Identification of consensus hairpin loop structure among the negative sense subgenomic RNAs of SARS-CoV-2

BACKGROUND: SARS-CoV-2 is the causative agent of worldwide pandemic disease coronavirus disease 19. SARS-CoV-2 bears positive sense RNA genome that has organized and complex pattern of replication/transcription process including the generation of subgenomic RNAs. Transcription regulatory sequences have important role in the pausing of replication/transcription and generation of subgenomic RNAs. RESULTS: In the present bioinformatics analysis, a consensus secondary structure was identified among negative sense subgenomic RNAs of SARS-CoV-2. This consensus region is present at the adjacent of initiation codon. CONCLUSIONS: This study proposed that consensus structured domain could involve in mediating the long pausing of replication/transcription complex and responsible for subgenomic RNA production. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42269-023-01002-3.