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How the novel coronavirus has evolved
- nmfisher 6y agoAnd I was downvoted on HN for merely asking the question whether coronavirus could mutate: https://news.ycombinator.com/item?id=24035686 https://news.ycombinator.com/item?id=24035686
- sadmann1 6y agoHN has an tendency of becoming a hivemind like reddit due to the intellectual pride of the overpaid CRUD technologists that reside here
- DubiousPusher 6y agolooks up from writing a fancy Azure function that manages a blob store Hey!
- googlryas 6y agoHN votes more on delivery style than substance. A short post in plain language espousing human rights will generally do worse than a long, academically styled post restating Nazi ideals.
- redis_mlc 6y ago> HN votes more on delivery style than substance. It's much worse than that. Because most HNers have almost no actual knowledge or experience, you have to provide two links for them to read to get up to speed on virtually any topic. I've done experiments on HN readers where virtually all of my posts are downvoted or flagged, but adding 2 links will usually get them upvoted. No difference in tone or opinion. So if you read HN, you're also my personal guinea pig. Thanks! :)
- nadaver 6y agoWow, that was salty. Better wash it down with some whine. Oh, wait, I see you already have some there.
- kolinko 6y agoThat is by design. You should upvote/dovnvote good/bad ways of expression, and if you disagree with something then argue why you do.
- abhinav22 6y agoThe stuff I get downvoted for boggles my mind (e.g. get downvoted for saying thank you this was a good post). They should rename HN to HM, HiveMind.
- tempestn 6y agoA comment that just says "thank you this was a good post" is basically an up-vote in the form of a comment; it doesn't add any substance to the conversation. That would be a polite response in another context, but on HN the goal of the guidelines as I understand them is to keep the signal to noise ratio high - basically to increase the density of useful information and insightful argument in comments. In order to do that, comments that don't add substance to the discussion are discouraged here.
- abhinav22 6y agoThank you for the note, I suspected as much but I do appreciate your elaboration on the topic. I don’t agree with the approach (I would say for submissions that don’t have as many upvotes that somebody who took the time to write a thank you note reflects they actually read the article and it was worth the effort to write a note (which takes more effort than an upvote). This can be a important signal for others. It also I think is a nice feedback to the author, I always want to try and encourage people — when I receive positive feedback, it makes my day). In some ways it’s a reflection of how the community (at large, not any individual in particular) views itself — to be such stringent guardians of information density, when in fact a large portion of the comments are relatively useless and misinformed (usually the most knowledgeable people speak less as they are busy actually working in their field, although they pop up from time to time). However, when in Rome, do as the romans do.
- kolinko 6y agoYou imploed that mutation is the same as a „change in any way biologically”. Coronaviruses mutate slowly, and the majority of mutations chamge nothing in the way the virus mutates. So far, out of all the strains, only one has been shown to modify it’s behaviour.
- oefrha 6y agoIn case there's further whining about this comment being downvoted: I didn't downvote due to hivemind mentality or agreement/disagreement about the original, I downvoted because whining about downvotes makes boring reading. https://news.ycombinator.com/newsguidelines.html https://news.ycombinator.com/newsguidelines.html Additionally, it takes a single, random HN user with 500 karma to put a comment into "downvoted" state. It takes three or four to be "heavily downvoted" (which doesn’t apply to your original comment). Just not a very meaningful thing to draw conclusions from.
- My7thAccount 6y agoTalking about karma makes for boring reading too.
- My7thAccount 6y agoIt takes like a week of posting articles to get to 500 karma. I've done it 12 times now which means if I want to, I can make anyone's comment instantly go dead. But they are imaginary points so don't care too much
- melling 6y ago“If the virus changes substantially, particularly the spike proteins, then it might escape a vaccine. We want to slow transmission globally to slow the clock,” Is this why some are saying we might need a booster shot in a few years?
