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

Abstract

Previous research investigation determined the abundance levels of subgenomic RNAs from the COVID-19 patient samples (Alexandersen et al. 2020). Authors mapped the NGS reads data to subgenomic RNAs in order to identify the abundance of particular subgenomic RNA from the patient samples (Alexandersen et al. 2020). NGS reads mapped results revealed that Orf7a and N subgenomic were in high abundance, whereas Orf8, Orf6, and E subgenomic were relatively low (in an increasing order). These subgenomic RNAs are present several fold higher in comparison with whole genome fragments. Therefore, the present study seek to identify the possible conserved regions nearby the TRS or initiation codon which could mediate significant roles in the generation or expression of subgenomic RNAs.