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

被引：84

作者：

Gong, Yu-Nong ^{[1
,2
]}

Tsao, Kuo-Chien ^{[1
,2
,3
]}

Hsiao, Mei-Jen ^{[2
]}

Huang, Chung-Guei ^{[2
,3
]}

Huang, Peng-Nien ^{[1
,4
]}

Huang, Po-Wei ^{[2
]}

Lee, Kuo-Ming ^{[1
]}

Liu, Yi-Chun ^{[2
]}

Yang, Shu-Li ^{[2
,3
]}

Kuo, Rei-Lin ^{[1
,3
,5
,6
]}

Chen, Kuan-Fu ^{[7
,8
,9
]}

Liu, Yen-Chin ^{[1
]}

Huang, Sheng-Yu ^{[1
]}

Huang, Hsing-I. ^{[1
,3
,5
,10
]}

Liu, Ming-Tsan ^{[11
]}

Yang, Ji-Rong ^{[11
]}

Chiu, Cheng-Hsun ^{[12
,13
]}

Yang, Cheng-Ta ^{[14
,15
]}

Chen, Guang-Wu ^{[1
,2
,16
]}

Shih, Shin-Ru ^{[1
,2
,3
,17
,18
]}

机构：

[1] Chang Gung Univ, Coll Med, Res Ctr Emerging Viral Infect, 259,Wenhua 1st Rd, Taoyuan, Taiwan

[2] Linkou Chang Gung Mem Hosp, Dept Lab Med, Taoyuan, Taiwan

[3] Chang Gung Univ, Coll Med, Dept Med Biotechnol & Lab Sci, Taoyuan, Taiwan

[4] Linkou Chang Gung Mem Hosp, Dept Pediat, Div Infect Dis, Taoyuan, Taiwan

[5] Chang Gung Univ, Grad Inst Biomed Sci, Coll Med, Taoyuan, Taiwan

[6] Linkou Chang Gung Mem Hosp, Dept Pediat, Div Asthma Allergy & Rheumatol, Taoyuan, Taiwan

[7] Chang Gung Mem Hosp, Dept Emergency Med, Keelung, Taiwan

[8] Chang Gung Univ, Clin Informat & Med Stat Res Ctr, Taoyuan, Taiwan

[9] Chang Gung Mem Hosp, Community Med Res Ctr, Keelung, Taiwan

[10] Linkou Chang Gung Mem Hosp, Dept Pediat, Taoyuan, Taiwan

[11] Ctr Dis Control, Taipei, Taiwan

[12] Chang Gung Univ, Chang Gung Mem Hosp, Dept Pediat, Div Pediat Infect Dis,Coll Med, Taoyuan, Taiwan

[13] Chang Gung Univ, Chang Gung Mem Hosp, Mol Infect Dis Res Ctr, Coll Med, Taoyuan, Taiwan

[14] Chang Gung Univ, Coll Med, Dept Resp Therapy, Taoyuan, Taiwan

[15] Linkou Chang Gung Mem Hosp, Dept Thorac Med, Taoyuan, Taiwan

[16] Chang Gung Univ, Sch Elect & Comp Engn, Coll Engn, Dept Comp Sci & Informat Engn, Taoyuan, Taiwan

[17] Chang Gung Univ Sci & Technol, Res Ctr Chinese Herbal Med, Res Ctr Food & Cosmet Safety, Coll Human Ecol, Taoyuan, Taiwan

[18] Chang Gung Univ Sci & Technol, Grad Inst Hlth Ind Technol, Coll Human Ecol, Taoyuan, Taiwan

来源：

EMERGING MICROBES & INFECTIONS | 2020年 / 9卷 / 01期

关键词：

COVID-19; SARS-CoV-2; genome sequencing; Phylogeny; ORF8; deletion; CORONAVIRUS; IDENTIFICATION; REPLICATION; SEQUENCE; FIDELITY;

D O I：

10.1080/22221751.2020.1782271

中图分类号：

R392 [医学免疫学]; Q939.91 [免疫学];

学科分类号：

100102 ;

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.

引用

页码：1457 / 1466

页数：10

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