Skip to main content

Molecular Methods of Virus Detection in Foods

  • Chapter
Viruses in Foods

Part of the book series: Food Microbiology and Food Safety ((FMFS))

8.0. Summary

Molecular assays are now available for the detection of the enteric viruses most commonly associated with the transmission of food-borne illness. Some of these assays, such as RT-PCR and NASBA, are able to detect very small quantities of virus genome and are suitable tools for the identification of viruses in foods. The application of these assays to foods has been facilitated by the development of methods for the concentration and purification of viral nucleic acids, but inhibitory substances may persist in processed samples and can lead to false-negative results. Thus, it is important to use positive and negative controls in every analysis to allow appropriate interpretation of assay results. There are now several reports of the successful identification of the same virus identified as the cause of a food-borne outbreak in the food implicated by the epidemiologic investigation. Additional studies are needed to determine the role molecular assays will have in food-safety programs.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 209.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 269.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

9.0. References

  • Abd El Galil, K. H., El Sokkary, M. A., Kheira, S. M., Salazar, A. M., Yates, M. V., Chen, W., and Mulchandani, A., 2004, Combined immunomagnetic separation-molecular beacon-reverse transcription-PCR assay for detection of hepatitis A virus from environmental samples. Appl. Environ. Microbiol. 70:4371–4374.

    Article  CAS  Google Scholar 

  • Abu Al-Soud, W., and Radstrom, P., 1998, Capacity of nine thermostable DNA polymerases to mediate DNA amplification in the presence of PCR-inhibiting samples. Appl. Environ. Microbiol. 64:3748–3753.

    CAS  Google Scholar 

  • Allard, A., Albinsson, B., and Wadell, G., 1992, Detection of adenoviruses in stools from healthy persons and patients with diarrhea by two-step polymerase chain reaction. J. Med. Virol. 37:149–157.

    Article  CAS  Google Scholar 

  • Allard, A., Kajon, A., and Wadell, G., 1994, Simple procedure for discrimination and typing of enteric adenoviruses after detection by polymerase chain reaction. J. Med. Virol. 44:250–257.

    CAS  Google Scholar 

  • Atmar, R. L., and Estes, M. K., 2001, Diagnosis of noncultivatable gastroenteritis viruses, the human caliciviruses. Clin. Microbiol. Rev. 14:15–37.

    Article  CAS  Google Scholar 

  • Atmar, R. L., Metcalf, T. G., Neill, F. H., and Estes, M. K., 1993, Detection of enteric viruses in oysters by using the polymerase chain reaction. Appl. Environ. Microbiol. 59:631–635.

    CAS  Google Scholar 

  • Atmar, R. L., Neill, F. H., Romalde, J. L., Le Guyader, F., Woodley, C. M., Metcalf, T. G., and Estes, M. K., 1995, Detection of Norwalk virus and hepatitis A virus I inshellfish tissues with the PCR. Appl. Environ. Microbiol. 61:3014–3018.

    CAS  Google Scholar 

  • Atmar, R. L., Neill, F. H., Woodley, C. M., Manger, R., Fout, G. S., Burkhardt, W., Leja, L., McGovern, E. R., Le Guyader, F., Metcalf, T. G., and Estes, M. K., 1996, Collaborative evaluation of a method for the detection of Norwalk virus in shell-fish tissues by PCR. Appl. Environ. Microbiol. 62:254–248.

    CAS  Google Scholar 

  • Belliot, G., Laveran, H., and Monroe, S. S., 1997, Detection and genetic differentiation of human astroviruses: phylogenetic grouping varies by coding region. Arch. Virol. 142:1323–1334.

    Article  CAS  Google Scholar 

  • Bidawid, S., Farber, J., and Sattar, S., 2000, Rapid concentration and detection of HAV from lettuce and strawberries. J. Virol. Methods 88:175–185.

    Article  CAS  Google Scholar 

  • Boom, R., Sol, C. J., Salimans, M. M., Jansen, C. L., Wertheim-van Dillen, P. M., and van der Noordaa, J., 1990, Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28:495–503.

