High-resolution phylogeographical surveillance of Hantaan orthohantavirus using rapid amplicon-based Flongle sequencing, Republic of Korea

Jongwoo Kim, Kyungmin Park, Kijin Kim, Juyoung Noh, Seong Gyu Kim, Eunyoung Yang, Hee Kyung Cho, Seung Ho Lee, Jin Sun No, Geum Young Lee, Daesang Lee, Dong Hyun Song, Se Hun Gu, Man Seong Park, Nam Hyuk Cho, Seong Tae Jeong, Won Keun Kim, Jin Won Song

Research output: Contribution to journalArticlepeer-review


Orthohantaviruses, etiological agents of hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome, pose a critical public health threat worldwide. Hantaan orthohantavirus (HTNV) outbreaks are particularly endemic in Gyeonggi Province in northern area of the Republic of Korea (ROK). Small mammals were collected from three regions in the Gyeonggi Province during 2017 and 2018. Serological and molecular prevalence of HTNV was 25/201 (12.4%) and 10/25 (40%), respectively. A novel nanopore-based diagnostic assay using a cost-efficient Flongle chip was developed to rapidly and sensitively detect HTNV infection in rodent specimens within 3 h. A rapid phylogeographical surveillance of HTNV at high-resolution phylogeny was established using the amplicon-based Flongle sequencing. In total, seven whole-genome sequences of HTNV were newly obtained from wild rodents collected in Paju-si (Gaekhyeon-ri) and Yeoncheon-gun (Hyeonga-ri and Wangnim-ri), Gyeonggi Province. Phylogenetic analyses revealed well-supported evolutionary divergence and genetic diversity, enhancing the resolution of the phylogeographic map of orthohantaviruses in the ROK. Incongruences in phylogenetic patterns were identified among HTNV tripartite genomes, suggesting differential evolution for each segment. These findings provide crucial insights into on-site diagnostics, genome-based surveillance, and the evolutionary dynamics of orthohantaviruses to mitigate hantaviral outbreaks in HFRS-endemic areas in the ROK.

Original languageEnglish
Article numbere29346
JournalJournal of Medical Virology
Issue number1
Publication statusPublished - 2024 Jan

Bibliographical note

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© 2024 Wiley Periodicals LLC.


  • Flongle sequencing
  • Hantaan orthohantavirus
  • evolutionary dynamics
  • hemorrhagic fever with renal syndrome
  • phylogeographical surveillance

ASJC Scopus subject areas

  • Infectious Diseases
  • Virology


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