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Kim J, Park K, Kim K, Noh J, Kim SG, Yang E, Cho HK, Lee SH, No JS, Lee GY, Lee D, Song DH, Gu SH, Park MS, Cho NH, Jeong ST, Kim WK, Song JW. High-resolution phylogeographical surveillance of Hantaan orthohantavirus using rapid amplicon-based Flongle sequencing, Republic of Korea. J Med Virol 2024; 96:e29346. [PMID: 38178580 DOI: 10.1002/jmv.29346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/04/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024]
Abstract
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.
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Affiliation(s)
- Jongwoo Kim
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kyungmin Park
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kijin Kim
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Juyoung Noh
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seong-Gyu Kim
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Eunyoung Yang
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hee-Kyung Cho
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seung-Ho Lee
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Jin Sun No
- Division of High-Risk Pathogens, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Geum-Young Lee
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Daesang Lee
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Dong-Hyun Song
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Se Hun Gu
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Nam-Hyuk Cho
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Seong Tae Jeong
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon, Republic of Korea
| | - Won-Keun Kim
- Department of Microbiology, Hallym University, Chuncheon, Republic of Korea
- Institute of Medical Research, Hallym University, Chuncheon, Republic of Korea
| | - Jin-Won Song
- Department of Microbiology, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Korea University College of Medicine, Seoul, Republic of Korea
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