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

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.

中国台湾地区曾出现两波新型冠状病毒肺炎（Coronavirus Disease 2019, COVID-19）输入性疫情。本研究旨在探究中国台湾地区分离的严重急性呼吸综合征冠状病毒2（severe acute respiratory syndrome coronavirus 2, SARS-CoV-2）的基因组变异特征，并将其进化轨迹与全球毒株进行对比。
研究团队对SARS-CoV-2毒株开展病毒培养及全基因组测序，并进行系统发育分析。2020年2月4日，研究人员从一名有武汉旅行史的患者体内分离得到一株中国台湾地区毒株，该毒株的开放阅读框8（open reading frame 8, ORF8）区域存在一段382个核苷酸的缺失。第一波疫情的感染者还包含多例散发性本地传播病例。
从聚集性感染病例中测序获得的5株病毒基因组，除被归入ORF8-L84S、ORF3a-G251V及S-D614G这3个优势进化分支外，还被归类为一个携带ORF1ab-V378I突变的全新进化分支。该受关注的进化分支同时涵盖部分从有土耳其、伊朗旅行史的患者体内分离得到的毒株。
第二波疫情主要由有欧洲及美洲旅行史的感染者引发。所有中国台湾地区分离的SARS-CoV-2毒株均被划分至不同的进化分支中。对中国台湾地区SARS-CoV-2的基因组监测工作，发现了一株携带ORF8缺失的突变毒株，以及一个可能与中东地区感染相关的病毒进化分支，该研究成果有助于深化对全球SARS-CoV-2传播动态的认知。