11 ms·
Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]
- jakewins 7y agoSo what is the probability that a lab that works with HIV normally, now working under extreme pressure, contaminated or mixed up a sample? And what is the probability that this is not just a third type of major coronavirus, but in fact a secret bioweapon? Knowing how commonly there are arguments about mixed up samples in the biolabs friends work in, I know where I would place my bets.
- xvector 7y agoIt would be a pretty lame bioweapon given how few people it’s killed.
- fapjacks 7y agoBe advised that there are many posts on Chinese social media claiming the crematoriums are backlogged with people whose listed cause of death is "viral pneumonia" (or just "pneumonia") because hospitals are turning away so many and diagnostics are not catching up. Do not take statistical reporting for granted: The numbers are a best case scenario of definitive knowns. Also, bioweapons have as diverse a variety of use cases as any other class of weapon: They don't need to kill half of a population to be effective weapons.
- xvector 7y agoWhile I think China is hiding the number of infected, it'd be pretty hard to hide the proportion of dead to infected as the virus has already escaped Wuhan.
- ngcc_hk 7y agoThe question is not hard but no one really know. Would you test a body died recently? China is not very reliable in gdp (one top guy told us to look at the electricity and we look at pollution). It is very hard to get stat. So far touch wood no one died outside of China. The death rate should not be high unless the alternative saying hiv death rate after 1 month is 0%. The conspiracy theory in a proper sense is accidentally leaked for an experiment, like sars virus leaked (later and during study) by Beijing level 3 lab.
- Palptine 7y agoCould easily be "mixed samples" on the other end instead of intentional leaks. You know how old lab equipment could be really useful in a live seafood market.
- gus_massa 7y agoThe article claims that the new coronavirus is an "hybrid" of an usual coronavirus with some parts of HIV. If you mix both virus in a bottle of water, you don't get the hybrid. If both virus infect a cell simultaneously, there is a small possibility that something like this happens. I think it's so small that is not possible to do it in a laboratory even on purpose, and definitively not by accident but IANAB. It is easier with other virus. For example mixing variants of flu, because they have (IIRC) 8 strands of DNA. There are avian, swine, human, others flu, and each of them has many subvariants. If some animal get infected with two variants at the same time, a cell may have a double infection and the viral offspring may have a mix. But the mix is a mix of the strands of DNA, like 3 swine flu + 5 human flu. This is usual, but you must consider that there are millions and millions of animals in the wild and farms. It's more difficult to do it in a small lab, but IANAB. The main difference is that the article claim that the usual coronavirus and the HIV parts are in a single strain, not a bunch of strains packed together.
- dcolkitt 7y agoIgnoring the political implications, how would HIV insertions change the virulence and epidemiology of the infection?
- droithomme 7y agoIn the paper they hypothesize: > Due to the presence of gp120 motifs in 2019-nCoV spike glycoprotein at its binding domain, we propose that these motif insertions could have provided an enhanced affinity towards host cell receptors. Further, this structural change might have also increased the range of host cells that 2019-nCoV can infect.
- herogreen 7y agoTwitter thread by Dr. Eric Feigl-Ding on this yet-unreviewd publication: https://threadreaderapp.com/thread/1221990534643929089.html https://threadreaderapp.com/thread/1221990534643929089.html
- remarkEon 7y agoto someone who doesn’t know anything about the relevant science (me) the use of the word “insertions” seems to imply this was engineered. Can someone who actually understands this explain what this document is saying?
- ceejayoz 7y agoInsertions can occur naturally. https://en.wikipedia.org/wiki/Insertional_mutagenesis https://en.wikipedia.org/wiki/Insertional_mutagenesis > Because many viruses integrate their own genomes into the genomes of their host cells in order to replicate, mutagenesis caused by viral infections is a fairly common occurrence. Not all integrating viruses cause insertional mutagenesis, however. This paper does seem to allege that these particular sets of insertions aren't via natural causes, though.
- asdf21 7y agoThere could be naturally occurring insertions, but they would generally look similar to an associated coronavirus, or something else local, not 4 discrete changes that are all nearly identical to a (very well studied) virus that should be completely unrelated..
