Comparison of different RT-qPCR assays for the detection of human and bovine group A rotaviruses and characterization by sequences analysis of genes encoding VP4 and VP7 capsid proteins

Journal of Applied Microbiology

Volumn 114, Issue 5, 2013, Pages 1435-1448

  Ward, P ^a   Poitras, E ^a   Leblanc, D ^a   Gagnon, C A ^b   Brassard, J ^a   Houde, A ^a  

^a FOOD RESEARCH AND DEVELOPMENT CENTRE   (Canada)

^b UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

Capsid protein sequences; Detection; Group A rotaviruses; Phylogenetic analysis; RT qPCR assays

Indexed keywords

CELL CULTURE; GENES; MAMMALS; POLYMERASE CHAIN REACTION; PROTEINS; RNA; STRAIN;

CAPSID PROTEIN SEQUENCE; CAPSID PROTEINS; DETECTION; FAECAL SAMPLES; GROUP A ROTAVIRUS; PHYLOGENETIC ANALYSIS; PROTEIN SEQUENCES; ROTAVIRUSES; RT-QPCR ASSAY; SEQUENCE ANALYSIS;

ASSAYS;

GLUCOSE 6 PHOSPHATE; PROTEIN VP4; PROTEIN VP7;

BIOASSAY; COMPARATIVE STUDY; GENE; GENETIC ANALYSIS; INFECTIOUS DISEASE; PROTEIN; RNA; SAMPLING; VIRUS;

AMINO ACID SEQUENCE; ANIMAL CELL; ARTICLE; CLINICAL ARTICLE; CONTROLLED STUDY; FECES; FECES ANALYSIS; HUMAN; HUMAN CELL; HUMAN ROTAVIRUS; NONHUMAN; PROTEIN ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA EXTRACTION; VIRUS CHARACTERIZATION; VIRUS DETECTION; VIRUS ISOLATION; VIRUS STRAIN;

BOVINAE; FELINE ROTAVIRUS; HUMAN ROTAVIRUS A; MIRIDAE; ROTAVIRUS; ROTAVIRUS A;

EID: 84876409214     PISSN: 13645072     EISSN: 13652672     Source Type: Journal    
DOI: 10.1111/jam.12165     Document Type: Article

References (50)

