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Volumn 346, Issue 4, 2006, Pages 1163-1172

Efficient amplification and cloning of near full-length hepatitis C virus genome from clinical samples

Author keywords

Cloning; Hepatitis C; Long RT PCR; Quasispecies

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENE AMPLIFICATION; GENE VECTOR; GENETIC RECOMBINATION; HEPATITIS C VIRUS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA STRUCTURE; RNA VIRUS; VIRUS GENOME; VIRUS MUTATION;

EID: 33745333404     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2006.06.039     Document Type: Article
Times cited : (15)

References (53)
  • 1
    • 0028211009 scopus 로고
    • PCR amplification of up to 35-kb DNA with high fidelity and high yield from lambda bacteriophage templates
    • Barnes W.M. PCR amplification of up to 35-kb DNA with high fidelity and high yield from lambda bacteriophage templates. Proc. Natl. Acad. Sci. USA 91 (1994) 2216-2220
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 2216-2220
    • Barnes, W.M.1
  • 2
    • 0028261194 scopus 로고
    • Effective amplification of long targets from cloned inserts and human genomic DNA
    • Cheng S., Fockler C., Barnes W.M., and Higuchi R. Effective amplification of long targets from cloned inserts and human genomic DNA. Proc. Natl. Acad. Sci. USA. 91 (1994) 5695-5699
    • (1994) Proc. Natl. Acad. Sci. USA. , vol.91 , pp. 5695-5699
    • Cheng, S.1    Fockler, C.2    Barnes, W.M.3    Higuchi, R.4
  • 3
    • 0028568553 scopus 로고
    • Reverse transcriptase can inhibit PCR and stimulate primer-dimer formation
    • Chumakov K.M. Reverse transcriptase can inhibit PCR and stimulate primer-dimer formation. PCR Meth. Appl. 4 (1994) 62-64
    • (1994) PCR Meth. Appl. , vol.4 , pp. 62-64
    • Chumakov, K.M.1
  • 4
    • 0036269759 scopus 로고    scopus 로고
    • Thermodynamic and phylogenetic prediction of RNA secondary structures in the coding region of hepatitis C virus
    • Tuplin A., Wood J., Evans D.J., Patel A.H., and Simmonds P. Thermodynamic and phylogenetic prediction of RNA secondary structures in the coding region of hepatitis C virus. RNA 8 (2002) 824-841
    • (2002) RNA , vol.8 , pp. 824-841
    • Tuplin, A.1    Wood, J.2    Evans, D.J.3    Patel, A.H.4    Simmonds, P.5
  • 5
    • 5444272324 scopus 로고    scopus 로고
    • Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods
    • Tuplin A., Evans D.J., and Simmonds P. Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods. J. Gen. Virol. 85 (2004) 3037-3047
    • (2004) J. Gen. Virol. , vol.85 , pp. 3037-3047
    • Tuplin, A.1    Evans, D.J.2    Simmonds, P.3
  • 6
    • 4344619191 scopus 로고    scopus 로고
    • Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: implications for virus evolution and host persistence
    • Simmonds P., Tuplin A., and Evans D.J. Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: implications for virus evolution and host persistence. RNA 10 (2004) 1337-1351
    • (2004) RNA , vol.10 , pp. 1337-1351
    • Simmonds, P.1    Tuplin, A.2    Evans, D.J.3
  • 7
    • 17644421360 scopus 로고    scopus 로고
    • A refined long RT-PCR technique to amplify complete viral RNA genome sequences from clinical samples: Application to a novel hepatitis C virus variant of genotype 6
    • Lu L., Nakano T., Smallwood G.A., Heffron T.G., Robertson B.H., and Hagedorn C.H. A refined long RT-PCR technique to amplify complete viral RNA genome sequences from clinical samples: Application to a novel hepatitis C virus variant of genotype 6. J. Virol. Methods 126 (2005) 139-148
    • (2005) J. Virol. Methods , vol.126 , pp. 139-148