- 317070 7y agoWell, the conclusion of this paper is that the odds of this virus coming to be naturally are very small. Which is a very scientific way of saying "we think this was man-made". But, that is what the paper is saying. Extraordinary claims, extraordinary evidence is what I think. I feel the evidence here is quite small, but I'm not a bio-data-scientist.
- ericb 7y agoIs it an extraordinary claim? The sequence matching should be easy to verify as the genome has been published. If the sequences are short or common enough maybe it would be a more likely coincidence. That said: What are the priors on a "natural" virus erupting in the only city in China with a level 4 biohazard facility? Source: http://english.www.gov.cn/state_council/ministries/2018/01/04/content_281476001535134.htm http://english.www.gov.cn/state_council/ministries/2018/01/0...
- ajna91 7y agoA thread by an epidemiologist on the new results: https://twitter.com/DrEricDing/status/1223305946723704832 https://twitter.com/DrEricDing/status/1223305946723704832
- Andhurati 7y agoWhat are the geopolitical ramifications if this is indeed a bioweapon?
- jdhn 7y agoPerhaps the US and EU will put aside squabbles caused by the trade war to have a united front against China?
- Consultant32452 7y agoI don't think it will be talked about in that way. Especially if this is a bioweapon created in China which accidentally escaped. No one wants the dirty laundry spilled of all the countries who are doing bioweapon research. China is too powerful economically and surely has too much dirt on everyone else to go down alone. So I believe the official position will be that it's either not engineered at all ("inconclusive"), or just an unfortunate accident related to legitimate non-weapon research. Worst case scenario is US, EU, etc. do a little finger wagging that China needs to "stop eating bats" and then it will be let go. Of course, that's just the official/public position.
- T-A 7y agoChina is a signatory to the Biological Weapons Convention [1]. The US State Department regularly issues a compliance report about it (and other international agreements). Here [2] is how it summarized China's compliance in August 2019: "Information indicates that the People’s Republic of China (China) engaged during the reporting period in biological activities with potential dual-use applications, which raises concerns regarding its compliance with the BWC. In addition, the United States does not have sufficient information to determine whether China eliminated its assessed biological warfare (BW) program, as required under Article II of the Convention." (That's followed by some more details, which you can read about in [2].) Given this ongoing scrutiny, it would be very surprising if a smoking gun that the PRC has in fact been developing bioweapons were just swept under the rug. [1] https://en.wikipedia.org/wiki/Biological_Weapons_Convention https://en.wikipedia.org/wiki/Biological_Weapons_Convention [2] https://www.state.gov/wp-content/uploads/2019/08/Compliance-Report-2019-August-19-Unclassified-Final.pdf https://www.state.gov/wp-content/uploads/2019/08/Compliance-...
- codingslave 7y agoThis would be a really scary outcome. As has been commented elsewhere, there's confirmed events of at least four virus leaks from labs in Beijing. Evidence/article on it here: https://thebulletin.org/2014/03/threatened-pandemics-and-laboratory-escapes-self-fulfilling-prophecies/ https://thebulletin.org/2014/03/threatened-pandemics-and-lab... Not only that, but just last year there was a case of a Chinese scientist who was banished from a Canadian bio lab level 4 for stealing virus samples, as well as a Harvard Academic found to be taking money from the Chinese gov to help develop the lab in Wuhan. None of this proves the lab theory, but I do believe that with enough genetic analysis the truth will come out.
- uwuhn 7y agoI don't like how people are saying that theories regarding it being accidentally leaked are conspiratorial in nature. Intentional leaking? Sure, I think it's fair to consider that a conspiracy theory. But not accidental.
- AndrewBissell 7y agoIt would be conspiratorial in nature because it questions the Chinese government's official narrative that the virus emerged from a seafood market, and implies they're covering up the truth. Of course, people usually use the term "conspiratorial" to be synonymous with "untrue" or even "patently absurd."
- busterarm 7y agoWe already know for sure that the initial cases did not originate in the seafood market and that the market was just an infection vector for subsequent cases. Recently available data shows that the first few cases happened in November.
