Archives of Virology

, Volume 97, Issue 3–4, pp 151–165 | Cite as

Advances in the use of nucleic acid probes in diagnosis of viral diseases of man

  • Mary Norval
  • R. W. Bingham
Brief Review


A variety of methods are now available for the preparation and labelling of viral nucleic acids for use as probes in diagnostic virology. Some of these are assessed including the use of synthetic oligonucleotides in place of molecularly cloned nucleic acids, and alternatives to labelling with radioactive isotopes such as biotin, enzymes and fluorochromes. Dot blot, sandwich, indirect sandwich and in situ hybridization are covered, and examples given of the current use of nucleic acid probes in detection of human viral infections. The potential and limitations of nucleic acid hybridization are discussed in the light of these new methods.


Infectious Disease Nucleic Acid Viral Infection Biotin Viral Disease 
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. 1.
    Aksamit AJ, Mourrain P, Sever JL, Major EO (1985) Progressive multifocal leukoencephalopathy investigation of three cases using in situ hybridization with JC virus biotinylated DNA probe. Ann Neurol 18: 490–496Google Scholar
  2. 2.
    Al-Nakib W, Stanway G, Forsyth M, Hughes PJ, Almond JW, Tyrrell DAJ (1986) Detection of human rhinoviruses and their molecular relationship using cDNA probes. J Med Virol 20: 289–296Google Scholar
  3. 3.
    Ambinder RF, Charache P, Staal S, Wright P, Forman M, Hayward SD, Hayward GS (1986) The vector homology problem in diagnostic nucleic acid hybridization of clinical specimens. J Clin Microbiol 24: 16–20Google Scholar
  4. 4.
    Ambinder RF, Wingard JR, Burns WH, Hayward SD, Sarai R, Perry HR, Santos GW, Hayward GS (1985) Detection of Epstein Barr virus DNA in mouth washes by hybridization. J Clin Microbiol 21: 353–356Google Scholar
  5. 5.
    Anand A, Gray ES, Brown T, Clewley JP, Cohen BJ (1987) Human parvovirus infection in pregnancy and hydrops fetalis. N Engl J Med 316: 183–186Google Scholar
  6. 6.
    Anderson MJ, Jones SE, Minson AC (1985) Diagnosis of human parvovirus infection by dot-blot hybridization using cloned viral DNA. J Med Virol 15: 163–172Google Scholar
  7. 7.
    Bauman JFG, Wiegant J, van Duijn P (1981) Cytochemical hybridization with fluorochrome-labelled RNA. I. Development of a method using nucleic acid bound to agarose beads as a model. J Histochem Cytochem 29: 227–237Google Scholar
  8. 8.
    Bauman JG, Wiegant J, van Duijn P (1981) Cytochemical hybridization with fluorochrome-labelled RNA. II. Applications. J Histochem Cytochem 29: 227–237Google Scholar
  9. 9.
    Beckmann AM, Myerson D, Daling JR, Kiviat N, Fenoglio CM, McDougall JK (1985) Detection and localization of human papilloma virus DNA in human genital condylomas by in situ hybridization with biotinylated probes. J Med Virol 16: 265–273Google Scholar
  10. 10.
    Bornkamm GW, Desgranges C, Gissmann L (1983) Nucleic acid hybridization for the detection of viral genomes. Curr Top Microbiol Immunol 104: 287–298Google Scholar
  11. 11.
    Brechot C, Hadchouel M, Scotts J, Degos F, Charnay P, Trepo C, Tiollais P (1981) Detection of hepatitis B DNA in liver and serum: a direct appraisal of the chronic carrier state. Lancet 2: 765–768Google Scholar
  12. 12.
    Bresser J, Doering J, Gillespie D (1983) Quick-blot—selective messenger-RNA or DNA immobilization from whole cells. DNA 2: 243–254Google Scholar
  13. 13.
    Chowdhury SI, Hammerschmidt W, Ludwig H, Thein P, Buhk H-J (1986) Rapid method for the identification and screening of herpesvirus by DNA finger printing combined with blot hybridization. J Virol Methods 14: 285–291Google Scholar
