> We did not find the 19-nucleotide sequence CTCCTCGGCGGGCACGTAG in any eukaryotic or viral genomes except SARS-CoV-2 with 100% coverage and identity in the BLAST database (Supplementary Tables 1–3).<p>Huh? I just run BLAST (blastn, specifically) with that nucleotide sequence and found several eukaryotic genomes containing it in non MutS-like contexts, aligning sense and anti-sense strands, with 100% coverage and 100% identity. Besides, there is no “BLAST” database (I used the non-redundant -nr- one, for instance; BLAST is just the name of the tool). One possible reason they didn’t find the sequences is that BLAST, by default, only returns the first 100 hits, which in their case might have been prokaryotic ones. I didn’t check viral genomes but might later.<p>Disclaimer: I know and have used BLAST since my undergrad years, about a decade and a half ago.
I am a molecular biologist but not a virologist. This article is stupid. The furin cleavage site, with almost identical sequences is present in several ancestral coronaviruses to Sars cov II. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7836551/" rel="nofollow">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7836551/</a><p>Serious virologists went over the furin cleavage site in close detail already and none of them seemed very convinced it was anything but natural in 2020.<p>Also, stick any 13 bp dna sequence into BLAST and you will find some strange matches if you include the right databases. That this particular 13 base pairs matches some bit of the human genome (inverted, mind you) is not really that surprising.
Interestingly, the observation in this paper was surfaced on a substack several months ago.
<a href="https://arkmedic.substack.com/p/how-to-blast-your-way-to-the-truth" rel="nofollow">https://arkmedic.substack.com/p/how-to-blast-your-way-to-the...</a><p>I do not see the substack author among the paper authors or references to that writeup. I wonder if there was any collaboration or if this was an independent finding?<p>That substack made the rounds here about 5 weeks ago. While it was heavily critiqued for being a rather poor writeup, there was a fair bit of discussion about the observation itself that should be relevant here: <a href="https://news.ycombinator.com/item?id=29938732" rel="nofollow">https://news.ycombinator.com/item?id=29938732</a>
This has been known for a while, but I'm not complaining about it. Ever since this whole thing started, several scientists have been finding things which are "interesting to take a look into them further", to put it in some way.<p>I have a close friend who works w/ population genetics and basically does phylogenies all day. For those who don't know, a phylogeny is an analysis where you study how similar/dissimilar are sequences between known things in order to infer what are the most plausible evolutionary relationships that (could have) happened.<p>So, this friend of mine has been taking a look at some of the published sequences ever since they came out and his personal conclusion is that there is no way that SARS-CoV-2 came to be in a "natural" way.<p>Among other interesting things, he claims that the virus does not seem to have a single "origin". I'll try to explain, so while you're figuring out what the "history" of something is (i.e. ancestors, lineage), you usually get some sort of tree-like arrangement where some structural rules are strongly (but not completely) preserved, like if A -> B and B -> C then A -> C, you get the idea. In SARS-CoV-2's case, such rules (or lack thereof) suggest that different regions of the sequence cannot be assumed to have followed the same evolutionary history; which is kind of weird, honestly. This is something that has been observed naturally, but under very specific constraints which are unlikely to apply to SARS-CoV-2 and how it has spread throughout the world.<p>Anyway, I'm happy that these sort of studies are finally coming to light and that, for whatever reason, people are now allowed to talk about it. The whole point of science is to engage in rational discussion and build on each other's knowledge in order to attain the truth.<p>PS: I have degrees in Genomics and Molecular Biology, and have worked for around 15 years on the field.
>> Examination of SEQ ID11652 revealed that the match extends beyond the 12-nucleotide insertion to a 19-nucleotide sequence: 5′-CTACGTGCCCGCCGAGGAG-3′ (nt 2733-2751 of SEQ ID11652), such that the resulting mRNA would have 3′- GAUGCACGGGCGGCUCCUC-5′, or equivalently 5′- CU CCU CGG CGG GCA CGU AG-3′ (nucleotides 23547-23565 in the SARS-CoV-2 genome, in which the four bold codons yield PRRA, amino acids 681–684 of its spike protein). This is very rare in the NCBI BLAST database.<p>I don't like "<i>this is very rare</i>"<p>How rare?<p>It's a database. Query it, and confidently give numbers to support your statement.