    CAS  Google Scholar 

  • Buesa, J., Colomina, J., Raga, J., Villanueva, A., and Prat, J. 1996, Evaluation of reverse transcription and polymerase chain reaction (RT/PCR) for the detection of rotaviruses: applications of the assay. Res. Virol. 147:353–361.

    Article  CAS  Google Scholar 

  • Calder, L., Simmons, G., Thornley, C., Taylor, P., Pritchard, K., Greening, G., and Bishop, J., 2003, An outbreak of hepatitis A associated with consumption of raw blueberries. Epidemiol. Infect. 131:745–751.

    Article  CAS  Google Scholar 

  • Chizhikov, V., Wagner, M., Ivshina, A., Hoshino, Y., Kapikian, A. Z., and Chumakov, K., 2002, Detection and genotyping of human group A rotaviruses by oligonucleotide microarray hybridization. J. Clin. Microbiol. 40:2398–2407.

    Article  CAS  Google Scholar 

  • Cline, J., Braman, J. C., and Hogrefe, H. H., 1996, PCR fidelity of Pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res. 24:3546–3551.

    Article  CAS  Google Scholar 

  • Cromeans, T. L., Nainan, O.V., and Margolis, H. S., 1997, Detection of hepatitis A virus RNA in oyster meat. Appl. Environ. Microbiol. 63:2460–2463.

    CAS  Google Scholar 

  • Dimitrov, D. H., Graham, D. Y., and Estes, M. K., 1985, Detection of rotaviruses by nucleic acid hybridization with cloned DNA of simian rotavirus SA11 genes. J. Infect. Dis. 152:293–300.

    CAS  Google Scholar 

  • Dubois, E., Agier, C., Traore, O., Hennechart, C., Merle, G., Cruciere, C., and Laveran, H., 2002, Modified concentration method for the detection of enteric viruses on fruits and vegetables by reverse transcriptase-polymerase chain reaction or cell culture. J. Food Prot. 65:1962–1969.

    CAS  Google Scholar 

  • Espy, M. J., Smith, T. F., and Persing, D. H., 1993, Dependence of polymerase chain reaction product inactivation protocols on amplicon length and sequence composition. J. Clin. Microbiol. 31:2361–2365.

    CAS  Google Scholar 

  • Formiga-Cruz, M., Tofino-Quesada, G., Bofill-Mas, S., Lees, D. N., Henshilwood, K., Allard, A. K., Conden-Hansson, A. C., Hernroth, B. E., Vantarakis, A., Tsibouxi, A., Papapetropoulou, M., Furones, M. D., and Girones, R., 2002, Distribution of human virus contamination in shellfish from different growing areas in Greece, Spain, Sweden, and the United Kingdom. Appl. Environ. Microbiol. 68:5990–5998.

    Article  CAS  Google Scholar 

  • Gentsch, J. R., Glass, R. I., Woods, P., Gouvea, V., Gorziglia, M., Flores, J., Das, B. K., and Bhan, M. K., 1992, Identification of group A rotavirus Gene 4 types by polymerase chain reaction. J. Clin. Microbiol. 30:1365–1373.

    CAS  Google Scholar 

  • Gilpatrick, S. G., Schwab, K. J., Estes, M. K., and Atmar, R. L., 2000, Development of an immunomagnetic capture reverse transcription-PCR assay for the detection of Norwalk virus. J. Virol. Methods 90:69–78.

    Article  CAS  Google Scholar 

  • Gouvea, V., Glass, R. I., Woods, P., Taniguchi, K., Clark, H. F., Forrester, B., and Fang, Z.-F., 1990, Polymerase chain reaction amplification and typing of rotavirus nucleic acid from stool specimens. J. Clin. Microbiol. 28:276–282.

    CAS  Google Scholar 

  • Gouvea, V., Allen, J. R., Glass, R. I., Fang, Z.-Y., Bremont, M., Cohen, J., McCrae, M. A., Saif, L. J., Sinarachatanant, P., and Caul, E.O., 1991, Detection of group B and C rotaviruses by polymerase chain reaction. J. Clin. Microbiol. 29:519–523.