- contingencies 7y agoHaha, I like conspiracy theories. While we're at it: <s>Isn't it convenient that it appeared smack bang in the middle of China right about 2x incubation periods before Chinese New Year, the greatest annual migration in human history? Also that it's the first major virus outbreak to be described to the public as driven by asymptomatic carriers? And right after a 'trade war'? Before an election? What's to say it wasn't a ... drumroll please ... foreign or rogue scientist bioweapon?</s> cue for Dr. Evil cat stroking
- cwkoss 7y ago"The finding of 4 unique inserts in the 2019-nCoV, all of which have identity /similarity to amino acid residues in key structural proteins of HIV-1 is unlikely to be fortuitous in nature." Does this lend support to the theory that the coronavirus was engineered in Wuhan's bioweapons laboratory?
- mc32 7y agoIf that is ever proven and a cover up ensues I’d like to think the people would at last slough off their gov.
- PipeDreamer69 7y agoThe Chinese government has done a lot worse to its own people without being "sloughed" off in living memory.
- rednerrus 7y agoWorse than creating a super plague?
- ravenstine 7y agoHarvesting organs from political prisoners is pretty bad.
- ceejayoz 7y agoYes? https://en.wikipedia.org/wiki/Great_Leap_Forward https://en.wikipedia.org/wiki/Great_Leap_Forward > A lower-end estimate is 18 million and upper estimates find that some 45 million people died. That's more than virtually all epidemics. Black Death, Spanish flu, and (maybe) HIV exceed it.
- mc32 7y agoVery true but but people are better informed and are no longer powerless peasants and roboter. They have a bit more self determination.
- deleted 7y ago[deleted]
- yters 7y agoI thought detecting intelligent design in the genetic code was impossible and bad science.
- ceejayoz 7y agoDetecting intelligent design in things is done all the time. Teacup dachshunds are intelligently designed. So's corn and broccoli. Throwing your hands up and saying "God must've done it!" when you don't have an immediate explanation and can't be bothered to do some research into one is the bad science part.
- dang 7y agoPlease don't feed egregious comments by replying. This is in the site guidelines: https://news.ycombinator.com/newsguidelines.html https://news.ycombinator.com/newsguidelines.html. A religious flamewar on top of whatever else we've got here is the last thing this thread needs!
- ceejayoz 7y agoFair enough! I don't seem to be able to delete it; please feel free.
- yters 7y agoHow is this religious?
- dang 7y ago"Intelligent design" is an argument for the existence of God, which is a religious topic. The issue from an HN moderation point of view isn't religion; it's religious flamewar, which is what internet arguments about religion—at least in large public forums—inevitably degrade into. Therefore we don't go there.
- yters 7y ago
- tomrod 7y agoThat's very, very disturbing. If this is an engineered virus, why as a race do we keep doing these things to ourselves? Do we _really_ think that weapons of mass destruction won't be turned on us? Is our hubris so high that we think no one else can replicate what we built?
- daenz 7y agoIf a horrible weapon can be built, it will be built. And it is better to be the one building the weapon than the one at the mercy of those who built it.
- nexuist 7y ago>Is our hubris so high that we think no one else can replicate what we built? How do we know someone else hasn't already built what we've built? They don't exactly post these things on Facebook... ....which is why we have to build it too.
- ngcc_hk 7y agoOur eye and hand was developed mainly to focus against other humans. Our military has to study this ... But officially one has to study this as dual use as one has to prepare the natural evolution of say SARS to another strain. Can’t be sitting duck, let evolution run its course (2% death rate is not high but times 1.4 billion it is 28m people). Hence there is a case to study it, even change it. But then ... Just like we should fight hiv. But then someone in china use human to experiment on it. It is not there is no case. There are. Just stupidity of human ...
- heinrichhartman 7y ago2019-nCov is "The novel coronavirus (2019-nCoV), informally known as the Wuhan coronavirus." source: https://en.wikipedia.org/wiki/Novel_coronavirus_(2019-nCoV) https://en.wikipedia.org/wiki/Novel_coronavirus_(2019-nCoV)
- brutt 7y agoAs predicted in Contagion (2011). https://en.wikipedia.org/wiki/Contagion_(2011_film)#Scientific_response https://en.wikipedia.org/wiki/Contagion_(2011_film)#Scientif...
