[HN Gopher] Why is Delta so infectious? New tool spotlights litt...
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Why is Delta so infectious? New tool spotlights little-noticed
mutation
Author : infodocket
Score : 73 points
Date : 2021-11-04 20:16 UTC (2 hours ago)
(HTM) web link (www.science.org)
(TXT) w3m dump (www.science.org)
| zmmmmm wrote:
| It's fascinating to see how knowledge evolves over time. So far
| most of the emphasis has been on the spike protein and its
| cleavage mechanisms. Now we start to see that may even be a
| relatively minor factor compared to the nucleocapsid.
|
| It is quite important to understand all these things if we are
| seeing new variants arise and need to assess how dangerous they
| are likely to be. Most especially since vaccines are based on the
| spike protein on the premise that it is essential to the
| infectiousness. But what if a variant can arise with a highly
| compromised spike protein yet compensate enough to still be
| highly infectious due to other factors?
|
| The most interesting thing is to think about where the other
| empty spaces in our knowledge are that are yet to be filled in -
| what will we know this time next year that will have us saying
| "previously we thought ...."
| mdp2021 wrote:
| Forthcoming vaccine Valneva will be based on inactivated virus.
| Nucleocapsid preserved.
| angelzen wrote:
| Novavax has also applied for approval in Canada, UK,
| Australia and NZ, and possibly already received EUA in
| Indonesia.
|
| https://news.ycombinator.com/item?id=29111197
|
| https://ir.novavax.com/press-releases?category=2
|
| https://www.forbes.com/sites/joshuacohen/2021/11/03/if-
| appro...
| fsh wrote:
| The Novavax vaccine is a recombinant protein vaccine and
| only contains the spike protein:
| https://mvec.mcri.edu.au/references/novavax-
| covid-19-vaccine...
| mdp2021 wrote:
| ...plus the 'Matrix-M1' adjuvant - saponin from tree
| bark.
|
| And, if you wish, _polysorbate 80_ to assemble the spike
| proteins into nanoparticle "parcels". In fact, I think
| the Novavax particles should be radial bunches of spike
| proteins tied at their "tail" - see e.g.
| https://www.nytimes.com/interactive/2020/health/novavax-
| covi...
|
| Adequately technical and well done is the description at
| https://www.sciencemediacentre.co.nz/2021/09/14/what-do-
| we-k...
| ak217 wrote:
| The nucleocapsid is inside the live virus - it's not accessible
| from the outside. So we don't currently know of a way to train
| the human immune system to bind to it to kill live virus
| particles. So while it's important to understand the role of
| the nucleocapsid in infectivity, it's not actionable for
| vaccine technology.
|
| Conversely, there is currently no evidence that the spike can
| be "highly compromised" without reducing infectivity. The spike
| has to bind specifically to ACE2 in order to enter the cell. As
| long as that's true, vaccines can continue to target live virus
| using the ACE2 receptor binding domain in the spike protein.
| dekhn wrote:
| I lived through the entire HIV cycle (from first announcements
| in the press to the current situation).
|
| There weren't really any credible origin stories for HIV for
| years after the discovery of the virus and the syndrome it
| causes (AIDS). Eventually (more than a decade later), a
| reasonably good origin narrative evolved, but not until there
| were plenty of now-discredited origin theories:
| https://en.wikipedia.org/wiki/Discredited_HIV/AIDS_origins_t...
| kordlessagain wrote:
| I guess if we start glowing, we'll know which lab leaked.
| jazzyjackson wrote:
| > But because it is stripped of the virus' RNA genome, it can't
| hijack a cell's machinery to replicate and burst out of the host
| cell to infect more cells. "It's a one-way ticket. It doesn't
| spread," says Charles Rice, a molecular virologist at Rockefeller
| University.
|
| Did these people not take Jurrasic Park seriously? Life finds a
| way!
| shadowgovt wrote:
| Probably best not to extrapolate too much from some fun but
| inaccurate science fiction when actual human lives are on the
| line.
