academic Press, Inc., San Diego.Google Scholar
  38. Isaacs, S. T., Tessman, J. W., Mitchette, K. C., Hearst, J. E. and Cimino, G. D. (1991) Nucl. Acids Res. 19, 109–116.PubMedCrossRefGoogle Scholar
  39. Jackson, J. B., Kwok, S. Y., Sninsky, J. J., Hopsicker, J. S., Sannerud, K. J., Rhame, F. S., Henry, K., Simpson, M. and Balfour, H. H. J. (1990) J. Clin. Microbiol. 28, 16–19.PubMedGoogle Scholar
  40. Japour, A. J., Chatis, P. A., Eigenrauch, H. A. and Crumpacker, C. S. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 3092–3096.PubMedCrossRefGoogle Scholar
  41. Kitchin, P. A., Szotyeri, Z., Fromhole, C. and Almond, N. (1990) Nature 344, 201.PubMedCrossRefGoogle Scholar
  42. Kwoh, D. Y., Davis, G. R., Whitfield, K. M., Chappelle, H. L., DiMichele, L. J. and Gingeras, T. R. (1989) Proc. Nati. Acad. Sci. U.S.A. 86, 1173–1177.CrossRefGoogle Scholar
  43. Kwoh, D. Y. and Kwoh, T. J. (1990) Am. Biotech. Lab. 8, 16–25.Google Scholar
  44. Kwok, S. and Higuchi, R. (1989) Nature 339, 237–238.PubMedCrossRefGoogle Scholar
  45. Kwok, S., Kellogg, D., Ehrlich, G., Poiesz, B., Bhagavati, S. and Sninsky, J. J. (1988)1. Infect. Dis. 158, 1193–1197.Google Scholar
  46. Landry, M. L. (1990) Clin. Biochem. 23, 267–277.PubMedCrossRefGoogle Scholar
  47. Larder, B. A., Chesebro, B. and Richman, D. D. (1990) Antimicrob. Agents Chemother. 34, 436–441.PubMedCrossRefGoogle Scholar
  48. Larder, B. A., Darby, G. and Richman, D. D. (1989) Science 243, 1731–1734.PubMedCrossRefGoogle Scholar
  49. Larder, B. A. and Kemp, S. D. (1989) Science 246 Google Scholar
  50. Larzul, D., Guigue, F., Sninsky, J. J., Mack, D. H., Bréchot, C. and Guesdon, J. L. (1988) J. Virol. Meth. 20, 227–237.CrossRefGoogle Scholar
  51. Laure, F., Courgnaud, V., Rouzioux, C., Blanche, S., Veber, F., Burgard, M., Jacomet, C., Griscelli, C. and Bréchot, C. (1988) Lancet 2, 538–541.PubMedCrossRefGoogle Scholar
  52. Lifson, A. R., Stanley, M., Pane, J., O’Malley, P. M., Wiber, J. C., Stanley, A., Jeffrey, B., Rutherford, G. W. and Sohmer, P. R. (1990) J. Infect. Dis. 161, 436–439.PubMedCrossRefGoogle Scholar
  53. Lizardi, P. M., Guerra, C. E., Lomeli, H., Tussie-Luna, I. and Kramer, F. R. (1988) Bio Technology 6, 1197–1201.CrossRefGoogle Scholar
  54. Longo, M. C., Berninger, M. S. and Hartley, J. L. (1990) Gene 93, 125–128.PubMedCrossRefGoogle Scholar
  55. López-Galíndez, C., Rojas, J. M., Nâjera, R., Richman, D. D. and Perucho, M. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 4280–4284.PubMedCrossRefGoogle Scholar
  56. McCabe, P. C., (1990) In PCR Protocols: A Guide to Methods and Applications (M. Innis, D. Gelfand, J. Sninsky and T. White, eds.), pp. 76–83, Academic Press, Inc., San Diego, CA.Google Scholar
  57. Morello, D., Duprey, P., Israel, A. and Babinet, C. (1985) Immunogenetics 22, 441–452.PubMedCrossRefGoogle Scholar
  58. Mullis, K. B. (1990) Scientific American 262, 56–61, 64–65.Google Scholar
  59. Mullis, K. B. and Faloona, F. A. (1987) Methods Enzymol. 155, 335–350.PubMedCrossRefGoogle Scholar
