Fig. 1: BA.5 displays enhanced innate immune antagonism during infection of airway epithelial cells.

a–g, Calu-3 infection with 2,000 E copies per cell of Delta (yellow, Ο), BA.1 (blue, Ο), BA.2 (blue, Δ), BA.4 (purple, O) and BA.5 (purple, Δ), n = 3: mean viral E copies at 2 h.p.i. across three independent experiments (a); viral replication over time measured by RT–qPCR for intracellular E copies per microgram RNA (b); infection levels measured by nucleocapsid expression (% N+ by flow cytometry) (c); expression of IFNB, CXCL10, IFIT1, IFIT2, RSAD2, MX1, MX2 and DDX58 in infected cells over time (d); IFNβ (e) and CXCL10 (f) secretion from infected Calu-3 cells measured by ELISA at 48 h.p.i.; rescue of viral replication by JAK1-inhibitor ruxolitinib in Calu-3 cells at 48 h.p.i., where relative infection levels are shown across three independent experiments determined by E copies per microgram RNA normalized to the median infection level of the untreated control (g). h–k, Primary bronchial HAEs were infected with the indicated variants at 1,500 E copies per cell: viral replication measured by intracellular E copies at 72 h.p.i. (h) and viral release into apical washes over time (i), with three biological replicates shown; expression of IFNB, CXCL10, IFIT1, IFIT2, DDX58 and RSAD2 in HAEs at 72 h.p.i., with six biological replicates shown (j); intracellular viral E copies in HAEs in the presence or absence of 5 μM ruxolitinib at 72 h.p.i., with three biological replicates shown (k). For a, one-way analysis of variance (ANOVA) with Bonferroni post-test was used. n.s., not significant at P > 0.05 for all comparisons. For b–h and j, one-way ANOVA and Dunnett’s post-test were used. For i, two-way ANOVA with a Bonferroni post-test was used. For k, one-tailed unpaired Student’s t-test was used. Replicate measurements from one of three independent experiments. Fold change over mock is shown. Mean ± s.e.m. or individual datapoints are shown. h.p.i., hours post infection.

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