SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East

Yu Nong Gong; Kuo Chien Tsao; Mei Jen Hsiao; Chung Guei Huang; Peng Nien Huang; Po Wei Huang; Kuo Ming Lee; Yi Chun Liu; Shu Li Yang; Rei Lin Kuo; Kuan Fu Chen; Yen Chin Liu; Sheng Yu Huang; Hsing I. Huang; Ming Tsan Liu; Ji Rong Yang; Cheng Hsun Chiu; Cheng Ta Yang; Guang Wu Chen; Shin Ru Shih

doi:10.1080/22221751.2020.1782271

SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East

Yu Nong Gong, Kuo Chien Tsao, Mei Jen Hsiao, Chung Guei Huang, Peng Nien Huang, Po Wei Huang, Kuo Ming Lee, Yi Chun Liu, Shu Li Yang, Rei Lin Kuo, Kuan Fu Chen, Yen Chin Liu, Sheng Yu Huang, Hsing I. Huang, Ming Tsan Liu, Ji Rong Yang, Cheng Hsun Chiu, Cheng Ta Yang, Guang Wu Chen^*, Shin Ru Shih^*

^*此作品的通信作者

研究成果: 期刊稿件 › 文章 › 同行評審

93 引文斯高帕斯（Scopus）

摘要

Taiwan experienced two waves of imported infections with Coronavirus Disease 2019 (COVID-19). This study aimed at investigating the genomic variation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Taiwan and compared their evolutionary trajectories with the global strains. We performed culture and full-genome sequencing of SARS-CoV-2 strains followed by phylogenetic analysis. A 382-nucleotides deletion in open reading frame 8 (ORF8) was found in a Taiwanese strain isolated from a patient on February 4, 2020 who had a travel history to Wuhan. Patients in the first wave also included several sporadic, local transmission cases. Genomes of 5 strains sequenced from clustered infections were classified into a new clade with ORF1ab-V378I mutation, in addition to 3 dominant clades ORF8-L84S, ORF3a-G251V and S-D614G. This highlighted clade also included some strains isolated from patients who had a travel history to Turkey and Iran. The second wave mostly resulted from patients who had a travel history to Europe and Americas. All Taiwanese viruses were classified into various clades. Genomic surveillance of SARS-CoV-2 in Taiwan revealed a new ORF8-deletion mutant and a virus clade that may be associated with infections in the Middle East, which contributed to a better understanding of the global SARS-CoV-2 transmission dynamics.

原文	英語
頁（從 - 到）	1457-1466
頁數	10
期刊	Emerging Microbes and Infections
卷	9
發行號	1
DOIs	https://doi.org/10.1080/22221751.2020.1782271
出版狀態	已出版 - 01 01 2020

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© 2020, © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group, on behalf of Shanghai Shangyixun Cultural Communication Co., Ltd.

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10.1080/22221751.2020.1782271

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Gong, Y. N., Tsao, K. C., Hsiao, M. J., Huang, C. G., Huang, P. N., Huang, P. W., Lee, K. M., Liu, Y. C., Yang, S. L., Kuo, R. L., Chen, K. F., Liu, Y. C., Huang, S. Y., Huang, H. I., Liu, M. T., Yang, J. R., Chiu, C. H., Yang, C. T., Chen, G. W., & Shih, S. R. (2020). SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. Emerging Microbes and Infections, 9(1), 1457-1466. https://doi.org/10.1080/22221751.2020.1782271

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title = "SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East",

abstract = "Taiwan experienced two waves of imported infections with Coronavirus Disease 2019 (COVID-19). This study aimed at investigating the genomic variation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Taiwan and compared their evolutionary trajectories with the global strains. We performed culture and full-genome sequencing of SARS-CoV-2 strains followed by phylogenetic analysis. A 382-nucleotides deletion in open reading frame 8 (ORF8) was found in a Taiwanese strain isolated from a patient on February 4, 2020 who had a travel history to Wuhan. Patients in the first wave also included several sporadic, local transmission cases. Genomes of 5 strains sequenced from clustered infections were classified into a new clade with ORF1ab-V378I mutation, in addition to 3 dominant clades ORF8-L84S, ORF3a-G251V and S-D614G. This highlighted clade also included some strains isolated from patients who had a travel history to Turkey and Iran. The second wave mostly resulted from patients who had a travel history to Europe and Americas. All Taiwanese viruses were classified into various clades. Genomic surveillance of SARS-CoV-2 in Taiwan revealed a new ORF8-deletion mutant and a virus clade that may be associated with infections in the Middle East, which contributed to a better understanding of the global SARS-CoV-2 transmission dynamics.",

