Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates

Peculiar among human RNA viruses, coronaviruses have large genomes containing accessory genes that are not required for replication. Numerous mutations within the SARS-CoV-2 genome have been described but few deletions in the accessory genes of SARS-CoV-2 have been reported. Here, we report two large deletions in ORF7a, both of which produce new open reading frames (ORFs) through the fusion of the N-terminus of ORF7a and a downstream ORF.