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Volumn 228, Issue , 2016, Pages 114-122

Design and testing of multiplex RT-PCR primers for the rapid detection of influenza A virus genomic segments: Application to equine influenza virus

Author keywords

Dual priming oligonucleotide (DPO); Equine influenza virus; H3N8; Influenza A virus; Multiplex RT PCR; Phylogenetic analysis; Reverse transcription polymerase chain reaction (RT PCR)

Indexed keywords

AMINO ACID; DUAL PRIMING OLIGONUCLEOTIDE; OLIGONUCLEOTIDE; UNCLASSIFIED DRUG; PRIMER DNA;

EID: 84949666738     PISSN: 01660934     EISSN: 18790984     Source Type: Journal    
DOI: 10.1016/j.jviromet.2015.11.012     Document Type: Article
Times cited : (6)

References (53)
  • 2
    • 0035992155 scopus 로고    scopus 로고
    • Heteroduplex mobility assay for detection of new avian influenza virus variants
    • Berinstein A., Seal B.S., Suarez D.L. Heteroduplex mobility assay for detection of new avian influenza virus variants. Avian Dis. 2002, 46:393-400.
    • (2002) Avian Dis. , vol.46 , pp. 393-400
    • Berinstein, A.1    Seal, B.S.2    Suarez, D.L.3
  • 3
    • 0141617541 scopus 로고    scopus 로고
    • The design of Jemboss: a graphical user interface to EMBOSS
    • Carver T., Bleasby A. The design of Jemboss: a graphical user interface to EMBOSS. Bioinformatics 2003, 19:1837-1843.
    • (2003) Bioinformatics , vol.19 , pp. 1837-1843
    • Carver, T.1    Bleasby, A.2
  • 6
    • 34247843070 scopus 로고    scopus 로고
    • Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene
    • Chun J.Y., Kim K.J., Hwang I.T., Kim Y.J., Lee D.H., Lee I.K., Kim J.K. Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene. Nucleic Acids Res. 2007, 35:e40.
    • (2007) Nucleic Acids Res. , vol.35 , pp. e40
    • Chun, J.Y.1    Kim, K.J.2    Hwang, I.T.3    Kim, Y.J.4    Lee, D.H.5    Lee, I.K.6    Kim, J.K.7
  • 7
    • 84902072507 scopus 로고    scopus 로고
    • Dual-priming oligonucleotide-based multiplex PCR using tissue samples in rapid urease test in the detection of Helicobacter pylori infection
    • Chung W.C., Jung S.H., Oh J.H., Kim T.H., Cheung D.Y., Kim B.W., Kim S.S., Kim J.I., Sin E.Y. Dual-priming oligonucleotide-based multiplex PCR using tissue samples in rapid urease test in the detection of Helicobacter pylori infection. World J. Gastroenterol.: WJG 2014, 20:6547-6553.
    • (2014) World J. Gastroenterol.: WJG , vol.20 , pp. 6547-6553
    • Chung, W.C.1    Jung, S.H.2    Oh, J.H.3    Kim, T.H.4    Cheung, D.Y.5    Kim, B.W.6    Kim, S.S.7    Kim, J.I.8    Sin, E.Y.9
  • 8
    • 67849128701 scopus 로고    scopus 로고
    • Primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies
    • Contreras-Moreira B., Sachman-Ruiz B., Figueroa-Palacios I., Vinuesa P. primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies. Nucleic Acids Res. 2009, 37:W95-W100.
    • (2009) Nucleic Acids Res. , vol.37 , pp. W95-W100
    • Contreras-Moreira, B.1    Sachman-Ruiz, B.2    Figueroa-Palacios, I.3    Vinuesa, P.4
  • 9
    • 84864453108 scopus 로고    scopus 로고
    • JModelTest 2: more models, new heuristics and parallel computing
    • Darriba D., Taboada G.L., Doallo R., Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat. Methods 2012, 9:772.
