[HN Gopher] New coronavirus variant: What do we know?
___________________________________________________________________
New coronavirus variant: What do we know?
Author : justforfunhere
Score : 132 points
Date : 2020-12-21 10:54 UTC (12 hours ago)
(HTM) web link (www.bbc.com)
(TXT) w3m dump (www.bbc.com)
| DrBazza wrote:
| A good visualization of the mutations, including the South
| African one that isn't related, but also increasing:
|
| https://nextstrain.org/groups/neherlab/ncov/S.N501?c=gt-S_50...
| robhu wrote:
| Ewan Birney (deputy directory of EMBL European Molecular Biology
| Laboratory)'s Twitter is a really good source of first class
| scientific information on this.
|
| You need to scroll back about 2 days to get the latest info (and
| he refers to the Twitter accounts of others in the field who can
| give more information).
|
| His Twitter profile is @ https://twitter.com/ewanbirney/
|
| (Ewan is awesome - he is also (co)director of EMBL-EBI European
| Bioinformatics Institute, and I had the honour (as a Computer
| Scientist) of working there for nine years)
| occamrazor wrote:
| Direct link to the thread where he explains why the evidence,
| although not conclusive, strongly supports a higher infectivity
| of the new variant:
| https://mobile.twitter.com/jcbarret/status/13407169016101724...
| maest wrote:
| Are there any non-twitter sources available? I can't access
| that website.
|
| Also, I doubt twitter is the place where that information
| should live long-term anyway.
| jghn wrote:
| I did see him mention on twitter the other day that he was
| going to be on a BBC segment talking about this, so there
| could be video archives on that front
| iso1631 wrote:
| https://threadreaderapp.com/thread/1340716901610172416.html
| _Microft wrote:
| Try nitter, it's a fast alternative to reading Twitter
| content on Twitter itself. I modified the link above for
| you:
|
| https://nitter.net/jcbarret/status/1340716901610172416
| muxator wrote:
| Visiting Hacker News with a text-mode browser (Links2, in
| this case) is so liberating! Twitter says that my browser is
| not supported (unsurprisingly enough).
|
| Well, I think I'll have to adapt to ditch a website that
| needs a shit-ton of JS to serve me a few KibiBytes of
| content.
| poma88 wrote:
| Boris needed a news piece to lock the City down.
| hestefisk wrote:
| That's not very helpful.
| poma88 wrote:
| Mutations are pervasive and not well flagged.
| anonymousDan wrote:
| The talk of the virus potentially being on a path to vaccine
| escape is very worrying. Sounds like we might end up in a
| situation where we have seasonal COVID like we do with the flu :(
| herbst wrote:
| At this point i heavy doubt we dont. If this mutation took
| place after one year, what will come in two or three.
| jjgreen wrote:
| There's been a certain amount of public arguments between the
| government in the UK (yay Christmas) and scientists (boo
| Christmas). I really hope that this is not a tactical
| exaggeration used by the latter to get their way that's got way
| out of hand ...
| plutonorm wrote:
| It seems to me to be possible. I'm undecided either way. Also,
| isn't it suspicious that anyone who has suggested this is
| downvoted into oblivion/flagged?
| [deleted]
| gns24 wrote:
| I think most people seem to be underestimating just how bad this
| is. During the recent 4-week lockdown it was already clear that
| something odd was going on in Kent; whilst case counts were
| dropping in the rest of the country, they continued to rise
| significantly there. Something was clearly different.
|
| Now high case counts are spreading from the South East into the
| rest of the country. We don't know whether we can even stop the
| growth. During the last lockdown schools remained open; I suspect
| that it may be necessary to close them in order to just stop the
| growth. A significant reduction in cases looks impossible.
|
| This strain has probably already spread to tens of other
| countries. Every country which is just about holding things
| together, whatever their strategy, is going to struggle with a
| significantly more transmissible variant of the virus.
| numpad0 wrote:
| I think what most people has is issues with resolving double
| binds; there's only one way out and it's hard lockdown with
| rationing, which kind of require willful sacrifices, of jobs to
| say super least.
|
| The general public anywhere isn't ready for trolley problems
| even if told to optimize for least body counts. Basically the
| whole free world is in disbelief of the story that there are
| people on tracks(except TW/AU/NZ?).
| oliwarner wrote:
| It was only a lockdown in name. Schools were in. Shops were
| open. Ministers have even been supplying pubs with methods to
| skirt the rules (scotch eggs ffs).
|
| Not saying it's not bad, just that very little is actually
| being done to prevent the spread. Govt care more about keeping
| people in work.
| iso1631 wrote:
| Yet it worked well. In Cheshire (not badly hit), daily cases
| halved between the start of lockdown and end, having doubled
| in the previous month. In Cumbria it was even more of a drop
|
| Overnight covid paitents in the NW went from a peak above
| that of April in Mid November (i.e. had caught it in
| October), dropping to 70% of the peak a month later, same in
| NE+Yorks.
| stubbedtoe wrote:
| For those interested in looking at the raw data,
| https://coronavirus.data.gov.uk/details/interactive-map is a
| useful visualisation of cases by region, over time.
| LatteLazy wrote:
| I don't disagree, but it would be really nice if we could
| classify lockdowns better. The original lockdown furloughed a
| LOT of workers, closed schools and closed virtually all shops.