|
| The odds of creating a super-virus researching Delta with this
| method are far, far lower than the odds of Delta continuing to
| stack up a body-count if we can't understand it better.
| jazzyjackson wrote:
| If you want to tell the truth, write fiction.
|
| The odds of COVID19 escaping a BSL4 facility were also pretty
| low but here we are.
| civilized wrote:
| > The odds of COVID19 escaping a BSL4 facility were also
| pretty low but here we are.
|
| Only a small fraction of scientists actually believe the
| lab leak hypothesis, so it's a bit ridiculous to speak as
| if it's an established fact.
| shadowgovt wrote:
| The Chrichton story about a virus escaping a laboratory is
| the Andromeda Strain.
|
| Sometimes, fiction is just fiction.
| tejtm wrote:
| Or that movie where all the wanted posters turned into clones
| of the outlaws they represent. Hate it when that happens in
| real life
| themitigating wrote:
| Remember in TNG when it turned out warp engines damage space?
| jazzyjackson wrote:
| Fair counterpoint, but in my defense there really are animals
| that switch sex when their population is lacking one or the
| other, so there's not much fictional about it: the scientists
| were confident in their plan because they didn't know one of
| nature's tricks.
| rolph wrote:
| for general edification:
|
| https://en.wikipedia.org/wiki/Coronavirus_nucleocapsid_prote...
| alfor wrote:
| Let's try in a (safe) lab to make it more infectious, you know
| for science ! Hey, while we are doing this why not try on MERS,
| immagine the number of citation I could get for this !
|
| Let's think for one second the cost of a leak to the world
| population.
|
| It seems to me that we are doomed to self destruction if we don't
| get wiser fast.
| travoc wrote:
| Don't forget to lie about it when you get caught.
| jdavis703 wrote:
| Viruses will always mutate. We can either let nature beat us to
| the punch or we can attempt to race nature. Also there's a lot
| of literature on BSL 4 labs with crazy safety lapses (e.g. labs
| using duct tape to seal leaks and what not). If we wanted to
| treat BSL 4 with the same safety culture of modern nuclear
| technology we could. This is ultimately a policy problem, not a
| technical problem (e.g. shutting down dangerous labs and
| defunding the researchers running offending labs).
| frankfrankfrank wrote:
| What I find most shocking about all of this is that we can't even
| publicly or openly discuss things anymore because even if it is
| no longer done, there is surely still a latent deterrent effect
| from all the censorship and public persecution of anyone who was
| not willing to tow the regime message.
|
| When a culture of fear and intimidation sets it, it is extremely
| dangerous and usually in my experience even terminal for things
| like organizations and companies.
| belltaco wrote:
| I blame the rampant misinformation and taking things out of
| context for that.
|
| > public persecution of anyone who was not willing to tow the
| regime message
|
| What regime? The side that tried to tell us covid was harmless?
| e.g.
|
| https://www.youtube.com/watch?v=NAh4uS4f78o
| ashtonkem wrote:
| ... we're openly discussing this here. What are you talking
| about?
| netflixandkill wrote:
| He's trying to waste people's time trolling.
| mdp2021 wrote:
| Or was just clumsy and communicationally ineffective while
| attempting to note some trends and events which are not
| negligible at all: yes, we are discussing matters in a cool
| civilized manner (in general and sufficiently) here, while
| elsewhere moderators banned users who objected that
| vaccines should be a topic at all in sections dealing with
| the cutesy of small cats with big eyes (Reddit), or
| platforms decided that no discussion can be made about
| vaccine toxicity (YouTube), etc.
|
| It is refreshing that relative visibility and a better
| median allow us a proper environment. It's not granted.
| kordlessagain wrote:
| You find it shocking that, even thought it's no longer done,
| discussing things openly will open up someone to censorship and
| public persecution?
|
| What did we do 25 years ago to discuss things? It sure the hell
| wasn't Twitter or Facebook. It was sitting down with the people
| around us and having a reasonable conversation that didn't
| include snippets from stupid corners of some webby thing.
|
| It required thought and a reasonable search of the information
| at hand, which was slower back then. We were more methodical in
| forming our opinions and what we put our attention on.
