Deciphering the initial steps of SARS-CoV2 infection in whole human lungs identifies macrophages as primary targets and reveals subset-specific responses.

Several in vitro models have been established to mimic the initial interaction between lung cell types and SARS-CoV-2, mainly using explant-based techniques that generated contrasted results about the cell types that were infected. These contrasting results could be due to biases in the various tissue-culture conditions. Furthermore, all these systems do not respect the spatial tissue architecture and the anatomic constraints that shape cell type interactions with viruses. In this study, we used whole human lungs maintained alive ex vivo for 10 h, based on a technique used in lung transplantation (ex vivo lung perfusion or EVLP), to analyze the first steps of SARS-CoV-2 infection in the lung. Five human donor lungs declined for transplantation were perfused and ventilated at 37°C and three of them were infected with SARS-CoV-2 using nebulization of the Wuhan lineage and D614G variants. Single-cell RNA-sequencing (scRNA-seq) using 10x Genomics 3' (v3 Chemistry) has been performed on these samples. Donor lungs used in this study were from donation after brain death and were determined to be unsuitable for transplantation. Donor lung retrieval was carried out according to current clinical practice. After transportation at 4°C, lungs were processed to EVLP, with or without virus nebulization. Lung biopsies were taken just before EVLP (0 h) and after 10 h EVLP, and analyzed using scRNAseq. *************************************************************** Submitter states that missing raw files are due to patient privacy concerns. ***************************************************************