    CAS  Google Scholar 

  • Gouvea, V., Santos, N., Carmo Timenetsky, M., Estes, M. K., 1994, Identification of Norwalk virus in artificially seeded shellfish and selected foods. J. Virol. Methods 48:177–187.

    Article  CAS  Google Scholar 

  • Greene, S. R., Moe, C. L., Jaykus, L.-A., Cronin, M., Grosso, L., and van Aarle, P., 2003, Evaluation of the NucliSens® basic kit assay for detection of Norwalk virus RNA in stool specimens. J. Virol. Methods 108:123–131.

    Article  CAS  Google Scholar 

  • Grimm, A. C., and Fout, G. S., 2002, Development of a molecular method to identify hepatitis E virus in water. J. Virol. Methods 101:175–188.

    Article  CAS  Google Scholar 

  • Grimm, A. C., Cashdollar, J. L., Williams, F. P., and Fout, G. S., 2004, Development of an astrovirus RT-PCR detection assay for use with conventional, real-time, and integrated cell culture/RT-PCR. Can. J. Microbiol. 50:269–278.

    Article  CAS  Google Scholar 

  • Hale, A. D., Tanaka, T. N., Kitamoto, N., Ciarlet, M., Jiang, X., Takeda, N., Brown, D. W., and Estes, M. K., 2000, Identification of an epitope common to genogroup 1 Norwalk-like viruses. J. Clin. Microbiol. 38:1656–1660.

    CAS  Google Scholar 

  • Haqqi, T. M., Sarkar, G., David C.S., and Sommer, S. S., 1988, Specific amplification with PCR of a refractory segment of genomic DNA. Nucleic Acids Res. 16:11844.

    Article  CAS  Google Scholar 

  • Harrington, P. R., Vinjé, J., Moe, C. L., and Baric, R. S., 2004, Norovirus capture with histo-blood group antigens reveals novel virus-ligand interactions. J. Virol. 78: 3035–3045.

    Article  CAS  Google Scholar 

  • Hutin, Y. J. F., Pool, V., Cramer, E. H., Nainan, O.V., Weth, J., Williams, I.T., Goldstein, S. T., Gensheimer, K. F., Bell, B. P., Shapiro, C. N., Alter, M. J., and Margolis, J. S., for the National Hepatitis A Investigation Team, 1999, A multistate, foodborne outbreak of hepatitis A. N. Engl. J. Med. 340:595–602.

    Article  CAS  Google Scholar 

  • Iturriza-Gomara, M., Green, J., Brown, D.W.G., Desselberger, U., and Gray, J. J., 1999, Comparison of specific and random priming in the reverse transcriptase polymerase chain reaction for genotyping group A rotaviruses. J. Virol. Methods 78:93–103.

    Article  CAS  Google Scholar 

  • Jansen, R. W., Newbold, J. E., and Lemon, S. M., 1985, Combined immunoaffinity cDNA-RNA hybridization assay for detection of hepatitis A virus in clinical specimens. J. Clin. Microbiol. 22:984–989.

    CAS  Google Scholar 

  • Jansen, R.W., Siegl, G., and Lemon, S. M., 1990, Molecular epidemiology of human hepatitis A virus defined by an antigen-capture polymerase chain reaction. Proc. Natl. Acad. Sci. U.S.A 87:2867–2871.

    Article  CAS  Google Scholar 

  • Jaykus, L. A., 2003, Challenges to developing real-time methods to detect pathogens in foods. ASM News 69:341–347.

    Google Scholar 

  • Jean, J., Blais, B., Darveau, A., and Fliss, I., 2001, Detection of hepatitis A virus by the nucleic acid sequence-based amplification technique and comparison with reverse transcription-PCR. Appl. Environ. Microbiol. 67:5593–5600.

