Novel algorithm characterizes RNA motifs in SARS-CoV and SARS-CoV-2 SciReports Cambridge_Uni RNA SARSCoV2 SARSCoV virus virology
By Neha MathurAug 1 2023Reviewed by Sophia Coveney In a recent study published in Scientific Reports, researchers developed a novel algorithm to analyze large genomic datasets of ribonucleic acid viruses, applying it to severe acute respiratory syndrome coronavirus 2 and severe acute respiratory syndrome coronavirus .
Moreover, it was scale-agnostic in determining regions of nucleic acid conservation like its predecessors. It increased its ability to find previously unidentified features of interest, which might lack analogs in host organisms and therefore had reduced risk of toxicity as drug targets. SARS-CoV and SARS-CoV-2 have low overall inter-sequence variability. So, the researchers made three key improvements to their investigation protocol. First, they applied a weighting to each gene loci, with weights proportional to data on nucleotide conservation provided by a gene loci beyond that needed for amino acid conservation.
When they did not find the most conserved region in a sequence, researchers re-run the analysis after removing the next most conserved region as it likely was causing interference. They marked regions found to be significant after a re-analysis because the false positive rate for such genomic regions might be slightly higher.
They generated folds of a series of conserved regions with slightly different lengths from the identified conserved region. One stem-loop in the middle of the larger conserved region remained consistently predicted. So, they postulated that this stem-loop is a candidate for the RNA packaging signal in this region.
Note that the study protocol highlighted the presence of primer sites only within regions shorter than 250 nucleotides identified as conserved. So, a conserved region overlapping a primer binding site should be viewed as a possible contribution to observed conservation, not as a sole explanation.
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