Broadly reactive TaqMan® assay for real-time RT-PCR detection of rotavirus in clinical and environmental samples

Journal of Virological Methods

Volumn 155, Issue 2, 2009, Pages 126-131

  Jothikumar, N ^a   Kang, G ^b   Hill, V R ^a  

^a NATIONAL CENTER FOR EMERGING AND ZOONOTIC INFECTIOUS DISEASES   (United States)

^b CHRISTIAN MEDICAL COLLEGE   (India)

Author keywords

Clinical; Real time RT PCR; Rotavirus; TaqMan ; Waterborne

Indexed keywords

NONSTRUCTURAL PROTEIN 3; PLASMID DNA; TAP WATER;

ARTICLE; CONTROLLED STUDY; CROSS REACTION; ENTERIC VIRUS; FECES ANALYSIS; GENOTYPE; INDIA; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; ROTAVIRUS; SENSITIVITY AND SPECIFICITY; VALIDATION PROCESS; VIRUS DETECTION; WATER SAMPLING;

FRESH WATER; GASTROENTERITIS; HUMANS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; ROTAVIRUS; ROTAVIRUS INFECTIONS; SENSITIVITY AND SPECIFICITY; TAQ POLYMERASE; VIRAL NONSTRUCTURAL PROTEINS;

ROTAVIRUS;

EID: 57849101993     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2008.09.025     Document Type: Article

References (30)

