Detection and genotyping of human rotavirus VP4 and VP7 genes by reverse transcriptase PCR and reverse hybridization

Journal of Clinical Microbiology

Volumn 47, Issue 9, 2009, Pages 2704-2712

  Van Doorn, Leen Jan ^a   Kleter, Bernhard ^a   Hoefnagel, Evert ^a   Stainier, Isabelle ^b   Poliszczak, Annick ^b   Colau, Brigitte ^b   Quint, Wim ^a  

^a DDL DIAGNOSTIC LABORATORY   (Netherlands)

^b GLAXOSMITHKLINE BIOLOGICALS   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; PROTEIN VP4; PROTEIN VP7; ROTAVIRUS VACCINE; VIRUS RNA;

ARTICLE; ENZYME LINKED IMMUNOSORBENT ASSAY; FECES ANALYSIS; GENOTYPE; HUMAN; HUMAN ROTAVIRUS; MAJOR CLINICAL STUDY; MIXED INFECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; ROTAVIRUS; SEQUENCE ANALYSIS; VIRUS DETECTION; VIRUS INFECTION;

ANIMALS; ANTIGENS, VIRAL; CAPSID PROTEINS; DNA PRIMERS; FECES; GENOTYPE; HUMANS; NUCLEIC ACID HYBRIDIZATION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; ROTAVIRUS; ROTAVIRUS INFECTIONS; SENSITIVITY AND SPECIFICITY;

HUMAN ROTAVIRUS A; ROTAVIRUS;

EID: 69949084477     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.00378-09     Document Type: Article

References (51)