    Article  CAS  Google Scholar 

  • Jean, J., Blais, B., Darveau, A., and Fliss, I., 2002, Simultaneous detection and identification of hepatitis A virus and rotavirus by multiplex nucleic acid sequence-based amplification (NASBA) and microtiter plate hybridization system. J. Virol. Methods 105:123–132.

    Article  CAS  Google Scholar 

  • Jean, J., D’Souza, D., and Jaykus, L.-A., 2003, Transcriptional enhancement of RTPCR for rapid and sensitive detection of noroviruses. FEMS Microbiol. Lett. 226:339–345.

    Article  CAS  Google Scholar 

  • Jean, J., D’Souza, D., and Jaykus, L.-A., 2004, Multiplex nucleic acid sequence-based amplification for simultaneous detection of several enteric viruses in model ready-to-eat foods. Appl. Environ. Microbiol. 70:6603–6610.

    Article  CAS  Google Scholar 

  • Jiang, X., Estes, M. K., and Metcalf, T. G., 1989, In situ hybridization for quantitative assay of infectious hepatitis A virus. J. Clin. Microbiol. 27:874–879.

    Google Scholar 

  • Jiang, X., Wang, J., Graham, D.Y., and Estes, M. K., 1992, Detection of Norwalk virus in stool by polymerase chain reaction. J. Clin. Microbiol. 30:2529–2534.

    CAS  Google Scholar 

  • Jiang, Y.-J., Liao, G.-Y., Zhao, W., Sun, M.-B., Qian, Y., Bian, C.-X., and Jiang, S.-D., 2004, Detection of infectious hepatitis A virus by integrated cell culture/strand-specific reverse transcriptase-polymerase chain reaction. J. Appl. Microbiol. 97: 1105–1112.

    Article  CAS  Google Scholar 

  • Jonassen, T. O., Monceyron, C., Lee, T.W., Kurtz, J. B., and Grinde, B., 1995, Detection of all serotypes of human astrovirus by the polymerase chain reaction. J. Virol. Methods 52:327–334.

    Article  CAS  Google Scholar 

  • Kageyama, T. S., Kojima, S., Shinohara, M., Uchida, K., Fukushi, S., Hoshino, F. B., Takeda, N., and Katayama, K., 2003, Broadly reactive and highly sensitive assay for Norwalk-like viruses based on real-time quantitative reverse transcription-PCR. J. Clin. Microbiol. 41:1548–1557.

    Article  CAS  Google Scholar 

  • Kobayashi, S., Natori, K., Takeda, N., and Sakae, K., 2004, Immunomagnetic capture rt-PCR for detection of norovirus from foods implicated in a foodborne outbreak. Microbiol. Immunol. 48:201–204.

    CAS  Google Scholar 

  • Koopmans, M., Vennema, H., Heersma, H., van Strien, E., van Duynhoven, Y., Brown, D., Reacher, M., and Lopman, B., for the European Consortium on Foodborne Viruses, 2003, Early identification of common-source foodborne virus outbreaks in Europe. Emerg. Infect. Dis. 9:136–1142.

    Google Scholar 

  • Kwok, S., and Higuchi, R., 1989,Avoiding false positives with PCR. Nature 339:237–238.

    Article  CAS  Google Scholar 

  • Le Cann, P., Ranarijaona, S., Monpoeho, S., Le Guyader, F., and Ferré, V., 2004, Quantification of human astroviruses in sewage using real-time RT-PCR. Res. Microbiol. 155:11–15.

    Article  CAS  Google Scholar 

  • Le Guyader, F. S., Neill, F. H., Estes M. K., Monroe, S. S., Ando, T., and Atmar, R. L., 1996, Detection and analysis of a small round-structured virus strain in oysters implicated in an outbreak of acute gastroenteritis. Appl. Environ. Microbiol. 62:4268–4272.

    Google Scholar 

  • Le Guyader, F. S., Haugarreau, L., Miossec, L., Dubois, E., and Pommepuy, M., 2000, Three-year study to assess human enteric viruses in shellfish. Appl. Environ. Microbiol. 66:3241–3248.

