Genotyping and Molecular Diagnosis of Hepatitis A Virus in Human Clinical Samples Using Multiplex PCR-Based Next-Generation Sequencing

Geum Young Lee, Won Keun Kim, Seungchan Cho, Kyungmin Park, Jongwoo Kim, Seung Ho Lee, Jingyeong Lee, Young-Sun Lee, Ji Hoon Kim, Kwan Soo Byun, Jin Won Song

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)


Hepatitis A virus (HAV) is a serious threat to public health worldwide. We used multiplex polymerase chain reaction (PCR)-based next-generation sequencing (NGS) to derive information on viral genetic diversity and conduct precise phylogenetic analysis. Four HAV genome sequences were obtained using multiplex PCR-based NGS. HAV whole-genome sequence of one sample was obtained by conventional Sanger sequencing. The HAV strains demonstrated a geographic cluster with sub-genotype IA strains in the Republic of Korea. The phylogenetic pattern of HAV viral protein (VP) 3 region showed no phylogenetic conflict between the whole-genome and partial-genome sequences. The VP3 region in serum and stool samples showed sensitive detection of HAV with differences of quantification that did not exceed <10 copies/µL than the consensus VP4 region using quantitative PCR (qPCR). In conclusion, multiplex PCR-based NGS was implemented to define HAV genotypes using nearly whole-genome sequences obtained directly from hepatitis A patients. The VP3 region might be a potential candidate for tracking the genotypic origin of emerging HAV outbreaks. VP3-specific qPCR was developed for the molecular diagnosis of HAV infection. This study may be useful to predict for the disease management and subsequent development of hepatitis A infection at high risk of severe illness.

Original languageEnglish
Article number100
Issue number1
Publication statusPublished - 2022 Jan

Bibliographical note

Funding Information:
Funding: This work was supported by the Institute of Biomedical Science and Food Safety (IBF) (K2108991). In addition, the research was a project titled “Diagnosis, treatment and control technology based on big data of infectious virus in the marine environment” funded by the Korea Institute of Marine Science & Technology Promotion (Ref. No. 21210466) of the Ministry of Oceans and Fisheries (MOF) of South Korea. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Publisher Copyright:
© 2022 by the authors. Licensee MDPI, Basel, Switzerland.


  • Genotypic analysis
  • Hepatitis A virus
  • Multiplex polymerase chain reaction
  • Next-generation sequencing
  • Phylogenetic analysis

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)
  • Virology


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