Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 510000, China.
Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, 510000, China.
Curr Med Sci. 2021 Apr;41(2):228-235. doi: 10.1007/s11596-021-2340-3. Epub 2021 Apr 20.
Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) with unknown origin spread rapidly to 222 countries, areas or territories. To investigate the genomic evolution and variation in the early phase of COVID-19 pandemic in Guangdong, 60 specimens of SARS-CoV-2 were used to perform whole genome sequencing, and genomics, amino acid variation and Spike protein structure modeling analyses. Phylogenetic analysis suggested that the early variation in the SARS-CoV-2 genome was still intra-species, with no evolution to other coronaviruses. There were one to seven nucleotide variations (SNVs) in each genome and all SNVs were distributed in various fragments of the genome. The Spike protein bound with human receptor, an amino acid salt bridge and a potential furin cleavage site were found in the SARS-CoV-2 using molecular modeling. Our study clarified the characteristics of SARS-CoV-2 genomic evolution, variation and Spike protein structure in the early phase of local cases in Guangdong, which provided reference for generating prevention and control strategies and tracing the source of new outbreaks.
严重急性呼吸综合征冠状病毒 2（SARS-CoV-2），其来源不明，迅速传播至 222 个国家、地区或领土。为研究广东省 COVID-19 大流行早期 SARS-CoV-2 的基因组进化和变异情况，本研究使用 60 份 SARS-CoV-2 标本进行全基因组测序，并进行基因组学、氨基酸变异和 Spike 蛋白结构建模分析。系统进化分析表明，SARS-CoV-2 基因组的早期变异仍在种内，没有进化为其他冠状病毒。每个基因组中有 1 到 7 个核苷酸变异（SNV），所有的 SNV 都分布在基因组的不同片段中。利用分子建模发现，SARS-CoV-2 的 Spike 蛋白与人受体结合，形成一个氨基酸盐桥和一个潜在的弗林裂解位点。本研究阐明了广东省本地病例 SARS-CoV-2 基因组进化、变异和 Spike 蛋白结构的特征，为制定防控策略和追溯新疫情源头提供了参考。