- DubiousPusher 6y agoI don't think so. I believe that is related to the immune system's ability to "forget". I believe a new strain which evades the current vaccine schemes would need an entirely new or significantly altered vaccine.
- CyanBird 6y agoNo, different reason, booster shots, are needed to "remind" your immune system that the virus is still out there, and keep it on fighting shape, and as far as I am aware, the early discussions for booster shots, were about 6, to 9 months. But all of that is up in the air, there's no data for how the vaccine will develop that much into the future yet Anyhow, if the spike proteins vary too much, then we'll need a new vaccine all together, not just a booster for the current one
- akkawwakka 6y agoTo correct the quoted assertion... There is little selection pressure on the virus for the spike proteins to evolve and change. SARS-CoV-2 infects human cells just fine using its current spike protein. [1] [1]: https://www.nature.com/articles/d41586-020-02544-6 https://www.nature.com/articles/d41586-020-02544-6
- divbzero 6y agoThanks for that Nature news feature, it summarized the research on SARS-CoV-2 mutations quite well. We’ll have to watch for signs of selection pressure as more and more of us get vaccinated to recognize the spike protein. Hopefully SARS-CoV2 mutates too slowly to escape the vaccines, or can only escape with sharply reduced infectivity and virulence.
- 6y ago
- Izkata 6y agoSo it's finally okay to say there's multiple strains with different infectiousness and (possibly) severity? Back in February-ish (I forget exactly when), we had confirmed community spread in Washington (West-coast state in the US), with the belief that it had been spreading for weeks and no one noticed, because of how few cases there were, and no bump in hospitalizations. This was likely the Wuhan strain, which likewise had been spreading in Wuhan for at least a month and a half before it was detected. On the flipside, when it reached Italy, it hit that country hard. It wasn't clear why, but I remember a report sometime during the summer that the most prevalent version of the virus in Italy was distinct from the Wuhan one, and could possibly be labeled a different strain because of its increased infectiousness, that mutation apparently occurring somewhere in Europe and spreading out from there (France was also hit hard at the same time IIRC, but Germany for example was not). Not long after that I remember a cross-country comparison that said the primary version of the virus in New York (US East coast, also hit hard) matched the one in Italy, but not the Wuhan one, and that what we had in Chicago was a mix of the different strains with (at the time) no one winning out over the others. Nice to finally see confirmation about there actually being different strains that are shifting over time, but unfortunately the timing makes it look like lockdowns may have selected for the more virulent version and caused the pandemic to be worse than it otherwise would have been (see the graphs in the "G strains take over" section, where the cases spike only after, well, the "G" strains take over and the Wuhan "L" strain has been pushed out).
- jstanley 6y agoCan you elaborate on why a lockdown would select for a more virulent strain?
- Izkata 6y agoI'm mainly basing it on the graphs provided: The cases don't spike until after the "G" strain is present, no matter how long the "L" and "S" strains were present beforehand. Actually I think I should have said "infective" rather than "virulent" there; basically lockdowns select for versions of the virus that can spread despite the lockdowns. It only looks more virulent because of the larger number of total infections.
- yumraj 6y agoSo which strain are the various vaccines targeting? Or are they multi strain vaccines like the flu vaccine?
- m-ee 6y agoIt’s not like the flu. The strains aren’t functionally different, with the possible exception to the one that spilled back over from infected mink which was slightly less responsive to human antibodies in lab experiments. Unless there’s more significant change the vaccine should work for all the different variants. EDIT- Be careful reading too far into statements like “XYZ mutation makes it easier to bond to ACE2 therefore it’s more contagious” Infection is more than just binding to a receptor, even if lower quality preprints jump the gun in their conclusions
- rossdavidh 6y agoThere was a suggestion that one of the variants seen in Denmark's mink infection, might make at least some of the vaccines slightly less effective. But even in that case the effect was not large, and in any event the variant in question hasn't been seen since September.
