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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

High-resolution HAV genotyping using amplicon-based NGS read mapping and quantification.

Huiping Chen1, Arthur Löve1, Brynja Ármannsdóttir1

  • 1Department of Microbiology, University Hospital of Iceland, Iceland.

Diagnostic Microbiology and Infectious Disease
|July 8, 2026
PubMed
Summary

Next-generation sequencing (NGS) precisely genotypes Hepatitis A virus (HAV), detecting mixed infections missed by Sanger sequencing. This method enhances molecular surveillance and outbreak investigations for public health.

Keywords:
GenotypingHAVMixed infectionNGSQCMDQuantification

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Area of Science:

  • Virology
  • Genetics
  • Molecular Epidemiology

Background:

  • High-resolution genotyping of Hepatitis A virus (HAV) is essential for effective molecular surveillance and outbreak investigations.
  • Conventional Sanger sequencing of the VP1/2A region is limited in its ability to accurately identify mixed HAV infections.

Purpose of the Study:

  • To develop and validate an amplicon-based next-generation sequencing (NGS) method for precise HAV genotyping.
  • To enhance the detection of mixed HAV infections.
  • To trace the geographical origin of clinical HAV samples using sequence data.

Main Methods:

  • An amplicon-based NGS workflow targeting the VP1/2A region of HAV was established.
  • The method was validated using Quality Control for Molecular Diagnostics (QCMD) samples and clinical HAV-positive samples.
  • NGS reads were mapped to reference HAV sequences for genotype quantification, with results compared to Sanger sequencing and nanopore sequencing.

Main Results:

  • The NGS method demonstrated 100% concordance with expected results for QCMD samples and successfully genotyped all clinical samples.
  • A mixed infection of HAV subgenotypes IA and IB was identified, which was undetectable by Sanger sequencing but confirmed by nanopore sequencing.
  • A localized outbreak of HAV subgenotype IA was detected in Iceland, and the probable origin of clinical samples was determined.

Conclusions:

  • Amplicon-based NGS provides a rapid, high-resolution approach for HAV genotyping.
  • This NGS method significantly improves the detection of mixed HAV infections compared to traditional Sanger sequencing.
  • The validated NGS method is suitable for routine diagnostic applications and epidemiological studies of Hepatitis A virus.