tetano
Editor, Senior Moderator
Emerg Microbes Infect
. 2020 Jun 16;1-37.
doi: 10.1080/22221751.2020.1782271. Online ahead of print.
SARS-CoV-2 Genomic Surveillance in Taiwan Revealed Novel ORF8-deletion Mutant and Clade Possibly Associated With Infections in Middle East
Yu-Nong Gong[SUP] 1 2 [/SUP], Kuo-Chien Tsao[SUP] 1 2 3 [/SUP], Mei-Jen Hsiao[SUP] 2 [/SUP], Chung-Guei Huang[SUP] 2 3 [/SUP], Peng-Nien Huang[SUP] 1 4 [/SUP], Po-Wei Huang[SUP] 2 [/SUP], Kuo-Ming Lee[SUP] 1 [/SUP], Yi-Chun Liu[SUP] 2 [/SUP], Shu-Li Yang[SUP] 2 3 [/SUP], Rei-Lin Kuo[SUP] 1 3 5 6 [/SUP], Kuan-Fu Chen[SUP] 7 8 9 [/SUP], Yen-Chin Liu[SUP] 1 [/SUP], Sheng-Yu Huang[SUP] 1 [/SUP], Hsing-I Huang[SUP] 1 3 5 10 [/SUP], Ming-Tsan Liu[SUP] 11 [/SUP], Ji-Rong Yang[SUP] 11 [/SUP], Cheng-Hsun Chiu[SUP] 12 13 [/SUP], Cheng-Ta Yang[SUP] 14 15 [/SUP], Guang-Wu Chen[SUP] 1 2 16 [/SUP], Shin-Ru Shih[SUP] 1 2 3 17 [/SUP]
Affiliations
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; Genome Sequencing; ORF8 Deletion; Phylogeny; SARS-CoV-2.
. 2020 Jun 16;1-37.
doi: 10.1080/22221751.2020.1782271. Online ahead of print.
SARS-CoV-2 Genomic Surveillance in Taiwan Revealed Novel ORF8-deletion Mutant and Clade Possibly Associated With Infections in Middle East
Yu-Nong Gong[SUP] 1 2 [/SUP], Kuo-Chien Tsao[SUP] 1 2 3 [/SUP], Mei-Jen Hsiao[SUP] 2 [/SUP], Chung-Guei Huang[SUP] 2 3 [/SUP], Peng-Nien Huang[SUP] 1 4 [/SUP], Po-Wei Huang[SUP] 2 [/SUP], Kuo-Ming Lee[SUP] 1 [/SUP], Yi-Chun Liu[SUP] 2 [/SUP], Shu-Li Yang[SUP] 2 3 [/SUP], Rei-Lin Kuo[SUP] 1 3 5 6 [/SUP], Kuan-Fu Chen[SUP] 7 8 9 [/SUP], Yen-Chin Liu[SUP] 1 [/SUP], Sheng-Yu Huang[SUP] 1 [/SUP], Hsing-I Huang[SUP] 1 3 5 10 [/SUP], Ming-Tsan Liu[SUP] 11 [/SUP], Ji-Rong Yang[SUP] 11 [/SUP], Cheng-Hsun Chiu[SUP] 12 13 [/SUP], Cheng-Ta Yang[SUP] 14 15 [/SUP], Guang-Wu Chen[SUP] 1 2 16 [/SUP], Shin-Ru Shih[SUP] 1 2 3 17 [/SUP]
Affiliations
- PMID: 32543353
- DOI: 10.1080/22221751.2020.1782271
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; Genome Sequencing; ORF8 Deletion; Phylogeny; SARS-CoV-2.