- lvs 6y agoThe very first strain isolated in Wuhan, but the most prevalent S protein mutations in subsequent strains are fairly buried. None have yet been shown to affect immune recognition, as far as I know.
- ketamine__ 6y agoCommentary by Derek Lowe that links this graphic. https://blogs.sciencemag.org/pipeline/archives/2020/12/10/the-latest-on-coronavirus-mutations https://blogs.sciencemag.org/pipeline/archives/2020/12/10/th...
- bostik 6y agoTowards the end of the article is a particularly good nugget of information. > Since then, there have been documented reports of individuals being reinfected with different versions of the virus. Yes, reinfections have been extremely rare so far. But if the immunity really is strain-specific, the warnings about Covid becoming endemic in the global population should now carry a lot more weight. The virus will mutate. In a likely scenario, previous immunisations are likely to be less useful, and we all need annual shots against the newly emerging strains. On the upside, if Covid strains become just another aspect of the flu jab, then we at least already have an existing infrastructure to manage it in the future. Production capacity of vaccines will take some time to ramp up, though. Maybe now would be a good time to invest in drug manufacturing and logistics? Planet Money did an episode on Covid vaccine logistics and one data point stuck with me. The global production of vaccines is between 3.5B and 5B doses a year. That's for ALL vaccines, across the entire spectrum of diseases and treatments. Adding another 12B to 16B doses on top of that is going to require a lot of new infrastructure, from production facilities to all the materials needed in the logistics chain.
- chimprich 6y ago> > Since then, there have been documented reports of individuals being reinfected with different versions of the virus. > [...] But if the immunity really is strain-specific Reinfections have been recorded from different strains because it's much easier to demonstrate that someone has been reinfected with a new strain. If someone has been reinfected with the same strain then it is hard to distinguish that from an infection that wasn't fully cleared originally. It doesn't necessarily mean that immunity is strain-specific. (I don't know why you were downvoted; your comment seems reasonable to me!)
- dontTango 6y agoPeople are really enjoying WFH and don't want it to end. It's important to keep the fear strong. Meanwhile, I am baffled we didn't prioritize n95(or kn95) masks. Well... It's government, I'm not that baffled A significantly more rational policy would have been to prioritize masks with filters and for the less than 1/12 of elderly people who live with younger generations, move them into a hotel room and pay for food delivery and care services. All of this is cheaper and healthier than what was done.
- deleted 6y ago[deleted]
- stevenjohns 6y agoSince this will continue to be misunderstood, it's important to emphasise that the article explicitly mentions that there is 1. No evidence to support the idea of strains that have any impact on infection 2. No evidence to support the idea that the strains will resist the vaccines or weaken vaccine efficacy. This is not a "strain" in the sense of the flu, COVID-19 hasn't fundamentally changed in any meaningful way that lets us do anything other than track the pandemic's spread.
- riccia 6y agoNot questioning anything you wrote, but it would be interesting to know the strains of virus in people who acquired COVID in the mRNA vaccine trials. I imagine this is in the trial data but haven't seen it.
- CyberDildonics 6y agoHow many people actually acquired COVID in the mRNA vaccine trials?
- lvs 6y agoIn the BioNTech vaccine Phase 2/3, it was 50 any time after the first dose, but 11 after the second dose.
- CyberDildonics 6y agoThose were people who caught covid or people that had antibodies?
- lvs 6y agoPatients who received one or two doses of the vaccine who later tested positive for covid.
- rossdavidh 6y agoWell, that's _mostly_ true, but the very fact that one virus variant displaces another over the course of a month or two, while by no means definitive proof of anything, is at the very least suggestive that for one reason or another it is better able to spread. It _could_ be a neutral mutation that just spread due to a "founder affect" or something, but it would not be in any way surprising if a virus which is brand new in humans, evolved in the direction of adapting better to that new environment. What spreads better in bats, may not be the same as what spreads better in humans, and there is no particular reason to expect that this virus wouldn't be mutating in the direction that allows it to adapt to its new host. Now, that could even be a good thing, if it was adapting in the direction of not triggering the host's immune system as strongly, since it is largely an immune system overreaction that kills the host. But, while by no means definitive, I don't think we can say that there is _no_ evidence to support the idea that strains have any impact on infection. the very fact that the initial strain has been largely displaced by others, suggests at least the possibility that it has.
