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SARS-CoV-2 contains part of a patented genetic sequence
- tptacek 5y agoWe get stories like this about once every other week. Here's a recent one, with some expert contributions: https://news.ycombinator.com/item?id=30279180 https://news.ycombinator.com/item?id=30279180
- TedDoesntTalk 5y agoDoes that make them any less accurate or valid? (Sincere question not rhetorical)
- meepmorp 5y agoYou should have a look at the linked thread to see what people had to say about a previous, similar story.
- xtracto 5y agoNo, he shouldn't. There's no point in giving any value to anything argued here in news.ycombinator.com (a computer programming, technology entrepreneur forum) related to a genomics/biology subject. People here only argue to argue, and the level of discourse in these subjects are terrible, in both "sides" (the fact that people take sides is even a demonstration of how terrible the discourse is). What has to be done with this scientific paper, from a scientific journal is to read it, maybe go to scholar.google.com to look for its references or other sibling papers. And maybe go to science.reddit.com askscientists.reddit.com or any other internet forum were people educated in the subject interact, to get some good quality dialogue. Over here at HN? we are just speculating.
- MockObject 5y agoOn the other hand, even in this very thread are biologists with many years of experience.
- PragmaticPulp 5y agoThey tend to glue together a scientific fact and some vague conspiracy-esque implied conclusions that are anywhere from debatable to entirely nonsense. In this case, it’s accurate to say that the same sequence found in SARS-CoV-2 is indeed found in a patent. That’s valid and accurate. The claim that the occurrence is an impossibly unlikely random chance is the flawed part, though. Generic fragments aren’t actually random because they correspond to actual functions of the virus, and it shouldn’t be surprising that viruses with similar functions have similar genetic code fragments. It’s like if someone examined the binaries of two executables from different companies, identified a small sequence of bits that was common to both, then tried to imply that they were secretly written by the same author because it’s statistically unlikely for that random sequence of bits to appear twice. As a programmer you’d immediately dismiss the claim because that small sequence of bits could be common code like a standard library part or a common algorithm. But the claim may appear to be proof of a conspiracy to the uneducated. That’s basically what’s going on with this article, but swap bits for genetic code.
- TedDoesntTalk 5y agoExcellent explanation. Thank you.
- ImaCake 5y agoYes and they are frustrating to see as someone with some understanding of molecular biology. The science is so far very clear cut that there is no evidence for a lab engineered virus and only circumstantial evidence for a lab leak (but plausible). But people keep falling back on political arguments which have nothing more compelling than an argument from some authority. Programmers can see that the media and govt lies when there is a “hack” which was just a result of poor management, and extend that to literally anything reported on by the news.
- deleted 5y ago[deleted]
- WaxedChewbacca 5y ago
- mabbo 5y agoMy 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. Can someone tell me what the real implications of this are, and what the totally reasonable explanations might be?
- b112 5y agoSure, the implication is that you can be sued for catching COVID, for patent infringement.
- native_samples 5y agoNo, the implication is that Moderna was involved in gain of function research that led to the creation of SARS-CoV-2 which explains why they happened to conveniently have a vaccine available right from the start. Which, if true, would be one of the greatest scandals in history.
- nimajneb 5y agoI just tried to read it and got nothing out of it. The whole thing is above my head, lol.
- IncRnd 5y ago> The presence in SARS-CoV-2 of a 19-nucleotide RNA sequence encoding an FCS at amino acid 681 of its spike protein with 100% identity to the reverse complement of a proprietary MSH3 mRNA sequence is highly unusual. Potential explanations for this correlation should be further investigated.
- deleted 5y ago[deleted]
- mizzack 5y ago> 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 That seems like a pretty small number.
- fabian2k 5y agoI don't find that calculation convincing as it ignores that these viruses already have a furin cleavage site that by definition must be pretty similar to the sequence here. So the probablity would have to be calculated as "how likely is it that a virus with a related furin cleavage site accumulates the number of mutations necessary to arrive at this particular optimized one". And even then as this sequence provides a fitness advantage a naive calculation could be seriously off as well.