1. Abid, I., Guix, S., Aouni, M., Pinto, R. and Bosch, A. (2007) Detection and characterization of human group C rotavirus in the pediatric population of Barcelona, Spain. J Clin Virol 38, 78-82.
2. Ahmed, H.E., Coulter, J.B.S., Nakagomi, O., Hart, C.A., Zaki, J.M., Al-Rabaty, A.A., Dove, W. and Cunliffe, N.A. (2006) Molecular characterization of rotavirus gastroenteritis strains, Iraqi Kurdistan. Emerg Infect Dis 12, 824-826.
3. Alfieri, A.F., Alfieri, A.A., Bacellar Barreiros, M.A., Gagliardi Leite, J.P. and Richtzenhain, L.J. (2004) G and P genotypes of group A rotavirus strains circulating in calves in Brazil, 1996-1999. Vet Microbiol 99, 167-173.
4. Badaracco, A., Garaicoechea, L., Rodriguez, D., Uriarte, E.L., Odeon, A., Galarza, R., Abdala, A., Fernandez, F. et al. (2012) Bovine rotavirus strains circulating in beef and dairy herds in Argentina from 2004-2010. Vet Microbiol 158, 394-399.
5. Banyai, K., Esona, M.D., Mijatovic, S., Kerin, T.K., Pedreira, C., Mercado, J., Balmaseda, A., Perz, M.C. et al. (2009) Zoonotic bovine rotavirus strain in diarrheic child, Nicaragua. J Clin Virol 46, 391-393.
6. Bishop, R.F., Davidson, G.P., Holmes, I.H. and Ruck, B.J. (1973) Virus particles in epithelial cells of duodenal mucosa from children with acute non-bacterial gastroenteritis. Lancet 2, 1281-1283.
7. Brassard, J., Seyer, K., Houde, A., Simard, C. and Trottier, Y.-L. (2005) Concentration and detection of hepatitis A and rotavirus in spring water samples by reverse transcription-PCR. J Virol Methods 123, 163-169.
8. Escobar-Herrera, J., Cancio, C., Guzman, G.I., Villegas-Sepulveda, N., Estrada-Garcia, T., Garcia-Lozano, H., Gomez-Santiago, F. and Gutierrez-Escolano, A.L. (2006) Construction of an internal RT-PCR standard control for the detection of human caliciviruses in stool. J Virol Methods 137, 334-338.
9. Freeman, M.M., Kerin, T., Hull, J., McCaustland, K. and Gentsch, J. (2008) Enhancement of detection and quantification of rotavirus in stool using a modified real-time RT-PCR assay. J Med Virol 80, 1489-1496.
10. 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.
11. Gentsch, J.R., Laird, A.R., Bielfelt, B., Griffin, D.D., Banyai, K., Ramachandran, M., Jain, V., Cunliffe, N.A. et al. (2005) Serotype diversity and reassortment betweem human and animal rotavirus strains: implication for rotavirus vaccine programs. J Infect Dis 192, S146-S159.
12. Gouvea, V., Glass, R.I., Woods, P., Taniguchi, K., Clark, H.F., Forrester, B. and Fang, Z.-Y. (1990) Polymerase chain reaction amplification and typing of rotavirus nucleic acid from stool specimens. J Clin Microbiol 28, 276-282.
13. Gutiérrez-Aguirre, I., Steyer, A., Boben, J., Gruden, K., Poljsak-Prijatelj, M. and Ravnikar, M. (2008) Sensitive detection of multiple rotavirus genotypes with a single reverse transcription-real-time quantitative PCR assay. J Clin Microbiol 46, 2547-2554.
14. van der Heide, R., Koopmans, M.P.G., Shekary, N., Houwers, D.J., van Duynhoven, T.T.H.P. and van der Poel, W.H.M. (2005) Molecular characterizations of human and animal group A rotaviruses in the Netherlands. J Clin Microbiol 43, 669-675.
15. Houde, A., Guévremont, E., Poitras, E., Leblanc, D., Ward, P., Simard, C. and Trottier, Y.-L. (2007) Comparative evaluation of new TaqMan real-time assays for the detection of hepatitis A virus. J Virol Methods 140, 80-89.
16. Houde, A., Mattison, K., Ward, P. and Plante, D. (2009) Molecular detection and characterization of food and waterborne viruses. In Bacterial DNA, DNA Polymerase and DNA Helicases ed. Knudsen, W.D. and Bruns, S.S. pp. 137-185. New York, USA: Nova Publishers.
17. Isegawa, Y., Nakagomi, O., Nakagomi, T., Ishida, S., Uesugi, S. and Ueda, S. (1993) Determination of bovine rotavirus G and P serotypes by polymerase chain reaction. Mol Cell Probes 7, 277-284.
