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Virus Genome Detection by the Polymerase Chain Reaction (PCR)

  • Julian G. Hoad
  • Thomas F. Schulz
Part of the Methods in Molecular Biology book series (MIMB, volume 8)

Abstract

Since the polymerase chain reaction (PCR) technique was developed in 1986 (1), it has found wide application in molecular biology and is now regarded as an irreplaceable tool in many laboratories. This chapter will deal with its use for the detection of virus genomes for diagnostic and experimental purposes.

Keywords

Polymerase Chain Reaction Polymerase Chain Reaction Product Polymerase Chain Reaction Reaction Polymerase Chain Reaction Fragment Polymerase Chain Reaction Mixture 
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.

References

  1. 1.
    Saiki, R. K., Gelfand, D. H., Stoffel, S., Scharf, S. J., Higuchi, R, Horn, G. T., Mullis, K. B., and Erlich, H. A. (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239, 487–491.PubMedCrossRefGoogle Scholar
  2. 2.
    Goodenow, M., Huet, T., Saurin, W., Kwok, S., Sninsky, J., and Wain-Hobson, S. (1989) HIV-1 isolates are rapidly evolving quasispecies: Evidence for viral mixtures and preferred nucleotide substitutions. J. Acqu. Immunodefic. Syndr. 2, 344–352.Google Scholar
  3. 3.
    Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd Ed. (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY).Google Scholar
  4. 4.
    Rodgers, M. F., Ou, C.-Y, Rayfield, M., Thomas, P. A., Schoenbaum, E. E., Abrams, E., Krasinski, K., Selwyn, P. A., Moore, J., Kaul, A., Grimm, K. T., Bamji, M, and Schochetman, G. (1989) Use of the polymerase chain reaction for early detection of the proviral sequences of human immunodeficiency virus in infants born to seropositive mothers. N. Engl. J. Med. 320, 1649–1654.CrossRefGoogle Scholar
  5. 5.
    Simmonds, P., Balfe, P., Peutherer, J. F., Ludlam, C. A., Bishop, J. O., and Brown, A. J. L. (1990) Human immunodeficiency virus-infected individuals contain provirus in small numbers of peripheral mononuclear cells and at low copy numbers. J. Virol. 64, 864–872.PubMedGoogle Scholar
  6. 6.
    Abbott, M. A., Poiesz, B. J., Byrne, B. C., Kwok, S., Sninsky, J. J., and Ehrlich, G. D. (1988) Enzymatic gene amplification: Qualitative and quantitative methods for detecting proviral DNA amplified in vitro. J. Infect. Dis 158, 1158–1169.PubMedGoogle Scholar
  7. 7.
    Ou, C.-Y., Kwok, S., Mitchell, S. W., Mack, D., Sninsky J. J., Krebs, J. W, Feorino, P., Warfield, D., and Schochetman, G. (1988) DNA amplification for direct detection of HIV-1 in DNA of peripheral blood mononuclear cells. Science 239, 295–297PubMedCrossRefGoogle Scholar
  8. 8.
    Chen, E. Y. and Seeburg, P. H. (1985) Supercoil sequencing: A fast and simple method for sequencing plasmid DNA. DNA 4(2), 165–170.PubMedCrossRefGoogle Scholar
  9. 9.
    Winship, P. R. (1989) An improved method for directly sequencing PCR amplified material using dimethyl sulphoxide. Nucleic Acids Res 17, 1266.PubMedCrossRefGoogle Scholar
  10. 10.
    Gyllensten, U. B. and Erlich, H. A. (1988) Generation of single stranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQA locus. Proc. Nat. Acad. Sa. USA 85, 7652–7656.CrossRefGoogle Scholar
  11. 11.
    Reddy, P., Sandberg-Wollheim, M., and Mettus, R. (1989) Amplification and molecular cloning of HTLV-1 sequences from DNA of MS patients. Science 243, 529–533PubMedCrossRefGoogle Scholar
  12. 12.
    Richardson, J., Wucherpfennig, K, Endo, N., Rudge, P., Dalgleish, A. G., and Hafler, D. A. (1989) PCR analysis of DNA from MS patients for the presence of HTLV-1. Science 246, 821–823.CrossRefGoogle Scholar
