Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea
DC Field | Value | Language |
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dc.contributor.author | Park, Kyungmin | - |
dc.contributor.author | Lee, Seung-Ho | - |
dc.contributor.author | Kim, Jongwoo | - |
dc.contributor.author | Lee, Jingyeong | - |
dc.contributor.author | Lee, Geum-Young | - |
dc.contributor.author | Cho, Seungchan | - |
dc.contributor.author | Lee, Seung Ho | - |
dc.contributor.author | Park, Kkothanahreum | - |
dc.contributor.author | No, Jin Sun | - |
dc.contributor.author | Budhathoki, Shailesh | - |
dc.contributor.author | Kim, Yu-Jin | - |
dc.contributor.author | Kim, Young-Su | - |
dc.contributor.author | Kim, Heung-Chul | - |
dc.contributor.author | Klein, Terry A. | - |
dc.contributor.author | Kim, Won-Keun | - |
dc.contributor.author | Song, Jin-Won | - |
dc.date.accessioned | 2021-11-21T01:41:10Z | - |
dc.date.available | 2021-11-21T01:41:10Z | - |
dc.date.created | 2021-08-30 | - |
dc.date.issued | 2021-05 | - |
dc.identifier.issn | 1999-4915 | - |
dc.identifier.uri | https://scholar.korea.ac.kr/handle/2021.sw.korea/128182 | - |
dc.description.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. | - |
dc.language | English | - |
dc.language.iso | en | - |
dc.publisher | MDPI | - |
dc.subject | HEMORRHAGIC-FEVER | - |
dc.subject | RENAL SYNDROME | - |
dc.subject | HANTAVIRUS INFECTION | - |
dc.subject | REAL-TIME | - |
dc.subject | VIRUS | - |
dc.subject | TRANSMISSION | - |
dc.subject | MINION | - |
dc.subject | GENOME | - |
dc.subject | RODENTS | - |
dc.subject | ORIGIN | - |
dc.title | Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea | - |
dc.type | Article | - |
dc.contributor.affiliatedAuthor | Song, Jin-Won | - |
dc.identifier.doi | 10.3390/v13050847 | - |
dc.identifier.scopusid | 2-s2.0-85106202004 | - |
dc.identifier.wosid | 000654615800001 | - |
dc.identifier.bibliographicCitation | VIRUSES-BASEL, v.13, no.5 | - |
dc.relation.isPartOf | VIRUSES-BASEL | - |
dc.citation.title | VIRUSES-BASEL | - |
dc.citation.volume | 13 | - |
dc.citation.number | 5 | - |
dc.type.rims | ART | - |
dc.type.docType | Article | - |
dc.description.journalClass | 1 | - |
dc.description.journalRegisteredClass | scie | - |
dc.description.journalRegisteredClass | scopus | - |
dc.relation.journalResearchArea | Virology | - |
dc.relation.journalWebOfScienceCategory | Virology | - |
dc.subject.keywordPlus | HEMORRHAGIC-FEVER | - |
dc.subject.keywordPlus | RENAL SYNDROME | - |
dc.subject.keywordPlus | HANTAVIRUS INFECTION | - |
dc.subject.keywordPlus | REAL-TIME | - |
dc.subject.keywordPlus | VIRUS | - |
dc.subject.keywordPlus | TRANSMISSION | - |
dc.subject.keywordPlus | MINION | - |
dc.subject.keywordPlus | GENOME | - |
dc.subject.keywordPlus | RODENTS | - |
dc.subject.keywordPlus | ORIGIN | - |
dc.subject.keywordAuthor | Hantaan virus (HTNV) | - |
dc.subject.keywordAuthor | hemorrhagic fever with renal syndrome (HFRS) | - |
dc.subject.keywordAuthor | next-generation sequencing (NGS) | - |
dc.subject.keywordAuthor | whole-genome sequencing | - |
dc.subject.keywordAuthor | amplicon-based NGS | - |
dc.subject.keywordAuthor | MinION sequencing | - |
dc.subject.keywordAuthor | phylogenetic analysis | - |
dc.subject.keywordAuthor | genetic diversity | - |
dc.subject.keywordAuthor | viral genome surveillance | - |
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