Whole-genome sequencing and genetic diversity of severe fever with thrombocytopenia syndrome virus using multiplex PCR-based nanopore sequencing, Republic of Korea

Jingyeong Lee; Kyungmin Park; Jongwoo Kim; Seung Ho Lee; Geum Young Lee; Seungchan Cho; Heung Chul Kim; Terry A. Klein; Jeong Ah Kim; Jeewan Choi; Juwan Park; Dong Hyun Song; Se Hun Gu; Hyeongseok Yun; Jung Eun Kim; Daesang Lee; Gyeung Haeng Hur; Seong Tae Jeong; Il Ung Hwang; Won Keun Kim; Jin Won Song

doi:10.1371/JOURNAL.PNTD.0010763

Whole-genome sequencing and genetic diversity of severe fever with thrombocytopenia syndrome virus using multiplex PCR-based nanopore sequencing, Republic of Korea

Jingyeong Lee, Kyungmin Park, Jongwoo Kim, Seung Ho Lee, Geum Young Lee, Seungchan Cho, Heung Chul Kim, Terry A. Klein, Jeong Ah Kim, Jeewan Choi, Juwan Park, Dong Hyun Song, Se Hun Gu, Hyeongseok Yun, Jung Eun Kim, Daesang Lee, Gyeung Haeng Hur, Seong Tae Jeong, Il Ung Hwang, Won Keun KimJin Won Song

Department of Biomedical Sciences

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

1 Citation (Scopus)

Abstract

Background Whole-genome sequencing plays a critical role in the genomic epidemiology intended to improve understanding the spread of emerging viruses. Dabie bandavirus, causing severe fever with thrombocytopenia syndrome (SFTS), is a zoonotic tick-borne virus that poses a significant public health threat. We aimed to evaluate a novel amplicon-based nanopore sequencing tool to obtain whole-genome sequences of Dabie bandavirus, also known as SFTS virus (SFTSV), and investigate the molecular prevalence in wild ticks, Republic of Korea (ROK). Principal findings A total of 6,593 ticks were collected from Gyeonggi and Gangwon Provinces, ROK in 2019 and 2020. Quantitative polymerase chain reaction revealed the presence of SFSTV RNA in three Haemaphysalis longicornis ticks. Two SFTSV strains were isolated from H. longicornis captured from Pocheon and Cheorwon. Multiplex polymerase chain reaction-based nano-pore sequencing provided nearly full-length tripartite genome sequences of SFTSV within one hour running. Phylogenetic and reassortment analyses were performed to infer evolutionary relationships among SFTSVs. Phylogenetic analysis grouped SFTSV Hl19-31-4 and Hl19-31-13 from Pocheon with sub-genotype B-1 in all segments. SFTSV Hl20-8 was found to be a genomic organization compatible with B-1 (for L segment) and B-2 (for M and S seg-ments) sub-genotypes, indicating a natural reassortment between sub-genotypes. Conclusion/Significance Amplicon-based next-generation sequencing is a robust tool for whole-genome sequencing of SFTSV using the nanopore platform. The molecular prevalence and geographical distribution of SFTSV enhanced the phylogeographic map at high resolution for sophisticated prevention of emerging SFTS in endemic areas. Our findings provide important insights into the rapid whole-genome sequencing and genetic diversity for the genome-based diagnosis of SFTSV in the endemic outbreak.

Original language	English
Article number	e0010763
Journal	PLoS Neglected Tropical Diseases
Volume	16
Issue number	9
DOIs	https://doi.org/10.1371/JOURNAL.PNTD.0010763
Publication status	Published - 2022

Bibliographical note

Funding Information:
This study was supported by the Agency for Defense Development (UE202026GD to J.-W. S.) and the Institute for Basic Science Korea (IBS-R801-D92022-a03 to J.-W.S.). In addition, this research was supported by Basic Research Program through the National ResearchFoundation of Korea (NRF) funded by the Ministry of Education (NRF-2021R1I1A2049607 to W.-K. K.). Partial funding was provided by the Armed Forces Health Surveillance Branch, Global Emerging Infections Surveillance and Response System (AFHSB-GEIS); Silver Spring, MD (ProMIS ID #P0025-2016-2018-ME to T.A.K.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Publisher Copyright:
© 2022 Lee et al.