    Article  Google Scholar 

  • Le Guyader, F. S., Neill, F. H., Dubois, E., Bon, F., Loisy, F., Kohli, E., Pommepuy, M., and Atmar, R. L., 2003, A semiquantitative approach to estimate Norwalk-like virus contamination of oysters implicated in an outbreak. Int. J. Food Microbiol. 87:107–12.

    Article  Google Scholar 

  • Le Guyader, F. S., Mittelholzer, C., Haugarreau, L., Hedlund, K.-O., Alsterlund, R., Pommepuy, M., and Svensson, L., 2004a, Detection of noroviruses in raspberries associated with a gastroenteritis outbreak. Int. J. Food Microbiol. 97:179–186.

    Article  Google Scholar 

  • Le Guyader, F. S., Schultz, A.-C, Haugarreau, L., Croci, L., Maunula, L., Duizer, E., Lodder-Verschoor, F., von Bonsdorff, C.-H., Suffredini, E., van der Poel, W. M. M., Reymundo, R., and Koopmans, M., 2004b, Round-robin comparison of methods for the detection of human enteric viruses in lettuce. J. Food Protect. 67:2315–2319.

    Google Scholar 

  • Lees, D. N., Henshilwood, K., and Doré, W. J., 1994, Development of a method for detection of enteroviruses in shellfish by PCR with poliovirus as a model. Appl. Environ. Microbiol. 60:2999–3005.

    CAS  Google Scholar 

  • Lees, D. N., Henshilwood, K., Green, J., Gallimore, C. I., and Brown, D.W. G., 1995, Detection of small round structured viruses in shellfish by reverse transcription-PCR. Appl. Environ. Microbiol. 61:4418–4424.

    CAS  Google Scholar 

  • Leggitt, P. R., and Jaykus, L. A., 2000, Detection methods for human enteric viruses in representative foods. J. Food Prot. 63:1738–1744.

    CAS  Google Scholar 

  • Lewis, G. D., and Metcalf, T. G., 1988, Polyethylene glycol precipitation for recovery of pathogenic viruses, including hepatitis A virus and human rotavirus, from oyster, water, and sediment samples. Appl. Environ. Microbiol. 54:1983–1988.

    CAS  Google Scholar 

  • Lovmar, L., Fock, C., Espinoza, F., Bucardo, F., Syvänen, A.-C., and Bondeson, K., 2003, Microarrays for genotyping human group A rotavirus by multiplex capture and type-specific primer extension. J. Clin. Microbiol. 41:5153–5158.

    Article  CAS  Google Scholar 

  • Mackay, I. M., Arden, K. E., and Nitsche, A., 2002, Real-time PCR in virology. Nucleic Acids Res. 30:1292–1305.

    Article  CAS  Google Scholar 

  • Moore, C., Clark, E. M., Gallimore, C. I., Corden, S. A., Gray, J. J., and Westmoreland, D., 2004, Evaluation of a broadly reactive nucleic acid sequence based amplification assay for the detection of noroviruses in faecal material. J. Clin. Virol. 29:290–296.

    Article  CAS  Google Scholar 

  • Muniain-Mujika, I., Girones, R., Lucena, F., 2000, Viral contamination of shellfish: evaluation of methods and analysis of bacteriophages and human viruses. J. Virol. Methods 89:109–118.

    Article  CAS  Google Scholar 

  • Mustafa, H., Palombo, E. A., and Bishop, R. F., 1998, Improved sensitivity of astrovirus-specific RT-PCR following culture of stool samples in CaCO-2 cells. J. Clin. Virol. 11:103–107.

    Article  CAS  Google Scholar 

  • Myers, T.W., and Gelfand, D. H., 1991, Reverse transcription and DNA amplification by a Thermus thermophilus DNA polymerase. Biochemistry 30:7661–7666.