1. Banerjee I., Ramani S., Primrose B., Iturriza-Gomara M., Gray J.J., Brown D.W., and Kang G. Modification of rotavirus multiplex RT-PCR for the detection of G12 strains based on characterization of emerging G12 rotavirus strains from South India. J. Med. Virol. 79 (2007) 1413-1421
2. Boccia D., Tozzi A.E., Cotter B., Rizzo C., Russo T., Buttinelli G., Caprioli A., Marziano M.L., and Ruggeri F.M. Waterborne outbreak of Norwalk-like virus gastroenteritis at a tourist resort, Italy. Emerg. Infect. Dis. 8 (2002) 563-568
3. Boom R., Sol C.J.A., Heijtink R., Wertheimvandillen P.M.E., and Vandernoordaa J. Rapid purification of hepatitis-B virus-DNA from serum. J. Clin. Microbiol. 29 (1991) 1804-1811
4. Borchardt M.A., Bertz P.D., Spencer S.K., and Battigelli D.A. Incidence of enteric viruses in groundwater from household wells in Wisconsin. Appl. Environ. Microbiol. 69 (2003) 1172-1180
5. Brassard J., Seyer K., Houde A., Simard C., and Trottier Y.L. Concentration and detection of hepatitis A virus and rotavirus in spring water samples by reverse transcription-PCR. J. Virol. Methods 123 (2005) 163-169
6. Divizia M., Gabrieli R., Donia D., Macaluso A., Bosch A., Guix S., Sanchez G., Villena C., Pinto R.M., Palombi L., Buonuomo E., Cenko F., Leno L., Bebeci D., and Bino S. Waterborne gastroenteritis outbreak in Albania. Water Sci. Technol. 50 (2004) 57-61
7. Estes M.K. Rotaviruses and their replication. In: Knipe D.M., and Howley P.M. (Eds). Fields Virology (2001), Lippincott Williams & Wilkins, Philadelphia 1747-1785
8. Gentsch J.R., Glass R.I., Woods P., Gouvea V., Gorziglia M., Flores J., Das B.K., and Bhan M.K. Identification of group A rotavirus gene 4 types by polymerase chain reaction. J. Clin. Microbiol. 30 (1992) 1365-1373
9. Glass R.I., Parashar U.D., Bresee J.S., Turcios R., Fischer T.K., Widdowson M.A., Jiang B., and Gentsch J.R. Rotavirus vaccines: current prospects and future challenges. Lancet 368 (2006) 323-332
10. Gouvea V., Glass R.I., Woods P., Taniguchi K., Clark H.F., Forrester B., and Fang Z.Y. Polymerase chain reaction amplification and typing of rotavirus nucleic acid from stool specimens. J. Clin. Microbiol. 28 (1990) 276-282
11. Griffin D.W., Donaldson K.A., Paul J.H., and Rose J.B. Pathogenic human viruses in coastal waters. Clin. Microbiol. Rev. 16 (2003) 129-143
12. Grimwood K., and Bines J.E. Rotavirus vaccines must perform in low-income countries too. Lancet 370 (2007) 1739-1740
13. Gutierrez M.F., Alvarado M.V., Martinez E., and Ajami N.J. Presence of viral proteins in drinkable water-sufficient condition to consider water a vector of viral transmission?. Water Res. 41 (2007) 373-378
14. Hill V.R., Kahler A.M., Jothikumar N., Johnson T.B., Hahn D., and Cromeans T.L. Multistate evaluation of an ultrafiltration-based procedure for simultaneous recovery of enteric microbes in 100-liter tap water samples. Appl. Environ. Microbiol. 73 (2007) 4218-4225
15. Hoshino Y., Jones R.W., Ross J., Honma S., Santos N., Gentsch J.R., and Kapikian A.Z. Rotavirus serotype G9 strains belonging to VP7 gene phylogenetic sequence lineage 1 may be more suitable for serotype G9 vaccine candidates than those belonging to lineage 2 or 3. J. Virol. 78 (2004) 7795-7802
16. Iturriza-Gomara M., Green J., Brown D.W., Desselberger U., and Gray J.J. Comparison of specific and random priming in the reverse transcriptase polymerase chain reaction for genotyping group A rotaviruses. J. Virol. Methods 78 (1999) 93-103
17. Jothikumar N., Khanna P., Paulmurugan R., Kamatchiammal S., and Padmanabhan P. A simple device for the concentration and detection of enterovirus, hepatitis E virus and rotavirus from water samples by reverse transcription-polymerase chain reaction. J. Virol. Methods 55 (1995) 401-415
18. Kapikian A.Z. Overview of viral gastroenteritis. Arch. Virol. Suppl. 12 (1996) 7-19
19. Koopmans M., von Bonsdorff C.H., Vinje J., de Medici D., and Monroe S. Foodborne viruses. FEMS Microbiol. Rev. 26 (2002) 187-205
20. Lepage P. Rotavirus infection in Europe: time for effective prevention?. Pediatr. Infect. Dis. J. 25 (2006) S5-6
21. Metcalf T.G., Melnick J.L., and Estes M.K. Environmental virology: from detection of virus in sewage and water by isolation to identification by molecular biology-a trip of over 50 years. Annu. Rev. Microbiol. 49 (1995) 461-487
22. Miller M. Particle Counting of Viruses. In: Hyat M.A. (Ed). Principles and Techniques of Electron Microscopy vol. 4 (1974), Von Nostrand-Reinhold, New York 89-128
23. Miller M.S. Proceedings of the Electron Microscopy Society of American, 37th Annual Meeting of Electron Microscopy Society (1979) 56-57
24. Min B.S., Noh Y.J., Shin J.H., Baek S.Y., Min K.I., Ryu S.R., Kim B.G., Park M.K., Choi S.E., Yang E.H., Park S.N., Hur S.J., and Ahn B.Y. Assessment of the quantitative real-time polymerase chain reaction using a cDNA standard for human group A rotavirus. J. Virol. Methods 137 (2006) 280-286
25. Pang X.L., Lee B., Boroumand N., Leblanc B., Preiksaitis J.K., and Yu Ip C.C. Increased detection of rotavirus using a real time reverse transcription-polymerase chain reaction (RT-PCR) assay in stool specimens from children with diarrhea. J. Med. Virol. 72 (2004) 496-501
26. Radstrom P., Knutsson R., Wolffs P., Lovenklev M., and Lofstrom C. Pre-PCR processing-strategies to generate PCR-compatible samples. Mol. Biotechnol. 26 (2004) 133-146
27. Richards A.F., Lopman B., Gunn A., Curry A., Ellis D., Cotterill H., Ratcliffe S., Jenkins M., Appleton H., Gallimore C.I., Gray J.J., and Brown D.W. Evaluation of a commercial ELISA for detecting Norwalk-like virus antigen in faeces. J. Clin. Virol. 26 (2003) 109-115
28. Sharp D. Proceedings of the 4th International Conference on Electron Microscopy (1960) 542-548
29. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 22 (1994) 4673-4680
30. Villena C., El-Senousy W.M., Abad F.X., Pinto R.M., and Bosch A. Group A rotavirus in sewage samples from Barcelona and Cairo: emergence of unusual genotypes. Appl. Environ. Microbiol. 69 (2003) 3919-3923