Identification of Hammerhead-variant ribozyme sequences in SARS-CoV-2

The SARS-CoV-2 RNA virus and variants, responsible for the COVID-19 pandemic has become endemic, raised a need for further understanding of the viral genome and biology. Despite vast research on SARS-CoV-2, no ribozymes have been found in the virus genome. Here we report the identification of 39 Hammerhead-variant ribozyme sequences (CoV-HHRz) in SARS-CoV-2. These sequences are highly conserved within SARS-CoV-2 variants but show large diversity among other coronaviruses. In vitro CoV-HHRz sequences possess the characteristics of typical ribozymes; cleavage is pH and ion dependent, although their activity is relatively low and Mn2+ is required for cleavage. The cleavage sites of four CoV-HHRz coincide with the breakpoint of expressed subgenomic RNA (sgRNAs) in SARS-CoV-2 transcriptome data suggesting in vivo activity. The CoV-HHRz are involved in processing sgRNAs for ORF7b, ORF 10 and ORF1ab nsp13 which are essential for viral packaging and life cycle.