Multiplex pcr-based nanopore sequencing and epidemiological surveillance of hantaan orthohantavirus in apodemus agrarius, republic of korea

Kyungmin Park, Seung Ho Lee, Jongwoo Kim, Jingyeong Lee, Geum Young Lee, Seungchan Cho, Seung Ho Lee, Kkothanahreum Park, Jin Sun No, Shailesh Budhathoki, Yu Jin Kim, Young Su Kim, Heung Chul Kim, Terry A. Klein, Won Keun Kim, Jin Won Song

Research output: Contribution to journalArticlepeer-review

Abstract

Whole-genome sequencing of infectious agents enables the identification and characterization of emerging viruses. The MinION device is a portable sequencer that allows real-time sequencing in fields or hospitals. Hantaan orthohantavirus (Hantaan virus, HTNV), harbored by Apodemus agrarius, causes hemorrhagic fever with renal syndrome (HFRS) and poses a critical public health threat world-wide. In this study, we aimed to evaluate the feasibility of using nanopore sequencing for whole-genome sequencing of HTNV from samples having different viral copy numbers. Amplicon-based next-generation sequencing was performed in A. agrarius lung tissues collected from the Republic of Korea. Genomic sequences of HTNV were analyzed based on the viral RNA copy numbers. Amplicon-based nanopore sequencing provided nearly full-length genomic sequences of HTNV and showed sufficient read depth for phylogenetic analysis after 8 h of sequencing. The average identity of the HTNV genome sequences for the nanopore sequencer compared to those of generated from Illumina MiSeq revealed 99.8% (L and M segments) and 99.7% (S segment) identities, respectively. This study highlights the potential of the portable nanopore sequencer for rapid generation of accurate genomic sequences of HTNV for quicker decision making in point-of-care testing of HFRS patients during a hantavirus outbreak.

Original languageEnglish
Article number847
JournalViruses
Volume13
Issue number5
DOIs
Publication statusPublished - 2021 May

Keywords

  • Amplicon-based NGS
  • Genetic diversity
  • Hantaan virus (HTNV)
  • Hemorrhagic fever with renal syndrome (HFRS)
  • MinION sequencing
  • Next-generation sequencing (NGS)
  • Phylogenetic analysis
  • Viral genome surveillance
  • Whole-genome sequencing

ASJC Scopus subject areas

  • Infectious Diseases
  • Virology

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