| Today's "super tier 4+ lockdown" doesn't seem to apply to shops
| at all (my local shops were all open this morning, is wrapping
| paper really an "essential"?). Workers are mostly going in.
| Schools that have remained open unless they already closed and
| childcare is still running.
|
| They've basically just shut restaurants. That's the only change
| I can see...
|
| I've posted elsewhere that my cynical view of the UK gov
| approach is that they are talking tough and doing nothing. So
| maybe I'm biased?
|
| Perhaps a move transmissible strain will force real action?
| lol768 wrote:
| > I've posted elsewhere that my cynical view of the UK gov
| approach is that they are talking tough and doing nothing. So
| maybe I'm biased?
|
| It's felt like this with all of the tiers to be honest.
|
| They just don't go far enough and the populace is fed up with
| taking much heed of the rules too.
|
| The November "lockdown" felt very, very different to March
| when the roads etc were quiet - and it actually felt like
| people were taking this seriously.
| sgt101 wrote:
| Schools were still open, and building sites - which made a
| very significant difference to movement and traffic.
|
| However, if you look at the graphs the dynamic of virus
| growth did seem to be significantly changed by the
| intervention.
| LatteLazy wrote:
| I have to be careful I don't wander into conspiracy
| theories but...
|
| I'm fed up because so many people flout the rules with no
| consequences. I suspect that the lack of consequences is
| intentional. If everyone flours the rules, the economic hit
| will be smaller and Bojo can claim he did something and its
| not his fault no one listened. The government have created
| a situation where the only logical action for normal people
| is business as usual, that means large excess deaths, and
| the government has plausible deniability. Whoops.
|
| /RantAndParanoia
| SideburnsOfDoom wrote:
| > If everyone flours the rules, the economic hit will be
| smaller
|
| Only assuming that there's no economic hit to a rampant
| pandemic spreading death, hospitalisation and illness.
| Which is a barking mad assumption. It never was "illness
| vs economy" you either have both good, or you have
| neither good. They can't be separated.
| iso1631 wrote:
| > I'm fed up because so many people flout the rules with
| no consequences.
|
| Been that way since Barnard's Castle.
|
| The latest decision that says MPs can see their siblings
| for Christmas Dinner on the 25th, but a Nurse working on
| the 25th can't see their parent with terminal cancer for
| dinner on the 26th, will hopefully be ignored.
| londons_explore wrote:
| What's especially funny is the latest Tier 4 Health
| Protection legislation has a _specific_ exception for
| groups meeting in the grounds of castles...
|
| I can't believe it hasn't made headlines yet...
| simonbarker87 wrote:
| There was a decent drop in cases in November from what I
| can see. You're right though, the first lock down felt very
| different.
|
| Sadly the rules are laxer than they should be but the
| government can't enforce the rules effectively so are
| putting in enough grey-area that people can sort of decide
| for themselves.
|
| Sadly people are very short term focussed and unable to
| make the most of the situation and instead complain and go
| about their normal lives with just enough changes that they
| "feel like they're doing their bit".
|
| I love the gym but the move to "keep gyms open" was the
| best example of people not really getting it and being sad
| that their toys had been taken away.
|
| The moto in our hose at the moment is "just because you can
| doesn't mean you should"
| sgt101 wrote:
| People are very short term focused on things like; not
| losing their houses, not losing their businesses,
| maintaining their families, maintaining their mental
| health, looking after children.
|
| I don't know your situation, but I have lived a very
| isolated existance for the last 9 months because I am
| able to. _MANY_ people I know are not in this position.
| simonbarker87 wrote:
| I wasn't referring to things people HAVE to do to survive
| - I'm talking about stuff they don't have to do but want
| to do because they "just want to be back to normal"
| bealesd wrote:
| Couldn't agree more. People who have already isolated in
| previous lockdowns, and lost income, probably can't
| afford to play it safe. Expecially if they percieve the
| risk of Covid to be less than the financial risk of
| playing it safe.
| detritus wrote:
| On my walk to work this morning, I detoured down a local main
| street, curious to see what shops were considering themselves
| 'essential' and remaining open.
|
| Apparently this time around, travel agents and jewellery
| sellers have added themselves to the list, with a few barbers
| clearly operating illicitly behind half-drawn shutters.
|
| I was bemused by the very chi-chi local middle class deli
| near my home insisting they'd be staying open when I enquired
| on Saturday evening. I mean, sure they sell food, but really
| - I'm unsure how vital to survival artisanal cheese and pasta
| is!
|
| Bluntly, without the sincere threat of fines or whatever, no
| action will be taken. UK-dwellers' sense of entitlement to
| 'freedoms' seems drastically diluted compared to what I
| witnessed on the continent a few months back, when I was
| able.
|
| We deserve everything we get.
|
| - ed, whups - clearly I meant something like 'drastically
| inflated', not 'diluted'.
| shalmanese wrote:
| > I was bemused by the very chi-chi local middle class deli
| near my home insisting they'd be staying open when I
| enquired on Saturday evening. I mean, sure they sell food,
| but really - I'm unsure how vital to survival artisanal
| cheese and pasta is!