1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Anderson, E. J., and S. G. Weber. 2004. Rotavirus infection in adults. Lancet Infect. Dis. 4:91-99.
3. Baggi, F., and R. Peduzzi. 2000. Genotyping of rotaviruses in environmental water and stool samples in southern Switzerland by nucleotide sequence analysis of 189 base pairs at the 5′ end of the VP7 gene. J. Clin. Microbiol. 38:3681-3685.
4. Bányai, K., V. Martella, F. Jakab, B. Melegh, and G. Szucs. 2004. Sequencing and phylogenetic analysis of human genotype P[6] rotavirus strains detected in Hungary provides evidence for genetic heterogeneity within the P[6] VP4 gene. J. Clin. Microbiol. 42:4338-4343.
5. Barman, P., S. Ghosh, S. Das, V. Varghese, S. Chaudhuri, S. Sarkar, T. Krishnan, S. K. Bhattacharya, A. Chakrabarti, N. Kobayashi, and T. N. Naik. 2004. Sequencing and sequence analysis of VP7 and NSP5 genes reveal emergence of a new genotype of bovine group B rotaviruses in India. J. Clin. Microbiol. 42:2816-2818.
6. Bok, K., D. O. Matson, and J. A. Gomez. 2002. Genetic variation of capsid protein VP7 in genotype G4 human rotavirus strains: simultaneous emergence and spread of different lineages in Argentina. J. Clin. Microbiol. 40:2016-2022.
7. Chizhikov, V., M. Wagner, A. Ivshina, Y. Hoshino, A. Z. Kapikian, and K. Chumakov. 2002. Detection and genotyping of human group A rotaviruses by oligonucleotide microarray hybridization. J. Clin. Microbiol. 40:2398-2407.
8. Das, S., A. Sen, G. Uma, V. Varghese, S. Chaudhuri, S. K. Bhattacharya, T. Krishnan, P. Dutta, D. Dutta, M. K. Bhattacharya, U. Mitra, N. Kobayashi, and T. N. Naik. 2002. Genomic diversity of group A rotavirus strains infecting humans in eastern India. J. Clin. Microbiol. 40:146-149.
9. Das, S., V. Varghese, S. Chaudhury, P. Barman, S. Mahapatra, K. Kojima, S. K. Bhattacharya, T. Krishnan, R. K. Ratho, G. P. Chhotray, A. C. Phukan, N. Kobayashi, and T. N. Naik. 2003. Emergence of novel human group A rotavirus G12 strains in India. J. Clin. Microbiol. 41:2760-2762.
10. DiStefano, D. J., N. Kraiouchkine, L. Mallette, M. Maliga, G. Kulnis, P. M. Keller, H. F. Clark, and A. R. Shaw. 2005. Novel rotavirus VP7 typing assay using a one-step reverse transcriptase PCR protocol and product sequencing and utility of the assay for epidemiological studies and strain characterization, including serotype subgroup analysis. J. Clin. Microbiol. 43:5876-5880.
11. Eing, B. R., G. May, H. G. Baumeister, and J. E. Kuhn. 2001. Evaluation of two enzyme immunoassays for detection of human rotaviruses in fecal specimens. J. Clin. Microbiol. 39:4532-4534.
12. Estes, M. K., and J. Cohen. 1989. Rotavirus gene structure and function. Microbiol. Rev. 53:410-449.
13. Estes, M. K., and A. Z. Kapikian. 2007. Rotaviruses, p. 1917-1974. In D. M. Knipe, P. M. Howley, D. E. Griffin, R. A. Lamb, M. A. Martin, B. Roizman, and S. E. Straus (ed.), Fields virology, 5th ed. Lippincott Williams & Wilkins, Philadelphia, PA.
14. Fang, Z. Y., H. Yang, J. Qi, J. Zhang, L. W. Sun, J. Y. Tang, L. Ma, Z. Q. Du, A. H. He, J. P. Xie, Y. Y. Lu, Z. Z. Ji, B. Q. Zhu, H. Y. Wu, S. E. Lin, H. P. Xie, D. D. Griffin, B. Ivanoff, R. I. Glass, and J. R. Gentsch. 2002. Diversity of rotavirus strains among children with acute diarrhea in China: 1998-2000 surveillance study. J. Clin. Microbiol. 40:1875-1878.
15. Fischer, T. K., J. Eugen-Olsen, A. G. Pedersen, K. Molbak, B. Bottiger, K. Rostgaard, and N. M. Nielsen. 2005. Characterization of rotavirus strains in a Danish population: high frequency of mixed infections and diversity within the VP4 gene of P[8] strains. J. Clin. Microbiol. 43:1099-1104.
16. Fischer, T. K., N. A. Page, D. D. Griffin, J. Eugen-Olsen, A. G. Pedersen, P. Valentiner-Branth, K. Molbak, H. Sommerfelt, and N. M. Nielsen. 2003. Characterization of incompletely typed rotavirus strains from Guinea-Bissau: identification of G8 and G9 types and a high frequency of mixed infections. Virology 311:125-133.
17. Fischer, T. K., H. Steinsland, and P. Valentiner-Branth. 2002. Rotavirus particles can survive storage in ambient tropical temperatures for more than 2 months. J. Clin. Microbiol. 40:4763-4764.
18. Gallimore, C. I., J. S. Cheesbrough, K. Lamden, C. Bingham, and J. J. Gray. 2005. Multiple norovirus genotypes characterised from an oyster-associated outbreak of gastroenteritis. Int. J. Food Microbiol. 103:323-330.
