SARS-CoV-2 variant spike and accessory gene mutations alter pathogenesis

To examine the effects of accessory protein mutations and other non-spike mutations on SARS-CoV-2 pathogenesis, we synthesized viruses possessing deletions in the accessory genes as well as viruses where the WA-1 spike is replaced by each variant spike gene in a SARS-CoV-2/WA-1 infectious clone, and compared replication and transcriptional responses to WA-1 and SARS-CoV-2 variants.