Wish to share something that has captured my attention, and that i am trying to dissect
Let me summarize the origin of the graph below
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a) NCBI sequences for sars cov 2 were obtained, which were grouped monthly by sample collection date. approximately 50,000 sequences per month
.b) the s2m were aligned and harvested, with no more clustering than the month of sample collection
c) 1529 polymorphic forms were detected (they were classified and named based on the mutations observed in the 41 nt)
d) it was determined the frequency (percentage for each one of them) and now I am trying to calculate the mutation rate and its cataloging as transversion or transition.
e) of the 1,528 polymorphisms, three present higher frequencies, which are graphed below
F) s2m represents the sequence ancestral for SARS COV 2, which suffers a population swept, but regains fixation again. s2m 15 G to T is the product of a transversion, a polymorphism that achieved fixation in the months of July 2021 to December 2021 s2m 7 to 33 del is a polymorphism that reached fixation in May 2022. It is initially present (January 2020 to May 2020) but its frequency does not seem to take off. https://pubs.acs.org/doi/10.1021/acsomega.2c05245
G) s2m was considered a conserved region and even a possible target for miRNA therapies. even a miRNA 1307 3p showed some complementarity. What is interesting is that the 15 G to T mutation caused a reduction in complementarity-
- DOI: 10.1261/rna.079627.123
H) interesting but not yet well studied the interaction between the N protein and s2m (in its GAGUA stem loop) and the intervention of hydroxychloroquine. doi: 10.1017/qrd.2021.12
I) is there any mutation on N that made the new s2m 7 32 del viable. the frequency of it was detected earlier, but became "successful" since may 2022 ist i hitchhiking or actual improvement on the viral adaptation t doi: https://doi.org/10.1101/2022.12.21.521431 ( Mechanism of LLPS of SARS-CoV-2 N protein)
how to learn more from this observation is this a case of Selection/adaptation or a Neutral theory of evolution? Seeing a dramatic shift tells is selection still needs to be read an learned about Please any direction or ideas are welcome
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