Cluster 5, which represented a small number of genes downregulated from baseline after infection (e.g. IRAK3, MRC1, MYC, APP, and PPARG) and may indicate a loss of alveolar macrophages, which has been previously described for SARS-CoV-2 infection (Figs 3A and S3) [2]. This evidence concerns the gene IRAK3 and infection.