Epithelial cells were computationally identified from scRNA-Seq from samples of tissue consisting of granuloma and adjacent, uninvolved lung samples from 10 Mtb-infected NHPs were collected with Seq-Well S^3. Here we show Type 1 Pneumocytes, Type 2 Pneumocytes, Secretory, and Multiciliated subsets of these single cells to facilitate inquiry into the susceptibility of these cells to respiratory viruses, specifically COVID-19. We find that Type 2 Pneumocytes are enriched for cells that co-express the COVID-19 receptor (ACE2) and associated protease (TMPRSS2) and these cells are more frequently found in samples from granulomatous regions of the lung.

Note that since this is a pre-publication dataset, we only include cell types which express ACE2 and metadata relevant to this inquiry. The full dataset will be released at a later date.

Analysis of this data to evaluate expression of COVID-19 receptor ACE2 and protease TMPRSS2 are described in the following manuscript: https://www.cell.com/cell/fulltext/S0092-8674(20)30500-6

And summarized here: http://shaleklab.com/resource/covid-19-resources/

Contributors (listed alphabetically): JoAnne L. Flynn, Sarah M. Fortune, Hannah P. Gideon, Travis K. Hughes, Philana Ling Lin, Sarah K. Nyquist, Alex K. Shalek, Marc H. Wadsworth, Caylin G. Winchell