    • Lu, L.1    Nakano, T.2    Smallwood, G.A.3    Heffron, T.G.4    Robertson, B.H.5    Hagedorn, C.H.6
  • 8
    • 0037386754 scopus 로고    scopus 로고
    • Full-length cDNA synthesis for long-distance RT-PCR of large mRNA transcripts
    • Hawkins P.R., Jin P., and Fu G.K. Full-length cDNA synthesis for long-distance RT-PCR of large mRNA transcripts. Biotechniques 34 (2003) 768-770
    • (2003) Biotechniques , vol.34 , pp. 768-770
    • Hawkins, P.R.1    Jin, P.2    Fu, G.K.3
  • 9
    • 0037083546 scopus 로고    scopus 로고
    • A highly efficient method for long-chain cDNA synthesis using trehalose and betaine
    • Spiess A.N., and Ivell R. A highly efficient method for long-chain cDNA synthesis using trehalose and betaine. Anal. Biochem. 301 (2002) 168-174
    • (2002) Anal. Biochem. , vol.301 , pp. 168-174
    • Spiess, A.N.1    Ivell, R.2
  • 10
    • 0023700869 scopus 로고
    • Structure-independent DNA amplification by PCR using 7-deaza-2′-deoxyguanosine
    • McConlogue L., Brow M.A., and Innis M.A. Structure-independent DNA amplification by PCR using 7-deaza-2′-deoxyguanosine. Nucleic Acids Res. 16 (1988) 9869
    • (1988) Nucleic Acids Res. , vol.16 , pp. 9869
    • McConlogue, L.1    Brow, M.A.2    Innis, M.A.3
  • 12
  • 13
    • 0031160039 scopus 로고    scopus 로고
    • Optimizing multiplex and LA-PCR with betaine
    • Hengen P.N. Optimizing multiplex and LA-PCR with betaine. Trends Biochem. Sci. 22 (1997) 225-226
    • (1997) Trends Biochem. Sci. , vol.22 , pp. 225-226
    • Hengen, P.N.1
  • 14
    • 0034219149 scopus 로고    scopus 로고
    • New specificity and yield enhancer of polymerase chain reactions
    • Kovarova M., and Draber P. New specificity and yield enhancer of polymerase chain reactions. Nucleic Acids Res. 28 (2000) E70
    • (2000) Nucleic Acids Res. , vol.28
    • Kovarova, M.1    Draber, P.2
  • 15
    • 0026718980 scopus 로고
    • Phosphorothioate primers improve the amplification of DNA sequences by DNA polymerases with proofreading activity
    • Skerra A. Phosphorothioate primers improve the amplification of DNA sequences by DNA polymerases with proofreading activity. Nucleic Acids Res. 20 (1992) 3551-3554
    • (1992) Nucleic Acids Res. , vol.20 , pp. 3551-3554
    • Skerra, A.1
  • 16
    • 85045499669 scopus 로고
    • Amplimers with 3′-terminal phosphorothioate linkages resist degradation by vent polymerase and reduce Taq polymerase mispriming
    • de Noronha C.M., and Mullins J.I. Amplimers with 3′-terminal phosphorothioate linkages resist degradation by vent polymerase and reduce Taq polymerase mispriming. PCR Meth. Appl. 2 (1992) 131-136
    • (1992) PCR Meth. Appl. , vol.2 , pp. 131-136
    • de Noronha, C.M.1    Mullins, J.I.2
  • 17
    • 1642332243 scopus 로고    scopus 로고
    • Single base extension (SBE) with proofreading polymerases and phosphorothioate primers: improved fidelity in single-substrate assays
    • Di Giusto D., and King G.C. Single base extension (SBE) with proofreading polymerases and phosphorothioate primers: improved fidelity in single-substrate assays. Nucleic Acids Res. 31 (2003) e7
    • (2003) Nucleic Acids Res. , vol.31
    • Di Giusto, D.1    King, G.C.2
  • 18
    • 0033729713 scopus 로고    scopus 로고
    • Controlled hot start and improved specificity in carrying out PCR utilizing touch-up and loop incorporated primers (TULIPS)
    • Ailenberg M., and Silverman M. Controlled hot start and improved specificity in carrying out PCR utilizing touch-up and loop incorporated primers (TULIPS). Biotechniques 29 (2000) 1018-1020
    • (2000) Biotechniques , vol.29 , pp. 1018-1020
