Fig. 2: Global RNA-seq and proteomics reveal innate immune suppression by Alpha.

a, Schematic of the experimental workflow. Calu-3 cells were infected with 5,000 E copies per cell of SARS-CoV-2 Alpha (red), early-lineage VIC (blue) or early-lineage IC19 (grey) or mock-infected (biological triplicates were performed for each time point). Phosphoproteomics and abundance proteomics analysis using a data-independent acquisition (DIA) and total RNA-seq were performed at 10 and 24 h. b, Unbiased pathway enrichment analysis. The −log₁₀(P) values were averaged for enrichments using Alpha/VIC and Alpha/IC19 at 10 and 24 hpi to rank terms. The top five terms are shown. Innate immune system terms are shown in bold. ECM, extracellular matrix; AMI, acute myocardial infarction. c, Heat map depicting the log₂-transformed fold change (log₂FC; colour) of ISGs²⁵ (by RNA-seq) comparing Alpha to VIC or IC19. Black outlines indicate P < 0.01. d, Box plots show log₂FC of ISGs between Alpha/VIC, Alpha/IC19 or IC19/VIC. Dots indicate different ISGs. Boxes indicate median (middle line) and interquartile range (upper and lower lines). Blue indicates comparisons with Alpha; black indicates comparisons between early-lineage viruses (IC19 and VIC). e, RT–qPCR analysis of bolded ISGs from c in cells infected with 2,000 E copies per cell. Mean ± s.e.m. f, Number of phosphorylation sites significantly dysregulated for Alpha, VIC or IC19 versus mock at an absolute log₂FC > 1 and adjusted P < 0.05. g, Kinase activities for the top enriched terms for the phosphoproteomics dataset ‘Reactome innate immune system’ (b, right). Two-tailed student’s t-test (d) or two-way ANOVA with Tukey’s multiple comparisons post-hoc test (e). Blue asterisks, Alpha versus VIC (blue bars); grey stars, Alpha versus IC19 (grey bars). *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001, or exact P value (d); NS, not significant.