Multiplex pcr-based nanopore sequencing and epidemiological surveillance of hantaan orthohantavirus in apodemus agrarius, republic of korea

Kyungmin Park; Seung Ho Lee; Jongwoo Kim; Jingyeong Lee; Geum Young Lee; Seungchan Cho; Seung Ho Lee; Kkothanahreum Park; Jin Sun No; Shailesh Budhathoki; Yu Jin Kim; Young Su Kim; Heung Chul Kim; Terry A. Klein; Won Keun Kim; Jin Won Song

doi:10.3390/v13050847

Multiplex pcr-based nanopore sequencing and epidemiological surveillance of hantaan orthohantavirus in apodemus agrarius, republic of korea

Kyungmin Park, Seung Ho Lee, Jongwoo Kim, Jingyeong Lee, Geum Young Lee, Seungchan Cho, Seung Ho Lee, Kkothanahreum Park, Jin Sun No, Shailesh Budhathoki, Yu Jin Kim, Young Su Kim, Heung Chul Kim, Terry A. Klein, Won Keun Kim, Jin Won Song

Department of Biomedical Sciences

Research output: Contribution to journal › Article › peer-review

7 Citations (Scopus)

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 world-wide. 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.

Original language	English
Article number	847
Journal	Viruses
Volume	13
Issue number	5
DOIs	https://doi.org/10.3390/v13050847
Publication status	Published - 2021 May

Bibliographical note

Funding Information:
Funding: This study was supported by the Research Program to Solve Social Issues of the National Research Foundation of Korea (NRF) funded by the Ministry of Science and Information and Communication Technology (ICT; NRF-2017M3A9E4061992) and the Agency for Defense Development (UE202026GD). Partial funding was provided by the Research Program to Solve Social Issues of the NRF funded by the Ministry of Science and ICT (NRF-2019R1I1A2A01060902); the Armed Forces Health Surveillance Branch, Global Emerging Infections Surveillance and Response System (AFHSB-GEIS); Silver Spring, MD (ProMIS ID #P0025-2016-2018-ME); and the 65th Medical Brigade, Camp Humphreys, Republic of Korea.

Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Keywords

Amplicon-based NGS
Genetic diversity
Hantaan virus (HTNV)
Hemorrhagic fever with renal syndrome (HFRS)
MinION sequencing
Next-generation sequencing (NGS)
Phylogenetic analysis
Viral genome surveillance
Whole-genome sequencing

ASJC Scopus subject areas

Infectious Diseases
Virology

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.3390/v13050847

Cite this

Park, K., Lee, S. H., Kim, J., Lee, J., Lee, G. Y., Cho, S., Lee, S. H., Park, K., No, J. S., Budhathoki, S., Kim, Y. J., Kim, Y. S., Kim, H. C., Klein, T. A., Kim, W. K., & Song, J. W. (2021). Multiplex pcr-based nanopore sequencing and epidemiological surveillance of hantaan orthohantavirus in apodemus agrarius, republic of korea. Viruses, 13(5), Article 847. https://doi.org/10.3390/v13050847

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title = "Multiplex pcr-based nanopore sequencing and epidemiological surveillance of hantaan orthohantavirus in apodemus agrarius, republic of korea",

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 world-wide. 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.",

keywords = "Amplicon-based NGS, Genetic diversity, Hantaan virus (HTNV), Hemorrhagic fever with renal syndrome (HFRS), MinION sequencing, Next-generation sequencing (NGS), Phylogenetic analysis, Viral genome surveillance, Whole-genome sequencing",

author = "Kyungmin Park and Lee, {Seung Ho} and Jongwoo Kim and Jingyeong Lee and Lee, {Geum Young} and Seungchan Cho and Lee, {Seung Ho} and Kkothanahreum Park and No, {Jin Sun} and Shailesh Budhathoki and Kim, {Yu Jin} and Kim, {Young Su} and Kim, {Heung Chul} and Klein, {Terry A.} and Kim, {Won Keun} and Song, {Jin Won}",

note = "Funding Information: Funding: This study was supported by the Research Program to Solve Social Issues of the National Research Foundation of Korea (NRF) funded by the Ministry of Science and Information and Communication Technology (ICT; NRF-2017M3A9E4061992) and the Agency for Defense Development (UE202026GD). Partial funding was provided by the Research Program to Solve Social Issues of the NRF funded by the Ministry of Science and ICT (NRF-2019R1I1A2A01060902); the Armed Forces Health Surveillance Branch, Global Emerging Infections Surveillance and Response System (AFHSB-GEIS); Silver Spring, MD (ProMIS ID #P0025-2016-2018-ME); and the 65th Medical Brigade, Camp Humphreys, Republic of Korea. Publisher Copyright: {\textcopyright} 2021 by the authors. Licensee MDPI, Basel, Switzerland.",

year = "2021",

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doi = "10.3390/v13050847",

language = "English",

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journal = "Viruses",

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AU - Park, Kyungmin

AU - Lee, Seung Ho

AU - Kim, Jongwoo

AU - Lee, Jingyeong

AU - Lee, Geum Young

AU - Cho, Seungchan

AU - Lee, Seung Ho

AU - Park, Kkothanahreum

AU - No, Jin Sun

AU - Budhathoki, Shailesh

AU - Kim, Yu Jin

AU - Kim, Young Su

AU - Kim, Heung Chul

AU - Klein, Terry A.

AU - Kim, Won Keun

AU - Song, Jin Won

N1 - Funding Information: Funding: This study was supported by the Research Program to Solve Social Issues of the National Research Foundation of Korea (NRF) funded by the Ministry of Science and Information and Communication Technology (ICT; NRF-2017M3A9E4061992) and the Agency for Defense Development (UE202026GD). Partial funding was provided by the Research Program to Solve Social Issues of the NRF funded by the Ministry of Science and ICT (NRF-2019R1I1A2A01060902); the Armed Forces Health Surveillance Branch, Global Emerging Infections Surveillance and Response System (AFHSB-GEIS); Silver Spring, MD (ProMIS ID #P0025-2016-2018-ME); and the 65th Medical Brigade, Camp Humphreys, Republic of Korea. Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

PY - 2021/5

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N2 - 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 world-wide. 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.

AB - 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 world-wide. 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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KW - Phylogenetic analysis

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Multiplex pcr-based nanopore sequencing and epidemiological surveillance of hantaan orthohantavirus in apodemus agrarius, republic of korea

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

UN SDGs

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