  14. 14.
    Conner BJ, Reyes AA, Murin C, Itakura K, Teplitz RL, Wallace RB (1983) Detection of sickle cell βS-globulin allele by hybridization with synthetic oligonucleotides. Proc Natl Acad Sci USA 80: 278–282Google Scholar
  15. 15.
    Danos O, Katinka M, Yaniv M (1980) Molecular cloning, refined physical map and heterogeneity of methylation sites of papilloma virus type 1 a DNA. Eur J Biochem 109: 475–461Google Scholar
  16. 16.
    de Villiers E-M, Gissmann L, zur Hausen H (1981) Molecular cloning of viral DNA from human genital warts. J Virol 40: 932–935Google Scholar
  17. 17.
    Diaz-Mitroma F, Preiksaitis JK, Leung WC, Tyrrell DLJ (1987) DNA dot hybridization to detect Epstein-Barr virus in throat washings. J Infect Dis 155: 297–303Google Scholar
  18. 18.
    Diegutis PS, Keirnan E, Burnett L, Nightingale BN, Cossart YE (1986) False-positive results with hepatitis B DNA dot-hybridization in hepatitis B surface antigennegative specimes. J Clin Microbiol 23: 797–799Google Scholar
  19. 19.
    Durst M, Kleinheinz A, Hotz M, Gissmann L (1985) The physical state of human papillomavirus type 16 DNA in benign and malignant genital tumours. J Gen Virol 66: 1515–1522Google Scholar
  20. 20.
    Fleckenstein B, Muller I, Collins J (1982) Cloning of the complete human cytomegalovirus in cosmids. Gene 18: 39–46Google Scholar
  21. 21.
    Flewett TH (1985) Rapid diagnosis of virus diseases. Br Med Bull 41: 315–321Google Scholar
  22. 22.
    Forster AC, McInnes JL, Skingle DC, Symons RH (1985) Non-radioactive hybridization probes prepared by the chemical labelling of DNA and RNA with a novel reagent, photobiotin. Nucleic Acids Res 13: 745–761Google Scholar
  23. 23.
    Galloway DA, Swain M (1980) Cloning of Herpes simplex virus type 2 DNA fragments in a plasmid vector. Gene 11: 253–257Google Scholar
  24. 24.
    Gendelman HE, Moench TR, Narayan O, Graffin DE, Clements JE (1985) A double labeling technique for performing immunocytochemistry and in situ hybridization in virus infected cell cultures and tissues. J Virol Methods 11: 93–103Google Scholar
  25. 25.
    Goldin AL, Sandri-Goldin RM, Levine M, Glorioso JC (1981) Cloning of herpes simplex type 1 sequences representing the whole genome. J Virol 38: 50–58Google Scholar
  26. 26.
    Gomes SA, Sascimin JP, Siqueira MM, Krawczuk MM, Pereira HG, Russell WC (1985) In situ hybridization with biotinylated DNA probes: a rapid diagnostic test for adenovirus upper respiratory infection. J Virol Methods 12: 105–110Google Scholar
  27. 27.
    Habermehl K-O (ed) (1985) Rapid methods and automation in microbiology and immunology. Springer Verlag, Berlin Heidelberg New York TokyoGoogle Scholar
  28. 28.
    Henchal EA, Narupiti S, Feighny R, Padmanabhan P, Vakharia V (1987) Detection of dengue virus RNA using nucleic acid hybridization. J Virol Methods 15: 187–200Google Scholar
  29. 29.
    Hernandez-Jairegui P, Eriksson A, Perez RT, Pettersson U, Moreno-Lopez J (1987) Human papillomavirus type 13 DNA in focal epithelial hyperplasia among Mexicans. Arch Virol 93: 131–137Google Scholar
  30. 30.
    Hyypia T, Stalhandske P, Vainionpaa R, Pettersson U (1984) Detection of Enteroviruses by spot hybridization. J Clin Microbiol 19: 436–438Google Scholar
  31. 31.
    Khan AM, Wright PJ (1987) Detection of flavivirus RNA in infected cells using photobiotin-labelled hybridization probes. J Virol Methods 15: 121–130Google Scholar
  32. 32.
    Kulski JK, Norval M (1985) Nucleic acid probes in diagnosis of viral diseases of man. Arch Virol 83: 3–15Google Scholar
