Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein
Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein
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DOI：
10.1186/s13073-020-00763-0
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发表时间：
2020-07-28
期刊：
影响因子：
12.3
通讯作者：
Matthews, David A.
中科院分区：
文献类型：
--
作者：
Davidson, Andrew D.;Williamson, Maia Kavanagh;Matthews, David A.
背景SARS-CoV-2是近年来出现的一种严重影响全球人类健康的呼吸道病原体。我们想要快速描述这种新型冠状病毒的转录组、蛋白质组和磷蛋白质组图景，以提供对病毒基因组和蛋白质组潜力的基本描述。方法用RNA直接测序法测定SARS-CoV-2在Vero E6细胞中的转录组。使用最近开发的以ORF为中心的管道对病毒转录组进行分析。与此相结合，我们使用串联质谱仪研究了同一病毒感染细胞的蛋白质组和磷酸蛋白质组。结果我们的综合分析表明，病毒转录物(即亚基因组mRNAs)基本符合冠状病毒的预期转录模型。重要的是，在编码尖峰蛋白(S)糖蛋白的亚基因组mRNAs中检测到24nT的框内缺失，并被预测从S糖蛋白中移除了一个拟议的Furin裂解位点。串联质谱仪在病毒感染细胞中鉴定出500多个病毒多肽和44个磷酸肽，几乎覆盖了SARS-CoV-2基因组预测的所有编码蛋白，包括S糖蛋白缺失变体特有的多肽。结论在疫苗的主要靶点S糖蛋白的Furin裂解位点检测到一个明显可行的缺失，这表明该蛋白和其他区域的SARS-CoV-2蛋白可能很容易发生突变。在病毒进入或退出过程中，Furin位点引导S糖蛋白裂解成功能亚基，可能与该病毒的致病和人畜共患病密切相关。我们的数据强调，在用于研究、动物挑战模型和潜在临床样本的病毒库增长期间，应该仔细监测病毒基因组序列。这种变异可能会导致不同程度的毒力、发病率和死亡率。
Background SARS-CoV-2 is a recently emerged respiratory pathogen that has significantly impacted global human health. We wanted to rapidly characterise the transcriptomic, proteomic and phosphoproteomic landscape of this novel coronavirus to provide a fundamental description of the virus's genomic and proteomic potential. Methods We used direct RNA sequencing to determine the transcriptome of SARS-CoV-2 grown in Vero E6 cells which is widely used to propagate the novel coronavirus. The viral transcriptome was analysed using a recently developed ORF-centric pipeline. Allied to this, we used tandem mass spectrometry to investigate the proteome and phosphoproteome of the same virally infected cells. Results Our integrated analysis revealed that the viral transcripts (i.e. subgenomic mRNAs) generally fitted the expected transcription model for coronaviruses. Importantly, a 24 nt in-frame deletion was detected in over half of the subgenomic mRNAs encoding the spike (S) glycoprotein and was predicted to remove a proposed furin cleavage site from the S glycoprotein. Tandem mass spectrometry identified over 500 viral peptides and 44 phosphopeptides in virus-infected cells, covering almost all proteins predicted to be encoded by the SARS-CoV-2 genome, including peptides unique to the deleted variant of the S glycoprotein. Conclusions Detection of an apparently viable deletion in the furin cleavage site of the S glycoprotein, a leading vaccine target, shows that this and other regions of SARS-CoV-2 proteins may readily mutate. The furin site directs cleavage of the S glycoprotein into functional subunits during virus entry or exit and likely contributes strongly to the pathogenesis and zoonosis of this virus. Our data emphasises that the viral genome sequence should be carefully monitored during the growth of viral stocks for research, animal challenge models and, potentially, in clinical samples. Such variations may result in different levels of virulence, morbidity and mortality.