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Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea

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 he...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8148566/
https://www.ncbi.nlm.nih.gov/pubmed/34066592
http://dx.doi.org/10.3390/v13050847
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author 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
author_facet 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
author_sort Park, Kyungmin
collection PubMed
description 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.
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spelling pubmed-81485662021-05-26 Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea 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 Viruses Article 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. MDPI 2021-05-06 /pmc/articles/PMC8148566/ /pubmed/34066592 http://dx.doi.org/10.3390/v13050847 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
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
Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea
title Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea
title_full Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea
title_fullStr Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea
title_full_unstemmed Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea
title_short Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea
title_sort multiplex pcr-based nanopore sequencing and epidemiological surveillance of hantaan orthohantavirus in apodemus agrarius, republic of korea
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8148566/
https://www.ncbi.nlm.nih.gov/pubmed/34066592
http://dx.doi.org/10.3390/v13050847
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