Journal Article

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

Lee, Kuo-Ming, Huang, Peng-Nien, Yang, Cheng-Ta, Liu, Yen-Chin, Huang, Chung-Guei, Kuo, Rei-Lin, Shih, Shin-Ru, Chen, Kuan-Fu, Hsiao, Mei-Jen, Chiu, Cheng-Hsun, Yang, Shu-Li, Huang, Po-Wei, Huang, Hsing-I., Tsao, Kuo-Chien, Liu, Yi-Chun, Gong, Yu-Nong, Huang, Sheng-Yu, Liu, Ming-Tsan, Yang, Ji-Rong, Chen, Guang-Wu

2020

Overview

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.

• Publisher: Taylor & Francis,Taylor & Francis Ltd,Taylor & Francis Group
• Subject: Animals / Betacoronavirus - classification / Betacoronavirus - genetics / Betacoronavirus - isolation & purification / Cell Line / Chlorocebus aethiops / Coronavirus Infections - virology / Coronaviruses / COVID-19 / Disease transmission / genome sequencing / Genome, Viral / Haemophilus parainfluenzae - isolation & purification / Humans / Infections / Middle East / Open Reading Frames / ORF8 deletion / Pandemics / Phylogeny / Pneumonia, Viral - virology / RNA, Viral / SARS-CoV-2 / Sequence Deletion / Severe acute respiratory syndrome coronavirus 2 / Taiwan / Travel / Vero Cells / Virus Cultivation / Whole Genome Sequencing