- brutt 7y agoSeriously, this particular mutation of unknown bat virus + HIV is predicted in film. I recommend to watch it: it's very scientific, and has almost no action.
- aqme28 7y ago"...unlikely to be fortuitous." Ignoring the odd word-choice, this ties in to the conspiracy theory that this was a Wuhan biolab containment leak. I have been writing it off as a crackpot conspiracy until now, depending on peer review.
- jszymborski 7y agoI think the important things to know here are: 1. A group of scientist have submitted a manuscript for review with a number of exceptionally (and uncharacteristically) bold claims. 2. A huge amount of scrutiny and additional reproducibility will necessarily need to be conducted before conclusions of this nature can be drawn. 3. This manuscript hasn't even passed the normal muster... a biorxiv post isn't much different than a Medium post. Claims like these require many eyes. EDIT: My sentiment echoed by someone who know more than I https://twitter.com/DrEricDing/status/1223325141364592640?s=20 https://twitter.com/DrEricDing/status/1223325141364592640?s=...
- cs702 7y agoAs regards #3, I agree: the more eyes who see this unconfirmed claim, the better. That's the main reason I upvoted the OP. A great outcome would be if reputable scientists see this on HN or Twitter or learn about it through colleagues, and subsequently refute it or dismiss it as bad science.
- im3w1l 7y ago> the more eyes who see this unconfirmed claim, the better. Isn't it a waste of those eyes' time if it turns out to be false? When there are plenty of confirmed things they could be reading?
- folli 7y ago#2: replicating their BLAST search is easy: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=398N4CSR01R https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=398N4CS... and it shows that the matches of these short inserts are completely by chance and don't constitute any statistically significant relationship.
- cs702 7y agoThank you for posting this here -- and thank you for taking a quick look at that paper and debunking it. I just upvoted your comment at https://news.ycombinator.com/item?id=22206393 https://news.ycombinator.com/item?id=22206393.
- narrator 7y agoIf someone with deep pockets may be liable, there will be a well funded effort to debunk this.
- tkems 7y agohttps://web.archive.org/web/20200131195339/https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.full.pdf https://web.archive.org/web/20200131195339/https://www.biorx...
- thorum 7y agoThis is especially interesting since there have been reports that China was testing HIV treatments on patients with the coronavirus: https://www.reuters.com/article/us-china-health-abbvie-hiv/china-testing-hiv-drug-as-treatment-for-new-coronavirus-abbvie-says-idUSKBN1ZP0QK https://www.reuters.com/article/us-china-health-abbvie-hiv/c...
- deleted 7y ago[deleted]
- Arete314159 7y agoYes they are BUT it's my understanding those HIV drugs had already been used against SARS and found helpful in an anecdotal way. So it would be an obvious first go-to drug.
- sct202 7y agoHIV drugs were used on SARS over a decade ago. https://www.ncbi.nlm.nih.gov/pubmed/15144898 https://www.ncbi.nlm.nih.gov/pubmed/15144898 It shouldn't be surprising that this new virus that is related to SARS can also be treated by HIV antiviral drugs.
- JulianMorrison 7y agoI wonder if this could happen because someone with a retrovirus got both infections at once?
- zozbot234 7y agoIt's not even necessarily someone with HIV - HIV is just one virus that is especially well-studied. If horizontal gene transfer in viruses is more common than we expect it to be, this genetic material could've been picked up from just about anywhere and we wouldn't necessarily know about that source.
- charliemil4 7y agoDoes anyone know the extent of the symptoms of 2019-nCoV? Does the virus get fully expelled from a person when they are recovered? Or is there a secondary effect / reemergence?
- greesil 7y agoMaybe we should wait for peer review before we jump to any conclusions.
- seaghost 7y agoHave in mind that this paper is not peer reviewed.
- lisk1 7y agoMy dose of speculation. So far we have strong evidence that this is a biolab virus, probably they were experimenting with this virus on animals the lab personal didn't realize on time how easy this virus could be transmitted by air, probably they were using the public transport from home to work during the incubation period thats how it boomed all of a sudden.