- XorNot 5y agoThe probability is also some argument by increduality anyway: 10-11, or you know, an occurrence rate of 10 after a trillion attempts. In an "average" COVID-19 infection course in an adult human, it is estimated that at peak infection a person has 10^9 to 10^11 virion particles in their body alone. Multiply by the all the people infected, + all the animals, + parallel gene transfer with other viruses in the ecosystem... [1] https://www.pnas.org/content/118/25/e2024815118 https://www.pnas.org/content/118/25/e2024815118
- PragmaticPulp 5y agoEach virus copy isn’t a different random sequence though. They have to share most of their code to work.
- XorNot 5y agoOf course, but if you're going to make arguments about probability in nature, they only mean something compared to the attempt space.
- uxp100 5y ago
- sebastien_b 5y agoIf this occurred naturally, shouldn’t that automatically invalidate the patent?
- agd 5y agoI think the point is that it might not have occurred naturally in this case.
- imglorp 5y agoCould part of it have existed naturally in the past, and the patent captured this part? Surely nobody is writing the entire organism from scratch; they're still making tweaks to natural sequences?
- rd_police 5y agoIsn't your statement dangerous?
- grosswait 5y agoYes. That’s why so few dare think it.
- jacquesm 5y agoNo, it's not that they don't dare to think it, it's that they realize it is stupid.
- graphpercolator 5y agoSo now we are back to the idea that this coming from a lab is dangerous idea that shouldn't be talked abbout? It was something to consider last summer but now it is a dangerous idea again. We have become such a total joke intellectually.
- dekhn 5y agoNo. We should consider all non-impossible hypotheses, weighted by their prior probabilities. What's dangerous is to proceed with sanctions against china without having an airtight case (with multiple cross-consistent supporting data inspecting by many parties). Nobody has made an airtight case that the virus was human-engineered (for whatever reason) or leaked (intentionally or accidentally). ANd it's most likely any evidence that did exist has been scrubbed. However, that's all speculation, not fact.
- 1970-01-01 5y agoSequence is here: https://seqdata.uspto.gov/?pageRequest=viewSequence&DocID=US09587003B2&seqID=11652 https://seqdata.uspto.gov/?pageRequest=viewSequence&DocID=US...
- cf141q5325 5y agoI looked a while for this. Thank you, i really mean it.
- Semaphor 5y agoHaving 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? [0]: https://old.reddit.com/r/science/comments/sysag6/msh3_homology_and_potential_recombination_link_to/hy2df2w/?context=3 https://old.reddit.com/r/science/comments/sysag6/msh3_homolo...
- alufers 5y agoImagine that a virus is detected in your body and then you get sued by a patent troll for having unlicensed genetic sequences in your body.
- lsllc 5y agoOr GM seeds apparently getting blown into your fields and then getting sued for growing unlicensed crops: https://www.washingtonpost.com/archive/politics/2001/03/30/farmer-liable-for-growing-biotech-crops/e4d32d97-a3d8-4ab7-9f69-d49bcc88198a/ https://www.washingtonpost.com/archive/politics/2001/03/30/f...
- spiderfarmer 5y agoThe main reason why the EU bans GMO crops.
- daughart 5y agoFederal patent law defines patent infringement as “mak[ing], us[ing], offer[ing] to sell, or sell[ing]” a patented invention. Not an attorney, but seems like it would be quite a stretch to argue that becoming infected with a virus would fall under one of those categories.
- theta_d 5y agoWell, a virus replicates by forcing your cells to make more of the virus. Just sayin'.
- servytor 5y agoI swear that's the plot to something I have heard of... wish I could be more helpful and suggest a link.
- ajross 5y agoHeadline 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. 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.
- jaywalk 5y agoThis isn't smoking gun by itself, but there sure are a lot of warm guns laying around this particular topic.
- grosswait 5y agoCould you elaborate on what “complement to a genuine human sequence “ means?
- deleted 5y ago[deleted]
- Nathanael_M 5y agoI would love some clarification on what "patented" does mean. For instance, I can find a "patent" here: https://seqdata.uspto.gov/?pageRequest=viewSequence&DocID=US09587003B2&seqID=11652 https://seqdata.uspto.gov/?pageRequest=viewSequence&DocID=US... that categorizes it as an "Artificial Sequence". Is this more like a naturally occurring sequence that has been documented before, isolated, and then claimed by the team that isolated it?