  33. 33.
    Langdale JA, Malcolm ADB (1985) A rapid method of gene detection using DNA bound to Sephacryl. Gene 36: 201–210Google Scholar
  34. 34.
    Lehtomaki K, Julkunen I, Sandelin K, Salonen J, Virtanen M, Ranki M, Hovi T (1986) Rapid diagnosis of respiratory adenovirus infection in young adult men. J Clin Microbiol 24: 108–111Google Scholar
  35. 35.
    Lin HJ, Wu P-C, Lai C-L (1987) An oligonucleotide probe for the detection of hepatitis B virus DNA in serum. J Virol Methods 15: 139–149Google Scholar
  36. 36.
    Maniatis T, Fritsch EF, Sambrook J (1982) Molecular cloning. A laboratory manual. Cold Spring Harbor Laboratory, New YorkGoogle Scholar
  37. 37.
    McCance DJ (1986) Human papillomaviruses and cancer. Biochem Biophys Acta 823: 195–205Google Scholar
  38. 38.
    McKeating JA, Al-Nakib W, Greenaway PJ, Griffith PD (1985) Detection of cytomegalovirus by DNA-DNA hybridization employing probes labelled with32-phosphorus or biotin. J Virol Methods 11: 207–216Google Scholar
  39. 39.
    Meanwell CA, Cox MF, Blackledge G, Maitland N (1987) HPV 16 DNA in normal and malignant cervical epithelium: implication for the aetiology and behaviour of cervical neoplasia. Lancet 1: 703–707Google Scholar
  40. 40.
    Meinkoth J, Wahl G (1984) Hybridization of nucleic acids immobilized on solid supports. Anal Biochem 138: 267–284Google Scholar
  41. 41.
    Messing J (1983) New M 13 vectors for cloning. In: Wu R, Grossman L, Moldave K (eds) Methods in enzymology, vol 101. Academic Press, New York, pp 20–78Google Scholar
  42. 42.
    Mitchell R, Ambros P, Gosden JR, Morten JE, Porteous DJ (1986) Gene mapping and physical arrangements of human chromation in transformed, hybrid cells: fluorescent and autoradiographic in situ hybridization compared. Somatic Cell Mol Genet 12: 313–324Google Scholar
  43. 43.
    Moench TR, Gendelman HE, Clements JE, Narayan O, Griffin DE (1985) Efficiency of in situ hybridization as a function of probe size and fixation method. J Virol Methods 11: 119–130Google Scholar
  44. 44.
    Monroe JE, Andrews C, Sullivan JL, Mulder C (1987) Use of cytoplasmic dot-blot hybridization to detect human immunodeficiency virus RNA sequences in cultures of peripheral blood. J Infect Dis 155: 320–322Google Scholar
  45. 45.
    Morace G, van der Helm K, Jilg W, Deinhardt F (1985) Detection of hepatitis B viral DNA in serum by a rapid-filtration hybridization assay. J Virol Methods 12: 235–242Google Scholar
  46. 46.
    Parkkinen S, Mantyjarvi R, Syrjanen K, Ranki M (1986) Detection of human papillomavirus DNA by the nucleic acid sandwich hybridization method from cervical scrapings. J Med Virol 20: 279–288Google Scholar
  47. 47.
    Pettersson U, Hyypia T (1985) Nucleic acid hybridization — an alternative tool in diagnostic microbiology. Immunol Today 6: 268–272Google Scholar
  48. 48.
    Ranki M, Virtanen M, Palva A, Laaksonen M, Pettersson R, Kaariainen L, Halonen P, Soderlund H (983) Nucleic acid sandwich hybridization in adenovirus diagnosis. Curr Top Microbiol Immunol 104: 307–318Google Scholar
  49. 49.
    Renz M, Kurz C (1984) A colorimetric method for DNA hybridization. Nucleic Acids Res 12: 3435–3444Google Scholar
  50. 50.
    Richman DD, Cleveland PH, Redfield DC, Oxman MN, Wahl GM (1984) Rapid viral diagnosis. J Infect Dis 149; 298–310Google Scholar
  51. 51.
    Rotbard HA, Levin MJ, Villarreal LP, Tracy SM, Semler BL, Wimmer E (1985) Factors affecting the detection of enteroviruses in cerebrospinal fluid with Coxsackie B3 and poliovirus 1 cDNA probes. J Clin Microbiol 22: 220–224Google Scholar
  52. 52.