|
| Let's not repeat the mistakes of the first lockdown. If you
| close down too many places, all that causes is everyone
| cramming into the same few places still open, causing
| superspreader events. At one point, LA shut down outdoor
| farmers markets and many cities including London slashed
| their public transit schedules, leading to overpacked
| busses and trains.
| jkinudsjknds wrote:
| I don't know if I agree that a restaurant selling artisinal
| cheeses should be held to different standards than the
| lowest common denominator of nutrient gruel restauranteers.
| jmnicolas wrote:
| > UK-dwellers' sense of entitlement to 'freedoms'
|
| Seriously?
|
| We (the West, I'm not from the UK) are losing our freedom
| at an unimaginable speed even a few years ago and you think
| freedom is negotiable? I find this appalling how easy we
| ease into a dictatorship everywhere in Europe.
| LatteLazy wrote:
| It's interesting that no one seems to give a shit about
| real freedoms like free speech or democracy, detention
| without trial or access to lawyers. But when you close
| the pubs (or the artisnal pasta makers), suddenly we're
| on a dictatorship.
| jmnicolas wrote:
| This is so unjust: you don't know me but you basically
| reduce me to an angry guy that can't get drunk with his
| friends.
|
| ALL our freedoms are attacked: the social media
| censorship reached crazy levels lately, and let's not
| talk about democracy given the disgusting spectacle the
| US has shown this year (my country doesn't fare any
| better).
|
| When someone is condemned to financial ruin because her
| shop is not allowed to open, this is not a matter of self
| entitlement, yes I think these are the beginnings of
| dictatorship.
|
| As I said I'm not from the UK but as far as I know people
| in London had more freedom during the WWII aerial
| bombings.
| onion2k wrote:
| _When someone is condemned to financial ruin because her
| shop is not allowed to open, this is not a matter of self
| entitlement, yes I think these are the beginnings of
| dictatorship._
|
| On the other hand, people are actually dying of Covid.
| Given the choice I'd take financial ruin over death.
| detritus wrote:
| During Rationing, you mean?
| jtbayly wrote:
| Yes. During rationing.
| im3w1l wrote:
| To many people democracy is just a means to an end. And
| the end goal is a simple life with simple pleasures.
| detritus wrote:
| Hence my enclosing Freedoms in single quotes.
|
| I tend to communicate quite drily - that's often hard to
| put across online.
| LatteLazy wrote:
| I think you're exactly correct.
|
| It drives me nuts when people talk about freedom, they
| have no actual idea what freedom is or takes and their
| actions undermine it. Freedom doesn't mean "I can do
| whatever I like with no consequences", but that's what
| people really want.
|
| Freedom is just a better sounding word than selfishness
| these days :(
|
| <Steps-down-from-soapbox>
| carlmr wrote:
| >Freedom doesn't mean "I can do whatever I like with no
| consequences"
|
| Depends on your definition of freedom. The issue with
| this kind of freedom is that your freedom encroaches on
| other people's freedoms, so most societies agreed that we
| should have less freedom in favor of fairness.
|
| Exactly where the trade-off is to be made is subjective
| and cannot be derived from facts alone.
|
| We have a lot of freedoms that encroach on other people's
| freedoms, it's impossibly to make a clear cut on where
| fair ends and personal freedom begins.
|
| Allowing people the freedom to sell sugar will inevitably
| lead to more diabetes and earlier death. It tastes good
| and it's addictive.
|
| Sugar costs a lot of people some of their freedom to live
| and move. But if we didn't allow selling sugar we would
| take away the seller's freedom and the freedom to choose
| from the consumer.
| jtbayly wrote:
| Your sugar example is no good. Sugar doesn't take
| people's freedoms away. It has no agency and doesn't
| enforce anything. Like any action, eating sugar may have
| consequences good or bad for the individual, but that has
| nothing to do with freedoms unless the government starts
| telling people they may not eat more than x grams per day
| or something like that.
| tinus_hn wrote:
| In the Netherlands, although not in every city, in some
| COVID-19 is an excuse for banning demonstrations.
| adwww wrote:
| Re the deli and other quasi essential shops, it would seem
| unfair if they closed when you can still buy your fancy
| cheese and olives in a supermarket.
| tonyedgecombe wrote:
| I don't know why you expect it to be fair. The policy
| needs to be effective first and foremost. Schemes like
| furlough are there to support people who are most
| affected.
| LatteLazy wrote:
| The issue isn't really whether that shop is essential.
| The issue is that the greeting card store next door is
| also open, because they've decided they're essential. And
| none of these stores (including the super market) is
| enforcing mask requirements because none of the others
| are and they don't want to be the only one.
|
| In 1000 little steps you are suddenly miles away from a
| real lockdown. You're basically BAU, but the pub is shut
| ever other week (unless you buy a scotch egg in which
| case it is also essential).
|
| I don't care if people are eating gourmet olives. But we
| need to realise that making excuses for doing nothing is
| still doing nothing.
| Izkata wrote:
| It's essential to the owners or their employees, who may
| risk losing their home if they can't make a living.
|
| Lockdowns have gone on long enough that people are
| deciding to risk it because they have _far_ more pressing
| concerns.
| oli5679 wrote:
| Citymapper mobility index is quite interesting for
| quantifying level of lockdown.