- rflrob 5y agoI’m having trouble getting the patent to load on my phone, but my interpretation of the “codon optimized” patented sequence is that although the sequence codes for a naturally occurring protein sequence, the RNA triplets that are actually used are not naturally occurring. MolBio 102 for software engineers: each amino acid is coded for by 3 RNA bases. However, the number of possible RNA triplets (4^3=64) is greater than the number of amino acids (20), so some amino acids have multiple triplets assigned to them. For instance, both UUA and CUG code for the same amino acid (leucine), but one of them is more efficient to express. The implicit argument is that consistent preferential use of these optimal codons is evidence of genetic engineering rather than natural evolution.
- lettergram 5y agoWuhan discussing "synthetically derived viruses": https://web.archive.org/web/20200212011902/http://english.whiov.cas.cn/News/Events/201512/t20151204_157114.html https://web.archive.org/web/20200212011902/http://english.wh... 2017 conference at (Wuhan Institute of a virology) with gain of function research being top priority: http://web.archive.org/web/20200221213643/http://english.whiov.cas.cn/Exchange2016/International_Conferences2017/201712/t20171215_187977.html http://web.archive.org/web/20200221213643/http://english.whi... Ecohealth Alliance partnership: https://web.archive.org/web/20210323171425/http://english.whiov.cas.cn/International_Cooperation2016/Partnerships/ https://web.archive.org/web/20210323171425/http://english.wh... US Gov from state department: http://web.archive.org/web/20210116001621/https://www.state.gov/fact-sheet-activity-at-the-wuhan-institute-of-virology/ http://web.archive.org/web/20210116001621/https://www.state.... EcoHealth Alliance Peter Daszak discussing gene editing in coronaviruses in december 2019 - https://www.youtube.com/watch?v=5-Y843FFJvI https://www.youtube.com/watch?v=5-Y843FFJvI
- zmgsabst 5y ago
- matheweis 5y agoInterestingly, the observation in this paper was surfaced on a substack several months ago. https://arkmedic.substack.com/p/how-to-blast-your-way-to-the-truth https://arkmedic.substack.com/p/how-to-blast-your-way-to-the... 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? 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: https://news.ycombinator.com/item?id=29938732 https://news.ycombinator.com/item?id=29938732
- pcdoodle 5y ago
- titzer 5y agoThe article isn't about the vaccine, it's about the RNA sequence directly in COVID.
- 1970-01-01 5y ago>> 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. I don't like "this is very rare" How rare? It's a database. Query it, and confidently give numbers to support your statement.
- dnautics 5y ago> How rare? Zero other exact matches, in the database. An n of 1 has infinite variance. The relevant rarity, though is not the database, but rather "in the universe of viral sequences. The database biases for sequences that we've sequences, so at best you can give a really shitty estimate. Fwiw I believe the story that this was a stack overflow copy-paste operation from the moderna sequence, but I can only ever call this a strong belief[0], with no numbers behind it, unless someone comes forward and admits having done it. [0] why strong? Because it follows the scientific method. If the hypothesis is that it's a lab leak, then your prediction is that existing sequences would bleed through. A bit crazy that we only found this now, hell I could have done this blast search years ago, but it is what you would expect to find.
- sschueller 5y agoI would say statistically it is not rare. I mean it's a sequence of 12 where each item can only be C,T,A OR G from the little I understand about DNA. It would be quite a bad password even though it's 12 characters long.
- Workaccount2 5y agoWhat is the value of this comment?
- dekhn 5y agostatistics in sequence matching depend on underlying base rates; out of the 4*12 (2*24) possible sequences, you will see some never, some many, and many some times.
- titzer 5y ago> "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". This is just going to feed more conspiracy theory nutters. 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, Second, mutations, whether random or not, are subject to selective pressure and incremental progress. 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.
- samatman 5y ago> hundreds of millions of infections in humans This article is of course based on an early sequence of SARSCov2, from before the pandemic spread. Which means you didn't even begin to understand the question before spouting off, and everything you say on this subject can be disregarded. Do better.
- titzer 5y ago> an early sequence of SARSCov2 Which apparently had never replicated before and thus was not subject to evolution...? My point was just to illustrate how many trillions of replications happen for viruses in the wild. 100 billion is absolutely nothing for biology. The snide ad hominem that makes up the rest of your comment doesn't belong here. If you had just left it out, this would be a conversation and not an unnecessary source of anger and stress.
- samatman 5y ago> snide ad hominem You came straight out the gate with "conspiracy nutters", then typed two paragraphs of misleading nonsense which did nothing to further the conversation. This isn't a dialogue, this is me tagging you for other's sake as someone to ignore on this subject. Which is an important subject.
