3 ms·
It doesn't look like that nucleotide sequence is actually unique to both SARS-CoV-2 and Moderna's 2015/2016 patents. Just BLASTed that sequence with the "gss"
by yellowapple 5y ago
It doesn't look like that nucleotide sequence is actually unique to both SARS-CoV-2 and Moderna's 2015/2016 patents. Just BLASTed that sequence with the "gss" database and got hits¹ for a bunch of different species of grass (plus some other hits for everything from bacteria to a species of dolphin). Tried again with the "RefSeq_Gene" database (ostensibly the human genome, AFAICT) and got a bunch of hits² for that, too.
I ain't a geneticist, so it goes without saying that I don't really know what I'm doing and I'm probably using BLAST wrong, but it seems to me like (EDIT: something very close to) CTCCTCGGCGGGCACGTAG is pretty dang common even within the human genome (let alone other species), and it doesn't seem far-fetched to me that SARS-CoV-2 might've yanked (EDIT: something very close to) that sequence from one of its hosts at some point.
EDIT: I forgot to check the completeness of the matches, and it does look like the hits tend to have one or two nucleotides that don't match. Still, it's close enough that the article doesn't seem like it presents much of a smoking gun.
¹: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=Y3TZW9WB01R https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=Y3TZW9W...
²: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=Y3UU86PP013 https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=Y3UU86P...
- dnautics 5y agoDouble check the query coverage percentage on your searches.
- yellowapple 5y agoYep, you're right (and edited above to reflect that). After accounting for that, and after realizing that BLAST only returns the first 100 results, I searched on the "nt" database (where the article found "only" SARS-CoV-2 results) while excluding SARS-CoV-2 (taxid:2697049), "synthetic construct" (taxid:32630), and "other sequences" (taxid:28384). This¹ produced not just a lot of hits, but a lot of exact (i.e. 19/19) hits (mostly various microbes) - further suggesting that even the exact sequence in question ain't unique. I also ran a search on "nt" strictly on SARS-CoV (i.e. the original SARS virus)², and while no single result completely matches the query, there are a lot of results that could be concatenated/combined to produce the query - and while I'm (again) no geneticist, it doesn't seem to me like some sort of impossibility for that concatenation to happen through mutations in the wild. ¹: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=Y3WR4BPX013 https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=Y3WR4BP... ²: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=Y3YCNK2C013 https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=Y3YCNK2...
- dnautics 5y agoUnless there is a transposable element between them, Just so concatenations like that are two independent splicing events so you roughly expect a quadratic likelihood reduction (square the rarity)
- yellowapple 5y agoWhich would still be a lot more likely than "random chance" (as the article puts it - i.e. each of those 19 nucleotides being randomly selected), right?
- dnautics 5y agoI'm not going to defend any of the statistics in the article.