    Article  CAS  Google Scholar 

  • Noel, J. S., Lee, T.W., Kurtz, J. B., Glass, R. I., and Monroe, S. S., 1995, Typing of human astroviruses from clinical isolates by enzyme immunoassay and nucleotide sequencing. J. Clin. Microbiol. 33:797–801.

    CAS  Google Scholar 

  • Nolte, F. S., and Caliendo, A. M., 2003, Molecular detection and identification of microorganisms, in: Manual of Clinical Microbiology, 8th ed. (P. R. Murray, E. J. Baron, J. H. Jorgensen, M. A. Pfaller, and R. H. Yolken, eds.), ASM Press, Washington, DC, pp. 234–256.

    Google Scholar 

  • Notomi, T., Okayama, H., Masubuchi, H., Yonekawa, T., Watanabe, K., Amino, N., and Hase, T., 2000, Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 28:e63.

    Article  CAS  Google Scholar 

  • Nuanualsuwan, S., and Cliver, D. O., 2002, Pretreatment to avoid positive RT-PCR results with inactivated viruses. J. Virol. Methods 104:217–225.

    Article  CAS  Google Scholar 

  • Orrù, G., Masia, G., Orrù, G., Romanò, L., Piras, V., and Coppola, R. C., 2004, Detection and quantitation of hepatitis E virus in human faeces by real-time quantitative PCR. J. Virol. Methods 118:77–82.

    Article  CAS  Google Scholar 

  • Pang, J., Modlin, J., and Yolken, R., 1992, Use of modified nucleotides and uracil-DNA glycosylase (UNG) for the control of contamination in the PCR-based amplifi-cation of RNA. Mol. Cell. Probes 6:251–256.

    Article  CAS  Google Scholar 

  • Pang, X., Lee, B., Chui, L., Preiksaitis, J. K., and Monroe, S. S., 2004a, Evaluation and validation of real-time reverse transcription-PCR assay using the LightCycler system for detection and quantitation of norovirus. J. Clin. Microbiol. 42:4679–4685.

    Article  CAS  Google Scholar 

  • Pang, X. L., Lee, B., Boroumand, N., Leblanc, B., Preiksaitis, J. K., and Ip, C. C. Y., 2004b, Increased detection of rotavirus using a real time reverse transcriptionpolymerase chain reaction (RT-PCR) assay in stool specimens from children with diarrhea. J. Med. Virol. 72:496–501.

    Article  CAS  Google Scholar 

  • Parida, M., Posadas, G., Inoue, S., Hasebe, F., and Morita, K., 2004, Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of West Nile virus. J. Clin. Microbiol. 42:257–263.

    Article  CAS  Google Scholar 

  • Parshionikar, S. U., Cashdollar, J., and Fout, G. S., 2004, Development of homologous viral internal controls for use in RT-PCR assays of waterborne enteric viruses. J. Virol. Methods 121:39–48.

    Article  CAS  Google Scholar 

  • Pina, S., Puig, M., Lucena, F., Jofre, J., and Girones, R., 1998, Viral pollution in the environment and in shellfish: human adenovirus detection by PCR as an index of human viruses. Appl. Environ. Microbiol. 64:3376–3382.

    CAS  Google Scholar 

  • Pina, S., Buti, M., JardÍ, R., Clemente-Casares, P., Jofre, J., and Girones, R., 2001, Genetic analysis of hepatitis A virus strains recovered from the environment and from patients with acute hepatitis. J. Gen. Virol. 82:2955–2963.

    CAS  Google Scholar 

  • Prato, R., Lopalco, P. L., Chironna, M., Barbuti, G., Germinario, C., and Quarto, M., 2004, Norovirus gastroenteritis general outbreak associated with raw shellfish consumption in south Italy. BMC Infect. Dis. 4:37.

    Article  Google Scholar 

  • Ratcliff, R. M., Doherty, J. C., and Higgins G. D., 2002, Sensitive detection of RNA viruses associated with gastroenteritis by a hanging-drop single-tube nested reverse transcription-PCR method. J. Clin. Microbiol. 40:4091–4099.