keywords = "COVID-19, ORF8 deletion, Phylogeny, SARS-CoV-2, genome sequencing",

author = "Gong, {Yu Nong} and Tsao, {Kuo Chien} and Hsiao, {Mei Jen} and Huang, {Chung Guei} and Huang, {Peng Nien} and Huang, {Po Wei} and Lee, {Kuo Ming} and Liu, {Yi Chun} and Yang, {Shu Li} and Kuo, {Rei Lin} and Chen, {Kuan Fu} and Liu, {Yen Chin} and Huang, {Sheng Yu} and Huang, {Hsing I.} and Liu, {Ming Tsan} and Yang, {Ji Rong} and Chiu, {Cheng Hsun} and Yang, {Cheng Ta} and Chen, {Guang Wu} and Shih, {Shin Ru}",

note = "Publisher Copyright: {\textcopyright} 2020, {\textcopyright} 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group, on behalf of Shanghai Shangyixun Cultural Communication Co., Ltd.",

year = "2020",

month = jan,

day = "1",

doi = "10.1080/22221751.2020.1782271",

language = "英语",

volume = "9",

pages = "1457--1466",

journal = "Emerging Microbes and Infections",

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Gong, YN, Tsao, KC, Hsiao, MJ, Huang, CG, Huang, PN, Huang, PW, Lee, KM, Liu, YC, Yang, SL, Kuo, RL, Chen, KF, Liu, YC , Huang, SY , Huang, HI, Liu, MT, Yang, JR, Chiu, CH, Yang, CT, Chen, GW & Shih, SR 2020, 'SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East', Emerging Microbes and Infections, 卷 9, 編號 1, 頁 1457-1466. https://doi.org/10.1080/22221751.2020.1782271

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T1 - SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East

AU - Gong, Yu Nong

AU - Tsao, Kuo Chien

AU - Hsiao, Mei Jen

AU - Huang, Chung Guei

AU - Huang, Peng Nien

AU - Huang, Po Wei

AU - Lee, Kuo Ming

AU - Liu, Yi Chun

AU - Yang, Shu Li

AU - Kuo, Rei Lin

AU - Chen, Kuan Fu

AU - Liu, Yen Chin

AU - Huang, Sheng Yu

AU - Huang, Hsing I.

AU - Liu, Ming Tsan

AU - Yang, Ji Rong

AU - Chiu, Cheng Hsun

AU - Yang, Cheng Ta

AU - Chen, Guang Wu

AU - Shih, Shin Ru

PY - 2020/1/1

Y1 - 2020/1/1

N2 - Taiwan experienced two waves of imported infections with Coronavirus Disease 2019 (COVID-19). This study aimed at investigating the genomic variation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Taiwan and compared their evolutionary trajectories with the global strains. We performed culture and full-genome sequencing of SARS-CoV-2 strains followed by phylogenetic analysis. A 382-nucleotides deletion in open reading frame 8 (ORF8) was found in a Taiwanese strain isolated from a patient on February 4, 2020 who had a travel history to Wuhan. Patients in the first wave also included several sporadic, local transmission cases. Genomes of 5 strains sequenced from clustered infections were classified into a new clade with ORF1ab-V378I mutation, in addition to 3 dominant clades ORF8-L84S, ORF3a-G251V and S-D614G. This highlighted clade also included some strains isolated from patients who had a travel history to Turkey and Iran. The second wave mostly resulted from patients who had a travel history to Europe and Americas. All Taiwanese viruses were classified into various clades. Genomic surveillance of SARS-CoV-2 in Taiwan revealed a new ORF8-deletion mutant and a virus clade that may be associated with infections in the Middle East, which contributed to a better understanding of the global SARS-CoV-2 transmission dynamics.

AB - Taiwan experienced two waves of imported infections with Coronavirus Disease 2019 (COVID-19). This study aimed at investigating the genomic variation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Taiwan and compared their evolutionary trajectories with the global strains. We performed culture and full-genome sequencing of SARS-CoV-2 strains followed by phylogenetic analysis. A 382-nucleotides deletion in open reading frame 8 (ORF8) was found in a Taiwanese strain isolated from a patient on February 4, 2020 who had a travel history to Wuhan. Patients in the first wave also included several sporadic, local transmission cases. Genomes of 5 strains sequenced from clustered infections were classified into a new clade with ORF1ab-V378I mutation, in addition to 3 dominant clades ORF8-L84S, ORF3a-G251V and S-D614G. This highlighted clade also included some strains isolated from patients who had a travel history to Turkey and Iran. The second wave mostly resulted from patients who had a travel history to Europe and Americas. All Taiwanese viruses were classified into various clades. Genomic surveillance of SARS-CoV-2 in Taiwan revealed a new ORF8-deletion mutant and a virus clade that may be associated with infections in the Middle East, which contributed to a better understanding of the global SARS-CoV-2 transmission dynamics.

KW - COVID-19

KW - ORF8 deletion

KW - Phylogeny

KW - SARS-CoV-2

KW - genome sequencing

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U2 - 10.1080/22221751.2020.1782271

DO - 10.1080/22221751.2020.1782271

M3 - 文章

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AN - SCOPUS:85087315164

SN - 2222-1751

VL - 9

SP - 1457

EP - 1466

JO - Emerging Microbes and Infections

JF - Emerging Microbes and Infections

IS - 1

ER -

SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East

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