| kwertyoowiyop wrote:
| Where is it that you're not able to publicly or openly discuss
| things? There has never BEEN such a wealth of opinions and
| discussion freely accessible to everyone.
| rsj_hn wrote:
| Correct, which is why there is a such a strong push to get
| Facebook to increase censorship. All of this communication
| freedom is absolutely freaking elites out, as their ability
| to control the discourse has slipped substantially.
| PaulDavisThe1st wrote:
| OK, so by many standards I'm "elite" (in terms of net
| worth, education etc.). But I don't think I'm part of the
| "elite" you're referring to, and I'm still concerned about
| the information flows enabled by the internet. Does that
| make me a member of said elite, or is there something else
| going on?
| furgooswft13 wrote:
| It makes you a useful idiot.
| nawgz wrote:
| > by many standards I'm "elite" (in terms of net worth
|
| High 8 figures+ net worth? Generationally wealthy? With
| government connections? Otherwise I don't think anyone
| cares about you
| PaulDavisThe1st wrote:
| Inside the top 10% for net worth would be my criteria for
| this, and I think many other Americans too. No self-
| aggrandisement here, I just wouldn't want to pretend to
| be "an ordinary guy on the street" (whatever that
| actually means).
| nawgz wrote:
| That would make 30 million people "elite". We mean the
| 0.01% who enact laws and escape enforcement, not people
| who live a comfortable life lmao
| alexashka wrote:
| No, elite is defined by ability to affect non-trivial
| change within society.
|
| If you don't have that ability, you're just upper middle
| class.
| davidw wrote:
| So is the truck driver guy who got elected in NJ 'elite'
| or not?
| PaulDavisThe1st wrote:
| As he is likely to find out if he ever gets re-elected,
| he will be part of the elite soon, even if he rejects the
| label (which I am sure he will).
| throwaway6734 wrote:
| Elites are the people I don't like and the more I don't
| like them the more Elite they are.
| rsj_hn wrote:
| I'm not going to try to diagnose you, but in general, the
| outrage that people have that someone is saying the wrong
| thing online is exactly what I'm talking about.
|
| The definition of "elite" is of course murky, but that
| does not mean that it's not real. There is a very real
| process of preference cascades among the discourse of
| those who hold power in society together with the
| professional classes that identify with them (even if
| they themselves do not hold much power). The ability to
| control the public discourse has collapsed as centralized
| media has been converted into decentralized social media,
| which has led to panic and calls to bring social media
| back to heel.
|
| Part of this is the (correct) belief that Trump and other
| populist phenomena - for example Democratic Socialists
| and the rise of Bernie Sanders -- are made possible by
| people being able to communicate with each other
| directly, bypassing whatever Overton window the major
| media outlets try to set, and even forming their own
| tribal Overton windows with _no regard_ to what
| respectable people at the _Heritage Foundation_ or the
| _New York Times_ or members of the Davos-set think about
| this. These outsiders can then win elections or at least
| threaten to win elections. That creates a moral panic
| about wrongthink, "misinformation", fact-checker
| discourse, and general terror that ordinary people are
| able to communicate freely, form their own opinions, and
| coordinate without the supervision of elite consensus.
| PaulDavisThe1st wrote:
| The point is surely that many people without much power
| take issue with the discourse that the internet has
| enabled, and that therefore it is incorrect to hear such
| opinions and conclude that they can only be about the
| retention of some kind of power.
|
| If you'd like, you could accuse them of "false
| consciousness" (long a favorite derisive put down from
| Leninists and their friends), or of simply being patsies
| for the powerful (more typical of the current US right).
|
| So I'm wondering what your explanation of this concern
| among non-elites?
| rsj_hn wrote:
| > The point is surely that many people without much power
| take issue with the discourse that the internet has
| enabled
|
| Well sure, but that's always been the case. E.g. in the
| past, people who were outside the overton window had no
| choice but to get mad at views they disagreed with as
| they had great difficulty in getting their own voices
| heard.
