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Request for clarification/insight on 2019-nCoV recombination question.
#2
So in researching this further on my own I came upon the following papers which have helped to clarify this for me somewhat:

This paper talks about how the likelihood of recombination of non-homologous RNA depends on sequence similarity of the inserts (and probably also their location): https://www.ncbi.nlm.nih.gov/pmc/article...3-0383.pdf

This one addresses the findings of the disputed paper linked in my original post, specifically noting that "all four insertions are located outside the Receptor Binding Domain (RBD) of spike" which, combined with the exceptionally small sequences of the inserts, seems to suggest it would be extremely unlikely for recombination of HIV-1 components to be inherited by 2019-nCoV in a way that would modify its receptor binding behavior: https://arxiv.org/ftp/arxiv/papers/2002/2002.03173.pdf

(There is also some knowledge about these sort of small inserts being mobile in the larger sequence, and it doesn't perform any in-depth analysis of potential convergence in the receptor region relative to an HIV-1 analog as to explore potential recombination scenarios, so there is still uncertainty here, at least for me.)

Finally this last link is to the above author's bioinformatics lab page on 2019-nCoV where you can explore the various structures of the virus, their known or predicted function (based on database matches of highly homologous analogs), with sequence strings and interactive 3D models: https://zhanglab.ccmb.med.umich.edu/C-I-...2019-nCov/
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RE: Request for clarification/insight on 2019-nCoV recombination question. - by Iapetus - 03-11-2020, 12:20 AM
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Request for clarification/insight on 2019-nCoV recombination question.00