    • Ailenberg, M.1    Silverman, M.2
  • 19
    • 0030606308 scopus 로고    scopus 로고
    • Oligonucleotide inhibitors of Taq DNA polymerase facilitate detection of low copy number targets by PCR
    • Dang C., and Jayasena S.D. Oligonucleotide inhibitors of Taq DNA polymerase facilitate detection of low copy number targets by PCR. J. Mol. Biol. 64 (1996) 268-278
    • (1996) J. Mol. Biol. , vol.64 , pp. 268-278
    • Dang, C.1    Jayasena, S.D.2
  • 20
    • 0031559579 scopus 로고    scopus 로고
    • Inhibition of multiple thermostable DNA polymerases by a heterodimeric aptamer
    • Lin Y., and Jayasena S.D. Inhibition of multiple thermostable DNA polymerases by a heterodimeric aptamer. J. Mol. Biol. 271 (1997) 100-111
    • (1997) J. Mol. Biol. , vol.271 , pp. 100-111
    • Lin, Y.1    Jayasena, S.D.2
  • 21
    • 13944249457 scopus 로고    scopus 로고
    • Quasispecies heterogeneity within the E1/E2 region as a pretreatment variable during pegylated interferon therapy of chronic hepatitis C virus infection
    • Chambers T.J., Fan X., Droll D.A., Hembrador E., Slater T., Nickells M.W., Dustin L.B., and DiBisceglie A.M. Quasispecies heterogeneity within the E1/E2 region as a pretreatment variable during pegylated interferon therapy of chronic hepatitis C virus infection. J. Virol. 79 (2005) 3071-3083
    • (2005) J. Virol. , vol.79 , pp. 3071-3083
    • Chambers, T.J.1    Fan, X.2    Droll, D.A.3    Hembrador, E.4    Slater, T.5    Nickells, M.W.6    Dustin, L.B.7    DiBisceglie, A.M.8
  • 23
    • 0032052803 scopus 로고    scopus 로고
    • Stimulation and suppression of PCR-mediated recombination
    • Judo M.S., Wedel A.B., and Wilson C. Stimulation and suppression of PCR-mediated recombination. Nucleic Acids Res. 26 (1998) 1819-1825
    • (1998) Nucleic Acids Res. , vol.26 , pp. 1819-1825
    • Judo, M.S.1    Wedel, A.B.2    Wilson, C.3
  • 24
    • 0036053432 scopus 로고    scopus 로고
    • Factors affecting PCR-mediated recombination
    • Shafikhani S. Factors affecting PCR-mediated recombination. Environ. Microbiol. 4 (2002) 482-486
    • (2002) Environ. Microbiol. , vol.4 , pp. 482-486
    • Shafikhani, S.1
  • 26
    • 0024234855 scopus 로고
    • CLUSTAL: a package for performing multiple sequence alignment on a microcomputer
    • Higgins D.G., and Sharp P.M. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73 (1988) 237-244
    • (1988) Gene , vol.73 , pp. 237-244
    • Higgins, D.G.1    Sharp, P.M.2
  • 27
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16 (1980) 111-120
    • (1980) J. Mol. Evol. , vol.16 , pp. 111-120
    • Kimura, M.1
  • 28
    • 3242810318 scopus 로고    scopus 로고
    • MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment
    • Kumar S., Tamura K., and Nei M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5 (2004) 150-163
    • (2004) Brief. Bioinform. , vol.5 , pp. 150-163
    • Kumar, S.1    Tamura, K.2    Nei, M.3
  • 29
    • 0023375195 scopus 로고
    • The neighbor-joining method: a new method for reconstructing phylogenetic trees
    • Saitou N., and Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 (1987) 406-425
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 32
    • 0030740520 scopus 로고    scopus 로고
    • Transcripts from a single full-length cDNA clone of hepatitis C virus are infectious when directly transfected into the liver of a chimpanzee
    • Yanagi M., Purcell R.H., Emerson S.U., and Bukh J. Transcripts from a single full-length cDNA clone of hepatitis C virus are infectious when directly transfected into the liver of a chimpanzee. Proc. Natl. Acad. Sci. USA 94 (1997) 8738-8743
