Amplification of the entire genome of influenza A virus H1N1 and H3N2 subtypes by reverse-transcription polymerase chain reaction

Journal of Virological Methods

Volumn 136, Issue 1-2, 2006, Pages 38-43

  Chan, Chi Ho ^a   Lin, Keh Liang ^a   Chan, You ^a   Wang, Ya Li ^a   Chi, Yu Tsai ^a   Tu, Hsiao Li ^a   Shieh, Happy K ^b   Liu, Wu Tse ^c  

^a CHUNG SHAN MEDICAL UNIVERSITY   (Taiwan)

^b NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

^c Examination Yuan   (Taiwan)

Author keywords

Entire genome; Influenza A virus; RT PCR; Thermoscript reverse transcriptase

Indexed keywords

RNA DIRECTED DNA POLYMERASE;

ACCURACY; AMPLICON; ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; DENATURATION; DNA SEQUENCE; DNA SYNTHESIS; GENE AMPLIFICATION; GENE CONSTRUCT; INFLUENZA VIRUS A; NONHUMAN; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA EXTRACTION; SEQUENCE ANALYSIS; VIRUS CULTURE; VIRUS GENOME; VIRUS STRAIN; VIRUS TYPING;

DNA PRIMERS; GENOME, VIRAL; HUMANS; INFLUENZA A VIRUS, H1N1 SUBTYPE; INFLUENZA A VIRUS, H3N2 SUBTYPE; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL;

INFLUENZA A VIRUS;

EID: 33745915522     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2006.03.027     Document Type: Article

References (33)

1. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
2. Bae S.H., Cheong H.K., Lee J.H., Cheong C., Kainosho M., and Choi B.S. Structural features of an influenza virus promoter and their implications for viral RNA synthesis. Proc. Nat. Acad. Sci. U.S.A. 98 (2001) 10602-10607
3. Baez M., Taussig R., Zazra J.J., Young J.F., Palese P., Reisfeld A., and Skalka A.M. Complete nucleotide sequence of the influenza A/PR/8/34 virus NS gene and comparison with the NS genes of the A/Udorn/72 and A/FPV/Rostock/34 strains. Nucleic Acids Res. 11 (1980) 5845-5858
4. Chen W., Calvo P.A., Malide D., Gibbs J., Schubert U., and Bacik I. A novel influenza A virus mitochondrial protein that induces cell death. Nat. Med. 7 (2001) 1306-1312
5. Claas E.C., Sprenger M.J., Kleter G.E., van Beek R., Quint W.G., and Masurel N. Type-specific identification of influenza viruses A, B and C by the polymerase chain reaction. J. Virol. Methods 39 (1992) 1-13
6. Cox N.J., Black R.A., and Kendal A.P. Pathways of evolution of influenza A (H1N1) viruses from 1977 to 1986 as determined by oligonucleotide mapping and sequencing studies. J. Gen. Virol. 70 (1989) 299-313
7. Curry J., McHale C., and Smith M.T. Low efficiency of the Moloney murine leukemia virus reverse transcriptase during reverse transcription of rare t(8;21) fusion gene transcripts. Biotechniques 32 (2002) 754-755
8. Desselberger U., Racaniello V.R., Zazra J.J., and Palese P. The 3′ and 5′-terminal sequences of influenza A, B and C virus RNA segments are highly conserved and show partial inverted complementarity. Gene 8 (1980) 315-328
9. Ellis J.S., and Zambon M.C. Combined PCR-heteroduplex mobility assay for detection and differentiation of influenza A viruses from different animal species. J. Clin. Microbiol. 39 (2001) 4097-4102
10. Fuchs B., Zhang K., Rock M.G., Bolander M.E., and Sarkar G. High temperature cDNA synthesis by AMV reverse transcriptase improves the specificity of PCR. Mol. Biotechnol. 12 (1999) 237-240
11. Gavin P.J., and Thomson Jr. R.B. Review of rapid diagnostic tests for influenza. Clin. App. Immunol. Rev. 4 (2004) 151-172
12. Gerard G.F., Potter R.J., Smith M.D., Rosenthal K., Dhariwal G., Lee J., and Chatterjee D.K. The role of template-primer in protection of reverse transcriptase from thermal inactivation. Nucleic Acids Res. 30 (2002) 3118-3129
13. Gorman O.T., Bean W.J., Kawaoka Y., and Webster R.G. Evolution of the nucleoprotein gene of influenza A virus. J. Virol. 64 (1990) 1487-1497
14. Guo Y., Wang M., Zheng G.S., Li W.K., Kawaoka Y., and Webster R.G. Seroepidemiological and molecular evidence for the presence of two H3N8 equine influenza viruses in China in 1993-94. J. Gen. Virol. 76 (1995) 2009-2014
15. Hoffmann E., Stech J., Guan Y., Webster R.G., and Perez D.R. Universal primer set for the full-length amplification of all influenza A viruses. Arch. Virol. 146 (2001) 2275-2289
16. Holmes E.C., Ghedin E., Miller N., Taylor J., Bao Y., St. George K., Grenfell B.T., Salzberg S.L., Fraser C.M., Lipman D.J., and Taubenberger J.K. Whole-genome analysis of human influenza a virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol. 3 (2005) 1579-1589
17. Kawaoka Y., Yamnikova S., Chambers T.M., Lvov D.K., and Webster R.G. Molecular characterization of a new hemagglutinin, subtype H14, of influenza A virus. Virology 179 (1990) 759-767
18. Kessler N., Ferraris O., Palmer K., Marsh W., and Steel A. Use of the DNA flow-thru chip, a three-dimensional biochip, for typing and subtyping of influenza viruses. J. Clin. Microbiol. 42 (2004) 2173-2185
19. Lau L.T., Banks J., Aherne R., Brown I.H., Dillon N., Collins R.A., Chan K.Y., Fung Y.W., Xing J., and Yu A.C. Nucleic acid sequence-based amplification methods to detect avian influenza virus. Biochem. Biophys. Res. Commun. 313 (2004) 336-342
20. Lin Y.P., Shu L.L., Wright S., Bean W.J., Sharp G.B., Shortridge K.F., and Webster R.G. Analysis of the influenza virus gene pool of avian species from southern China. Virology 198 (1994) 557-566
21. Lopez-Galindez C., Lopez J.A., Melero J.A., De La Fuente L., Martinez C., Ortin J., and Perucho M. Analysis of genetic variability and mapping of point mutations in influenza virus by the RNase mismatch cleavage method. Proc. Nat. Acad. Sci. U.S.A. 85 (1988) 3522-3526
22. Lugovtsev V.Y., Vodeiko G.M., Strupczewski C.M., and Levandowski R.A. Simple and rapid strategy for genetic characterization of influenza B virus reassortants. J. Virol. Methods 124 (2005) 203-210
23. Phipps L.P., Essen S.C., and Brown I.H. Genetic subtyping of influenza A viruses using RT-PCR with a single set of primers based on conserved sequences within the HA2 coding region. J. Virol. Methods 122 (2004) 119-122
24. Reid A.H., and Taubenberger J.K. The origin of the 1918 pandemic influenza virus: a continuing enigma. J. Gen. Virol. 84 (2003) 2285-2292
25. Reid A.H., Fanning T.G., Janczewski T.A., Lourens R.M., and Taubenberger J.K. Novel origin of the 1918 pandemic influenza virus nucleoprotein gene. J. Virol. 78 (2004) 12462-12470
26. Saito R., Oshitani H., Masuda H., and Suzuki H. Detection of amantadine-resistant influenza A virus strains in nursing homes by PCR-restriction fragment length polymorphism analysis with nasopharyngeal swabs. J. Clin. Microbiol. 40 (2002) 84-88
27. Sakamoto S., Kino Y., Oka T., Herlocher M.L., and Maassab F. Gene analysis of reassortant influenza virus by RT-PCR followed by restriction enzyme digestion. J. Virol. Methods 56 (1996) 161-171
28. Schrader C., and Suss J. Molecular epidemiology of porcine H3N2 influenza A viruses isolated in Germany between 1982 and 2001. Intervirology 47 (2004) 72-77
29. Stone B., Burrows J., Schepetiuk S., Higgins G., Hampson A., Shaw R., and Kok T. Rapid detection and simultaneous subtype differentiation of influenza A viruses by real time PCR. J. Virol. Methods 117 (2004) 103-112
30. Suarez D.L., Spackman E., and Senne D.A. Update on molecular epidemiology of H1, H5, and H7 influenza virus infections in poultry in North America. Avian Dis. 47 (2003) 888-897
31. Xu X., Lindstrom S.E., Shaw M.W., Smith C.B., Hall H.E., Mungall B.A., Subbarao K., Cox N.J., and Klimov A. Reassortment and evolution of current human influenza A and B viruses. Virus Res. 103 (2004) 55-60
32. Yan X., Schielke E.G., Grace K.M., Hassell C., Marrone B.L., and Nolan J.P. Microsphere-based duplexed immunoassay for influenza virus typing by flow cytometry. J. Immunol. Methods 284 (2004) 27-38
33. Zou S. A practical approach to genetic screening for influenza virus variants. J. Clin. Microbiol. 35 (1997) 2623-2627