ABSTRACT

The mutations in the SARS-CoV-2 virus genome during COVID-19 dissemination are unclear. In 788 COVID-19 patients from Zhejiang province, we observed decreased rate of severe/critical cases compared with patients in Wuhan. For mechanisms exploration, we isolated one strain of SARS-CoV-2 (ZJ01) from a mild COVID-19 patient. Thirty-five specific gene mutations were identified. Phylogenetic and relative synonymous codon usage analysis suggested that ZJ01 may be a potential evolutionary branch of SARS-CoV-2. We classified 54 global virus strains based on the base (C or T) at positions 8824 and 28247 while ZJ01 has T at both sites. The prediction of the Furin cleavage site (FCS) and sequence alignment indicated that the FCS may be an important site of coronavirus evolution. ZJ01 mutations identified near the FCS (F1-2) caused changes in the structure and electrostatic distribution of the S surface protein, further affecting the binding capacity of Furin. Single-cell sequencing and ACE2-Furin co-expression results confirmed that the Furin expression was especially higher in glands, liver, kidneys, and colon. The evolutionary pattern of SARS-CoV-2 towards FCS formation may result in its clinical symptom becoming closer to HKU-1 and OC43 caused mild flu-like symptoms, further showing its potential in differentiating into mild COVID-19 subtypes.

摘要

COVID-19 传播期间 SARS-CoV-2 病毒基因组的突变尚不清楚。在浙江省的 788 名 COVID-19 患者中，我们观察到与武汉患者相比，重症/危重症病例发生率有所下降。为了探索机制，我们从一名轻度 COVID-19 患者身上分离出了一种 SARS-CoV-2 (ZJ01) 毒株。鉴定出 35 个特定基因突变。系统发育和相对同义密码子使用分析表明，ZJ01 可能是 SARS-CoV-2 的潜在进化分支。我们根据 8824 和 28247 位点的碱基（C 或 T）对 54 个全球病毒株进行了分类，而 ZJ01 在这两个位点上都有 T。Furin裂解位点（FCS）的预测和序列比对表明FCS可能是冠状病毒进化的重要位点。在FCS（F1-2）附近发现的ZJ01突变导致S表面蛋白的结构和静电分布发生变化，进一步影响弗林蛋白酶的结合能力。单细胞测序和ACE2-Furin共表达结果证实，Furin在腺体、肝脏、肾脏和结肠中的表达尤其较高。SARS-CoV-2向FCS形成的进化模式可能导致其临床症状变得更接近HKU-1，而OC43则引起轻度流感样症状，进一步显示其分化为轻度COVID-19亚型的潜力。