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^*

^*Corresponding author for this work

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

93 Scopus citations

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.

Original language	English
Pages (from-to)	1457-1466
Number of pages	10
Journal	Emerging Microbes and Infections
Volume	9
Issue number	1
DOIs	https://doi.org/10.1080/22221751.2020.1782271
State	Published - 01 01 2020

Bibliographical note

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

Keywords

COVID-19
ORF8 deletion
Phylogeny
SARS-CoV-2
genome sequencing

UN SDGs

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

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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",

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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, vol. 9, no. 1, pp. 1457-1466. https://doi.org/10.1080/22221751.2020.1782271

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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

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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.

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KW - Phylogeny

KW - SARS-CoV-2

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DO - 10.1080/22221751.2020.1782271

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SN - 2222-1751

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IS - 1

ER -

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

Abstract

Bibliographical note

Keywords

UN SDGs

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