Hepatitis C virus genotyping methods

Evaluation of amplisens® HCV-1/2/3-FRT compared to sequencing method

Nurul Azmawati Mohamed, Noor Zetti Zainol Rashid, Wong Kon Ken

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Background: Hepatitis C virus (HCV) genotyping is important for treatment and epidemiological purposes. The objective of this study was to evaluate the performance of AmpliSens® HCV-1/2/3-FRT kit in comparison to sequencing method for genotyping. Methods: A total of 17 samples collected from December 2009 to January 2011 were analyzed. Reverse transcriptase polymerase chain reaction (PCR) was performed, followed by sequencing technique. Results were analyzed based on sequence information in GenBank. A second genotyping method (AmpliSens® HCV-1/2/3-FRT) was done, which differentiates HCV genotypes by means of real-time hybridization-fluorescence detection. Results: From 17 samples, four were untypeable by AmpliSens® HCV-1/2/3-FRT. Eleven of 13 (84.6%) results showed concordant genotypes. A specimen that was determined as genotype 3a by sequencing was genotype 1 by the AmpliSens® HCV-1/2/3-FRT. Another specimen that was genotype 1 by sequencing was identified as genotype 3 by AmpliSens® HCV-1/2/3-FRT. Conclusion: HCV genotyping with AmpliSens® HCV-1/2/3-FRT using real-time PCR method provides a much simpler and more feasible workflow with shorter time compared to sequencing method. There was good concordance compared to sequencing method. However, more evaluation studies would be required to show statistical significance, and to troubleshoot discordant results. AmpliSens® HCV-1/2/3-FRT does differentiate between genotype but not until subtype level.

Original languageEnglish
Pages (from-to)224-228
Number of pages5
JournalJournal of Clinical Laboratory Analysis
Volume28
Issue number3
DOIs
Publication statusPublished - 2014

Fingerprint

Viruses
Hepacivirus
Genotype
Polymerase chain reaction
Workflow
RNA-Directed DNA Polymerase
Nucleic Acid Databases
Reverse Transcriptase Polymerase Chain Reaction
Real-Time Polymerase Chain Reaction
Fluorescence

Keywords

  • AmpliSens® HCV-1/2/3-FRT
  • HCV genotype
  • HCV subtype
  • Real time
  • RT-PCR
  • Sequencing methods

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, medical
  • Public Health, Environmental and Occupational Health
  • Hematology
  • Immunology and Allergy
  • Microbiology (medical)
  • Medical Laboratory Technology
  • Medicine(all)

Cite this

@article{181b066a8e074d22b14169d654d61cf8,
title = "Hepatitis C virus genotyping methods: Evaluation of amplisens{\circledR} HCV-1/2/3-FRT compared to sequencing method",
abstract = "Background: Hepatitis C virus (HCV) genotyping is important for treatment and epidemiological purposes. The objective of this study was to evaluate the performance of AmpliSens{\circledR} HCV-1/2/3-FRT kit in comparison to sequencing method for genotyping. Methods: A total of 17 samples collected from December 2009 to January 2011 were analyzed. Reverse transcriptase polymerase chain reaction (PCR) was performed, followed by sequencing technique. Results were analyzed based on sequence information in GenBank. A second genotyping method (AmpliSens{\circledR} HCV-1/2/3-FRT) was done, which differentiates HCV genotypes by means of real-time hybridization-fluorescence detection. Results: From 17 samples, four were untypeable by AmpliSens{\circledR} HCV-1/2/3-FRT. Eleven of 13 (84.6{\%}) results showed concordant genotypes. A specimen that was determined as genotype 3a by sequencing was genotype 1 by the AmpliSens{\circledR} HCV-1/2/3-FRT. Another specimen that was genotype 1 by sequencing was identified as genotype 3 by AmpliSens{\circledR} HCV-1/2/3-FRT. Conclusion: HCV genotyping with AmpliSens{\circledR} HCV-1/2/3-FRT using real-time PCR method provides a much simpler and more feasible workflow with shorter time compared to sequencing method. There was good concordance compared to sequencing method. However, more evaluation studies would be required to show statistical significance, and to troubleshoot discordant results. AmpliSens{\circledR} HCV-1/2/3-FRT does differentiate between genotype but not until subtype level.",
keywords = "AmpliSens{\circledR} HCV-1/2/3-FRT, HCV genotype, HCV subtype, Real time, RT-PCR, Sequencing methods",
author = "Mohamed, {Nurul Azmawati} and {Zainol Rashid}, {Noor Zetti} and {Kon Ken}, Wong",
year = "2014",
doi = "10.1002/jcla.21670",
language = "English",
volume = "28",
pages = "224--228",
journal = "Journal of Clinical Laboratory Analysis",
issn = "0887-8013",
publisher = "Wiley-Liss Inc.",
number = "3",

