library_construction_protocol: Human SAECs from one donor were infected with MERS-CoV at a moi 1. At 1 dpi cells were harvested and re-suspended into a single cell solution using TryplE digestion. The single cells were subsequently methanol fixed according to 10x Genomics demonstrated protocol “Methanol Fixation of Cells for Single Cell RNA Sequencing” and stored at -80°C until the day of the sequencing. Prior to loading the cells on the 10x Chromium chip, cells were rehydrated according to the same demonstrated protocol. Cells were filtered and counted. Library was performed at Single Cell Discoveries according to standard 10× Genomics 3' V3.1 chemistry protocol. In short, the cells were loaded on a 10x Genomics chip, and the chip was run on a Chromium controller to initiate GEM formation. Library preparation was performed, following standard 10x Genomics guidelines 3' v3.1, to generate Gene Expression (GEX) libraries. The resulting DNA libraries were paired-end sequenced on an Illumina Novaseq S4 with an Illumina 2×150 bp kit.