    Schuster V, Matz B, Wiegand H, Traub B, Kampa D, Neumann-Haefelin D (1986) Detection of human cytomegalovirus in urine by DNA-DNA and RNA-DNA hybridizations. J Infect Dis 154: 309–314Google Scholar
  53. 53.
    Spector SA, Rua JA, Spector DH, McMillan R (1984) Detection of human cytomegalovirus in clinical specimens by DNA-DNA hybridization. J Infect Dis 150: 121–126Google Scholar
  54. 54.
    Stalhandske P, Hyypia T, Gadler H, Halonen P, Pettersson U (1983) The use of molecular hybridization for demonstration of adenovirus in human stools. Curr Top Microbiol Immunol 104: 229–306Google Scholar
  55. 55.
    Stenlund A, Perricaudet M, Tiollais P, Pettersson U (1980) Construction of restriction enzyme fragment libraries containing DNA from human adenovirus types 2 and 5. Gene 10: 47–52Google Scholar
  56. 56.
    Straus SE, Owens J, Ruyechan WT, Takiff HE, Casey TA, vande Woude GF, Hay J (1982) Molecular cloning and physical mapping of varicella zoster virus DNA. Proc Natl Acad Sci USA 79: 993–997Google Scholar
  57. 57.
    Thomas HC, Karayian P, Fowler MJ, Monjardi I (1985) Clinical uses of hepatitis B virus-DNA assays. J Virol Methods 10: 291–294Google Scholar
  58. 58.
    Tourtellotte WW, Verity AN, Schmid P, Martinez S, Shapshak P (1987) Covalent binding of formalin fixed paraffin embedded brain tissue sections to glass slides suitable for in situ hybridization. J Virol Methods 15: 87–100Google Scholar
  59. 59.
    Unger ER, Budgeon LR, Myerson D, Brigati DJ (1986) Viral diagnosis by in situ hybridization. Am J Surg Pathol 10: 1–8Google Scholar
  60. 60.
    Virtanen M, Palva A, Laaksonen M, Halonen P, Soderlund H, Ranki M (1983) Novel test for rapid viral diagnosis: detection of adenovirus in nasopharyngeal mucus aspirates by means of nucleic-acid sandwich hybridization. Lancet 1: 381–383Google Scholar
  61. 61.
    Virtanen M, Syvanen A-C, Oram J, Soderlund H, Ranki M (1984) Cytomegalovirus in urine: detection of viral DNA by sandwich hybridization. J Clin Microbiol 20: 1083–1088Google Scholar
  62. 62.
    Viscidi RP, Connelly CJ, Yolken RH (1986) Novel chemical method for the preparation of nucleic acid for non-isotopic hybridization. J Clin Microbiol 23: 311–317Google Scholar
  63. 63.
    Vonsover A, Leventon-Kriss S, Langer A, Smetana Z, Zaizov R, Potaznick D, Cohen IJ, Gotlieb-Stematsky T (1987) Detection of varicella zoster virus in lymphocytes by DNA hybridization. J Med Virol 21: 57–66Google Scholar
  64. 64.
    Wickenden C, Steele A, Malcolm AD, Coleman DV (1985) Screening for wart virus infection in normal and abnormal cervices by DNA hybridization of cervical scrapes. Lancet 1: 65–67Google Scholar
  65. 65.
    Wolf H, Leser U, Haus M, Gu SY, Pathmanathan R (1986) Sandwich nucleic acid hybridization: a method with a universally usable labelled probe for various specific tests. J Virol Methods 13: 1–8Google Scholar
  66. 66.
    Yousaf SI, Carroll AR, Clarke BE (1984) A new and improved method for 3′-end labelling DNA using [α-32P] dd ATP. Gene 27: 309–313Google Scholar
  67. 67.
    Ziegler T, Hukkanen V, Artstila P, Auvinen P, Jalava A, Hyypia T (1985) Typing of herpes simplex virus isolates with monoclonal antibodies and by nucleic acid hybridization. J Virol Methods 12: 169–177Google Scholar

Copyright information

© Springer-Verlag 1987

Authors and Affiliations

  • Mary Norval
    • 1
  • R. W. Bingham
    • 2
  1. 1.Department of BacteriologyUniversity of Edinburgh Medical SchoolEdinburgh
  2. 2.Department of Veterinary Pathology, Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEdinburgh

Personalised recommendations