Study investigates long-range RNA-RNA interactions of SARS-CoV-2 IJMS_MDPI IUPUI colgateuniv RNA SARSCoV2 COVID19 coronavirus covid
By Pooja Toshniwal PahariaSep 26 2022Reviewed by Danielle Ellis, B.Sc. In a recent study published in the International Journal of Molecular Sciences, researchers explored RRIs [long-range ribonucleic acid -RNA interactions] in severe acute respiratory syndrome coronavirus 2 variants of concern genomes to assess evolutionary changes in SARS-CoV-2.
SARS-CoV-2 genome sequences of the Alpha VOC, Beta VOC, Delta VOC and Omicron VOC, originating from 92 different nations, were downloaded from the GISAID database. Eight long-range Orf1a and/or Orf1b RRIs were selected for the analysis, four of which were experimentally validated and obtained from the COMRADES experiment and the remaining four were obtained from computational predictions using the IntaRNA software.
In the eight long-span RRIs, no stem-loops or pseudoknots were observed. To improve understanding of how SARS-CoV-2 RRIs are conserved, irrespective of VOC, the average number of mutations per base for the sequences were compared for all eight RRIs. In addition, the mutations were categorized as compensatory or non-compensatory based on RNA base pair accommodation.Download a copy today
However, statistical R-scape analyses did not show significant co-variations for any RRI, and there was no significance for the top five hits using the SHAPE constraint. No evidence was found for the co-evolution of the two regions of an RRI within the sequences. Omicron, the most recent VOC, showed the greatest sequence divergence and the highest mutational rate , and Delta showed the lowest mutational rate .
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