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 8738-8743
    • Yanagi, M.1    Purcell, R.H.2    Emerson, S.U.3    Bukh, J.4
  • 33
    • 0030711744 scopus 로고    scopus 로고
    • Cloning and characterization of a complete open reading frame of the hepatitis C virus genome in only two cDNA fragments
    • Rispeter K., Lu M., Lechner S., Zibert A., and Roggendorf M. Cloning and characterization of a complete open reading frame of the hepatitis C virus genome in only two cDNA fragments. J. Gen. Virol. 78 (1997) 2751-2759
    • (1997) J. Gen. Virol. , vol.78 , pp. 2751-2759
    • Rispeter, K.1    Lu, M.2    Lechner, S.3    Zibert, A.4    Roggendorf, M.5
  • 34
    • 0346727194 scopus 로고    scopus 로고
    • Rapid RT-PCR amplification of full-length poliovirus genomes allows rapid discrimination between wild-type and recombinant vaccine-derived polioviruses
    • Boot H.J., Schepp R.M., van Nunen F.J., and Kimman T.G. Rapid RT-PCR amplification of full-length poliovirus genomes allows rapid discrimination between wild-type and recombinant vaccine-derived polioviruses. J. Virol. Methods 116 (2004) 35-43
    • (2004) J. Virol. Methods , vol.116 , pp. 35-43
    • Boot, H.J.1    Schepp, R.M.2    van Nunen, F.J.3    Kimman, T.G.4
  • 36
    • 0034307933 scopus 로고    scopus 로고
    • Analysis of ORF 1 in European porcine reproductive and respiratory syndrome virus by long RT-PCR and restriction fragment length polymorphism (RFLP) analysis
    • Nielsen H.S., Storgaard T., and Oleksiewicz M.B. Analysis of ORF 1 in European porcine reproductive and respiratory syndrome virus by long RT-PCR and restriction fragment length polymorphism (RFLP) analysis. Vet. Microbiol. 76 (2000) 221-228
    • (2000) Vet. Microbiol. , vol.76 , pp. 221-228
    • Nielsen, H.S.1    Storgaard, T.2    Oleksiewicz, M.B.3
  • 37
    • 0032842314 scopus 로고    scopus 로고
    • The complete consensus sequence of coxsackievirus B6 and generation of infectious clones by long RT-PCR
    • Martino T.A., Tellier R., Petric M., Irwin D.M., Afshar A., and Liu P.P. The complete consensus sequence of coxsackievirus B6 and generation of infectious clones by long RT-PCR. Virus Res. 64 (1999) 77-86
    • (1999) Virus Res. , vol.64 , pp. 77-86
    • Martino, T.A.1    Tellier, R.2    Petric, M.3    Irwin, D.M.4    Afshar, A.5    Liu, P.P.6
  • 38
    • 0036072684 scopus 로고    scopus 로고
    • Reevaluation of a North India isolate of hepatitis E virus based on the full-length genomic sequence obtained following long RT-PCR
    • Jameel S., Zafrullah M., Chawla Y.K., and Dilawari J.B. Reevaluation of a North India isolate of hepatitis E virus based on the full-length genomic sequence obtained following long RT-PCR. Virus Res. 86 (2002) 53-58
    • (2002) Virus Res. , vol.86 , pp. 53-58
    • Jameel, S.1    Zafrullah, M.2    Chawla, Y.K.3    Dilawari, J.B.4
  • 39
    • 19144362556 scopus 로고    scopus 로고
    • Long RT-PCR of the entire 8.5-kb NF1 open reading frame and mutation detection on agarose gels
    • Martinez J.M., Breidenbach H.H., and Cawthon R. Long RT-PCR of the entire 8.5-kb NF1 open reading frame and mutation detection on agarose gels. Genome Res. 6 (1996) 58-66
    • (1996) Genome Res. , vol.6 , pp. 58-66
    • Martinez, J.M.1    Breidenbach, H.H.2    Cawthon, R.3
  • 40
    • 0032894225 scopus 로고    scopus 로고
    • Long RT-PCR Amplification of the entire coding sequence of the polycystic kidney disease 1 (PKD1) gene
    • Thongnoppakhun W., Wilairat P., Vareesangthip K., and Yenchitsomanus P.T. Long RT-PCR Amplification of the entire coding sequence of the polycystic kidney disease 1 (PKD1) gene. Biotechniques 26 (1999) 126-132