|
| https://citymapper.com/cmi/london
| hammock wrote:
| >During the recent 4-week lockdown it was already clear that
| something odd was going on in Kent; whilst case counts were
| dropping in the rest of the country, they continued to rise
| significantly there. Something was clearly different.
|
| They said the same thing about overnight vote counts in Fulton
| County, GA... turns out it was nothing.
| saberdancer wrote:
| I am not from UK but I think this is an important and critical
| information. How is the daily deaths chart in Kent and London?
|
| Deaths will be visible later on than infections but by now
| there should be a visible effect if IFR/CFR is different. If
| there is no visible difference it's possible that R0 increased
| while IFR remains steady (which is bad enough).
| Shorel wrote:
| >During the last lockdown schools remained open
|
| Honestly, that doesn't sound like a real lockdown at all.
| ryandrake wrote:
| People really need to stop using the l-word. It grossly
| overstates what's happening. They called it that here in the
| USA too, and it was just as ridiculous. We had these so-
| called Stay At Home orders, which had tons of exceptions and
| were both ignored by the population and unenforced by the
| government. They might as well have been called Stay At Home
| Suggestions.
|
| An actual sustained lock-down would likely stop the virus's
| spread, allowing us to finally get back to normal. But nobody
| wants to claim ownership of the economic fallout, so instead
| they do these half-assed lock-downs which don't really
| accomplish much besides making the government look like
| they're doing something.
| fsh wrote:
| Without proper statistical analysis and epidemiological
| modelling this is nothing more than an anecdote. The last
| twelve months should really have taught us not to trust those.
| kashprime wrote:
| It's fortunate that Pfizer/BioNTech chose the whole spike
| protein mRNA as their vaccine candidate over the one that
| focused just on the receptor binding domain -- which the UK
| mutation changed. Wise choice, and hopefully it will work well
| against this new variant.
| https://www.nejm.org/doi/full/10.1056/NEJMoa2027906
|
| Moderna's vaccine was focused on the whole spike protein too.
| So even though there are crucial mutations in this mutation,
| both leading vaccine candidates hopefully will still be
| effective.
| lbeltrame wrote:
| > I think most people seem to be underestimating just how bad
| this is.
|
| No, there is no reason to panic yet. Concern, perhaps, but not
| panic.
|
| There are a truckload of confounding factors in the middle,
| including potential "founder effects" (when a variant becomes
| dominant because it is the first to take hold, and just outruns
| the others out of larger starting numbers).
|
| There is not yet solid proof of "70% more transmissible" given
| that all the data there are is the SAGE meeting minutes. We
| don't know from where the data came from, and how the
| estimations were made. There are huge uncertainties.
|
| Until the biological analyses are done, one needs to keep their
| cool. Sadly, that wasn't what the UK government did.
| gns24 wrote:
| Founder effects don't explain why this new strain took over
| as the dominant strain in London.
|
| Even if we suppose the chance of it being as bad as suggested
| is only 50%, we should panic now, rather than waiting until
| we have solid proof and risk having a public health disaster.
|
| Personally I suspect the UK didn't panic in its announcement
| and that this situation had been under surveillance for some
| weeks.
| hnarn wrote:
| This comment should be flagged, it's extremely sensationalist
| and below what I expect from HN.
|
| 1. On what basis do you say that people are underestimating the
| seriousness? Are you a doctor? An epidemiologist? Do you have
| any medical education?
|
| 2. Do you have any supporting evidence for your claim that it's
| obvious that something was "off" about Kent and that there is a
| spread attributable to this? Or are you just drawing lines
| between dots? You source nothing, so it's impossible to know.
|
| 3. On what basis do you claim that this strain "probably" has
| spread to tens of other countries? Who are you, and based on
| what do you make this guess?
|
| The pandemic is taxing enough on everybody as it is. We DO NOT
| need "educated guesses" from armchair epidemiologists that do
| not identify themselves or what sources they are drawing their
| conclusions from -- and I could expect as much from a random
| comment field on the internet, but not as the top voted comment
| on HN.
| gns24 wrote:
| 1. No, I don't have any relevant qualifications. But it's not
| the epidemiologists who I think are underestimating the
| seriousness - what's surprising me is that everyone else is
| largely ignoring this. I think people think 70% is not a big
| amount, rather than the difference between slight decrease
| and rapid exponential growth. Clearly a lot of foreign
| governments do think it's serious given the travel plans they
| have put in place.
|
| 2. I spend an unhealthy amount of time looking at data.
| Before this incident there were always random peaks which got
| explained by outbreaks at abattoirs or freshers' week, and
| national movements, but this change stood out. Week after
| week it kept behaving differently. My partner and I had
| already speculated about the change possibly being down to a
| mutation, since although that seemed incredibly unlikely
| nothing else explained what we were seeing, but dismissed
| that idea since obviously the authorities would have noticed.
| It turned out they had noticed, they just hadn't announced
| it.
|
| 3. A quick calculation: recent infection surveys suggest
| about 1% of people in the UK have the virus. The new strain
| makes up about 10%, so 1 in 1000 people have the new strain.
| In November 2020 from Heathrow alone, 240k people travelled
| to the EU, 68k to other European countries, 63k to Africa and
| 82k to North America.