- sillysaurusx 6y agoWhat does everyone think of the idea that there is an 80/20 rule in play for Coronavirus? Specifically, 80% of the infections come from 20% of the infected. I’ve heard some hearsay about it, but nothing conclusive; I was hoping someone knew either way.
- graderjs 6y agoI don't know either way about your question, but aren't these sort of power law dynamics common in everything? I don't think it would be surprising if that was the case with this "pandemic" nor would it make this virus special. Just like 90% of the content is created by 10% of the people in social media, or something like that.
- herendin2 6y agoIt's important because focussing on that 20% might be far more efficient and effective
- hutzlibu 6y agoYeah, but this is known and taken into consideration, as far as I know. Like health workers who visit lots of houses, gets tested often.
- Scarblac 6y agoI don't think anybody knows who are going to be part of that 20% in advance though.
- bonzini 6y agoMaybe not who they are, but what they do.
- learnstats2 6y agoI think we have already somewhat focussed on that 20%, by asking people not to hang out in big groups. Churches and meat-packing plants are still a concern.
- known 6y agoCurious to know how it evolved/infected prior to Dec 2019
- jl2718 6y agoAntibodies mostly target the attachment heads of RNA viruses, which mutate very quickly to evade them. But that mutation also applies to its own reproductive mechanisms, like RNA polymerase, which degrades in the presence of evolutionary pressure from the immune system against the attachment proteins, so the latter strains become dormant because they lose reproductive integrity. It then takes conditions lacking an immune response to evolve back to a working polymerase and attachment head. I think it is interesting to note that the immune system itself is largely responsible for spreading most RNA viruses: inflammation, coughing, sneezing etc. Is this us evolving population-level (probably more like Dunbar number than 8B) defense in response to the general threat of viruses, or is it a weakness that each individual virus evolves to exploit. It seems to me that this involuntary spreading behavior is much more pronounced in humans than other mammals. https://scopeblog.stanford.edu/2020/04/03/how-coronaviruses-infect-us-how-infectious-viruses-created-us/ https://scopeblog.stanford.edu/2020/04/03/how-coronaviruses-... https://mbio.asm.org/content/2/5/e00150-11 https://mbio.asm.org/content/2/5/e00150-11
- oarsinsync 6y ago> It seems to me that this involuntary spreading behavior is much more pronounced in humans than other mammals. (Anecdotal) This may be why I laugh so hard each time the dog sneezes. It doesn’t happen often, and it’s hilarious when it does.
- kordlessagain 6y agoWhen this started, I did some visualizing of the virus' code: https://github.com/kordless/covid19_viz https://github.com/kordless/covid19_viz That "spike" in the graph comes from sequences in the nucleotides coding the spike on the virus, which is somewhat expected given it's repeated on the surface of the virus membrane. Apparently most of the spike encoding is from a South Asian fish. Reference in the repo.
- neuronic 6y agoWhat do you mean by "most of the spike encoding is from a South Asian fish"? As in, that's where the virus evolved/stole it from?
- stanrivers 6y agoWhat does the South Asian fish comment mean?
- overgard 6y agoThis is why I get so frustrated with people justifying continued shutdowns "until it's cured by the vaccine". Almost every highly contagious virus mutates quickly. Same with bacteria. The cat is already out of the bag, even if we do manage to completely eradicate it it'll take years. (To be clear I'm not against virus control measures, I'm just frustrated with the flawed reasoning that all this will just go away when the vaccine is within reach. It couldn't be easier to get a flu shot and yet we'll probably be dealing with the flu long into the future. If we know this will stretch into say 2022 I have to imagine that will change a lot of peoples attitudes as to how society should react)
- deleted 6y ago[deleted]
- timbit42 6y agoThe virus hasn't yet mutated enough to make the vaccine not work against it.