    • (2012) Nat. Methods , vol.9 , pp. 772
    • Darriba, D.1    Taboada, G.L.2    Doallo, R.3    Posada, D.4
  • 10
    • 84949684042 scopus 로고    scopus 로고
    • Integrated DNA Technologies, Inc., Coralville, IA, USA
    • DECODED Newsletter Tips for Using BLAST to Locate PCR Primers, Pipet Tips, Integrated DNA Technologies 2014, Integrated DNA Technologies, Inc., Coralville, IA, USA, https://sg.idtdna.com/pages/decoded/decoded-articles/pipet-tips/decoded/2011/03/16/tips-for-using-blast-to-locate-pcr-primers.
    • (2014) Tips for Using BLAST to Locate PCR Primers, Pipet Tips, Integrated DNA Technologies
  • 13
    • 79251550432 scopus 로고    scopus 로고
    • Identification of novel conserved functional motifs across most Influenza A viral strains
    • ElHefnawi M., Alaidi O., Mohamed N., Kamar M., El-Azab I., Zada S., Siam R. Identification of novel conserved functional motifs across most Influenza A viral strains. Virol. J. 2011, 8:44.
    • (2011) Virol. J. , vol.8 , pp. 44
    • ElHefnawi, M.1    Alaidi, O.2    Mohamed, N.3    Kamar, M.4    El-Azab, I.5    Zada, S.6    Siam, R.7
  • 14
    • 0034764741 scopus 로고    scopus 로고
    • Combined PCR-heteroduplex mobility assay for detection and differentiation of influenza A viruses from different animal species
    • Ellis J.S., Zambon M.C. Combined PCR-heteroduplex mobility assay for detection and differentiation of influenza A viruses from different animal species. J. Clin. Microbiol. 2001, 39:4097-4102.
    • (2001) J. Clin. Microbiol. , vol.39 , pp. 4097-4102
    • Ellis, J.S.1    Zambon, M.C.2
  • 15
    • 0037403221 scopus 로고    scopus 로고
    • Animal influenza virus surveillance
    • Fouchier R. Animal influenza virus surveillance. Vaccine 2003, 21:1754-1757.
    • (2003) Vaccine , vol.21 , pp. 1754-1757
    • Fouchier, R.1
  • 16
    • 0025835627 scopus 로고
    • Evolution of influenza A virus nucleoprotein genes: implications for the origins of H1N1 human and classical swine viruses
    • Gorman O.T., Bean W.J., Kawaoka Y., Donatelli I., Guo Y.J., Webster R.G. Evolution of influenza A virus nucleoprotein genes: implications for the origins of H1N1 human and classical swine viruses. J. Virol. 1991, 65:3704-3714.
    • (1991) J. Virol. , vol.65 , pp. 3704-3714
    • Gorman, O.T.1    Bean, W.J.2    Kawaoka, Y.3    Donatelli, I.4    Guo, Y.J.5    Webster, R.G.6
  • 17
    • 0025187412 scopus 로고
    • Evolution of influenza A virus PB2 genes: implications for evolution of the ribonucleoprotein complex and origin of human influenza A virus
    • Gorman O.T., Donis R.O., Kawaoka Y., Webster R.G. Evolution of influenza A virus PB2 genes: implications for evolution of the ribonucleoprotein complex and origin of human influenza A virus. J. Virol. 1990, 64:4893-4902.
    • (1990) J. Virol. , vol.64 , pp. 4893-4902
    • Gorman, O.T.1    Donis, R.O.2    Kawaoka, Y.3    Webster, R.G.4
  • 18
    • 0035559445 scopus 로고    scopus 로고
    • Universal primer set for the full-length amplification of all influenza A viruses
    • Hoffmann E., Stech J., Guan Y., Webster R.G., Perez D.R. Universal primer set for the full-length amplification of all influenza A viruses. Arch. Virol. 2001, 146:2275-2289.
    • (2001) Arch. Virol. , vol.146 , pp. 2275-2289
    • Hoffmann, E.1    Stech, J.2    Guan, Y.3    Webster, R.G.4    Perez, D.R.5
  • 19
    • 84897138563 scopus 로고    scopus 로고
    • Identification and chronological analysis of genomic signatures in influenza A viruses
    • Hu Y.J., Tu P.C., Lin C.S., Guo S.T. Identification and chronological analysis of genomic signatures in influenza A viruses. PLoS ONE 2014, 9:e84638.
