Heat inactivation of Nipah virus for downstream single cell RNA sequencing

Single-cell RNA sequencing (scRNA-seq) has aided greatly in the study of viruses to distinguish responses from infected versus bystander cells in complex systems. Many of these workstreams, however, are not directly compatible with the more stringent biosafety regulations of BSL-3 and BSL-4 laboratories. Here we show that TCL buffer (Qiagen), inactivates both Ebola virus (EBOV) and SARS-CoV-2, representative BSL-4 and BSL-3 viruses. We show that additional heat treatment was additionally sufficient to inactivate EBOV-containing samples, and had minimal effects on extracted RNA quality and downstream sequencing results. Overall design: Human induced pluripotent stem cell-derived alveolar epithelial type II cells were dissociated into single cells, FACS-sorted on live cells, and analyzed using scRNA-seq. After loading the cells onto the 10x Genomics chip, cDNA synthesis was performed with samples 2 and 3 undergoing an additional 60C heat step for 30 min. All 3 samples are frozen at -20C, and subsequently thawed, with Sample 3 thawed in 5% MicroChem Plus. All three samples were then processed for Illumina sequencing.