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- Title
Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius , Republic of Korea.
- Authors
Park, Kyungmin; Lee, Seung-Ho; Kim, Jongwoo; Lee, Jingyeong; Lee, Geum-Young; Cho, Seungchan; Lee, Seung Ho; Park, Kkothanahreum; No, Jin Sun; Budhathoki, Shailesh; Kim, Yu-Jin; Kim, Young-Su; Kim, Heung-Chul; Klein, Terry A.; Kim, Won-Keun; Song, Jin-Won; Yoshimatsu, Kumiko; Kariwa, Hiroaki
- 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 worldwide. 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.
- Subjects
SOUTH Korea; HEMORRHAGIC fever with renal syndrome; APODEMUS; NUCLEOTIDE sequencing; GENETIC variation; MILITARY hospitals; PHARMACOGENOMICS
- Publication
Viruses (1999-4915), 2021, Vol 13, Issue 5, p847
- ISSN
1999-4915
- Publication type
Article
- DOI
10.3390/v13050847