|
| Now they can have their own voices heard. They can make
| their own overton window and completely ignore someone
| else's.
|
| Point being, there is a democratization at work, but
| whereas those on the outside always had to put up with
| disagreeable voices, now elites must also put up with it,
| which is something they are not used to, indeed they are
| offended by needing to - it's a real shock to them - and
| this is where the calls for censorship of social media
| are coming from.
| fallingknife wrote:
| You can rationally be concerned without being one of the
| "elite". But if your solution involves trusting the real
| "elites" to censor information, then you would have to be
| one of them because you trust them to act in your
| interests.
| [deleted]
| thenewnormal wrote:
| Let's pick an example - there is very little scientific
| evidence to support the idea that wearing a mask provides any
| net public health benefit against your exhaled viral
| particles (and this is bourne out by a consideration of the
| construction, mesh size, etc, of cloth masks, compared to the
| size of viral particles).
|
| As far as I can see it, this statement is non-controversial
| and supported by the evidence (or lack thereof).
| drusepth wrote:
| That's a great example of the type of topic I could see
| people shutting down arguments/conversations over.
|
| In a very general sense, it doesn't make a lot of sense for
| laypeople to argue among themselves over the findings and
| guidance of experts. At best you see an extremely-localized
| effect (e.g. you convince someone it's okay to not wear a
| mask and they happen to not catch COVID) and at worst you
| add to the pile of disinformation and confusion around the
| whole thing (e.g. you convince someone that masks aren't
| effective at viral load reductions).
|
| In another sense, presenting one side of an evolving,
| actively-researched subject and painting it as fact (e.g.
| "masks aren't effective") doesn't help either. What we know
| about the virus and its transmission lifecycle changes as
| we learn more about it and it's often prudent to err on the
| side of caution in the context of potential deaths,
| especially when there are arguments actively being made for
| the effectiveness of those tactics (e.g. masks are not
| completely ineffective).
|
| For your courtesy, I'll conclude with this and excuse
| myself from the thread, as I'm not here to argue: I wish
| more people got their news, guidance, and expertise from
| vocal experts in the field and those experts'
| interpretations, rather than forming their own personal
| interpretations bourne from individual studies, which vary
| wildly per study for innumerable reasons rarely obvious to
| a layperson. I say this to mean: don't bother taking the
| time to find individual studies that say masks aren't
| effective -- there are plenty of studies I could also dig
| up saying the opposite, and neither one of us should be
| forming conclusions based on strangers throwing links at
| each other on the internet.
|
| >Where is it that you're not able to publicly or openly
| discuss things? There has never BEEN such a wealth of
| opinions and discussion freely accessible to everyone.
| reply
|
| In a roundabout way, I'm agreeing with you here. Not
| because I think I'm right or you're wrong, but because
| there's really no point in either of us arguing over it
| here if neither of us are actually publishing papers,
| providing guidance, etc.
| thenewnormal wrote:
| "Just trust the experts and ignore anything else you
| might read." Sorry, you'll forgive me for completely
| ignoring that advice.
|
| >there are plenty of studies I could also dig up saying
| the opposite
|
| This has been promised to me many times, and never
| delivered.
| stonemetal12 wrote:
| How much evidence do you need? Here are 15 studies (a mix
| of experimental and epidemiological). That cloth masks
| help, and have no real determents.
|
| https://www.cdc.gov/coronavirus/2019-ncov/science/science-
| br...
| thenewnormal wrote:
| Assuming you live in the US, you'll get to find out the
| long term developmental and social effects that forcing
| toddlers and young children to both wear masks and see
| most faces in masks.
|
| I stopped reading your link when it presented its first
| case study as that story about two Covid-positive
| hairdressers. It also has to add the caveat that "Data
| regarding the "real-world" effectiveness of community
| masking are limited to observational and epidemiological
| studies."
| ceejayoz wrote:
| https://www.economist.com/graphic-detail/2021/09/03/real-
| wor...