|
| If I remember correctly cases have already been found in
| Denmark and Australia. Denmark does more sequencing than most
| countries (I don't have a good source for that, but there by-
| country filters here imply it:
| https://nextstrain.org/groups/neherlab/ncov/united-
| kingdom?c... )
|
| Based on this I'd argue that it's more likely than not to
| already be in tens of other countries. I'd certainly be
| interested to hear arguments to the contrary. But I don't
| believe it's sensationalist to suggest this - at this point
| I'd consider it a miracle if it hasn't spread too far. I hope
| I'm wrong.
| poma88 wrote:
| I feel embarassed because people vilified my comment about Boris
| using this piece of news with a political cover motive. I am
| sorry, saying this is different than being a negationist. I hope
| more people get it now that I honestly try to explain myself
| better. Thanks.
| sradman wrote:
| VUI - 202012/01 on Wikipedia [1]:
|
| > The first Variant Under Investigation in December 2020 (VUI -
| 202012/01), also known as lineage B.1.1.7, is a variant of SARS-
| CoV-2, the virus that causes COVID-19. The variant was first
| detected in the United Kingdom in October 2020 from a sample
| taken the previous month, and it quickly began to spread by mid-
| December. It is correlated with a significant increase in the
| rate of COVID-19 infection in England; this increase is thought
| to be at least partly because of mutation N501Y inside the spike
| glycoprotein's receptor-binding domain, which is needed for
| binding to ACE2 in human cells.
|
| Correlation does not equal causation. Most of the northern
| hemisphere is experiencing a significant increase in cases, i.e.,
| a second wave. It has not yet been established whether this
| variant exhibits a unique pathogenesis.
|
| [1] https://en.m.wikipedia.org/wiki/VUI_-_202012/01
| jsnell wrote:
| But it's not just about there being correlation between the
| variant appearing, and there being a new wave. That is a pretty
| weak data point by itself. We have more evidence and everything
| so far is pointing in the same direction.
|
| The big deal to me is that this variant is muscling out others
| in sequencing (+ PCR tests which by coincidence can tell the
| difference between this variant and the previously dominant
| ones), despite there being a high prevalence.
|
| And while the details are sparse, the NERVTAG minutes refer to
| evidence showing that the patients infected by the new variant
| have higher viral loads.
| raadore wrote:
| On dec 10 WHO released a statement on their website admitting
| that PCR tests are faulty, will detect anything we want them
| to detect and therefore medical staff need to look for
| symptoms which basically means you're sick if you have
| symptoms.
|
| https://www.who.int/news/item/14-12-2020-who-information-
| not...
|
| As a scientist that information tells me that all cases have
| to be considered faulty since the foundation is faulty. The
| results cannot be trusted.
| thanatosmin wrote:
| You are misrepresenting the WHO statement. It's covering a
| small technical issue that setting the Ct threshold for PCR
| tests can vary the false positive rate, particularly when
| there is low prevalence. Because use of this, it can be
| helpful to consider the Ct value of a positive result. It
| does not say the Ct threshold has been set incorrectly, or
| that PCR tests "are faulty."
| sradman wrote:
| Not relevant. Variants are detected using full sequencing.
| fsh wrote:
| The statement you linked to says no such thing.
| gewa wrote:
| In this case, the B.1.1.7 variant has shown to be highly
| abundant in recent COVID-19 cases in the UK. Much higher
| compared to other mutations which are tracked too. This is
| pretty clear evidence of an increased infection rate or
| evolutionary advantage as there has to be some driving force
| for this process. Take a look at this Report from the COVID-19
| Genomics UK Consortium. The B.1.1.7 mutations N501Y + D69-70
| and N501Y are very recent and mostly showed up during the last
| 28 days.
|
| [1] https://www.cogconsortium.uk/wp-
| content/uploads/2020/12/Repo...
| lbeltrame wrote:
| That doesn't rule out a combination of slightly increased
| infectiousness and a founder effect, which is equally
| possible at this stage.
| wongarsu wrote:
| It's not just that there is an increase in cases after the
| mutation appeared. It's that in the regions where this mutation
| is prevalent there are many more cases than in other parts of
| the same country (and in fact case numbers are growing in
| regions with this variant and falling elsewhere). The other
| hint is that the new mutation is becoming the prevalent strain
| in south-east England, which on it's own would already indicate
| that it has an evolutionary advantage over other strains that
| allows it to outcompete them. Combined with everything else we
| know it seems clear that this advantage is faster spread.
| Tycho wrote:
| Wouldn't there be an element of cherry picking to this whole
| variant story? Like, don't viruses mutate constantly, we just
| don't analyze them in a disciplined manner most of the time, so
| if you start doing that you're bound to find something like this,
| but so would anyone else conducting a similar analysis anywhere
| else and at any other point in the pandemic?
| mrfusion wrote:
| Just in time for Christmas too.