19. Gault, E., R. Chikhi-Brachet, S. Delon, N. Schnepf, L. Albiges, E. Grimprel, J. P. Girardet, P. Begue, and A. Garbarg-Chenon. 1999. Distribution of human rotavirus G types circulating in Paris, France, during the 1997-1998 epidemic: high prevalence of type G4. J. Clin. Microbiol. 37:2373-2375.
20. Gentsch, J. R., R. I. Glass, P. Woods, V. Gouvea, M. Gorziglia, J. Flores, B. K. Das, and M. K. Bhan. 1992. Identification of group A rotavirus gene 4 types by polymerase chain reaction. J. Clin. Microbiol. 30:1365-1373.
21. Gentsch, J. R., A. R. Laird, B. Bielfelt, D. D. Griffin, K. Banyai, M. Ramachandran, V. Jain, N. A. Cunliffe, O. Nakagomi, C. D. Kirkwood, T. K. Fischer, U. D. Parashar, J. S. Bresee, B. Jiang, and R. I. Glass. 2005. Serotype diversity and reassortment between human and animal rotavirus strains: implications for rotavirus vaccine programs. J. Infect. Dis. 192(Suppl. 1):S146-S159.
22. Gouvea, V., R. I. Glass, P. Woods, K. Taniguchi, H. F. Clark, B. Forrester, and Z. Y. Fang. 1990. Polymerase chain reaction amplification and typing of rotavirus nucleic acid from stool specimens. J. Clin. Microbiol. 28:276-282.
23. Gouvea, V., M. S. Ho, R. Glass, P. Woods, B. Forrester, C. Robinson, R. Ashley, M. Riepenhoff-Talty, H. F. Clark, K. Taniguchi, et al. 1990. Serotypes and electropherotypes of human rotavirus in the USA: 1987-1989. J. Infect. Dis. 162:362-367.
24. Iturriza Gómara, M., C. Wong, S. Blome, U. Desselberger, and J. Gray. 2002. Rotavirus subgroup characterisation by restriction endonuclease digestion of a cDNA fragment of the VP6 gene. J. Virol. Methods 105:99-103. (Pubitemid 34899538)
25. Iturriza-Gómara, M., J. Green, D. W. Brown, U. Desselberger, and J. J. Gray. 2000. Diversity within the VP4 gene of rotavirus P[8] strains: implications for reverse transcription-PCR genotyping. J. Clin. Microbiol. 38:898-901.
26. Jain, V., B. K. Das, M. K. Bhan, R. I. Glass, and J. R. Gentsch. 2001. Great diversity of group A rotavirus strains and high prevalence of mixed rotavirus infections in India. J. Clin. Microbiol. 39:3524-3529.
27. Jiraphongsa, C., J. S. Bresee, Y. Pongsuwanna, P. Kluabwang, U. Poonawagul, P. Arporntip, M. Kanoksil, N. Premsri, and U. Intusoma. 2005. Epidemiology and burden of rotavirus diarrhea in Thailand: results of sentinel surveillance. J. Infect. Dis. 192(Suppl. 1):S87-S93.
28. Khamrin, P., S. Peerakome, L. Wongsawasdi, S. Tonusin, P. Sornchai, V. Maneerat, C. Khamwan, F. Yagyu, S. Okitsu, H. Ushijima, and N. Maneekarn. 2006. Emergence of human G9 rotavirus with an exceptionally high frequency in children admitted to hospital with diarrhea in Chiang Mai, Thailand. J. Med. Virol. 78:273-280.
29. Khetawat, D., T. Ghosh, M. K. Bhattacharya, S. K. Bhattacharya, and S. Chakrabarti. 2001. Molecular characterization of the VP7 gene of rotavirus isolated from a clinical sample of Calcutta, India. Virus Res. 74:53-58. (Pubitemid 32168193)
30. Laird, A. R., J. R. Gentsch, T. Nakagomi, O. Nakagomi, and R. I. Glass. 2003. Characterization of serotype G9 rotavirus strains isolated in the United States and India from 1993 to 2001. J. Clin. Microbiol. 41:3100-3111.
31. Laird, A. R., V. Ibarra, G. Ruiz-Palacios, M. L. Guerrero, R. I. Glass, and J. R. Gentsch. 2003. Unexpected detection of animal VP7 genes among common rotavirus strains isolated from children in Mexico. J. Clin. Microbiol. 41:4400-4403.
32. Lovmar, L., C. Fock, F. Espinoza, F. Bucardo, A. C. Syvanen, and K. Bondeson. 2003. Microarrays for genotyping human group A rotavirus by multiplex capture and type-specific primer extension. J. Clin. Microbiol. 41:5153-5158.
33. Martella, V., V. Terio, G. Del Gaudio, M. Gentile, P. Fiorente, S. Barbuti, and C. Buonavoglia. 2003. Detection of the emerging rotavirus G9 serotype at high frequency in Italy. J. Clin. Microbiol. 41:3960-3963.
34. Matthijnssens, J., M. Ciarlet, M. Rahman, H. Attoui, K. Bányai, M. K. Estes, J. R. Gentsch, M. Iturriza-Gómara, C. D. Kirkwood, V. Martella, P. P. Mertens, O. Nakagomi, J. T. Patton, F. M. Ruggeri, L. J. Saif, N. Santos, A. Steyer, K. Taniguchi, U. Desselberger, and M. Van Ranst. 2008. Recommendations for the classification of group A rotaviruses using all 11 genomic RNA segments. Arch. Virol. 153:1621-1629.
35. Maunula, L., and C. H. Von Bonsdorff. 2002. Frequent reassortments may explain the genetic heterogeneity of rotaviruses: analysis of Finnish rotavirus strains. J. Virol. 76:11793-11800. (Pubitemid 35304280)