    Article  CAS  Google Scholar 

  • Richards, G. P., 1999, Limitations of molecular biological techniques for assessing the virological safety of foods. J. Food Protect. 62:691–697.

    CAS  Google Scholar 

  • Robertson, B. H., Khanna, B., Nainan, O.V., and Margolis, H. S., 1991, Epidemiologic patterns of wild-type hepatitis A virus determined by genetic variation. J. Infect. Dis. 163:286–292.

    CAS  Google Scholar 

  • Rousell, J., Zajdel, M. E., Howdle, P. D., and Blair, G. E., 1993, Rapid detection of enteric adenoviruses by means of the polymerase chain reaction. J. Infect. 27: 271–275.

    Article  CAS  Google Scholar 

  • Saiki, R. K., Scharf, S. J., Faloona, F., Mullis, K. B., Horn, G. T., Erlich, H. A., and Arnheim, N., 1985, Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230:1350–1354.

    Article  CAS  Google Scholar 

  • Saiki, R. K., Gelfand D. H., Stoffel, S., Scharf, S. J., Higuchi, R., Mullis, K. B., Horn G. T., and Ehrlich H. A., 1988, Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491.

    Article  CAS  Google Scholar 

  • Sair, A. I., D’Souza, D. H., Moe, C. L., and Jaykus, L. A., 2002, Improved detection of human enteric viruses in foods by RT-PCR. J. Virol. Methods 100:57–69.

    Article  CAS  Google Scholar 

  • Schlauder, G. G., and Mushahwar, I. K., 2001, Genetic heterogeneity of hepatitis E virus. J. Med. Virol. 65:282–292, 2001.

    Article  CAS  Google Scholar 

  • Schlauder, G. G., Frider, B., Sookoian, S., Castano, G. C., and Mushahwar, I. K., 2000, Identification of two novel isolates of hepatitis E virus in Argentina. J. Infect. Dis. 182:294–297.

    Article  CAS  Google Scholar 

  • Schreier, E., Doring, F., and Kunkel, U., 2000, Molecular epidemiology of outbreaks of gastroenteritis associated with small round structured viruses in Germany in 1997/98. Arch. Virol. 145:443–453.

    Article  CAS  Google Scholar 

  • Schwab, K. J., Neill, F. H., Fankhauser, R. L., Daniels, N. A., Monroe, S. S., Bergmire-Sweat, D. A., Estes, M. K., and Atmar, R. L., 2000, Development of methods to detect “Norwalk-like viruses” (NLVs) and hepatitis A virus in delicatessen foods: application to a food-borne NLV outbreak. Appl. Environ. Microbiol. 66:213–218.

    CAS  Google Scholar 

  • Schwab, K. J., Neill, F. H., LeGuyader, F., Estes, M. K., and Atmar, R. L., 2001, Development of an RT-PCR-DNA enzyme immunoassay for the detection of Norwalk viruses in shellfish. Appl. Environ. Microbiol. 67:742–749.

    Article  CAS  Google Scholar 

  • Shieh, Y.-S. C., Calci, K. R., and Baric, R. S., 1999, A method to detect low levels of enteric viruses in contaminated oysters. Appl. Environ. Microbiol. 65:4709–4714.

    CAS  Google Scholar 

  • Soares, C. C., Volotao, E. M., Albuquerque, M. C. M., Nozawa, C. M., Linhares, R. E. C., Volokhov, D., Chizhikov, V., Lu, X., Erdman, D., and Santos, N., 2004, Genotyping or enteric adenoviruses by using single-stranded conformation polymorphism analysis and heteroduplex mobility assay. J. Clin. Microbiol. 42:1723–1726.

    Article  CAS  Google Scholar 

  • Sugieda, M., Nakajima, K., and Nakajima, S., 1996, Outbreaks of Norwalk-like virusassociated gastroenteritis traced to shellfish: coexistence of two genotypes in one specimen. Epidemiol. Infect. 116:339–346.

    Article  CAS  Google Scholar 

  • Svensson, L., 2000, Diagnosis of foodborne viral infections in patients. Int. J. Food Microbiol. 59:117–126.