ASJC Scopus subject areas

Public Health, Environmental and Occupational Health
Infectious Diseases

UN SDGs

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

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10.1371/JOURNAL.PNTD.0010763

Cite this

Lee, J., Park, K., Kim, J., Lee, S. H., Lee, G. Y., Cho, S., Kim, H. C., Klein, T. A., Kim, J. A., Choi, J., Park, J., Song, D. H., Gu, S. H., Yun, H., Kim, J. E., Lee, D., Hur, G. H., Jeong, S. T., Hwang, I. U., ... Song, J. W. (2022). Whole-genome sequencing and genetic diversity of severe fever with thrombocytopenia syndrome virus using multiplex PCR-based nanopore sequencing, Republic of Korea. PLoS Neglected Tropical Diseases, 16(9), Article e0010763. https://doi.org/10.1371/JOURNAL.PNTD.0010763

Lee, J, Park, K, Kim, J, Lee, SH, Lee, GY, Cho, S, Kim, HC, Klein, TA, Kim, JA, Choi, J, Park, J, Song, DH, Gu, SH, Yun, H, Kim, JE, Lee, D, Hur, GH, Jeong, ST, Hwang, IU, Kim, WK & Song, JW 2022, 'Whole-genome sequencing and genetic diversity of severe fever with thrombocytopenia syndrome virus using multiplex PCR-based nanopore sequencing, Republic of Korea', PLoS Neglected Tropical Diseases, vol. 16, no. 9, e0010763. https://doi.org/10.1371/JOURNAL.PNTD.0010763

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title = "Whole-genome sequencing and genetic diversity of severe fever with thrombocytopenia syndrome virus using multiplex PCR-based nanopore sequencing, Republic of Korea",

abstract = "Background Whole-genome sequencing plays a critical role in the genomic epidemiology intended to improve understanding the spread of emerging viruses. Dabie bandavirus, causing severe fever with thrombocytopenia syndrome (SFTS), is a zoonotic tick-borne virus that poses a significant public health threat. We aimed to evaluate a novel amplicon-based nanopore sequencing tool to obtain whole-genome sequences of Dabie bandavirus, also known as SFTS virus (SFTSV), and investigate the molecular prevalence in wild ticks, Republic of Korea (ROK). Principal findings A total of 6,593 ticks were collected from Gyeonggi and Gangwon Provinces, ROK in 2019 and 2020. Quantitative polymerase chain reaction revealed the presence of SFSTV RNA in three Haemaphysalis longicornis ticks. Two SFTSV strains were isolated from H. longicornis captured from Pocheon and Cheorwon. Multiplex polymerase chain reaction-based nano-pore sequencing provided nearly full-length tripartite genome sequences of SFTSV within one hour running. Phylogenetic and reassortment analyses were performed to infer evolutionary relationships among SFTSVs. Phylogenetic analysis grouped SFTSV Hl19-31-4 and Hl19-31-13 from Pocheon with sub-genotype B-1 in all segments. SFTSV Hl20-8 was found to be a genomic organization compatible with B-1 (for L segment) and B-2 (for M and S seg-ments) sub-genotypes, indicating a natural reassortment between sub-genotypes. Conclusion/Significance Amplicon-based next-generation sequencing is a robust tool for whole-genome sequencing of SFTSV using the nanopore platform. The molecular prevalence and geographical distribution of SFTSV enhanced the phylogeographic map at high resolution for sophisticated prevention of emerging SFTS in endemic areas. Our findings provide important insights into the rapid whole-genome sequencing and genetic diversity for the genome-based diagnosis of SFTSV in the endemic outbreak.",

author = "Jingyeong Lee and Kyungmin Park and Jongwoo Kim and Lee, {Seung Ho} and Lee, {Geum Young} and Seungchan Cho and Kim, {Heung Chul} and Klein, {Terry A.} and Kim, {Jeong Ah} and Jeewan Choi and Juwan Park and Song, {Dong Hyun} and Gu, {Se Hun} and Hyeongseok Yun and Kim, {Jung Eun} and Daesang Lee and Hur, {Gyeung Haeng} and Jeong, {Seong Tae} and Hwang, {Il Ung} and Kim, {Won Keun} and Song, {Jin Won}",

note = "Funding Information: This study was supported by the Agency for Defense Development (UE202026GD to J.-W. S.) and the Institute for Basic Science Korea (IBS-R801-D92022-a03 to J.-W.S.). In addition, this research was supported by Basic Research Program through the National ResearchFoundation of Korea (NRF) funded by the Ministry of Education (NRF-2021R1I1A2049607 to W.-K. K.). Partial funding was provided by the Armed Forces Health Surveillance Branch, Global Emerging Infections Surveillance and Response System (AFHSB-GEIS); Silver Spring, MD (ProMIS ID #P0025-2016-2018-ME to T.A.K.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: {\textcopyright} 2022 Lee et al.",

year = "2022",

doi = "10.1371/JOURNAL.PNTD.0010763",

language = "English",

volume = "16",

journal = "PLoS Neglected Tropical Diseases",

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T1 - Whole-genome sequencing and genetic diversity of severe fever with thrombocytopenia syndrome virus using multiplex PCR-based nanopore sequencing, Republic of Korea

AU - Lee, Jingyeong

AU - Park, Kyungmin

AU - Kim, Jongwoo

AU - Lee, Seung Ho

AU - Lee, Geum Young

AU - Cho, Seungchan

AU - Kim, Heung Chul

AU - Klein, Terry A.