- hirenj 7y agoThis looks like a whole lot of rubbish to me. They're excited they managed to get blast hits for these short inserts. But in the spirit of open-mindedness, what do I need to be convinced this is even interesting? First I want to see where on gp120 these inserts align to. Are they receptor/carbohydrate binding regions? Where do they map to on the coronavirus? These structures are known, so I don't know why this isn't in this manuscript. If somehow this is engineered, I am honestly impressed that someone could take features from one protein and estimate how to engineer those same features in another protein altogether, with little homology. It's like engineering a monkey tail onto an elephant and somehow getting the elephant to swing through the trees.
- fapjacks 7y agoI appreciate your skepticism (and your sense of humor) but for the benefit of other readers, it is not like engineering a monkey tail onto an elephant and expecting the elephant to swing through the trees.
- sam36 7y agoThe amazing thing is last week someone on 4chan posted this: https://i.imgur.com/Jkq8tYK.png https://i.imgur.com/Jkq8tYK.png Which shows that the virus had been modified. 4chan wins once again at sleuthing.
- codingslave 7y agoThis lab theory has been systematically censored across the internet for the last week or so. For me it has been fascinating to watch content on it pop up and then disappear.
- LargoLasskhyfv 7y agoPsyberwar in action...
- thu2111 7y agoMaybe I'm missing something obvious but nothing in that image shows the virus has been modified? Or at least the commentary doesn't say that.
- hnarn 7y agoI'm not saying I believe the conspiracies, but it would be a pretty scary future if a totalitarian nation decided to quietly immunize their population (or just a selected elite) from a pathogen designed by themselves, and if push comes to shove you have a bioweapon that will do the job for you, which you know the people you care about can't contract. It's like a smart nuke.
- mcantelon 7y agoGiven historical experimentation by the military and intelligence agencies it seems pretty likely that this sort of research is happening.
- Tenoke 7y agoWhy was this submission suddenly so heavily penalized by the mod(s)?
- ctoth 7y agoAlso curious about this.
- codingslave 7y agoI noticed this as well. Censorship...
- akamaka 7y agoUsers can press the “flag” button for content that is off-topic. I flagged this article because it is an unreviewed pre-print paper that has been rushed out by its authors, who clearly have not investigated any of the most obvious follow-up questions, such as “what is the probability of this occurring naturally?”
- mcantelon 7y ago>who clearly have not investigated any of the most obvious follow-up questions, such as “what is the probability of this occurring naturally?” If it's true then the cause is an entirely different question.
- ctoth 7y agoOkay so we definitely need to flag any machine learning papers from Arxiv because hey preprint. Further, do you assume that other members cannot read the preprint warning and decide for themselves? This strikes me as some sort of bizarre way to patronize the entire community.
- akamaka 7y agoI’m not a biologist, so I’m really not interested in this type of paper, and I expressed my opinion through the voting mechanism. Also, there are thousands of researchers studying this new virus. If this turns out to be an important finding, I can wait until it is validated. At this point, this paper looks poor quality, and it was a waste of time for me to click on it and read it.
- jonplackett 7y agoHow long would it take for any other scientists to confirm or deny this?
- perseusprime11 7y agoIt does seem like something escaped a lab or a human trial gone wrong. Here's a better explanation: https://jameslyonsweiler.com/2020/01/30/on-the-origins-of-the-2019-ncov-virus-wuhan-china/ https://jameslyonsweiler.com/2020/01/30/on-the-origins-of-th...
- rafaelm 7y agoSome comments on this Biorxiv site from an epidemiologist: https://twitter.com/aetiology/status/1223328143647236097 https://twitter.com/aetiology/status/1223328143647236097 "For non-scientists, if you see something posted from a site called BioRxiv, have some skepticism. It could be a fantastic paper! (I've used it!)--but. The site is for preprints, which means they haven't undergone peer review yet."
- drtillberg 7y agoI generally agree with the folks who flagged this posting on HN (I didn't though) because the thought of ... airborne, highly contagious HIV in an early phase pandemic ... is a really very un-HN-like thought ... the mere theoretical possibility it could be true is the sort of thing I'd hope might inspire a generation to make our leaders globally take a time out on heated rhetoric and the ongoing technological arms race.