    • (2014) PLoS ONE , vol.9 , pp. e84638
    • Hu, Y.J.1    Tu, P.C.2    Lin, C.S.3    Guo, S.T.4
  • 20
    • 0022838916 scopus 로고
    • Proofreading function associated with the RNA-dependent RNA polymerase from influenza virus
    • Ishihama A., Mizumoto K., Kawakami K., Kato A., Honda A. Proofreading function associated with the RNA-dependent RNA polymerase from influenza virus. J. Biol. Chem. 1986, 261:10417-10421.
    • (1986) J. Biol. Chem. , vol.261 , pp. 10417-10421
    • Ishihama, A.1    Mizumoto, K.2    Kawakami, K.3    Kato, A.4    Honda, A.5
  • 21
    • 84883721961 scopus 로고    scopus 로고
    • High resolution melting analysis: rapid and precise characterisation of recombinant influenza A genomes
    • Kalthoff D., Beer M., Hoffmann B. High resolution melting analysis: rapid and precise characterisation of recombinant influenza A genomes. Virol. J. 2013, 10:284.
    • (2013) Virol. J. , vol.10 , pp. 284
    • Kalthoff, D.1    Beer, M.2    Hoffmann, B.3
  • 22
    • 84875619226 scopus 로고    scopus 로고
    • MAFFT multiple sequence alignment software version 7: improvements in performance and usability
    • Katoh K., Standley D.M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 2013, 30:772-780.
    • (2013) Mol. Biol. Evol. , vol.30 , pp. 772-780
    • Katoh, K.1    Standley, D.M.2
  • 23
    • 40849101514 scopus 로고    scopus 로고
    • Direct detection of lamivudine-resistant hepatitis B virus mutants by a multiplex PCR using dual-priming oligonucleotide primers
    • Kim J.K., Lee H.J., Lee Y.J., Chun J.Y., Lee I.K., Lim Y.S., Suh D.J., Ko S.Y., Kim M.H., Oh H.B. Direct detection of lamivudine-resistant hepatitis B virus mutants by a multiplex PCR using dual-priming oligonucleotide primers. J. Virol. Methods 2008, 149:76-84.
    • (2008) J. Virol. Methods , vol.149 , pp. 76-84
    • Kim, J.K.1    Lee, H.J.2    Lee, Y.J.3    Chun, J.Y.4    Lee, I.K.5    Lim, Y.S.6    Suh, D.J.7    Ko, S.Y.8    Kim, M.H.9    Oh, H.B.10
  • 25
    • 80053535579 scopus 로고    scopus 로고
    • High-resolution melting approach to efficient identification and quantification of H275Y mutant influenza H1N1/2009 virus in mixed-virus-population samples
    • Lee H.K., Lee C.K., Loh T.P., Tang J.W., Tambyah P.A., Koay E.S. High-resolution melting approach to efficient identification and quantification of H275Y mutant influenza H1N1/2009 virus in mixed-virus-population samples. J. Clin. Microbiol. 2011, 49:3555-3559.
    • (2011) J. Clin. Microbiol. , vol.49 , pp. 3555-3559
    • Lee, H.K.1    Lee, C.K.2    Loh, T.P.3    Tang, J.W.4    Tambyah, P.A.5    Koay, E.S.6
  • 26
    • 40749096880 scopus 로고    scopus 로고
    • Rapid differentiation of influenza A virus subtypes and genetic screening for virus variants by high-resolution melting analysis
    • Lin J.H., Tseng C.P., Chen Y.J., Lin C.Y., Chang S.S., Wu H.S., Cheng J.C. Rapid differentiation of influenza A virus subtypes and genetic screening for virus variants by high-resolution melting analysis. J. Clin. Microbiol. 2008, 46:1090-1097.
    • (2008) J. Clin. Microbiol. , vol.46 , pp. 1090-1097
    • Lin, J.H.1    Tseng, C.P.2    Chen, Y.J.3    Lin, C.Y.4    Chang, S.S.5    Wu, H.S.6    Cheng, J.C.7
  • 27
    • 12344314160 scopus 로고    scopus 로고
    • Simple and rapid strategy for genetic characterization of influenza B virus reassortants
    • Lugovtsev V.Y., Vodeiko G.M., Strupczewski C.M., Levandowski R.A. Simple and rapid strategy for genetic characterization of influenza B virus reassortants. J. Virol. Methods 2005, 124:203-210.