  13. 13.
    Sarkar, G. and Sommer, S S (1990) Shedding light on PCR contamination Nature 343, 27.PubMedCrossRefGoogle Scholar
  14. 14.
    Bell, J. and Ratner, L. (1989) Specificity of polymerase chain amplification reactions for human immunodeficiency virus type 1 DNA sequences. AIDS Res Hum. Retroviruses 5, 87–95.PubMedCrossRefGoogle Scholar
  15. 15.
    Laure, F., Courgnaud, V., Rouzioux, C., Blanche, S., Veber, F., Burgard, M., Jacomet, C., Griscelli, C., and Brechot, C. (1988) Detection of HTV-1 DNA in infants and children by means of the polymerase chain reaction. Lancet 2, 538–541.PubMedCrossRefGoogle Scholar
  16. 16.
    Loche, M. and Mach, B. (1988) Identification of HFV-infected seronegative individuals by a direct diagnostic test based on hybridisation to amplified viral DNA Lancet 2, 418–421.PubMedCrossRefGoogle Scholar
  17. 17.
    Ou, C.-Y., Kwok, S., Mitchell, S. W., Mack, D. H., Sninsky, J. J., Krebs, J. W., Feorino, P., Warfield, D., and Schochetman, G. (1988) DNA amplification for direct detection of HIV-1 in DNA of peripheral blood mononuclear cells. Science 239, 295–297.PubMedCrossRefGoogle Scholar
  18. 18.
    Arrigo, S. J., Weitsman, S., Rosenblatt, J D, and Chen, I S. (1989) Analysis of rev gene function on human immunodeficiency virus type 1 replication in lymphoid cells by using a quantitative polymerase chain reaction method. J. Virol. 63, 4875–4881PubMedGoogle Scholar
  19. 19.
    Weber, J., Clapham, P., McKeating, J., Stratton, M., Robey, E., and Weiss, R. (1989) Infection of brain cells by diverse human immunodeficiency virus isolates: Role of CD4 as receptor. J. Gen. Virol 70, 2653–2660.PubMedCrossRefGoogle Scholar
  20. 20.
    Hart, C., Schochetman, G., Spira, T., Iifson, A., Moore, J., Galphin, J., Sninsky, J., and OU, C.-Y. (1988) Direct detection of HTV RNA expression in seropositive subjects Lancet 2, 596–599.PubMedCrossRefGoogle Scholar
  21. 21.
    Rayfield, M., De-Cock, K., Heyward, W., Goldstein, L., Krebs, J., Kwok, S., Lee, S, McCormick, J., Moreau, J. M., Odehouri, K., Schochetman, G., Sninski, J, and Ou, C-Y. (1988) Mixed human immunodeficiency virus (HIV) infection in an individual. Demonstration of both HIV type 1 and type 2 proviral sequences by using polymerase chain reaction. J. Infect. Dis. 158, 1170–1176.PubMedGoogle Scholar
  22. 22.
    Lynas, C., Cook, S. D., Laycock, K. A., Bradfield, J. W, and Maitland, N. J. (1989) Detection of latent virus mRNA in tissues using the polymerase chain reaction. J. Pathol. 157, 285–289.PubMedCrossRefGoogle Scholar
  23. 23.
    Cao, M., Xiao, X, Egbert, B., Darragh, T M, and Yen, T S (1989) Rapid detection of cutaneous herpes simplex virus infection with the polymerase chain reaction. J. Invest. Dermatol. 92, 391–392.PubMedCrossRefGoogle Scholar
  24. 24.
    Gama, R. E., Horsnell, P. R, Hughes, P. J, North, C., Bruce, C. B., al-Nakib, W., and Stanway, G. (1989) Amplification of rhinovirus specific nucleic acids from clinical samples using the polymerase chain reaction. J Med. Virol. 28, 73–77.PubMedCrossRefGoogle Scholar
  25. 25.
    Saito, I., Servenius, B., Compton, T., and Fox, R. I. (1989) Detection of Epstein-Barr virus DNA by polymerase chain reaction in blood and tissue biopsies from patients with Sjogren’s syndrome. J. Exp. Med. 169, 2191–2198.PubMedCrossRefGoogle Scholar
  26. 26.
    Thiers, V., Nakajima, E., Kremsdorf, D., Mack, D., Schellekens, H., Driss, F., Goudeau, A., Wands, J., Sninsky, J., Tiollais, P., and Brechot, C. (1988) Transmission of hepatitis B from hepatitis-B seronegative subjects. Lancet 2, 1273–1276.PubMedCrossRefGoogle Scholar