}

TY - JOUR

T1 - Hepatitis C virus genotyping methods

T2 - Evaluation of amplisens® HCV-1/2/3-FRT compared to sequencing method

AU - Mohamed, Nurul Azmawati

AU - Zainol Rashid, Noor Zetti

AU - Kon Ken, Wong

PY - 2014

Y1 - 2014

N2 - Background: Hepatitis C virus (HCV) genotyping is important for treatment and epidemiological purposes. The objective of this study was to evaluate the performance of AmpliSens® HCV-1/2/3-FRT kit in comparison to sequencing method for genotyping. Methods: A total of 17 samples collected from December 2009 to January 2011 were analyzed. Reverse transcriptase polymerase chain reaction (PCR) was performed, followed by sequencing technique. Results were analyzed based on sequence information in GenBank. A second genotyping method (AmpliSens® HCV-1/2/3-FRT) was done, which differentiates HCV genotypes by means of real-time hybridization-fluorescence detection. Results: From 17 samples, four were untypeable by AmpliSens® HCV-1/2/3-FRT. Eleven of 13 (84.6%) results showed concordant genotypes. A specimen that was determined as genotype 3a by sequencing was genotype 1 by the AmpliSens® HCV-1/2/3-FRT. Another specimen that was genotype 1 by sequencing was identified as genotype 3 by AmpliSens® HCV-1/2/3-FRT. Conclusion: HCV genotyping with AmpliSens® HCV-1/2/3-FRT using real-time PCR method provides a much simpler and more feasible workflow with shorter time compared to sequencing method. There was good concordance compared to sequencing method. However, more evaluation studies would be required to show statistical significance, and to troubleshoot discordant results. AmpliSens® HCV-1/2/3-FRT does differentiate between genotype but not until subtype level.

AB - Background: Hepatitis C virus (HCV) genotyping is important for treatment and epidemiological purposes. The objective of this study was to evaluate the performance of AmpliSens® HCV-1/2/3-FRT kit in comparison to sequencing method for genotyping. Methods: A total of 17 samples collected from December 2009 to January 2011 were analyzed. Reverse transcriptase polymerase chain reaction (PCR) was performed, followed by sequencing technique. Results were analyzed based on sequence information in GenBank. A second genotyping method (AmpliSens® HCV-1/2/3-FRT) was done, which differentiates HCV genotypes by means of real-time hybridization-fluorescence detection. Results: From 17 samples, four were untypeable by AmpliSens® HCV-1/2/3-FRT. Eleven of 13 (84.6%) results showed concordant genotypes. A specimen that was determined as genotype 3a by sequencing was genotype 1 by the AmpliSens® HCV-1/2/3-FRT. Another specimen that was genotype 1 by sequencing was identified as genotype 3 by AmpliSens® HCV-1/2/3-FRT. Conclusion: HCV genotyping with AmpliSens® HCV-1/2/3-FRT using real-time PCR method provides a much simpler and more feasible workflow with shorter time compared to sequencing method. There was good concordance compared to sequencing method. However, more evaluation studies would be required to show statistical significance, and to troubleshoot discordant results. AmpliSens® HCV-1/2/3-FRT does differentiate between genotype but not until subtype level.

KW - AmpliSens® HCV-1/2/3-FRT

KW - HCV genotype

KW - HCV subtype

KW - Real time

KW - RT-PCR

KW - Sequencing methods

UR - http://www.scopus.com/inward/record.url?scp=84899621138&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84899621138&partnerID=8YFLogxK

U2 - 10.1002/jcla.21670

DO - 10.1002/jcla.21670

M3 - Article

VL - 28

SP - 224

EP - 228

JO - Journal of Clinical Laboratory Analysis

JF - Journal of Clinical Laboratory Analysis

SN - 0887-8013

IS - 3

ER -