| Mvandenbergh wrote:
| Sure, there's constant mutation and most of it is
| phenotypically meaningless. What caused the concern is that
| this particular set of mutations seem to be associated with a
| part of the country where the measured dose-response of
| lockdown measures suddenly went way down. In other words, the
| effectiveness of a particular set of lockdown measures seemed
| to suddenly go down in Kent and London but not other parts of
| the country including parts of the country that had previously
| shown similar responses to lockdown measures. Either everyone
| in Kent is suddenly breaking the rules more than people
| elsewhere, this is unfortunate random variation driven by a few
| super spreading events (totally possible), or this is the first
| phenotypically distinct variant (as opposed to irrelevant
| sequence mutations) which has emerged.
|
| Let's hope it's nothing but I'm glad that measures have been
| taken now.
| spuz wrote:
| Yes variants occur all the time but they don't tend to become
| dominant. This variant went from 30% of all infections in
| November to 60% three weeks later. In order for a given variant
| to supplant all the others and become dominant it must have
| some characteristics that make it more transmissible. That is
| why they are particularly worried about this variant.
| raphaelj wrote:
| Could it still be that this variant is as infectious as
| others, but just happens to be the dominant one in the
| regions where the virus circulates the most, for reasons that
| have nothing to do with the genetics of the virus?
|
| London and the South East are some of the densest populated
| areas in the UK, and one could expect exponential growth of
| infections there while other less populated areas could
| manage to keep their Rt around or bellow zero. If this strain
| was more prevalent in these regions, you would also see it
| taking a larger share of the infections nationwide.
|
| However, the precautionary principle has been the keystone of
| good handling in the pandemic, so they are right to apply
| precautionary measures before it's too late. We will learn
| more about this strain in the next few weeks.
| jsnell wrote:
| Look at the prevalence graph in the article, you can see
| that the new variant has been gradually taking over the
| turf from the other ones. This cannot be explained by just
| the founder effect unlike most other cases, since the
| prevalence was high to start with. It cannot be explained
| away by a single super-spreader event, since a single event
| will just cause a single step-change. This has been a
| continuous process.
|
| It could be random chance or a selective advantage, but
| then it comes down to just a modeling exercise. How likely
| is it that this could happen by chance? And it appears
| quite unlikely: instead the best way to explain the data is
| a significantly increased transmission.
| lbeltrame wrote:
| Is this also taking out potential confounders out of the
| equation? I believe the currently available data (as
| opposed to the SAGE minutes, which has the conclusions)
| is not sufficient to rule that out.
| jsnell wrote:
| What confounders would you suggest? Elsewhere in the
| thread you've been suggesting it's a founder effect. It
| should be plainly obvious why it's not that, nor
| something you could attribute to a single super-spreader
| event.
| spuz wrote:
| I don't know enough about epidemiology but I would imagine
| they have done modelling to determine the likely
| transmissibility or R number of this new variant to be 70%
| higher. The probability that this new variant has come to
| dominate by pure chance must be small.
|
| You are right that London is a densely populated area prone
| to easy spread for the virus but the same must be true for
| all variants. This variant started its existence as a
| single strand of viral DNA and has managed to spread far
| enough to become the dominant strand against competition
| from many other well established variants.
| occamrazor wrote:
| This variant was not dominant in London some weeks ago, and
| now is.
| [deleted]
| raphaelj wrote:
| Also, the UK seems to do way more sequencing of the virus than
| any other country, so one would expect such cherry picking to
| actually happen in the UK.
| Closi wrote:
| Also the UK detected this new strain right next to the Dover
| Crossing - Isn't it pretty likely it came from mainland
| Europe and was detected at our port rather than we
| coincidentally had a mutation right on the border?
| mjul wrote:
| According to the Danish Serum Institute, the UK is sequencing
| about 10% of the positive test results. The UK is considered
| a leader in this field in Europe including the British Isles.
|
| For comparison, the Danish Serum Institute has a sequencing
| capacity about 5000 positive tests a week, a rate of around
| 25% of the positives at the current level.
|
| Source, in Danish, from the Serum Institute:
|
| https://www.ssi.dk/aktuelt/nyheder/2020/ny-covid-
| virusstamme...
| maxerickson wrote:
| Not really. Thousands of variations have ben sequenced, the
| notable thing here is the (potentially) faster spread.
| bigbizisverywyz wrote:
| Whilst the consensus seems to be that this variant is
| spreading faster than other variants - is there any
| information on exactly how it does so?
| Bombthecat wrote:
| Yeah, i read somewhere 70%.
| [deleted]
| fabian2k wrote:
| As far as I understand, that is what happened with previous
| concerns about mutated strains. In the end they turned out to
| be no different than the wildtype, and greate distribution was
| simply because those strains were present in populations that
| caused more spreading.
|
| There is not enough data right now to be sure whether this new
| strain is more infectious or not, but from what I read there
| are a few more reasons to be concerned this time compared to
| the previous times when mutated strains were reported.
| jhrmnn wrote:
| AFAIK, this strand is different because of the number of
| mutations. See figure 2 here
| https://virological.org/t/preliminary-genomic-characterisati...
| twic wrote:
| This is a really good report on the new strain, and I urge
| everyone to read it.
| plutonorm wrote:
| Very suspicious that this story breaks just as Boris needs to
| lock down the country over christmas.