Wuhan discussing "synthetically derived viruses":<p><a href="https://web.archive.org/web/20200212011902/http://english.whiov.cas.cn/News/Events/201512/t20151204_157114.html" rel="nofollow">https://web.archive.org/web/20200212011902/http://english.wh...</a><p>2017 conference at (Wuhan Institute of a virology) with gain of function research being top priority:<p><a href="http://web.archive.org/web/20200221213643/http://english.whiov.cas.cn/Exchange2016/International_Conferences2017/201712/t20171215_187977.html" rel="nofollow">http://web.archive.org/web/20200221213643/http://english.whi...</a><p>Ecohealth Alliance partnership:<p><a href="https://web.archive.org/web/20210323171425/http://english.whiov.cas.cn/International_Cooperation2016/Partnerships/" rel="nofollow">https://web.archive.org/web/20210323171425/http://english.wh...</a><p>US Gov from state department:<p><a href="http://web.archive.org/web/20210116001621/https://www.state.gov/fact-sheet-activity-at-the-wuhan-institute-of-virology/" rel="nofollow">http://web.archive.org/web/20210116001621/https://www.state....</a><p>EcoHealth Alliance Peter Daszak discussing gene editing in coronaviruses in december 2019 - <a href="https://www.youtube.com/watch?v=5-Y843FFJvI" rel="nofollow">https://www.youtube.com/watch?v=5-Y843FFJvI</a>
My imagination has a lot of ideas about what this means. But I also dropped biology in high school and went into computers, so I'm very poorly armed to assess this.<p>Can someone tell me what the real implications of this are, and what the totally reasonable explanations might be?
> Conventional biostatistical analysis indicates that the probability of this sequence randomly being present in a 30,000-nucleotide viral genome is 3.21 ×10−11<p>That seems like a pretty small number.
Headline here on HN seems somewhat misleading, and I fear for how this is likely to be spun. In this context "patented" does not mean "engineered" or "artificial". This is the complement to a genuine human sequence we all have. It's 19 nucleotides (28 bits) long, so unlikely (but not impossible in a cryptographic sense) to have arisen randomly. We do know viruses will pick up these sequences from their hosts though, so by itself this doesn't actually say much absent some statistics about how common that is.<p>Basically: please be careful here, a lot of people are going to want to treat this as a smoking gun, and it's not. It sure is interesting though.
That some gene is patented does in itself means nothing. At some point in the nineties the patent offices around the world started accepting patents for discovered gene sequences (i.e. sequences read out of some organism). This meant that patents rights could be granted for any drug targeting the protein the gene codes for, and not just a specific drug that does it. It does not mean that this is an invented DNA sequence. In fact it seems like one that is naturally occurring in humans. The fact that the sequence is patented is irrelevant, and should be ignored. It does not seem like the article make much fuzz about it either.
> "Conventional biostatistical analysis indicates that the probability of this sequence randomly being present in a 30,000-nucleotide viral genome is 3.21×10^−11".<p>This is just going to feed more conspiracy theory nutters.<p>First, a 1 in a 100 billion chance is absolutely nothing. There have been hundreds of millions of infections in humans, each representing billions upon billions of replications of the virus. Every replication carries the chance of mutation. Given that,<p>Second, mutations, whether random or not, are subject to <i>selective pressure</i> and <i>incremental progress</i>. A mutation that moves a sequence just slightly in the right direction, coding for a slightly different but close protein, will be selected for. Basically, evolution optimizes some structures (and therefore sequences) by hill climbing, accepting mutations that improve fitness and discarding mutations that don't. It doesn't roll all the dice at once and start over every time.
