Table_4_Identification of a SARS-CoV-2 virus-derived vmiRNA in COVID-19 patients holding potential as a diagnostic biomarker.xlsx

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a lasting threat to public health. To minimize the viral spread, it is essential to develop more reliable approaches for early diagnosis of the infection and immediate suppression of the viral replication. Herein, through computational prediction of SARS-CoV-2 genome and screening analysis of specimens from covid-19 patients, we predicted 15 precursors for SARS-CoV-2-encoded miRNAs (CvmiRNAs) containing 20 mature CvmiRNAs, in which CvmiR-2 was successfully detected by quantitative analysis in both serum and nasal swab samples of patients. CvmiR-2 showed high specificity in distinguishing covid-19 patients from normal controls, and high conservation between SARS-CoV-2 and its mutants. A positive correlation was observed between the CvmiR-2 expression level and the severity of patients. The biogenesis and expression of CvmiR-2 were validated in the pre-CvmiR-2-transfected A549 cells, showing a dose-dependent pattern. The sequence of CvmiR-2 was validated by sequencing analysis of human cells infected by either SARS-CoV-2 or pre-CvmiR-2. Target gene prediction analysis suggested CvmiR-2 may be involved in the regulation of the immune response, muscle pain and/or neurological disorders in covid-19 patients. In conclusion, the current study identified a novel v-miRNA encoded by SARS-CoV-2 upon infection of human cells, which holds the potential to serve as a diagnostic biomarker or a therapeutic target in clinic.

严重急性呼吸综合征冠状病毒2（SARS-CoV-2）已对公共卫生构成长期威胁。为最大限度减少病毒传播，开发更可靠的感染早期诊断方法以及快速抑制病毒复制的手段至关重要。本研究通过对SARS-CoV-2基因组开展计算预测，并对新冠（COVID-19）患者的临床标本进行筛选分析，共预测得到15个SARS-CoV-2编码的微RNA前体，对应20条成熟的新冠病毒编码微RNA（CvmiRNAs）；其中CvmiR-2可通过定量分析在患者血清与鼻拭子样本中成功检出。CvmiR-2在区分新冠患者与正常对照人群时表现出极高的特异性，且在SARS-CoV-2及其突变株之间具有高度保守性。研究发现，CvmiR-2的表达水平与患者的病情严重程度呈正相关。本研究在转染了CvmiR-2前体的A549细胞中验证了CvmiR-2的生物发生与表达模式，其表达呈现剂量依赖性特征。通过对感染SARS-CoV-2或转染CvmiR-2前体的人源细胞进行测序分析，验证了CvmiR-2的序列正确性。靶基因预测分析显示，CvmiR-2可能参与调控新冠患者的免疫应答、肌肉疼痛及/或神经系统病症。综上，本研究鉴定出一种在SARS-CoV-2感染人源细胞后表达的新型病毒编码微RNA，其具备作为临床诊断生物标志物或治疗靶点的潜力。