3 ms·
there's a 23? bp sequence that is directly lifted from the moderna hiv vaccine patent (which preceded covid-19 by a decade). now an exact match of that length
by throwawaymaths 2y ago
there's a 23? bp sequence that is directly lifted from the moderna hiv vaccine patent (which preceded covid-19 by a decade).
now an exact match of that length isn't impossible, but which is more likely? that this managed to be exactly correct on accident? or some grad student was told to just copypasta every furin cleavage site in the database into a GOF library and surprise surprise the most virulent form that became a pandemic came from the sequence that is engineered to be efficient.
any scientist that has any molecular biology wet experience will tell you this is exactly what they would have done (though us researchers would probably not have pulled from the patented BLAST sequences, since that selector is turned off by default by the NCBI)
- cakealert 2y agoCan you estimate the entropy of the sequence? Maybe by walking to it from other known sequences?
- throwawaymaths 2y agorough estimate worse than 1 in 3^7 (based on # of wobble codons) but its even lower likelihood if you also allow AA variation in the universe of all furin cleavage sites
- nickburns 2y ago> there's a 23? bp sequence that is directly lifted from the moderna hiv vaccine patent (which preceded covid-19 by a decade). could you cite this? not because i'm questioning the statement's credibility, but because i'm curious (and you could save me a lot of time from even knowing where to begin to look for credible information for myself—full disclosure, lol).
- throwawaymaths 2y agosorry. it was 19bp Here. you can do it yourself. databases are public. CTCCTCGGCGGGCACGTAG
- nickburns 2y agooh, i counted your earlier post lol. thanks for posting all the above.
- 110bpm 2y agoI wanted to learn more about where this claim comes from and found this article [0]. The linked commentary [1] raises several interesting points. "Unfortunately, the authors did not provide details of their BLAST research. The patent database that they used contained 24,712 sequences. Yet, by querying BLAST, we obtained a database of 46,121,617 patent sequences with an average length of 560 nucleotides. The authors should give more details and justification for their query, especially if they queried the full database but a posteriori restricted their computation. Of note, with such a large database, and despite the fact that the average sequence length decreased, the probability of finding at least one sequence containing one of the 16 patterns previously mentioned may rise to 68% under assumption 2." 0: https://www.frontiersin.org/journals/virology/articles/10.3389/fviro.2022.834808/full https://www.frontiersin.org/journals/virology/articles/10.33... 1: https://www.frontiersin.org/journals/virology/articles/10.3389/fviro.2022.914888/full https://www.frontiersin.org/journals/virology/articles/10.33...
- throwawaymaths 2y agoFTA: The absence of CTCCTCGGCGGGCACGTAG from any mammalian or viral genome in the BLAST database makes recombination in an intermediate host an unlikely explanation for its presence in SARS-CoV-2. You can verify for yourself that there are no other sequences with an exact match. The subsequent comment about statistics of blast searching is irrelevant.
- ndr42 2y agoSo the conclusion of the comment-article cited in the parent of your comment is false? "According to the current phylogeny, FCS appeared independently six times in the Betacoronavirus lineages, demonstrating that FCS insertion is compatible with natural evolution (2, 7, 8). [...] 7. Wu Y, Zhao S. Furin cleavage sites naturally occur in coronaviruses. Stem Cell Res (2021) 50:102115. doi: 10.1016/j.scr.2020.102115"
- throwawaymaths 2y agoit's incompatible. Why is there COVID speculation in Stem Cell Res?