Journal
EMERGING MICROBES & INFECTIONS
Volume 9, Issue 1, Pages 1457-1466Publisher
TAYLOR & FRANCIS LTD
DOI: 10.1080/22221751.2020.1782271
Keywords
COVID-19; SARS-CoV-2; genome sequencing; Phylogeny; ORF8 deletion
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Funding
- Research Center for Emerging Viral Infections from The Featured Areas Research Center Program within the framework of the Higher Education Sprout Project by the Ministry of Education (MOE) in Taiwan
- Ministry of Science and Technology (MOST), Taiwan [MOST 109-2634-F-182-001, MOST 107-2221-E-182-064-MY2, MOST 106-2320-B-182A-013-MY3]
- Linkou Chang Gung Memorial Hospital Taiwan [CLRPG3B0048, CMRPD1H0231-3]
- Johns Hopkins CEIRS, United States [HHSN272201400007C]
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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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