|
| "everyone is going to hate me, quick think of something to
| blame.".... Eureka .... "There's a new virus strain, totally
| unforeseeable, don't blame me for the lock downs"
|
| Just sayin'
| oneeyedpigeon wrote:
| Why did he need to lockdown the country _other than_ because of
| this? Given that he said 3 days earlier that this would be
| tantamount to "cancelling Christmas", and he now looks like a
| fool and a hypocrite for ridiculing the leader of the
| opposition over it, what possible benefit does he have to gain?
| plutonorm wrote:
| "Why did he need to lockdown the country other than because
| of this?"
|
| Imagine for a moment that the current case number was
| entirely predictable. i.e. it is due to Boris ignoring
| scientific advice, believing he knows better. So the need to
| close for christmas is a result of not locking down sooner
| and harder. Now due to that failure to sell the hard truth,
| people wont be able to meet over christmas and he wants to
| find a way of shifting the blame.
| standardUser wrote:
| These days, it seems like everyone is "Just sayin'" some sort
| of nonsense conspiracy theory with no evidence. I wish people
| would stop sayin'.
| poma88 wrote:
| I agree
| zpeti wrote:
| There's so many questions that this raises.
|
| - Is it more infectious or just bypasses current immunities?
|
| - Will the vaccines basically be voided by this?
|
| - Is it less lethal? Could it create more general immunity in
| communities without killing?
|
| - Has is spread yet? I've read the UK gov knew about this in
| october... seems like it's probably everywhere by now
| makomk wrote:
| It seems the answer is that we don't know if it's spread yet.
| To quote the ECDC's briefing, "However, most EU/EEA countries
| sequence much smaller proportions of virus isolates than the
| UK, so ongoing circulation of this variant outside of the UK
| cannot be excluded".
| https://www.ecdc.europa.eu/sites/default/files/documents/SAR...
|
| Basically, the UK is just better set up to detect variants like
| this than a lot of other countries. The other possibility is
| that even if this variant hasn't spread yet, there are other
| variants out there with similar properties that just haven't
| been detected due to the lack of widespread RNA sequencing.
| South Africa apparently has one that's similar but unrelated.
| imeron wrote:
| https://twitter.com/The_Soup_Dragon/status/13403496399466291.
| ..
|
| If this chart is true EU countries announcing the closing
| borders the last couple of days is waaay to late to prevent
| the spread of the new strain in Europe.
| makomk wrote:
| Yeah, all the evidence seems to point to the border
| closures being a stupid, counterproductive attempt to close
| the stable doors after the horse has bolted and maybe shoot
| the messenger in the process. Unfortunately, there seems to
| be a bit of a push here in the UK to spin this as a
| necessary and inevitable measure that the government should
| have anticipated, including the closure of the border to
| road freight - which I think is a siginificant escalation
| compared to the previous EU border closures - for,
| basically, Brexit-related partistan political reasons.
| Someone wrote:
| I think it may be too late, but if it isn't, bordering of
| a population where it is more widespread will help. Even
| if it is too late to prevent this variant from leaving
| Britain, it will lower the speed at which it spreads,
| giving time to prepare (assuming it is more widespread in
| Britain than elsewhere)
|
| Because of that, I think this move may be overcautious,
| but I don't see how it can be stupid or
| counterproductive.
| Closi wrote:
| Being a little more cynical, the strain probably started
| somewhere else in Europe and came across the border.
|
| It's probably not a coincidence that this strain was first
| detected as spreading right next to the Dover crossing.
| hordeallergy wrote:
| Yes, it's in other countries too eg Australia and Netherlands.
| robbiep wrote:
| If may have been detected in Australia in returned travellers
| but it is not in Australia in the community.
|
| Yesterday Australia had 15 community acquired cases (yes, 15
| in total, with a further 11 from international travel in
| hotel quarantine) in the country and a quarter of sydney is
| in lockdown due to it, the virus variant is an American
| strain.
| lucideer wrote:
| No answers on most of those Qs, but the messaging on (2) "Will
| the vaccines basically be voided by this?" is that no, vaccines
| should still be effective.
|
| I'm not sure how they can no that without restarting extensive
| trials, but as a sibling commenter points out, viruses mutate
| constantly so I guess dealing with variants is pretty common
| when it comes to vaccination.
| SifJar wrote:
| My understanding is as long as the variant has the same spike
| protein, vaccines "should" remain effective. So while trials
| haven't been done yet to verfiy the vaccines are still
| effective, I'm assuming the spike protein has been observed
| to be the same so there's no reason to suggest vaccines
| wouldn't be effective.
|
| EDIT: Actually, sounds like a couple of the mutations _are_
| in the spike protein and there is some evidence of reduced
| antibody effectiveness against the mutated version.
| lbeltrame wrote:
| N501Y is properly neutralized by vaccination (there's a
| paper in Science with these data, but I don't have a link
| handy right now).
|
| The deletion _seems_ to reduce antibody neutralization,
| but:
|
| - In the preprint where this was shown, only 4 convalescent
| sera were tested;
|
| - The same 4 sera had _large_ variation in neutralization
| activity per se;
|
| - There is no investigation on potential impaired T cell
| reactivity (cellular immunity): FTR, the "mink mutation",
| although it exhibited slightly lower antibody
| neutralization, did not change the reaction of T cells to
| it.
| xiphias2 wrote:
| Safety is the hardest part of trials, and also the vaccines
| that were approved are in Phase 4 (post market surveillence).