Having no idea what this means, I checked reddit. I found this comment [0] which I think says this could have happened naturally, but it uses a lot of words that sound like a Star Trek episode, so maybe someone can translate it?<p>[0]: <a href="https://old.reddit.com/r/science/comments/sysag6/msh3_homology_and_potential_recombination_link_to/hy2df2w/?context=3" rel="nofollow">https://old.reddit.com/r/science/comments/sysag6/msh3_homolo...</a>
Sequence is here:<p><a href="https://seqdata.uspto.gov/?pageRequest=viewSequence&DocID=US09587003B2&seqID=11652" rel="nofollow">https://seqdata.uspto.gov/?pageRequest=viewSequence&DocID=US...</a>
We get stories like this about once every other week. Here's a recent one, with some expert contributions:<p><a href="https://news.ycombinator.com/item?id=30279180" rel="nofollow">https://news.ycombinator.com/item?id=30279180</a>
This really can't be taken seriously if they don't even bother addressing the BANAL-52 or RmYN02 sequences which very nearly have a functioning FCS:<p><a href="https://ibb.co/T1YtShy" rel="nofollow">https://ibb.co/T1YtShy</a><p>There is a QTQTN deletion in circulating SARS-CoV-2 at the flanking region at 675-679 which has been observed in circulating human strains at the level of a few percent along with mouse-adapted strains. RmYN02 is closer in nucleotide sequences to those variants of SARS-CoV-2 than to ancestral (the SARS-CoV-2 variants carrying that deletion not show in that figure).<p>If there are variants of RmYNO2 which retain the QTQT sequence at 675-679 then that virus would be one amino acid insertion away from a functioning QTQTNSPRAAR FCS sequence. Then flipping another amino acid would give the SARS-CoV-2 sequence. The relative probably would be discovered with a higher level of surveillance and sequencing of sarbecoviruses in wildlife.<p>And the rest of the argument in this paper is some weird genetic numerology.
I am not a molecular biologist or virologist, far from it. I am reading the manner in which people who are those things are responding. Some quite scientifically, and others dogmatically. The one tidbit of information I had heard about the FCS was that the SARS-COV-2 had the exact 12-nucleotide sequence, no more no less, so it was an exact match for an FCS proposed for study that was rejected by the DoD, DARPA, or some other U.S. government agency. I believe this is not the same in the other SARS-COV viruses, at least not exactly 12, but found somewhere along a sequence. Can someone here clarify this for me as a layman? I'd appreciate it. It is fascinating to me, and as a result I just picked up an Introduction to Genomics book by Arthur Lesk. Thank you.
something are so clearly obvious (I don't think "obvious" is the exact word I need) that to consider them property of the intellectual kind is silly.<p>I'm thinking about certain mathematically expressed concepts and ideas which are nonetheless patented and treated as property nowadays; I don't see why DNA would be any different.<p>It's silly for anybody to "own" (with the exclusivity, royalties deserving modern way it is being done) a gene sequence.<p>I think that whomever has it already owns it and these things can and in reality are non-exclusively owned. because what is next? "oh you have so and so patented genes hence you must pay the owners royalties?"<p>I like thinking about who really owns the English (or any natural) language to try and makes sense of how it ought to be....<p>then again who wouldn't like to come up with some idea and then keep getting paid for this until they die? this is similar to rent-seeking, it is rent-found.
David Martin went to EUPACO in 2007 and predicted the 2008 crisis there.<p>His company M-Cam is copied all the patents in the world, and making intelligence reports based on that.<p>They made an analysis about all the DNA sequences of SARS-CoV-2, and came to the conclusion that it was manipulated by man.<p>Someone would have to request them the scripts and the patents to be able to reproduce their assessment. Which was flagged as 'complotist'.<p><a href="https://un-denial.com/2021/07/20/dr-david-martin-covid-is-a-manufactured-illusion/comment-page-1/" rel="nofollow">https://un-denial.com/2021/07/20/dr-david-martin-covid-is-a-...</a>