    • (2005) J. Virol. Methods , vol.124 , pp. 203-210
    • Lugovtsev, V.Y.1    Vodeiko, G.M.2    Strupczewski, C.M.3    Levandowski, R.A.4
  • 28
    • 79960384534 scopus 로고    scopus 로고
    • Influenza A viruses: new research developments
    • Medina R.A., Garcia-Sastre A. Influenza A viruses: new research developments. Nat. Rev. Microbiol. 2011, 9:590-603.
    • (2011) Nat. Rev. Microbiol. , vol.9 , pp. 590-603
    • Medina, R.A.1    Garcia-Sastre, A.2
  • 29
    • 77956646043 scopus 로고    scopus 로고
    • Simultaneous detection and subtyping of porcine endogenous retroviruses proviral DNA using the dual priming oligonucleotide system
    • Moon H.-J., Park S.-J., Kim H.-K., Ann S.-K., Rho S., Keum H.-O., Park B.-K. Simultaneous detection and subtyping of porcine endogenous retroviruses proviral DNA using the dual priming oligonucleotide system. J. Vet. Sci. 2010, 11:269.
    • (2010) J. Vet. Sci. , vol.11 , pp. 269
    • Moon, H.-J.1    Park, S.-J.2    Kim, H.-K.3    Ann, S.-K.4    Rho, S.5    Keum, H.-O.6    Park, B.-K.7
  • 30
    • 53849125470 scopus 로고    scopus 로고
    • Host restriction of avian influenza viruses at the level of the ribonucleoproteins
    • Naffakh N., Tomoiu A., Rameix-Welti M.A., van der Werf S. Host restriction of avian influenza viruses at the level of the ribonucleoproteins. Annu. Rev. Microbiol. 2008, 62:403-424.
    • (2008) Annu. Rev. Microbiol. , vol.62 , pp. 403-424
    • Naffakh, N.1    Tomoiu, A.2    Rameix-Welti, M.A.3    van der Werf, S.4
  • 31
    • 33847044691 scopus 로고    scopus 로고
    • The evolution of epidemic influenza
    • Nelson M.I., Holmes E.C. The evolution of epidemic influenza. Nat. Rev. Genet. 2007, 8:196-205.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 196-205
    • Nelson, M.I.1    Holmes, E.C.2
  • 32
    • 67649297821 scopus 로고    scopus 로고
    • Emergence and pandemic potential of swine-origin H1N1 influenza virus
    • Neumann G., Noda T., Kawaoka Y. Emergence and pandemic potential of swine-origin H1N1 influenza virus. Nature 2009, 459:931-939.
    • (2009) Nature , vol.459 , pp. 931-939
    • Neumann, G.1    Noda, T.2    Kawaoka, Y.3
  • 33
    • 84888376200 scopus 로고    scopus 로고
    • Cross talk between animal and human influenza viruses
    • Ozawa M., Kawaoka Y. Cross talk between animal and human influenza viruses. Annu. Rev. Anim. Biosci. 2013, 1:21-42.
    • (2013) Annu. Rev. Anim. Biosci. , vol.1 , pp. 21-42
    • Ozawa, M.1    Kawaoka, Y.2
  • 35
    • 19444384553 scopus 로고    scopus 로고
    • CODEHOP-mediated PCR-a powerful technique for the identification and characterization of viral genomes
    • Rose T.M. CODEHOP-mediated PCR-a powerful technique for the identification and characterization of viral genomes. Virol. J. 2005, 2:20.
    • (2005) Virol. J. , vol.2 , pp. 20
    • Rose, T.M.1
  • 37
    • 0029670112 scopus 로고    scopus 로고
    • Gene analysis of reassortant influenza virus by RT-PCR followed by restriction enzyme digestion
    • Sakamoto S., Kino Y., Oka T., Herlocher M.L., Maassab F. Gene analysis of reassortant influenza virus by RT-PCR followed by restriction enzyme digestion. J. Virol. Methods 1996, 56:161-171.
