Fig. 1

Transcriptome analysis of COVID-19 patients infected with KR-mutant and wild-type SARS-CoV-2. A Boxplot showing viral copy numbers (log10 transformed) of RG-patients and KR-patients (two-tailed t-test, KR-patients versus RG-patients, p-value < 0.0001 (****)). The copy numbers were calculated using standard curve from Ct values (RT-qPCR) of the N1 primer pairs after normalization with RNase P Ct values. Extracted RNA (by Direct-Zol kit, Zymo Research) was subjected to RT-qPCR using one-step TaqPath kit (Applied Biosystems) and nucleocapsid gene (N1) and RNAseP primers. B Plot showing the number of mild and severe cases in the RG and KR COVID-19 patient cohorts (severe = ICU/deceased and mild = not admitted to ICU). C PCA on transcriptome of nasopharyngeal samples from Healthy control, KR-Patients, and RG-Patients. PCA plot is based on all differentially expressed (DE) genes and autoscaling of data was used. D Tree shows hierarchical clustering between samples (Healthy control, KR-Patients, and RG-Patients) based on the expression level of cytokine and interferon stimulated (ISG) genes. The sample names are colored according to the group. The majority of KR-patients samples clustered together as shown in shaded. E Volcano plot showing significant (adj p-value < 0.05 and log2 fold-change cutoff ≥ 1.5) differentially expressed (DE) genes comparing KR-Patients versus Healthy controls (KR-vs-H) and RG-Patients versus Healthy controls (RG-vs-H) as determined by the method EdgeR. Genes with significant up-regulation are shown in red and down-regulated are shown in blue. All other non-significant genes are shown in gray. F Heatmap shows normalized expression of top significantly differentially expressed genes in KR-patient versus Healthy controls (KR-vs-H) (adj p-value < 0.05 and log2 fold-change ≥ 1.5). KR-Patients (n = 39), RG-Patients (n = 39), and Healthy controls (n = 34). The sample names represent COVID-19 disease status (severe, mild, and healthy) as in B. The heatmap was generated by the visualization module in the ExpressAnalyst