    Article  CAS  Google Scholar 

  • Tai, J. H., Ewert, M. S., Belliot, G., Glass, R. I., and Monroe, S. S., 2003, Development of a rapid method using nucleic acid sequence-based amplification for the detection of astrovirus. J. Virol. Methods 110:119–127.

    Article  CAS  Google Scholar 

  • Takiff, H. E., Seidlin, M., Krause, P. Rooney, J., Brandt, C., Rodriguez, W., Yolken, R., and Straus, S. E., 1985, Detection of enteric adenoviruses by dot-blot hybridization using a molecularly cloned viral DNA probe. J. Med. Virol. 16:107–118.

    CAS  Google Scholar 

  • Traore, O., Arnal, C., Mignotte, B., Maul, A., Laveran, H., Billaudel, S., and Schwartzbrod, L., 1998, Reverse transcriptase PCR detection of astrovirus, hepatitis A virus, and poliovirus in experimentally contaminated mussels: comparison of several extraction and concentration methods. Appl. Environ. Microbiol. 64:3118–3122.

    CAS  Google Scholar 

  • Urdea, M. S., Horn, T., Fultz, T. J., Anderson, M., Running, J. A., Hamren, S., Ahle, D., and Chang, C. A., 1991, Branched DNA amplification multimers for the sensitive, direct detection of human hepatitis viruses. Nucleic Acids Symp. Ser. 24:197–200.

    CAS  Google Scholar 

  • Vinjé, J., and Koopmans, M. P. G., 2000, Simultaneous detection and genotyping of “Norwalk-like viruses” by oligonucleotide array in a reverse line blot hybridization format. J. Clin. Microbiol. 38:2595–2601.

    Google Scholar 

  • Vinjé, J., Vennema, H., Maunula, L., von Bonsdorff, C. H., Hoehne, M., Schreier, E., Richards, A., Green, J., Brown, D., Beard, S. S., Monroe, S. S., de Bruin, E., Svensson, L., and Koopmans, M. P., 2003, International collaborative study to compare reverse transcriptase PCR assays for detection and genotyping of noroviruses. J. Clin. Microbiol. 41:1423–1433.

    Article  CAS  Google Scholar 

  • Walker, G. T., Little, M. C., Nadeau, J. G., and Shank, D. D., 1992, Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system. Proc. Natl. Acad. Sci. U.S.A. 89:392–396.

    Article  CAS  Google Scholar 

  • Willcocks, M. M., Carter, M. J., Silcock, J. G., and Madeley, C. R., 1991, A dot-blot hybridization procedure for the detection of astrovirus in stool samples. Epidemiol. Infect. 107:405–410.

    CAS  Google Scholar 

  • Williams, F. P. Jr., and Fout, G. S., 1992, Contamination of shellfish by stool-shed viruses: methods of detection. Environ. Sci. Technol. 26:689–696.

    Article  Google Scholar 

  • Wu, D. Y., and Wallace, R. B., 1989, The ligation amplification reaction (LAR)—amplification of specific DNA sequences using sequential rounds of template-dependent ligation. Genomics 4:560–569.

    Article  CAS  Google Scholar 

  • Xu, W., McDonough, M. C., and Erdman, D. D., 2000, Species-specific identification of human adenoviruses by a multiplex PCR assay. J. Clin. Microbiol. 38:4114–4120.

    CAS  Google Scholar 

  • Zhou, Y.-J., Estes, M. K., Jiang, X., and Metcalf, T. G., 1991, Concentration and detection of hepatitis A virus and rotavirus from shellfish by hybridization tests. Appl. Environ. Microbiol. 57:2963–2968.

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Atmar, R.L. (2006). Molecular Methods of Virus Detection in Foods. In: Goyal, S.M. (eds) Viruses in Foods. Food Microbiology and Food Safety. Springer, Boston, MA. https://doi.org/10.1007/0-387-29251-9_5

Download citation

Publish with us

Policies and ethics