- ImaCake 5y agoI 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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7836551/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7836551/ 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. 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.
- loceng 5y agoSo this is the very beginning of an argument. "Serious virologists" isn't proof. Which virologists think it's natural, and which think it's unnatural? Now lets see the data and thorough reasoning by each, and see the rebuttals of each for their opposition's reasoning, etc. Until this is laid out clearly it's all shallow discussion - that no one should blindly trust or believe. The above is the scientific process, method. There clearly isn't consensus yet.
- ajross 5y ago> Which virologists think it's natural, and which think it's unnatural? Literally no one, including the authors of this paper, contends the sequence is "unatural".
- alephnil 5y agoThat 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.
- cryptos 5y agoDo we have to pay license fees now, if we already enjoyed SARS-CoV-2? SCNR
- zemariagp 5y agoSomeone call Moderna, they filed the patent so I’m sure they will clarify
- zemariagp 5y agoSomeone call Moderna. They filed the patent so I’m sure they will clarify
- lobocinza 5y agoI though this claim was BS but indeed you're right. https://patents.google.com/patent/US9587003B2/en https://patents.google.com/patent/US9587003B2/en
- bsedlm 5y agosomething 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. 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. It's silly for anybody to "own" (with the exclusivity, royalties deserving modern way it is being done) a gene sequence. 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?" I like thinking about who really owns the English (or any natural) language to try and makes sense of how it ought to be.... 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.
- 1970-01-01 5y ago>oh you have so and so patented genes hence you must pay the owners royalties?" This is exactly how new plant foods are created. Here is a potato as an example: https://ctl.cornell.edu/wp-content/uploads/plants/Cornell_potato_varieties_comparison_chart.pdf https://ctl.cornell.edu/wp-content/uploads/plants/Cornell_po...
- GuB-42 5y agoExcellent news! Now patent lawyers will sue SARS-CoV-2 to oblivion and end this illegal pandemic. /s
- hanselot 5y ago
- moralestapia 5y agoThis 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. 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. 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. 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. 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. PS: I have degrees in Genomics and Molecular Biology, and have worked for around 15 years on the field.
- shadowgovt 5y ago> same origin Sure, but that can also indicate it's a virus resulting from natural stitching together of DNA sequences from multiple infections in one living host, like HIV. How do we disambiguate novel virus arising from multi-infection interference from human synthesis?
- moralestapia 5y ago>How do we disambiguate novel virus arising from multi-infection interference from human synthesis? Best you can do is work with probabilities and try to infer which theory is more plausible than others.
- zoobab 5y agoDavid Martin went to EUPACO in 2007 and predicted the 2008 crisis there. His company M-Cam is copied all the patents in the world, and making intelligence reports based on that. They made an analysis about all the DNA sequences of SARS-CoV-2, and came to the conclusion that it was manipulated by man. Someone would have to request them the scripts and the patents to be able to reproduce their assessment. Which was flagged as 'complotist'. https://un-denial.com/2021/07/20/dr-david-martin-covid-is-a-manufactured-illusion/comment-page-1/ https://un-denial.com/2021/07/20/dr-david-martin-covid-is-a-...
- rrock 5y agoGenerally, the reverse complement of a translated sequence is uninteresting. The function is not encoded in the reverse complement.
- flobosg 5y ago> 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). 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. Disclaimer: I know and have used BLAST since my undergrad years, about a decade and a half ago.
- y4mi 5y agoThat sounds more like an issue in the reporting being unclear about the constraints used for the identification then the actual finding.
- flobosg 5y agoExactly, and that could change the interpretation of their findings completely. I haven’t checked their credentials, but I would be surprised if any of the authors has a background in bioinformatics or computational biology. BLAST is used on a daily basis by a lot of scientists (its paper is among the most cited of all time), but many of them lack the theoretical knowledge to analyze in depth their results. This paper doesn’t have a single line about methodological details, such as the parameters used in their BLAST runs. The authors don’t even refer to P- or E-values either, despite being prominently displayed on the output table of every run!
- eggy 5y agoI 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.
- lamontcg 5y agoThis 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: https://ibb.co/T1YtShy https://ibb.co/T1YtShy 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). 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. And the rest of the argument in this paper is some weird genetic numerology.