While some genes were either constitutively expressed or mildly responding to the infection (for example, HSP90AA1 and YY1), many were broadly activated upon infection and/or enriched in the ‘highly infected clusters’ (for example, GADD45B, BCL2L11, NFΚBIA, CDKN1A and BNIP3), whereas others were subject to more cell-type-specific changes (for example, CD83, CDKN1A, PLK3 and E2F3) (Supplementary Data Fig. 3a). Here, CDKN1A is linked to infection.