Development of Multiplex RT-PCR Assays for Rapid Detection and Subtyping of Influenza Type A Viruses from Clinical Specimens

  • Chang, Hee-Kyoung (College of Medicine and Medical Research Institute, Chungbuk National University) ;
  • Park, Jeung-Hyun (College of Medicine and Medical Research Institute, Chungbuk National University) ;
  • Song, Min-Suk (College of Medicine and Medical Research Institute, Chungbuk National University) ;
  • Oh, Taek-Kyu (College of Medicine and Medical Research Institute, Chungbuk National University) ;
  • Kim, Seok-Young (College of Medicine and Medical Research Institute, Chungbuk National University) ;
  • Kim, Chul-Jung (College of Veterinary Medicine, Chungnam National University) ;
  • Kim, Hyung-Gee (Division of Bioscience and Technology, College of Life and Environmental Science, Korea University) ;
  • Sung, Moon-Hee (Department of Bio and Nano Chemistry, College of Natural Sciences, Kookmin University) ;
  • Han, Heon-Seok (College of Medicine and Medical Research Institute, Chungbuk National University) ;
  • Hahn, Youn-Soo (College of Medicine and Medical Research Institute, Chungbuk National University) ;
  • Choi, Young-Ki (College of Medicine and Medical Research Institute, Chungbuk National University)
  • Published : 2008.06.30

Abstract

We developed multiplex RT-PCR assays that can detect and identify 12 hemagglutinin (H1-H12) and 9 neuraminidase (N1-N9) subtypes that are commonly isolated from avian, swine, and human influenza A viruses. RT-PCR products with unique sizes characteristic of each subtype were amplified by multiplex RT-PCRs, and sequence analysis of each amplicon was demonstrated to be specific for each subtype with 24 reference viruses. The specificity was demonstrated further with DNA or cDNA templates from 7 viruses, 5 bacteria, and 50 influenza A virus-negative specimens. Furthermore, the assays could detect and subtype up to $10^5$ dilution of each of the reference viruses that had an original infectivity titer of $10^6\;EID_{50}/ml$. Of 188 virus isolates, the multiplex RT-PCR results agreed completely with individual RT-PCR subtyping results and with results obtained from virus isolations. Furthermore, the multiplex RT-PCR methods efficiently detected mixed infections with at least two different subtypes of influenza viruses in one host. Therefore, these methods could facilitate rapid and accurate subtyping of influenza A viruses directly from field specimens.

