PMID- 30050759
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20201001
IS  - 2215-0161 (Print)
IS  - 2215-0161 (Electronic)
IS  - 2215-0161 (Linking)
VI  - 5
DP  - 2018
TI  - Genotyping of hepatitis C virus by nucleotide sequencing: A robust method for a 
      diagnostic laboratory.
PG  - 414-418
LID - 10.1016/j.mex.2018.04.005 [doi]
AB  - Hepatitis C virus (HCV) is a globally significant blood-borne agent causing liver 
      diseases, and it has infected over 170 million people worldwide. HCV is a diverse 
      group of RNA viruses currently divided into genotypes 1-7 as well as subtypes. 
      HCV infection can be treated with antiviral drugs, but the HCV genotype has to be 
      determined for optimal selection of treatment strategy. The aim of this study was 
      to set up a sequencing-based HCV genotyping method suitable for the workflow of a 
      diagnostic laboratory. The established method is robust and stable, and it 
      utilizes a one-step reverse transcription and PCR amplification of the 5' 
      untranslated region (5'UTR) and partial Core region of the HCV genome. 
      Amplification products are sequenced using the standard Sanger method, and the 
      genotype is determined by using a freely accessible web-based genotyping tool. 
      The method was validated at the Helsinki University Hospital Laboratory using 238 
      previously genotyped serum samples. *A new one-step RT-PCR method for the 
      amplification of the 5' untranslated region and partial Core region of hepatitis 
      C virus was established.*HCV genotype is determined using Sanger sequencing and a 
      freely accessible, easy-to-use web-based genotyping tool.*The method is robust, 
      reproducible and suitable for diagnostic laboratory workflow, and it requires no 
      costly instrumentation or specialized sequence analysis skills.
FAU - Virtanen, Elina
AU  - Virtanen E
AD  - Department of Virology, University of Helsinki and Helsinki University Hospital 
      Laboratory, Helsinki, Finland.
FAU - Mannonen, Laura
AU  - Mannonen L
AD  - Department of Virology, University of Helsinki and Helsinki University Hospital 
      Laboratory, Helsinki, Finland.
FAU - Lappalainen, Maija
AU  - Lappalainen M
AD  - Department of Virology, University of Helsinki and Helsinki University Hospital 
      Laboratory, Helsinki, Finland.
FAU - Auvinen, Eeva
AU  - Auvinen E
AD  - Department of Virology, University of Helsinki and Helsinki University Hospital 
      Laboratory, Helsinki, Finland.
LA  - eng
PT  - Journal Article
DEP - 20180416
PL  - Netherlands
TA  - MethodsX
JT  - MethodsX
JID - 101639829
PMC - PMC6060086
OTO - NOTNLM
OT  - 5'UTR
OT  - Amplification
OT  - Genotype
OT  - HCV
OT  - HCV genotyping
OT  - HCV, hepatitis C virus
OT  - LiPA, line probe assay
OT  - PCR
OT  - PCR, polymerase chain reaction
OT  - RT, reverse transcription
OT  - Sanger
OT  - UTR, untranslated region
EDAT- 2018/07/28 06:00
MHDA- 2018/07/28 06:01
PMCR- 2018/04/16
CRDT- 2018/07/28 06:00
PHST- 2017/08/04 00:00 [received]
PHST- 2018/04/09 00:00 [accepted]
PHST- 2018/07/28 06:00 [entrez]
PHST- 2018/07/28 06:00 [pubmed]
PHST- 2018/07/28 06:01 [medline]
PHST- 2018/04/16 00:00 [pmc-release]
AID - S2215-0161(18)30058-X [pii]
AID - 10.1016/j.mex.2018.04.005 [doi]
PST - epublish
SO  - MethodsX. 2018 Apr 16;5:414-418. doi: 10.1016/j.mex.2018.04.005. eCollection 
      2018.