AU - Kim, Jeong Ah

AU - Choi, Jeewan

AU - Park, Juwan

AU - Song, Dong Hyun

AU - Gu, Se Hun

AU - Yun, Hyeongseok

AU - Kim, Jung Eun

AU - Lee, Daesang

AU - Hur, Gyeung Haeng

AU - Jeong, Seong Tae

AU - Hwang, Il Ung

AU - Kim, Won Keun

AU - Song, Jin Won

N1 - Funding Information: This study was supported by the Agency for Defense Development (UE202026GD to J.-W. S.) and the Institute for Basic Science Korea (IBS-R801-D92022-a03 to J.-W.S.). In addition, this research was supported by Basic Research Program through the National ResearchFoundation of Korea (NRF) funded by the Ministry of Education (NRF-2021R1I1A2049607 to W.-K. K.). Partial funding was provided by the Armed Forces Health Surveillance Branch, Global Emerging Infections Surveillance and Response System (AFHSB-GEIS); Silver Spring, MD (ProMIS ID #P0025-2016-2018-ME to T.A.K.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: © 2022 Lee et al.

PY - 2022

Y1 - 2022

N2 - Background Whole-genome sequencing plays a critical role in the genomic epidemiology intended to improve understanding the spread of emerging viruses. Dabie bandavirus, causing severe fever with thrombocytopenia syndrome (SFTS), is a zoonotic tick-borne virus that poses a significant public health threat. We aimed to evaluate a novel amplicon-based nanopore sequencing tool to obtain whole-genome sequences of Dabie bandavirus, also known as SFTS virus (SFTSV), and investigate the molecular prevalence in wild ticks, Republic of Korea (ROK). Principal findings A total of 6,593 ticks were collected from Gyeonggi and Gangwon Provinces, ROK in 2019 and 2020. Quantitative polymerase chain reaction revealed the presence of SFSTV RNA in three Haemaphysalis longicornis ticks. Two SFTSV strains were isolated from H. longicornis captured from Pocheon and Cheorwon. Multiplex polymerase chain reaction-based nano-pore sequencing provided nearly full-length tripartite genome sequences of SFTSV within one hour running. Phylogenetic and reassortment analyses were performed to infer evolutionary relationships among SFTSVs. Phylogenetic analysis grouped SFTSV Hl19-31-4 and Hl19-31-13 from Pocheon with sub-genotype B-1 in all segments. SFTSV Hl20-8 was found to be a genomic organization compatible with B-1 (for L segment) and B-2 (for M and S seg-ments) sub-genotypes, indicating a natural reassortment between sub-genotypes. Conclusion/Significance Amplicon-based next-generation sequencing is a robust tool for whole-genome sequencing of SFTSV using the nanopore platform. The molecular prevalence and geographical distribution of SFTSV enhanced the phylogeographic map at high resolution for sophisticated prevention of emerging SFTS in endemic areas. Our findings provide important insights into the rapid whole-genome sequencing and genetic diversity for the genome-based diagnosis of SFTSV in the endemic outbreak.

AB - Background Whole-genome sequencing plays a critical role in the genomic epidemiology intended to improve understanding the spread of emerging viruses. Dabie bandavirus, causing severe fever with thrombocytopenia syndrome (SFTS), is a zoonotic tick-borne virus that poses a significant public health threat. We aimed to evaluate a novel amplicon-based nanopore sequencing tool to obtain whole-genome sequences of Dabie bandavirus, also known as SFTS virus (SFTSV), and investigate the molecular prevalence in wild ticks, Republic of Korea (ROK). Principal findings A total of 6,593 ticks were collected from Gyeonggi and Gangwon Provinces, ROK in 2019 and 2020. Quantitative polymerase chain reaction revealed the presence of SFSTV RNA in three Haemaphysalis longicornis ticks. Two SFTSV strains were isolated from H. longicornis captured from Pocheon and Cheorwon. Multiplex polymerase chain reaction-based nano-pore sequencing provided nearly full-length tripartite genome sequences of SFTSV within one hour running. Phylogenetic and reassortment analyses were performed to infer evolutionary relationships among SFTSVs. Phylogenetic analysis grouped SFTSV Hl19-31-4 and Hl19-31-13 from Pocheon with sub-genotype B-1 in all segments. SFTSV Hl20-8 was found to be a genomic organization compatible with B-1 (for L segment) and B-2 (for M and S seg-ments) sub-genotypes, indicating a natural reassortment between sub-genotypes. Conclusion/Significance Amplicon-based next-generation sequencing is a robust tool for whole-genome sequencing of SFTSV using the nanopore platform. The molecular prevalence and geographical distribution of SFTSV enhanced the phylogeographic map at high resolution for sophisticated prevention of emerging SFTS in endemic areas. Our findings provide important insights into the rapid whole-genome sequencing and genetic diversity for the genome-based diagnosis of SFTSV in the endemic outbreak.

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Whole-genome sequencing and genetic diversity of severe fever with thrombocytopenia syndrome virus using multiplex PCR-based nanopore sequencing, Republic of Korea

Abstract

Bibliographical note

ASJC Scopus subject areas

UN SDGs

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