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2025 Vol.55, Issue 2 Preview Page

Original Article

Amplicon-based MinION Sequencing, Genomic Characterization, and Zoonotic Potential of Patient-derived Chikungunya Virus Imported from Thailand, Republic of Korea
Seonghyeon Lee1†
,
Seung Soon Lee2†
,
Bohyeon Kim1†
,
Haryo Seno Pangestu1
,
Augustine Natasha1
,
Jae Hwan Byun3
,
Jieun Park1
,
Sara Puspareni Prayitno1
,
Woan Lee3
,
Yeonsu Oh4
,
Kyu Sung Shin5*
,
Won-Keun Kim16*
1Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
2Division of Infectious Diseases, Department of Internal Medicine, Hallym University Chuncheon Sacred Heart Hospital, Hallym University College of Medicine, Chuncheon 24253, Republic of Korea
3Gangwon-do Institute of Health & Environment, Chuncheon 24203, Republic of Korea
4College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon 24341, Republic of Korea
5Department of Laboratory Medicine, Hallym University Chuncheon Sacred Heart Hospital, Hallym University College of Medicine, Chuncheon 24253, Republic of Korea
6Institute of Medical Research, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
*sjjajang@hallym.or.kr
*wkkim1061@hallym.ac.kr
†These authors equally contributed to this work.
30 June 2025. pp. 120-130
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Abstract

Chikungunya virus (CHIKV), causing Chikungunya fever (CF), is transmitted by Aedes mosquitoes primarily in tropical regions. CHIKV infection poses a public health burden owing to international travel and climate change. Implementation of Next-generation sequencing (NGS) for whole-genome sequencing (WGS) contributes to the formulation of effective public health and travel medicine policies to mitigate emerging CHIKV in non-endemic areas. A patient with CF, who traveled to Thailand, was enrolled at Sacred Chuncheon Hospital (Chuncheon, Republic of Korea). Amplicon-based NGS was performed using the patient’s sera on days 2 and 6 after hospitalization. The nearly whole genome sequence of CHIKV was recovered from day 2 post-hospitalization, while only 9% on day 6. The phylogenetic inference demonstrated that the CHIKV genotype belonged to the East/Central/South African lineage. In addition, zoonotic potential was evaluated by the machine learning model. This study highlights the effectiveness of amplicon-based MinION sequencing derived from a patient who traveled from an endemic area. Collection of patient samples early in infection is strongly correlated with genomic acquisition and genotypic identification. Therefore, this study provides insight into the active surveillance for NGS-based genomic diagnosis and characterization of emerging CHIKV outbreak in endemic and non-endemic areas.

Keywords
Chikungunya virus
Amplicon-based nanopore sequencing
Phylogenetic analysis
Zoonotic potential
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Information
  • Publisher :The Korean Society for Microbiology and The Korean Society of Virology
  • Publisher(Ko) :대한미생물학회‧대한바이러스학회
  • Journal Title :JOURNAL OF BACTERIOLOGY AND VIROLOGY
  • Volume : 55
  • No :2
  • Pages :120-130
  • Received Date : 2025-03-27
  • Revised Date : 2025-05-30
  • Accepted Date : 2025-06-09
  • DOI :https://doi.org/10.4167/jbv.2025.55.2.120
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