    • (1996) J. Virol. Methods , vol.56 , pp. 161-171
    • Sakamoto, S.1    Kino, Y.2    Oka, T.3    Herlocher, M.L.4    Maassab, F.5
  • 39
    • 0141923868 scopus 로고    scopus 로고
    • Molecular detection and identification of influenza viruses by oligonucleotide microarray hybridization
    • Sengupta S., Onodera K., Lai A., Melcher U. Molecular detection and identification of influenza viruses by oligonucleotide microarray hybridization. J. Clin. Microbiol. 2003, 41:4542-4550.
    • (2003) J. Clin. Microbiol. , vol.41 , pp. 4542-4550
    • Sengupta, S.1    Onodera, K.2    Lai, A.3    Melcher, U.4
  • 40
    • 84898617984 scopus 로고    scopus 로고
    • Rapid strategy for screening by pyrosequencing of influenza virus reassortants-candidates for live attenuated vaccines
    • Shcherbik S.V., Pearce N.C., Levine M.L., Klimov A.I., Villanueva J.M., Bousse T.L. Rapid strategy for screening by pyrosequencing of influenza virus reassortants-candidates for live attenuated vaccines. PLoS ONE 2014, 9:e92580.
    • (2014) PLoS ONE , vol.9 , pp. e92580
    • Shcherbik, S.V.1    Pearce, N.C.2    Levine, M.L.3    Klimov, A.I.4    Villanueva, J.M.5    Bousse, T.L.6
  • 42
    • 84860434973 scopus 로고    scopus 로고
    • RaxmlGUI: a graphical front-end for RAxML
    • Silvestro D., Michalak I. raxmlGUI: a graphical front-end for RAxML. Org. Diversity Evol. 2011, 12:335-337.
    • (2011) Org. Diversity Evol. , vol.12 , pp. 335-337
    • Silvestro, D.1    Michalak, I.2
  • 46
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 47
    • 1642378785 scopus 로고    scopus 로고
    • Rapid detection and simultaneous subtype differentiation of influenza A viruses by real time PCR
    • Stone B., Burrows J., Schepetiuk S., Higgins G., Hampson A., Shaw R., Kok T. Rapid detection and simultaneous subtype differentiation of influenza A viruses by real time PCR. J. Virol. Methods 2004, 117:103-112.
    • (2004) J. Virol. Methods , vol.117 , pp. 103-112
    • Stone, B.1    Burrows, J.2    Schepetiuk, S.3    Higgins, G.4    Hampson, A.5    Shaw, R.6    Kok, T.7
  • 48
    • 77954202497 scopus 로고    scopus 로고
    • DendroPy: a Python library for phylogenetic computing
    • Sukumaran J., Holder M.T. DendroPy: a Python library for phylogenetic computing. Bioinformatics 2010, 26:1569-1571.
    • (2010) Bioinformatics , vol.26 , pp. 1569-1571
    • Sukumaran, J.1    Holder, M.T.2
  • 49
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28:2731-2739.
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5    Kumar, S.6
  • 52
    • 55949113802 scopus 로고    scopus 로고
    • Evaluation of dual priming oligonucleotide-based multiplex PCR for detection of HBV YMDD mutants
    • Woo H.Y., Park H., Kim B.I., Jeon W.K., Kim Y.J. Evaluation of dual priming oligonucleotide-based multiplex PCR for detection of HBV YMDD mutants. Arch. Virol. 2008, 153:2019-2025.
    • (2008) Arch. Virol. , vol.153 , pp. 2019-2025
    • Woo, H.Y.1    Park, H.2    Kim, B.I.3    Jeon, W.K.4    Kim, Y.J.5
  • 53
    • 82655181926 scopus 로고    scopus 로고
    • Evolutionary dynamics of influenza A nucleoprotein (NP) lineages revealed by large-scale sequence analyses
    • Xu J., Christman M.C., Donis R.O., Lu G. Evolutionary dynamics of influenza A nucleoprotein (NP) lineages revealed by large-scale sequence analyses. Infect. Genet. Evol. 2011, 11:2125-2132.
    • (2011) Infect. Genet. Evol. , vol.11 , pp. 2125-2132
    • Xu, J.1    Christman, M.C.2    Donis, R.O.3    Lu, G.4


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