Table 1:

Availability of data analyzed in this paper.

Sample	Methods	Data shown in	DOI	GEO accession
Lung autopsy samples from COVID-19 patients	Bulk RNA sequencing; RNA-ISH	Fig. 3a	https://doi.org/10.1038/s41467-020-20139-7	GSE150316
Self-collected saliva, anterior nares swab, and oropharyngeal swab samples from individuals enrolled in a COVID-19 household transmission study	Bulk RNA sequencing with viral surveillance panel enrichment (Illumina Cat. 20040536 and 20088154); RT-qPCR	Fig. 3a	https://doi.org/10.1128/spectrum.03873-22 https://doi.ore/10.1093/pnasnexus/pead033	Raw sequencing data is not publicly available per participant privacy practices
SARS-CoV-2 infected human iPSC derived cardiomyocytes	SMART-Seq V4	Fig. 3a	https://doi.org/10.1016/j.xcrm.2020.100052	GSM4548303
Blood samples from rhesus macaques infected with Zaire ebolavirus	Seq-Well S3; RT-qPCR	Fig. 2–8; Extended Data Fig. 1–9	https://doi.org/10.1016/j.cell.2020.10.002	GSE158390
Lungs from APOE knock-in mice infected with SARS-CoV-2	SPLiT-Seq (Parse Biosciences)	Extended Data Fig. 4c	https://doi.org/10.1038/s41586-022-05344-2	GSM5974202