- buboard 7y agoThe study is probably bunk and sensational. check the comments by this redditor : https://www.reddit.com/r/China_Flu/comments/ewt9ep/scientific_paper_uncanny_similarity_of_unique/fg4ewbn/ https://www.reddit.com/r/China_Flu/comments/ewt9ep/scientifi... https://www.reddit.com/r/China_Flu/comments/ewuotw/discussion_biorxiv_preprint_on_2019ncov_spike/fg4jjrq/ https://www.reddit.com/r/China_Flu/comments/ewuotw/discussio... The real question is: how far are we from this becoming real ?
- zozbot234 7y agoInteresting, that user claims to be especially familiar with the 'gag' protein where the paper claims to find a match. User explicitly says that the "matching" portions claimed in the paper are so tiny as to be negligible, and not unique to HIV. They claim that this is easily verifiable with a simple 'blast' search. Could someone comment on these claims?
- TimonKnigge 7y agosee https://twitter.com/trvrb/status/1223337991168380928 https://twitter.com/trvrb/status/1223337991168380928
- protein_lense 7y agoI BLASTed all 4 2019-nCoV insert sequences and agree with that user. The sequences are short and found in many other proteins. It is appropriate to trim out the gaps (relative to the HIV sequences) in inserts 3 & 4, reducing the length of the query. In other words, we have 4 sequences of lengths: 6, 6, 8, & 12 amino acids, where the alphabet of naturally occurring amino acids is N=20. Amino acid frequency in proteins in non-uniform.
- deleted 7y ago[deleted]
- folli 7y agoSorry, but it's very easy to verify that these claims are crap by replicating their study, i.e. doing a simple blast search of the insert sequence against the virus database. Here's the result of the first insert: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=398N4CSR01R https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=398N4CS... Although, there are some hits against HIV, there are also equally matching hits against bacteriophages; viruses that only target bacterias, they are completely unrelated to any viruses that target humans and animals. Furthermore, the E value is around 170, that means that matches are statistically completely insignificant, meaning they happened by chance only. Such a high E value corresponds to a p-value of very, very close to 1 (https://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html https://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html). These guys that published such a paper are either completely clueless or nefarious in trying to stir up conspiracy theories.
- Palptine 7y agoWhat's the chance of hitting all 4 of them though? This is a good step in verification but you are awfully too quick to reject their claim.
- folli 7y agoRead the paper, they actually only match 2 inserts, the other two inserts are modified by the authors in such a way that they are made to match (Table 1). Both inserts 1 and 2 also match to Streptococcus phage, but a bacteriophage would of course not be such a bold claim as HIV matches are. Also, be aware that because of the scientific interest in HIV, there are hundreds of HIV strains sequenced, a virus known for its mutation rate (especially in these two proteins gp120 and gag, as they are under pressure to mutate in order to evade the immunesystem). So in such a large library of protein sequences one is bound to find a match of a short 6 letter (amino acid) sequence. That's why E values exist to make a statement about the statistical significance.
- folli 7y agoFor posteriority, here's the link to the Blast results for the second insert: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=39ACRKV3014 https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=39ACRKV...
- shanebkk 7y agoThis is all just guys stirring up trouble, conspiracy theories abound.
- ngcc_hk 7y agoThe virus is real. How it spread and where it comes from is an important analysis needed. SARS seems from eating wild cat and they are not sold there (there after decade there are selling in that market still but not those type). You learn. But so far due to the source is far away from more reliable scientific base (hk in 2003), no one knows. Hence one have to reconstruct. These might be wrong but investigation is needed. “ For his contemporaries, the ideas presented by Copernicus were not markedly easier to use than the geocentric theory and did not produce more accurate predictions of planetary positions. ” Let the river flow. Dead water you can step in twice is not good water.
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- hprotagonist 7y agoThis work was subsequently retracted: https://www.statnews.com/2020/02/03/retraction-faulty-coronavirus-paper-good-moment-for-science/ https://www.statnews.com/2020/02/03/retraction-faulty-corona...