|
| Real-world test of both cloth masks and surgical masks,
| demonstrating a decreased prevalence in towns randomly
| selected for mask distribution and education (not mandates,
| which is important; nowhere near 100% compliance, with 13%
| vs 42% masking) across 350,000 subjects.
|
| > The distribution of surgical masks resulted in a striking
| 35% reduction in confirmed symptomatic cases among people
| aged 60 or older.
|
| Again, that's without a masking _mandate_ or even 50% mask
| compliance.
| themitigating wrote:
| You created your account one day ago and it's name is even
| an anti-mask anti-government slogan.
|
| This site had just been overwhelmed with people who don't
| want discourse or even to change minds. They want to make
| their fringe views seem more popular than they really.
|
| The worst part is all the effort people have to do finding
| studies to disprove you while all you do is spout
| unverified conclusions.
|
| I know it's against the rules to attack a poster but I'll
| risk it.
| threeseed wrote:
| In South Korea, major study found mandatory wearing of
| masks reduced COVID-19 rates by 93.5% and practicing both
| social distancing with masks on public transport during
| peak hours reduced infection rates by 98.1%.
|
| https://www.science.org/doi/10.1126/sciadv.abg3691?utm_camp
| a...
| ipaddr wrote:
| The modeling is based on masks no one is using. If your
| mask doesn't cost at least $300 dollars it will not have
| the same effect.
| threeseed wrote:
| In Australia at least you do see N95 masks being used.
| And K80/K94 ones are very popular especially amongst
| Asian communities.
|
| But the type of mask is irrelevant to the discussion.
| It's about whether they are effective in preventing
| transmission. And on that point the answer is
| unequivocally yes.
| SketchySeaBeast wrote:
| KF94 masks are the rough equivalent of N95s, which are
| relatively cheap and plentiful. When I go out I now use a
| CAN99 mask.
| azinman2 wrote:
| This one was getting a lot of media attention:
| https://www.washingtonpost.com/outlook/2021/09/09/masks-
| rand...
|
| A list of 49 studies that back it:
| https://www.kxan.com/news/coronavirus/do-face-masks-work-
| her...
| strogonoff wrote:
| Proper mask wearing and replacement, understanding how
| masks work--all the things I observe in every study
| concerning masks as prevention for COVID and yet almost
| never in real life.
|
| (FWIW I wear a mask, except when I only have a used cheap
| surgical one and almost nobody around is wearing a mask
| correctly. I'm not doing society any good by getting sick
| from breathing in whatever badness has stuck in the mask
| during use, and I can't save the situation by being the
| one person properly wearing a mask.)
| thenewnormal wrote:
| It's all modelling. They also have to also say:
|
| > The limited number and type of experiments in this
| study means that there is uncertainty associated with our
| extrapolated findings.
|
| All results also use masks that are designed and rated
| for particular filtration properties, and are fitted with
| no leakage. I see basically none of the above in my day
| to day life. I'll say it again - there is incredibly
| limited evidence that the masks we all wear every day,
| with amount to random bits of cloth with gaping holes
| around the face (and are typically applied, removed, and
| re-used in a remarkably causal fashion for something
| that's supposed to contain biohazardous waste), do anyone
| any good.
| threeseed wrote:
| a) There are cited references within the paper that are
| based on real-world analysis. The onus is on you to
| refute the paper on its merits as well as those cited
| instead of dismissing anything based on modelling.
|
| b) Don't move the goalposts. You said that masks provide
| no net public health benefit. They clearly do. Some masks
| are obviously more effective than others but that doesn't
| change the fact that they are effective.
| ipaddr wrote:
| Social media, youtube, the press. Anyplace comments can be
| censored.
| eckmLJE wrote:
| I find your comment to be very vague -- what are you talking
| about exactly?
| fallingknife wrote:
| From the description it seems like the nucleocapsid protein
| mutation is something that would make the virus more effective in
| any given host. Whereas a spike protein mutation would be
| specific to the host since that is a part of the virus that
| interfaces with the host cell. In that case I would expect such a
| protein to already be very optimized (even in a lab leak
| scenario). Am I missing something here?
