title: Development of a sensitive RT-PCR method for amplifying and sequencing near full-length HCV genotype 1 RNA from patient samples.
abstract: BACKGROUND
  Direct-acting antiviral (DAAs) agents for hepatitis C virus (HCV) span a variety of targets, including proteins encoded by the NS3/4A, NS4B, NS5A, and NS5B genes. Treatment with DAAs has been shown to select variants with sequence changes in the HCV genome encoding amino acids that may confer resistance to the treatment. In order to assess these effects in patients, a Reverse Transcription Polymerase Chain Reaction (RT-PCR) method was developed to sequence these regions of HCV from patient plasma.
  
  
  METHODS
  A method was developed to amplify and sequence genotype 1 HCV RNA from patient plasma. Optimization of HCV RNA isolation, cDNA synthesis, and nested PCR steps were performed. The optimization of HCV RNA isolation, design of RT-PCR primers, optimization of RT-PCR amplification conditions and reagents, and the evaluation of the RT-PCR method performance is described.
  
  
  RESULTS
  The optimized method is able to successfully, accurately, and reproducibly amplify near full-length genotype 1 HCV RNA containing a wide range of concentrations (103 to 108 IU/mL) with a success rate of 97%. The lower limit of detection was determined to be 1000 IU/mL HCV RNA.
  
  
  CONCLUSIONS
  This assay allows viral sequencing of all regions targeted by the most common DAAs currently in development, as well as the possibility to determine linkage between variants conferring resistance to multiple DAAs used in combination therapy.
authors: Vertex Pharmaceuticals Incorporated, 130 Waverly Street, Cambridge, MA 02139-4242, USA.
authors: Eileen Z
authors: EZ
authors: Zhang
authors: Doug J
authors: DJ
authors: Bartels
authors: J Dan
authors: JD
authors: Frantz
authors: Sheila
authors: S
authors: Seepersaud
authors: Judith A
authors: JA
authors: Lippke
authors: Benjamin
authors: B
authors: Shames
authors: Yi
authors: Y
authors: Zhou
authors: Chao
authors: C
authors: Lin
authors: Ann
authors: A
authors: Kwong
authors: Tara L
authors: TL
authors: Kieffer
mesh_terms: D000998:Antiviral Agents / Q000627:therapeutic use; D024882:Drug Resistance, Viral; D016679:Genome, Viral; D005838:Genotype; D016174:Hepacivirus / Q000235:genetics* / Q000302:isolation & purification; D006526:Hepatitis C / Q000188:drug therapy / Q000821:virology; D006801:Humans; D008967:Molecular Biology / Q000379:methods*; D009154:Mutation; D010949:Plasma / Q000821:virology; D016133:Polymerase Chain Reaction / Q000379:methods*; D012367:RNA, Viral / Q000235:genetics* / Q000302:isolation & purification; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D014773:Virology / Q000379:methods*
chemical_list: D000998:Antiviral Agents; D012367:RNA, Viral
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