Decoding SARS-CoV-2 coding capacity. Decoding SARS-CoV-2 coding capacity

SARS-CoV-2 is a coronavirus responsible for the COVID-19 pandemic. Although the SARS-CoV-2 trascriptome was reported recently, its coding capacity and the relative production of different viral proteins remained unclear. Utilizing a suit of ribosome profiling techniques, we present a high resolution map of the SARS-CoV-2 coding regions. Overall design: To capture the SARS-CoV-2 coding capacity, we applied a suits of ribosome profiling approaches to two types of infected cells, Vero 6 and Calu 3. The Vero 6 cells were infected for 5 and 24 hours with BavPat1/2020 EPI_ISL_406862, and the Calu 3 cells were infected for 7 hours with BavPat1/2020 Ref-SKU: 026V-03883. For each time point we mapped genome-wide translation events by preparing three different ribosome-profiling libraries. Two libraries facilitate mapping of translation initiation sites, by treating cells with lactimidomycin (LTM) or harringtonine (Harr), drugs that inhibit translation initiation, and the third library was prepared from cells treated with the translation elongation inhibitor cycloheximide (CHX). In parallel, we used a tailored RNA-seq protocol which on top of quantification of RNA levels allows identification of transcription start sites (TSSs).