  27. 27.
    Kaneko, S., Miller, R. H., Feinstone, S. M., Unoura, M., Kobayashi, K., Hattori, N., and Purcell, R. H. (1989) Detection of serum hepatitis B virus DNA in patients with chronic hepatitis using the polymerase chain reaction assay. Proc. Natl Acad. Sci USA 86, 312–316.PubMedCrossRefGoogle Scholar
  28. 28.
    Sumazaki, R, Motz, M, Wolf, H., Heinig, J., Jilg, W, and Deinhardt, F. (1989) Detection of hepatitis B virus in serum using amplification of viral DNA by means of the polymerase chain reaction J. Med. Virol 27, 304–308.PubMedCrossRefGoogle Scholar
  29. 29.
    Shibata, D., Martin, W. J., Appleman, M. D, Causey, D. M., Leedom, J M., and Amheim, N. (1988) Detection of cytomegalovirus DNA in peripheral blood of patients infected with human immunodeficiency virus. J Infect. Dis. 158, 1185–1192.PubMedGoogle Scholar
  30. 30.
    Demmler, G. J., Buffone, G. J, Schimbor, C. M, and May, R A (1988) Detection of cytomegalovirus in urine from newborns by using polymerase chain reaction DNA amplification. J. Infect. Dis. 158, 1177–1184.PubMedGoogle Scholar
  31. 31.
    Young, L. S., Bevan, I. S., Johnson, M. A., Blomfield, P. I, Bromidge, T., Maitland, N. J., and Woodman, C. B. (1989) The polymerase chain reaction: A new epidemiological tool for investigating cervical human papillomavirus infection. Br. Med. J. 298, 14–18.CrossRefGoogle Scholar
  32. 32.
    Maitland, N. J., Bromidge, T., Cox, M. F., Crane, I. J., Prime, S. S., and Scully, C. (1989) Detection of human papillomavirus genes in human oral tissue biopsies and cultures by polymerase chain reaction. Br.J. Cancer 59, 698–703.PubMedCrossRefGoogle Scholar
  33. 33.
    Shibata, D. K., Arnheim, N., and Martin, W.J. (1988) Detection of human papilloma virus in paraffin-embedded tissue using the polymerase chain reaction. J. Exp. Med. 167, 225–230.PubMedCrossRefGoogle Scholar
  34. 34.
    Kinoshita, T., Shimoyama, M., Tobinai, K., Ito, M., Ito, S., Ikeda, S., Tajima, K., Shimotohno, K., and Sugimura, T. (1989) Detection of mRNA for the tax1/rex1 gene of human T-cell leukemia virus type I in fresh peripheral blood mononuclear cells of adult T-cell leukemia patients and viral carriers by using the polymerase chain reaction. Proc. Natl Acad. Sci. USA 86, 5620–5624.PubMedCrossRefGoogle Scholar
  35. 35.
    Greenberg, S. J., Ehrlich, G. D., Abbott, M. A., Hurwitz, B. J., Waldman, T. A., and Poiesz, B. J. (1989) Detection of sequences homologous to human retroviral DNA in multiple sclerosis by gene amplification. Proc. Natl. Acad. Sci. USA 86, 2878–2882.PubMedCrossRefGoogle Scholar
  36. 36.
    Arthur, R. R., Dagostin, S., and Shah, K. V. (1989) Detection of BK virus and JC virus in urine and brain tissue by the polymerase chain reaction. J. Clin. Microbiol. 27, 1174–1179.PubMedGoogle Scholar
  37. 37.
    Schulz, T. F, Whitby, D., Hoad, J. G., Corrah, T., Whittle, H., and Weiss, R. A Biological and molecular variability of HIV-2 isolates from the Gambia. J. Virol. 64(10), 5177–5182.Google Scholar
  38. 38.
    Lee, H., Swanson, P., Shorty, V. S., Zack, J. A., Rosenblatt, J. D., and Chen, I S. Y. (1989) High rate of HTLV-II infection in seropositive IV drug abusers in New Orleans. Science 244, 471–475.PubMedCrossRefGoogle Scholar

Copyright information

© The Humana Press Inc., Clifton, NJ 1991

Authors and Affiliations

  • Julian G. Hoad
    • 1
  • Thomas F. Schulz
    • 1
  1. 1.Chester Beatty LaboratoriesInstitute of Cancer ResearchLondonUK

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