| ak217 wrote:
| The virus evolved in bats, which have a much faster metabolism
| (to support the metabolic requirements of flight) and a
| constitutive (always on) immune response. This means in bats,
| the virus is always "on the run" from the host immune system
| and the host may never actually completely extinguish the
| infection, allowing it to continue at a low level while
| reducing inflammation.
|
| The trade-offs and selective pressures are different in the bat
| host compared to human. Packaging more copies of the mRNA per
| particle implies slowing down particle production so more mRNA
| can be made, but in bat that may unacceptably slow down the
| generation time. That's just one plausible mechanism of many,
| including simply that the protein structure was just not as
| "optimized" as you expect prior to the spillover event.
| [deleted]
| kwertyoowiyop wrote:
| Can any commenter who actually has a medical degree please
| indicate this, so we can separate the wheat from the chaff? :-)
| imnotlost wrote:
| Maybe Dr. Oz can help! (joking!)
| bena wrote:
| Why would someone with a medical degree be able to verify the
| works of research biologists?
|
| This comes from a team led by a woman whose credentials in this
| field are very nearly impeccable.
|
| Not to mention, this article is pretty much information that
| _we_ have no ability to act on. This is more like something you
| read and go "Huh, that's interesting" and then move on. It's
| an indicator that we're learning more. It doesn't need approval
| from your General Practitioner.
| ceejayoz wrote:
| People keep making this mistake. A medical degree here is about
| as relevant as asking a mechanic to opine on metallurgy.
| hcurtiss wrote:
| I get it. We need the tools. But, man, this all strikes me as
| super dicey. They're manipulating particles without the ability
| to replicate, but it sure feels like they're tinkering with
| humanity on the edge of a knife. I can't help but worry something
| could go wrong.
| [deleted]
| peakaboo wrote:
| It's too late now anyway. Humanity didnt listen to the warnings
| because the officials said the vaccine is safe.
|
| Lots of sickness on the way for humanity due to these vaccines.
| belltaco wrote:
| Nah, humanity ignored covid because their leaders told them
| it harmless.
|
| https://www.youtube.com/watch?v=NAh4uS4f78o
|
| We're still seeing the effects of harmful disinformation
| about the vaccine in East Europe.
| trhway wrote:
| There is no "the vaccine". There are several existing
| vaccines, and so far no one prevents infection, nor
| prevents spread. The only thing current vaccines do is
| making the illness softer. Yet the governments everywhere
| pushing the mandate which would have made sense only if the
| vaccines prevented infection and spread.
|
| Whole stuff of an emergency department in a Russian town
| resign refusing to get vaccinated. In addition to their
| main job they also work in the local covid hospital, and so
| far nobody of them has gotten ill. They are being forced to
| either get vaccinated or resign:
|
| https://www.rbc.ru/society/04/11/2021/6183924a9a794708a564a
| e...
|
| > but it sure feels like they're tinkering with humanity on
| the edge of a knife. I can't help but worry something could
| go wrong.
|
| well the current Covid is a result of such experiments -
| the original gain-of-function NIH grant channeled through
| the Dvorjac's EcoAlliance to the Wuhan lab even had the
| "Human Subjects Involved" checked. Gain-of-function in
| human model with human specific genetic modification of the
| virus (check the EcoAlliance's DARPA proposal) - what can
| go wrong... Well, now we know at least one such scenario
| for real.
| mcguire wrote:
| No vaccine _prevents_ infection, nor _prevents_ spread.
| trhway wrote:
| that is antivax propaganda. The main push of the
| antivaxxers these days is associating the successful,
| effective and well proven vaccines (like the ones against
| polio, etc.) with the obviously failing (except for the
| softening of illness effect) covid vaccines. The covid
| vaccines are at the level of those every year flu
| vaccines - make sense for vulnerable population,
| otherwise no effect on infection and spread.
| mrtesthah wrote:
| The sickness of which you speak is that of your own mind.
| Don't project your own mental illness out onto the rest of
| the world.
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(page generated 2021-11-04 23:00 UTC)