18. Jones, T.H., Houde, A., Poitras, E., Ward, P. and Johns, M.W. (2009) Development and evaluation of a multiplexed real-time TaqMan RT-PCR assay with a sample process control for detection of F-specific RNA coliphage genogroup I and IV. Food Environ Virol 1, 57-65.
19. Jothikumar, N., Kang, G. and Hill, V.R. (2009) Broadly reactive TaqMan assay for real-time RT-PCR detection of rotavirus in clinical and environmental samples. J Virol Methods 155, 126-131.
20. Kang, G., Iturriza-Gomara, M., Wheeler, J.G., Crystal, P., Monica, B., Ramani, S., Primrose, B., Moses, P.D. et al. (2004) Quantitation of group A rotavirus by real-time reverse-transcription-polymerase chain reaction: correlation with clinical severity in children in South India. J Med Virol 73, 118-122.
21. Khamrin, P., Maneekarn, N., Peerakome, S., Yagyu, F., Okitsu, S. and Ushijima, H. (2006) Molecular characterization of rare G3P[3] human rotavirus reassortant strain reveals evidence for multiple human-animal interspecies transmissions. J Med Virol 78, 986-994.
22. Koopmans, M. and Duizer, E. (2004) Foodborne viruses: an emerging problem. Int J Food Microbiol 90, 23-41.
23. Kottaridi, C., Spathis, A.T., Ntova, C.K., Papaevangelou, V. and Karakitsos, P. (2012) Evaluation of a multiplex real time reverse transcription PCR assay for the detection and quantification of the most common human rotavirus genotypes. J Virol Methods 180, 49-53.
24. Lamhoujeb, S., Cook, A., Pollari, F., Bidawid, S., Farber, J. and Mattison, K. (2010) Rotavirus from Canadian farms samples. Arch Virol 155, 1127-1137.
25. Lee, S.Y., Hong, S.K., Lee ., S.G., Suh, C.I., Park, S.W., Lee, J.H., Kim, J.H., Kim, D.S. et al. (2009) Human rotavirus genotypes in hospitalized children, South Korea, April 2005 to March 2007. Vaccine 27S, F97-F101.
26. Leung, A.K., Kellner, J.D. and Davis, H.D. (2005) Rotavirus gastroenteritis. Adv Ther 22, 476-487.
27. Logan, C., O'Leary, J.J. and O'Sullivan, N. (2006) Real-time reverse transcription-PCR for detection or rotavirus and adenovirus as causative agents of acute viral gastroenteritis in children. J Clin Microbiol 44, 3189-3195.
28. Loisy, F., Atmar, R.L., Guillon, P., Le Cann, P., Pommepuy, M. and Le Guyader, F.S. (2005) Real-time RT-PCR for norovirus screening in shellfish. J Virol Methods 123, 1-7.
29. Maes, R.K., Grooms, D.L., Wise, A.G., Han, C., Ciesicki, V., Hanson, L., Vickers, M.L., Kanitz, C. et al. (2003) Evaluation of a human group A rotavirus assay for on-site detection of bovine rotavirus. J Clin Microbiol 41, 290-294.
30. Martella, V., Banyai, K., Matthijnssens, J., Buonavoglia, C. and Ciarlet, M. (2010) Zoonotic aspects of rotaviruses. Vet Microbiol 140, 246-255.
31. Matthijnssens, J., Ciarlet, M., Rahman, M., Attoui, H., Banyai, K., Estes, M.K., Gentsch, J.R., Iturriza-Gomara, M. et al. (2008) Recommendations for the classification of group A rotaviruses using all 11 genomic RNA segments. Arch Virol 153, 1621-1629.
32. Matthijnssens, J., Ciarlet, M., McDonald, S.H., Attoui, H., Banyai, K., Brister, J.R., Buesa, J., Esona, M.D. et al. (2011) Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG). Arch Virol 156, 1397-1413.
33. Matthijnssens, J., Otto, P.H., Ciarlet, M., Desselberger, U., Van Ranst, M. and Johne, R. (2012) VP6-sequence-based cutoff values as a criterion for rotavirus species demarcation. Arch Virol 157, 1177-1182.
34. Mattison, K., Brassard, J., Gagné, M.-J., Ward, P., Houde, A., Lessard, L., Simard, C., Shukla, A. et al. (2009) The feline calicivirus as a sample process control for the detection of food and waterborne RNA viruses. Int J Food Microbiol 132, 73-77.
35. Min, B.-S., Noh, Y.-J., Shin, J.-H., Baek, S.-Y., Min, K.-I., Ryu, S.-R., Kim, B.-G., Park, M.-K. et al. (2006) Assessment of the quantitative real-time polymerase chain reaction using a cDNA standard for human group A rotavirus. J Virol Methods 137, 280-286.
