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SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East.
Emerg Microbes Infect. 2020 Dec; 9(1):1457-1466.EM

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.

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Authors+Show Affiliations

Gong YN
Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan. Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.
Tsao KC
Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan. Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan. Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
Hsiao MJ
Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.
Huang CG
Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan. Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
Huang PN
Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan. Division of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.
Huang PW
Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.
Lee KM
Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
Liu YC
Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.
Yang SL
Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan. Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
Kuo RL
Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan. Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan. Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan. Division of Asthma, Allergy, and Rheumatology, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.
Chen KF
Department of Emergency Medicine, Chang Gung Memorial Hospital, Keelung, Taiwan. Clinical Informatics and Medical Statistics Research Center, Chang Gung University, Taoyuan, Taiwan. Community Medicine Research Center, Chang Gung Memorial Hospital, Keelung, Taiwan.
Liu YC
Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
Huang SY
Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
Huang HI
Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan. Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan. Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan. Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.
Liu MT
Centers for Disease Control, Taipei, Taiwan.
Yang JR
Centers for Disease Control, Taipei, Taiwan.
Chiu CH
Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan. Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan.
Yang CT
Department of Respiratory Therapy, College of Medicine, Chang Gung University, Taoyuan, Taiwan. Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.
Chen GW
Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan. Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan. Department of Computer Science and Information Engineering, School of Electrical and Computer Engineering, College of Engineering, Chang Gung University, Taoyuan, Taiwan.
Shih SR
Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan. Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan. Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan. Research Center for Chinese Herbal Medicine, Research Center for Food and Cosmetic Safety, and Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan.

MeSH

AnimalsBetacoronavirusCOVID-19Cell LineChlorocebus aethiopsCoronavirus InfectionsGenome, ViralHaemophilus parainfluenzaeHumansMiddle EastOpen Reading FramesPandemicsPhylogenyPneumonia, ViralRNA, ViralSARS-CoV-2Sequence DeletionTaiwanTravelVero CellsVirus CultivationWhole Genome Sequencing

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32543353

Citation

Gong, Yu-Nong, et al. "SARS-CoV-2 Genomic Surveillance in Taiwan Revealed Novel ORF8-deletion Mutant and Clade Possibly Associated With Infections in Middle East." Emerging Microbes & Infections, vol. 9, no. 1, 2020, pp. 1457-1466.
Gong YN, Tsao KC, Hsiao MJ, et al. SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. Emerg Microbes Infect. 2020;9(1):1457-1466.
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 & Infections, 9(1), 1457-1466. https://doi.org/10.1080/22221751.2020.1782271
Gong YN, et al. SARS-CoV-2 Genomic Surveillance in Taiwan Revealed Novel ORF8-deletion Mutant and Clade Possibly Associated With Infections in Middle East. Emerg Microbes Infect. 2020;9(1):1457-1466. PubMed PMID: 32543353.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR 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 - 2020/6/17/pubmed PY - 2020/7/14/medline PY - 2020/6/17/entrez KW - COVID-19 KW - ORF8 deletion KW - Phylogeny KW - SARS-CoV-2 KW - genome sequencing SP - 1457 EP - 1466 JF - Emerging microbes & infections JO - Emerg Microbes Infect VL - 9 IS - 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. SN - 2222-1751 UR - https://www.unboundmedicine.com/medline/citation/32543353/SARS_CoV_2_genomic_surveillance_in_Taiwan_revealed_novel_ORF8_deletion_mutant_and_clade_possibly_associated_with_infections_in_Middle_East_ DB - PRIME DP - Unbound Medicine ER -