Keywords

References

  1. Alexander, D. J. 2000. A review of avian influenza in different bird species. Vet. Microbiol. 74: 3-13 https://doi.org/10.1016/S0378-1135(00)00160-7
  2. Aymard-Henry, M., M. T. Coleman, W. R. Dowdle, W. G. Laver, G. C. Schild, and R. G. Webster. 1973. Influenza virus neuraminidase and neuraminidase-inhibition test procedures. Bull. World Health Organ. 48: 199-202
  3. Butt, K. M., G. J. Smith, H. Chen, L. J. Zhang, Y. H. Leung, K. M. Xu, et al. 2005. Human infection with an avian H9N2 influenza A virus in Hong Kong in 2003. J. Clin. Microbiol. 43: 5760-5767
  4. Chan, P. K. 2002. Outbreak of avian influenza A (H5N1) virus infection in Hong Kong in 1997. Clin. Infect. Dis. 34(Suppl 2): S58-S64 https://doi.org/10.1086/338820
  5. Choi, Y. K., S. M. Goyal, S. W. Kang, M. W. Farnham, and H. S. Joo. 2002. Detection and subtyping of swine influenza H1N1, H1N2, and H3N2 viruses in clinical samples using two multiplex RT-PCR assays. J. Virol. Methods 102: 53-59 https://doi.org/10.1016/S0166-0934(01)00442-6
  6. Colman, P. M., J. N. Varghese, and W. G. Laver. 1983. Structure of the catalytic and antigenic sites in influenza virus neuraminidase. Nature 303: 41-44 https://doi.org/10.1038/303041a0
  7. Fouchier, R. A., V. Munster, A. Wallensten, T. M. Bestebroer, S. Herfst, D. Smith, G. F. Rimmelzwaan, B. Olsen, and A. D. Osterhaus. 2005. Characterization of a novel influenza a virus hemagglutinin subtype (H16) obtained from black-headed gulls. J. Virol. 79: 2814-2822 https://doi.org/10.1128/JVI.79.5.2814-2822.2005
  8. Guo, Y. J., J. W. Li, I. Cheung, M. Wang, Y. Zhou, and X. H. Li. 1999. Discovery of human infected by avian influenza A (H9N2) virus. Chin. J. Exp. Clin. Virol. 15: 105-108
  9. Hoffmann, E., J. Stech, Y. Guan, R. G. Webster, and D. R. Perez. 2001. Universal primer set for the full-length amplification of all influenza A viruses. Arch. Virol. 146: 2275-2289 https://doi.org/10.1007/s007050170002
  10. Jo, S. K., H. S. Kim, S. W. Cho, and S. H. Seo. 2007. Genetic and antigenic characterization of swine H1N2 influenza viruses isolated from Korean pigs. J. Microbiol. Biotechnol. 17: 868- 872
  11. Koopmans, M., B. Wilbrink, M. Conyn, G. Natrop, H. van der Nat, H. Vennema, et al. 2004. Transmission of H7N7 avian influenza A virus to human beings during a large outbreak in commercial poultry farms in The Netherlands. Lancet 363: 587-593 https://doi.org/10.1016/S0140-6736(04)15589-X
  12. Ong, W. T., A. R. Omar, A. Ideris, and S. S. Hassan. 2007. Development of a multiplex real-time PCR assay using SYBR Green 1 chemistry for simultaneous detection and subtyping of H9N2 influenza virus type A. J. Virol. Methods 144: 57-64 https://doi.org/10.1016/j.jviromet.2007.03.019
  13. Palmer, D. F., W. R. Dowdle, M. T. Coleman, and G. C. Schild. 1975. Advanced laboratory techniques for influenza diagnosis. U.S. Department of Health, Education and Welfare Immunology Series. U.S. Department of Health, Education and Welfare, Washington, D.C
  14. Park, K. J. and H. H. Lee. 2005. In vitro antiviral activity of aqueous extracts from Korean medicinal plants against influenza virus type A. J. Microbiol. Biotechnol. 15: 924-929
  15. Peiris, J. S., W. C. Yu, C. W. Leung, C. Y. Cheung, W. F. Ng, J. M. Nicholls, et al. 2004. Re-emergence of fatal human influenza A subtype H5N1 disease. Lancet 363: 617-619 https://doi.org/10.1016/S0140-6736(04)15595-5
  16. Peiris, M., K. Y. Yuen, C. W. Leung, K. H. Chan, P. L. Ip, R. W. Lai, W. K. Orr, and K. F. Shortridge. 1999. Human infection with influenza H9N2. Lancet 354: 916-917 https://doi.org/10.1016/S0140-6736(99)03311-5
  17. Poddar, S. K., R. Espina, and D. P. Schnurr. 2002. Evaluation of a single-step multiplex RT-PCR for influenza virus type and subtype detection in respiratory samples. J. Clin. Lab. Anal. 16: 163-166 https://doi.org/10.1002/jcla.10036
  18. Song, M. S., Y. H. Joo, E. H. Lee, J. Y. Shin, C. J. Kim, K. S. Shin, M. H. Sung, and Y. K. Choi. 2006. Genetic characterization of encephalomyocarditis virus isolated from aborted swine fetus in Korea. J. Microbiol. Biotechnol. 16: 1570-1576
  19. Steininger, C., M. Kundi, S. W. Aberle, J. H. Aberle, and T. Popow-Kraupp. 2002. Effectiveness of reverse transcription- PCR, virus isolation, and enzyme-linked immunosorbent assay for diagnosis of influenza A virus infection in different age groups. J. Clin. Microbiol. 40: 2051-2056 https://doi.org/10.1128/JCM.40.6.2051-2056.2002
  20. Takimoto, S., M. Grandien, M. A. Ishida, M. S. Pereira, T. M. Paiva, T. Ishimaru, E. M. Makita, and C. H. Martinez. 1991. Comparison of enzyme-linked immunosorbent assay, indirect immunofluorescence assay, and virus isolation for detection of respiratory viruses in nasopharyngeal secretions. J. Clin. Microbiol. 29: 470-474
  21. Tam, J. S. 2002. Influenza A (H5N1) in Hong Kong: An overview. Vaccine 20(Suppl 2): S77-S81 https://doi.org/10.1016/S0264-410X(02)00137-8
  22. Tran, T. H., T. L. Nguyen, T. D. Nguyen, T. S. Luong, P. M. Pham, V. C. Nguyen, et al. 2004. Avian influenza A (H5N1) in 10 patients in Vietnam. N. Engl. J. Med. 350: 1179-1188 https://doi.org/10.1056/NEJMoa040419
  23. Webster, R. G., W. J. Bean, O. T. Gorman, T. M. Chambers, and Y. Kawaoka. 1992. Evolution and ecology of influenza A viruses. Microbiol. Rev. 56: 152-179
  24. Xie, Z., Y. S. Pang, J. Liu, X. Deng, X. Tang, J. Sun, and M. I. Khan. 2006. A multiplex RT-PCR for detection of type A influenza virus and differentiation of avian H5, H7, and H9 hemagglutinin subtypes. Mol. Cell. Probes 20: 245-249 https://doi.org/10.1016/j.mcp.2006.01.003