- overgard 6y agoWe don't know that for sure, and it has 7 different (known) strains already. Why would this be any different than the flu in that regard? Besides, we already know there are a lot of ridiculous anti-vaxxers out there who will refuse the vaccine regardless. And a lot of those people are elderly or at risk! The longer this situation goes on, the less palatable shutting down huge chunks of society seems to me to be. If this is going to be endemic, which a lot of signs and common sense reasoning points to, then the management of the disease needs to change.
- Throwaway1771 6y agoI would like to know what is known, if anyone has it handy.
- raarts 6y agoI am pro-vaccines in general, but I'll refuse the Covid-19 vaccines.
- croes 6y agoAnd still there are people who deny that the virus exists.
- jader201 6y agoIs there any real concrete — or at least scientifically backed — reasons why we’re continuing to see numbers rise, in spite of more lockdowns in place and more people (supposedly?) wearing masks vs. in previous waves where the spread and deaths seem lower than now? This is especially baffling considering how much more prepared we are (or should be?) and how much more we (should) know about the virus now vs. before. It seems like one or more of the following is happening: - Actually fewer people are wearing masks, or are wearing them less vs. previously - Even though lockdown mandates/recommendations are increasing, they’re not being followed/enforced as much - Masks aren’t as effective as we think - It’s spreading in other ways that we’re unaware of I’d love an ELI5 of why we’re continuing to see record numbers of positive test rates + deaths + hospitalizations, in spite of (again, supposedly) more diligence with masks and lockdowns. To be clear, I’m a strong believer in wearing masks and staying home (I almost never leave my house, and when I do, I’m wearing a mask), but it’s baffling and a bit frustrating to see the numbers continue to rise without anyone seeming to have answers as to why.
- Triv888 6y ago> in spite of more lockdowns in place I've been to about 20 states during this pandemic and I have never seen lock-downs strictly enforced... and I don't blame them.
- sean2 6y agoI have no credentials or scientific evidence, but I never questioned the rising cases with each wave since I assume its just a property of the exponential nature of the virus spread: in march, say you had 5 people unknowingly carrying corona-virus arrive in your city and each of them spreads it to 5 more people in a two week period, your outbreak is 50 people (seems small now). But now in December, your city has about 350 people spreading the virus but only to 1.5 close contacts in a two week period, you'd expect the next outbreak to be 500 people. I think hospitalizations are still a somewhat consistent percentage of cases, and will increase as the number of cases go up.
- craftinator 6y ago> Is there any real concrete — or at least scientifically backed — reasons why we’re continuing to see numbers rise, in spite of more lockdowns in place Anthony Fauci summed this up pretty well a few days ago in a press release. He basically said that the USA is really bad at following rules, which we are, and that with the recent holidays (Halloween, Thanksgiving) and because of the cold weather (people stay indoors more, share the same air, air being recycled and heated in HVAC systems to reduce energy consumption), that numbers would rise. And so they are. I think these human explanations are the main source of the rise in numbers. Another interesting one was in a WHO release a few weeks ago, that people seem to be experiencing "mask fatigue", or what is more generally known as "caution fatigue", where people, after having to be cautious for a long time, and not experiencing the source of that caution personally, just lose their ability to pay attention to the problem. It's the same reason the TSA inserts fake firearm pictures into the x-rays of luggage, and the same reason the military regularly inspects guard posts in key locations.
- xony 6y agothis is a great lesson for mankind, next time isolate the country before it spread
- IamZeroBalance 6y agoI'm agree. Isolating the whole country can prevent the virus from spreading.