  60. Murakawa, G. J., Zaia, J. A., Apallone, P. A., Stephens, D. A., Kaplan, B. E., Wallace, R. B. and Rossi, J. J. (1988) DNA 7, 287–295.PubMedCrossRefGoogle Scholar
  61. Myers, R. M., Laren, Z. and Maniatis, T. (1985) Science 230, 1242–1246.PubMedCrossRefGoogle Scholar
  62. Noonan, K. E., Beck, C., Holzmayer, T. A., Chin, J. E., Wunder, J. S. Andrulis, I. L., Gazdar, A. F., William, C. L., Von Hoff, D. D. and Robinson, I. B. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 7160–7164.PubMedCrossRefGoogle Scholar
  63. Oser, A., Roth, W. K. and Valet, G. (1988) Nucl. Acids Res. 16, 1181–1196.PubMedCrossRefGoogle Scholar
  64. Ou, C.-Y., Kwok, S., Mitchell, S. W., Sninsky, J. J., Krebs, J. W., Feorino, P., Warfield, D. and Schochetman, G. (1988) Science 239, 295–297.PubMedCrossRefGoogle Scholar
  65. Ou, C.-Y., Moore, J. L. and Schochetman, G. (1991) Bio Techniques 10, 442–445.Google Scholar
  66. Ozawa, T., Tanaka, M., Ikebe, S.-I., Ohno, K., Kondo, T. and Mizuno, Y. (1990) Biochem. Biophys. Res. Comm. 172, 483–489.PubMedCrossRefGoogle Scholar
  67. Paterlini, P., Gerken, G., Nakajima, E., Terre, S., D’Errico, A., Grigioni, W., Nalpas, B., Franco, D., Wands, J., Kew, M., Pisi, E., Tiollais, P. and Bréchot, C. (1990a) N. Engl. J. Med. 323, 80–85.PubMedCrossRefGoogle Scholar
  68. Paterlini, P., Lallemant-Le Coeur, S., Lallemant, M., M’Pele, P., Dazza, M. C., Terre, S., Moncany, M., Jourdain, G., Courgnaud, V. and N’Zingoula, S. (1990b) J. Med. Virol. 30, 53–57.PubMedCrossRefGoogle Scholar
  69. Persing, D. H. (1991) J. Clin. Microbiol. 29, 1281–1285.PubMedGoogle Scholar
  70. Persing, D. H. and Landry, M. L. (1989) Yale J. Biol. Med. 62, 159–171.PubMedGoogle Scholar
  71. Pezzella, M., Rossi, P., Lombardi, V., Gemelli, V., Mariani Constantini, R., Mirolo, M., Fundaro, C., Moschese, V. and Wigzell, H. (1989) BMJ 298, 713–716.PubMedCrossRefGoogle Scholar
  72. Rayfield, M., DeCork, K., Heyward, W., Goldstein, L., Krebs, J., Kwok, S., Lee, S., McCormick, J., Moreau, J. M., Odebouri, K., Schochetman, G., Sninsky, J. and Ou, C. Y. (1988) J. Infect. Dis. 158, 1170–1176.PubMedCrossRefGoogle Scholar
  73. Richman, D., Rosenthal, A. S., Skoog, M., Eckner, R. J., Chou, T.-C., Sabo, J. P. and Merluzzi, V. J. (1991b) Antimicrob. Agents Chemotherap. 35, 305–308.CrossRefGoogle Scholar
  74. Richman, D. D. (1990) Rev. Infectious Diseases 12, S507 - S512.CrossRefGoogle Scholar
  75. Richman, D. D., Grimes, J. M. and Lagakos, S. W. (1990) J. AIDS 3, 743–746.Google Scholar
  76. Richman, D. D., McCutchan, J. A. and Spector, S. A. (1987) J. Infect. Dis. 156, 823–827.PubMedCrossRefGoogle Scholar
  77. Robinson, M. O. and Simon, M. I. (1991) Nucl. Acids Res. 19, 1557–1562.PubMedCrossRefGoogle Scholar
  78. Rogers, M. F., Ou, C.-Y., Rayfield, M., Thomas, P. A., Schoenbaum, E. E., Abrahms, E., Krasinski, K., Selwyn, P. A., Moore, J., Kaul, A., Grimm, K. T., Bamji, M. and Schochetman, G. (1989) N. Engl. J. Med. 320, 1649–1654.PubMedCrossRefGoogle Scholar
  79. Saiki, R. K., (1989). PCR Technology: Principles and Applications for DNA Amplification, Stockton Press, New York.Google Scholar
