IFNA1 and infection: We confirmed that viral stocks prepared in Caco-2 cells (the highest viral inoculum for each variant was 2,000 E copies per cell) did not contain measurable interferon (IFN)β and negligible IFNλ1/IFNλ3 (enzyme-linked immunosorbent assay, ELISA) (Extended Data Fig. 2a,b), ensuring differences in innate immune activation in Calu-3 infections were not a result of IFN carryover in the viral stocks.