A Development of Rapid Whole-Genome Sequencing of Seoul orthohantavirus Using a Portable One-Step Amplicon-Based High Accuracy Nanopore System

Kyungmin Park, Juyoung Noh, Kijin Kim, Jongwoo Kim, Hee Kyung Cho, Seong Gyu Kim, Eunyoung Yang, Won Keun Kim, Jin Won Song

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)


Whole-genome sequencing provides a robust platform for investigating the epidemiology and transmission of emerging viruses. Oxford Nanopore Technologies allows for real-time viral sequencing on a local laptop system for point-of-care testing. Seoul orthohantavirus (Seoul virus, SEOV), harbored by Rattus norvegicus and R. rattus, causes mild hemorrhagic fever with renal syndrome and poses an important threat to public health worldwide. We evaluated the deployable MinION system to obtain high-fidelity entire-length sequences of SEOV for the genome identification of accurate infectious sources and their genetic diversity. One-step amplicon-based nanopore sequencing was performed from SEOV 80–39 specimens with different viral copy numbers and SEOV-positive wild rats. The KU-ONT-SEOV-consensus module was developed to analyze SEOV genomic sequences generated from the nanopore system. Using amplicon-based nanopore sequencing and the KU-ONT-consensus pipeline, we demonstrated novel molecular diagnostics for acquiring full-length SEOV genome sequences, with sufficient read depth in less than 6 h. The consensus sequence accuracy of the SEOV small, medium, and large genomes showed 99.75–100% (for SEOV 80–39 isolate) and 99.62–99.89% (for SEOV-positive rats) identities. This study provides useful insights into on-site diagnostics based on nanopore technology and the genome epidemiology of orthohantaviruses for a quicker response to hantaviral outbreaks.

Original languageEnglish
Article number1542
Issue number7
Publication statusPublished - 2023 Jul

Bibliographical note

Funding Information:
This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIT) (2023R1A2C2006105), the Institute for Basic Science (IBS), Republic of Korea, under project code IBS-R801-D9-A03, and the Korea University. In addition, this study was funded by the Korea Institute of Marine Science and Technology Promotion (KIMST) fund by the Ministry of Oceans and Fisheries, Korea (20210466), and the Basic Research Program through the National Research Foundation of Korea (NRF) by the Ministry of Education (NRF-2021R1I1A2049607).

Publisher Copyright:
© 2023 by the authors.


  • molecular diagnosis
  • nanopore sequencing
  • portable diagnosis
  • Seoul virus
  • whole-genome sequencing

ASJC Scopus subject areas

  • Infectious Diseases
  • Virology


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