36. Pang, X.L., Lee, B., Boroumand, N., Leblanc, B. and Preiksaitis, K. (2004) 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, 496-501.
37. Pang, X., Cao, M., Zhang, M. and Lee, B. (2011) Increased sensitivity for various rotavirus genotypes in stool specimens by amending three mismatched nucleotides in the forward primer of a real-time RT-PCR assay. J Virol Methods 172, 85-87.
38. Pietruchinski, E., Benati, F., Lauretti, F., Kisielius, J., Ueda, M., Volotao, E.M., Soares, C.C., Hoshino, Y. et al. (2006) Rotavirus Diarrhea in children and adults in a Southern city of Brazil in 2003: distribution of G/P types and finding of rare G12 strain. J Med Virol 78, 1241-1249.
39. Plante, D., Bélanger, G., Leblanc, D., Ward, P., Houde, A. and Trottier, Y.-L. (2011) The use of bovine serum albumin to improve the RT-qPCR detection of foodborne viruses rinsed from vegetable surfaces. Lett Appl Microbiol 52, 239-244.
40. Rahman, M., Banik, S., Faruque, A.S.G., Taniguchi, K., Sack, D.A., Van Ranst, M. and Azim, T. (2005) Detection and characterization of human group C rotaviruses in Bangladesh. J Clin Microbiol 43, 4460-4465.
41. Raming, F., Ciarlet, M., Mertens, P.P.C. and Dermody, T.S. (2005) Rotavirus. In Virus Taxonomy; eight report of the international committee on taxonomy of viruses ed. Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U. and Ball, L.A. pp. 484-496. London: Elsevier Academic Press.
42. Rutjes, S.A., Lodder, W.J., Bouwknegt, M. and de Roda Husman, A.M. (2007) Increased hepatitis E virus prevalence on Dutch pig farms from 33 to 55% by using appropriate internal quality controls for RT-PCR. J Virol Methods 143, 112-116.
43. Schwarz, B.-A., Bange, R., Vahlenkamp, T.W., Johne, R. and Müller, H. (2002) Detection and quantitation of group A rotaviruses by competitive and real-time reverse transcription-polymerase chain reaction. J Virol Methods 105, 277-285.
44. Scipioni, A., Bourgot, I., Mauroy, A., Ziant, D., Saegerman, C., Daube, G. and Thiry, E. (2008) Detection and quantification of human and bovine noroviruses by a TaqMan RT-PCR assay with a control for inhibition. Mol Cell Probes 22, 215-222.
45. Steyer, A., Bajzelj, M., Iturriza-Gomara, M., Mladenova, Z., Korsun, N. and Poljsak-Prijatelj, M. (2010) Molecular analysis of human group A rotavirus G10P[14] genotype in Slovenia. J Clin Virol 49, 121-125.
46. Swiatek, D.L., Palombo, E.A., Lee, A., Coventry, M.J., Britz, M.L. and Kirkwood, C.D. (2010) Detection and analysis of bovine rotavirus strains circulating in Australian calves during 2004 and 2005. Vet Microbiol 140, 56-62.
47. Tate, J.E., Burton, A.H., Boschi-Pinto, C., Steele, A.D., Duque, J. and Parashar, U.D. (2012) 2008 estimate of worldwide rotavirus-associated mortality in children younger than 5 years before the introduction of universal rotavirus vaccination programmes: a systematic review and meta-analysis. Lancet Infect Dis 12, 137-141.
48. Tsugawa, T. and Hoshino, Y. (2008) Whole genome sequence and phylogenetic analyses reveal human rotavirus G3P[3] strains Ro1845 and HCR3A are examples of direct virion transmission of canine/feline rotaviruses to humans. Virology 380, 344-353.
49. Ward, P., Poitras, E., Leblanc, D., Letellier, A., Brassard, J., Plante, D. and Houde, A. (2009) Comparative analysis of different TaqMan real-time RT-PCR assays for the detection of swine Hepatitis E virus and integration of Feline calicivirus as internal control. J Appl Microbiol 106, 1360-1369.
50. Zeng, S.-Q., Halkosalo, A., Salminen, M., Szakal, E.D., Puustinen, L. and Vesikari, T. (2008) One-step quantitative RT-PCR for the detection of rotavirus in acute gastroenteritis. J Virol Methods 153, 238-240.