  80. Saiki, R. K., Gelfand, D. H., Stoffel, S., Scharf, S. J., Higuchi, R., Horn, G. T., Mullis, K. B. and Erlich, H. A. (1988) Science 230, 1350–1354.CrossRefGoogle Scholar
  81. Saiki, R. K., Scharf, S., Faloona, F. A., Mullis, K. B., Horn, G., Erlich, H. and Arnheim, W. (1985) Science 230, 1300–1354.CrossRefGoogle Scholar
  82. Sambrook, J., Fritsch, E. F. and Maniatis, T., (1989). Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.Google Scholar
  83. Sheppard, H. W., Ascher, M. S., Busch, M. B., Sohmer, P. R., Stanley, M., Luce, M. C., Chimera, J. A., Madej, R., Rodgers, G. C., Lynch, C. and The New York City Collaborative Study of maternal HIV Transmission and Montefiore Medical Center HIV Perinatal Transmission Study Group (1991) J. AIDS 4, 277–283.Google Scholar
  84. Shibata, D., Fu, Y. S., Gupta, J. W., Shah, K. V., Arnheim, N. and Martin, W. J. (1988a) Lab. Invest. 59, 555–559.PubMedGoogle Scholar
  85. Shibata, D., Martin, W. J., Appleman, M. D., Causey, D. M., Leedom, J. M. and Arnheim, N. (1988b) J. Infect. Dis. 158, 1185–1192.PubMedCrossRefGoogle Scholar
  86. Shibata, D. K., Arnheim, N. and Martin, W. J. (1988c) J. Exp. Med. 167, 225–230.PubMedCrossRefGoogle Scholar
  87. Thompson, J. D. and Gillespie, W. R. (1990) Clin. Biochem. 23, 261–265.PubMedCrossRefGoogle Scholar
  88. Varas, F., Leandro, M., Ballester, S. and Nâjera, R. (1991) Bio Techniques 11, 384–391.Google Scholar
  89. Wang, A. M., Doyle, M. V. and Mark, D. F. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 9717–9721.PubMedCrossRefGoogle Scholar
  90. Wang, A. M. and Mark, D. F., (1990) In PCR Protocols: A Guide to Methods and Applications (M. Innis, D. Gelfand, J. Sninsky and T. White, eds.), pp. 70–75, Academic Press, Inc., San Diego, California, USA.Google Scholar
  91. Wedell, A., Datta, S. Andersson, B. and Luthman, H. (1990) Technique 2, 23–26.Google Scholar
  92. Williams, P., Simmonds, P., Yap, P. L., Balfe, P., Bishop, J., Brettle, R., Hague, R., Hargreaves, D., Inglis, J. and Brown, A. L. (1990) AIDS 4, 393–398.PubMedCrossRefGoogle Scholar
  93. Winter, E., Yamamoto, F., Almoguera, C. and Perucho, M. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 7575–7579.PubMedCrossRefGoogle Scholar
  94. Wolinsky, S. M., Rinaldo, C. R., Kwok, S., Sninsky, J. J., Gupta, P., Imagawa, D., Farzadegan, H., Jacobson, L. P., Grovit, K. S. and Lee, M. H. (1989) Ann. Intern. Med. 111, 961–972.PubMedCrossRefGoogle Scholar
  95. Wu, D. Y. and Wallace, R. B. (1989) Genomics 4, 560–569.PubMedCrossRefGoogle Scholar
  96. Zeldis, J. B., Lee, J. H., Mamish, D., Finegold, D. J., Sircar, R., Ling, Q., Knudsen, P. J., Kuramoto, I. K. and Mimms, L. T. (1989) J. Clin. Invest. 84, 1503–1508.PubMedCrossRefGoogle Scholar
  97. Zignego, A. L., Deny, P., Feray, C., Ponzetto, A., Gentilini, P., Tiollais, P. and Bréchot, C. (1990) Mol. Cell. Probes 4, 43–51.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 1994

Authors and Affiliations

  • Deborah Y. Kwoh
    • 1
  • Thomas R. Gingeras
    • 1
  1. 1.Life Sciences Research LaboratoryBaxter Diagnostics, Inc.San DiegoUSA

Personalised recommendations