36. Nielsen, N. M., J. Eugen-Olsen, P. Aaby, K. Molbak, A. Rodrigues, and T. K. Fischer. 2005. Characterisation of rotavirus strains among hospitalised and non-hospitalised children in Guinea-Bissau, 2002. A high frequency of mixed infections with serotype G8. J. Clin. Virol. 34:13-21.
37. Parashar, U. D., C. J. Gibson, J. S. Bresse, and R. I. Glass. 2006. Rotavirus and severe childhood diarrhea. Emerg. Infect. Dis. 12:304-306.
38. Pongsuwanna, Y., R. Guntapong, M. Chiwakul, R. Tacharoenmuang, N. Onvimala, M. Wakuda, N. Kobayashi, and K. Taniguchi. 2002. Detection of a human rotavirus with G12 and P[9] specificity in Thailand. J. Clin. Microbiol. 40:1390-1394.
39. Reidy, N., F. O'Halloran, S. Fanning, B. Cryan, and H. O'Shea. 2005. Emergence of G3 and G9 rotavirus and increased incidence of mixed infections in the southern region of Ireland 2001-2004. J. Med. Virol. 77:571-578.
40. Rubilar-Abreu, E., K. O. Hedlund, L. Svensson, and C. Mittelholzer. 2005. Serotype G9 rotavirus infections in adults in Sweden. J. Clin. Microbiol. 43:1374-1376.
41. Ruiz-Palacios, G. M., I. Perez-Schael, F. R. Velázquez, H. Abate, T. Breuer, S. C. Clemens, B. Cheuvart, F. Espinoza, P. Gillard, B. L. Innis, Y. Cervantes, A. C. Linhares, P. López, M. Macías-Parra, E. Ortega-Barría, V. Richardson, D. M. Rivera-Medina, L. Rivera, B. Salinas, N. Pavía-Ruz, J. Salmerón, R. Rüttimann, J. C. Tinoco, P. Rubio, E. Nuñez, M. L. Guerrero, J. P. Yarzábal, S. Damaso, N. Tornieporth, X. Sáez-Llorens, R. F. Vergara, T. Vesikari, A. Bouckenooghe, R. Clemens, B. De Vos, and M. O'Ryan for the Human Rotavirus Vaccine Study Group. 2006. Safety and efficacy of an attenuated vaccine against severe rotavirus gastroenteritis. N. Engl. J. Med. 354:11-22.
42. Sánchez-Fauquier, A., I. Wilhelmi, J. Colomina, E. Cubero, and E. Roman. 2004. Diversity of group A human rotavirus types circulating over a 4-year period in Madrid, Spain. J. Clin. Microbiol. 42:1609-1613.
43. Santos, N., S. Honma, M. C. Timenetsky, A. C. Linhares, H. Ushijima, G. E. Armah, J. R. Gentsch, and Y. Hoshino. 2008. Development of a microtiter plate hybridization-based PCR-enzyme-linked immunosorbent assay for identification of clinically relevant human group A rotavirus G and P genotypes. J. Clin. Microbiol. 46:462-469.
44. Santos, N., and Y. Hoshino. 2005. Global distribution of rotavirus serotypes/ genotypes and its implication for the development and implementation of an effective rotavirus vaccine. Rev. Med. Virol. 15:29-56.
45. Shinozaki, K., M. Okada, S. Nagashima, I. Kaiho, and K. Taniguchi. 2004. Characterization of human rotavirus strains with G12 and P[9] detected in Japan. J. Med. Virol. 73:612-616.
46. Stelzmueller, I., K. M. Dunst, P. Hengster, H. Wykypiel, W. Steurer, S. Wiesmayr, R. Margreiter, and H. Bonatti. 2005. A cluster of rotavirus enteritis in adult transplant recipients. Transpl. Int. 18:470-474.
47. Steyer, A., M. Poljsak-Prijatelj, D. Barlic-Maganja, T. Bufon, and J. Marin. 2005. The emergence of rotavirus genotype G9 in hospitalised children in Slovenia. J. Clin. Virol. 33:7-11.
48. Suzuki, H. 1996. A hypothesis about the mechanism of assembly of doubleshelled rotavirus particles. Arch. Virol. Suppl. 12:79-85.
49. Vesikari, T., D. O. Matson, P. Dennehy, P. Van Damme, M. Santosham, Z. Rodriguez, M. J. Dallas, J. F. Heyse, M. G. Goveia, S. B. Black, H. R. Shinefield, C. D. Christie, S. Ylitalo, R. F. Itzler, M. L. Coia, M. T. Onorato, B. A. Adeyi, G. S. Marshall, L. Gothefors, D. Campens, A. Karvonen, J. P. Watt, K. L. O'Brien, M. J. DiNubile, H. F. Clark, J. W. Boslego, P. A. Offit, and P. M. Heaton for the Rotavirus Efficacy and Safety Trial (REST) Study Team. 2006. Safety and efficacy of a pentavalent human-bovine (WC3) reassortant rotavirus vaccine. N. Engl. J. Med. 354:23-33.
50. Yan, H., T. Abe, T. G. Phan, T. A. Nguyen, T. Iso, Y. Ikezawa, K. Ishii, S. Okitsu, and H. Ushijima. 2005. Outbreak of acute gastroenteritis associated with group A rotavirus and genogroup I sapovirus among adults in a mental health care facility in Japan. J. Med. Virol. 75:475-481.
51. Zhang, M., C. Q. Zeng, Y. Dong, J. M. Ball, L. J. Saif, A. P. Morris, and M. K. Estes. 1998. Mutations in rotavirus nonstructural glycoprotein NSP4 are associated with altered virus virulence. J. Virol. 72:3666-3672. (Pubitemid 28188663)