    • (1999) Biotechniques , vol.26 , pp. 126-132
    • Thongnoppakhun, W.1    Wilairat, P.2    Vareesangthip, K.3    Yenchitsomanus, P.T.4
  • 44
    • 0030774397 scopus 로고    scopus 로고
    • Amplification and fusion of long fragments of hepatitis C virus genome
    • Wang L.F., Radkowski M., Vargas H., Rakela J., and Laskus T. Amplification and fusion of long fragments of hepatitis C virus genome. J. Virol. Methods 68 (1997) 217-223
    • (1997) J. Virol. Methods , vol.68 , pp. 217-223
    • Wang, L.F.1    Radkowski, M.2    Vargas, H.3    Rakela, J.4    Laskus, T.5
  • 45
    • 0029956369 scopus 로고    scopus 로고
    • Long PCR and its application to hepatitis viruses: amplification of hepatitis A, hepatitis B, and hepatitis C virus genomes
    • Tellier R., Bukh J., Emerson S.U., Miller R.H., and Purcell R.H. Long PCR and its application to hepatitis viruses: amplification of hepatitis A, hepatitis B, and hepatitis C virus genomes. J. Clin. Microbiol. 34 (1996) 3085-3091
    • (1996) J. Clin. Microbiol. , vol.34 , pp. 3085-3091
    • Tellier, R.1    Bukh, J.2    Emerson, S.U.3    Miller, R.H.4    Purcell, R.H.5
  • 47
    • 11144347616 scopus 로고    scopus 로고
    • A strategy for obtaining near full-length HCV cDNA clones (assemblicons) by assembly PCR
    • Sheehy P., Scallan M., Kenny-Walsh E., Shanahan F., and Fanning L.J. A strategy for obtaining near full-length HCV cDNA clones (assemblicons) by assembly PCR. J. Virol. Methods 123 (2005) 115-124
    • (2005) J. Virol. Methods , vol.123 , pp. 115-124
    • Sheehy, P.1    Scallan, M.2    Kenny-Walsh, E.3    Shanahan, F.4    Fanning, L.J.5
  • 48
    • 0033555647 scopus 로고    scopus 로고
    • Differential priming of RNA templates during cDNA synthesis markedly affects both accuracy and reproducibility of quantitative competitive reverse-transcriptase PCR
    • Zhang J., and Byrne C.D. Differential priming of RNA templates during cDNA synthesis markedly affects both accuracy and reproducibility of quantitative competitive reverse-transcriptase PCR. Biochem. J. 337 (1999) 231-241
    • (1999) Biochem. J. , vol.337 , pp. 231-241
    • Zhang, J.1    Byrne, C.D.2
  • 49
    • 0034817076 scopus 로고    scopus 로고
    • Differential amplification of hypervariable region 1 of hepatitis C virus by partially mismatched primers
    • Fan X., Lyra A.C., Tan D., Xu Y., and Di Bisceglie A.M. Differential amplification of hypervariable region 1 of hepatitis C virus by partially mismatched primers. Biochem. Biophys. Res. Commun. 284 (2001) 694-697
    • (2001) Biochem. Biophys. Res. Commun. , vol.284 , pp. 694-697
    • Fan, X.1    Lyra, A.C.2    Tan, D.3    Xu, Y.4    Di Bisceglie, A.M.5
  • 50
    • 0027489427 scopus 로고
    • Defective interfering particles and virus evolution
    • Bangham C.R.M., and Kirkwood T.B.L. Defective interfering particles and virus evolution. Trends Microbiol. 1 (1993) 260-264
    • (1993) Trends Microbiol. , vol.1 , pp. 260-264
    • Bangham, C.R.M.1    Kirkwood, T.B.L.2
  • 51
    • 0029688801 scopus 로고    scopus 로고
    • Visualization of hepatitis C virons and putative defective interfering particles isolated from low-density lipoproteins
    • Prince A.M., Huima-Byron T., Parker T.S., and Levine D.M. Visualization of hepatitis C virons and putative defective interfering particles isolated from low-density lipoproteins. J. Viral Hepat. 3 (1996) 11-17
    • (1996) J. Viral Hepat. , vol.3 , pp. 11-17
    • Prince, A.M.1    Huima-Byron, T.2    Parker, T.S.3    Levine, D.M.4


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