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

Abstract

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
JournalMicroorganisms
Volume10
Issue number1
DOIs
Publication statusPublished - 2022 Jan

Keywords

  • 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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