| JetSetWilly wrote:
| > Will the vaccines basically be voided by this?
|
| It has been around since September - if vaccines were voided it
| would have shown up in trials. It seems the human immune system
| is pretty smart and manufactures many different antibodies
| against many different sites on the spike protein. So even if
| some parts of the spike protein mutate, you still have
| antibodies that will do the job.
|
| - Is it less lethal? Could it create more general immunity in
| communities without killing?
|
| It might be - it carries one mutation (a deletion) on a part of
| the genome that helps it evade the host immune system - but
| more data is needed. If it was less lethal that is a mechanism
| that can help it spread - people are asymptomatic for longer,
| or feel better so are out and about instead of in their bed.
| But although I have seen rumours on this there's nothing
| definite and no data.
|
| - Has is spread yet? I've read the UK gov knew about this in
| october...
|
| It has been detected in Denmark as well. The UK - especially
| obviously London where it is prevalent - is highly globally
| connected. This variant will be everywhere in the world now in
| small amounts and if it does spread better it is just a matter
| of time. The UK does a LOT of genome sequencing compares to
| most countries so it is well equipped to detect the emergence
| of new strains and their spread.
| glitchc wrote:
| Voided as a term doesn't make sense. The vaccine will be less
| effective for sure, correlated to the distribution of the
| variant vs. the original strain in the population.
| maxerickson wrote:
| It's not really clear how the vaccine and variant will
| interact. It can be the case that the vaccine confers
| strong immunity against the variant or that it doesn't
| confer any immunity at all, it's not necessarily
| predictable or linear.
|
| That said, what I've seen immunologists saying is that they
| expect the vaccine to still work well, because they
| wouldn't expect months of mutations to add up to the
| variant escaping the vaccine.
| spuz wrote:
| > It has been around since September - if vaccines were
| voided it would have shown up in trials.
|
| The variant didn't reach a significant proportion of
| infections until November. Evaluation of the efficacy of the
| Pfizer vaccine was done in July and August. We don't have
| data to understand how effective the Pfizer vaccine is
| against this variant yet.
| DoingIsLearning wrote:
| This should be the official position when communicating
| this information. There simply is not enough data at this
| point.
|
| I was really shocked to read German Minister statements
| saying the vacine is still effective for this variant. Sure
| theoretical the spike is majority unchanged but there is no
| evidence or data for a government official to make such an
| absolute statement.
| spuz wrote:
| The official message from the UK government when they
| announced concern about this new strain was "we have no
| evidence to suggest that the Pfizer vaccine is not just
| as effective against this new strain". Somehow that gets
| twisted by some people into "we believe the vaccine is
| just as effective against this new strain". I think it's
| party due to not wanting to appear to be doomsaying but
| also very misleading in terms of communicating the facts.
| DoingIsLearning wrote:
| My criticism was of Jens Spahn, Germany's Health
| minister. Claiming there was no evidence that the vacine
| would not be effective. [0] Which although true sounds
| incredibly misleading taking into the account the data we
| currently don't have.
|
| [0] https://metro.co.uk/2020/12/20/covid-vaccines-still-
| effectiv...
| detaro wrote:
| I thought Spahns full statement was reasonable. Deferring
| to what the health organizations report to him, saying
| that that "would be very good news" (would be, not is),
| emphasizing multiple times that this is "as of now,
| sunday evening". If you hear that and take away "we're
| definitively safe" ...
|
| (Of course I can't judge the biology and if that actually
| accurately represented the expert opinion behind it, but
| to me it communicated clearly enough that this isn't a
| certain claim, but reflecting a current snapshot of
| something that's actively looked at)
| mchusma wrote:
| The best reaction to this would be to pressure the NIH to lift
| the ban on the Astrazeneca vaccine. There is enough stockpiled
| supply to vaccinate most of the UK quickly and they would have a
| first mover advantage to getting a bunch of that vaccine.
| Evidence suggests this varient still has the same spike protein
| and seems like it would be still prevented by most if not all the
| vaccines.
| glitchc wrote:
| I am now suitably terrified. The vaccine won't be deployed fast
| enough. Coronavirus and humanity are in for a roller-coaster ride
| over the next few years...
| jonatron wrote:
| Two sources: https://www.cogconsortium.uk/wp-
| content/uploads/2020/12/Repo...
| https://www.bmj.com/content/371/bmj.m4857
| rubyist5eva wrote:
| I know I'm less afraid of it. More contagious generally means
| less deadly.
| throwaway4good wrote:
| The virus is already not deadly enough to kill itself as about
| 1/2 of the hosts have no symptoms.
| dgritsko wrote:
| My understanding was that because this virus can spread
| presymptomatically or even asymptomatically, there is little or
| no evolutionary pressure for it to become less deadly. It can
| easily spread to many people before the host even knows that
| they have it. Maybe I'm misunderstanding things, but if that is
| the case then it would seem that the normal "rules" for the
| virus becoming less deadly over time don't really apply.
| [deleted]
| parliament32 wrote:
| There's also no evolutionary incentive for it to be more
| deadly either. From the perspective of the virus, it has no
| incentive to kill its host -- if anything, it would want to
| keep them alive (and functioning) for as long as possible.
| Johnjonjoan wrote:
| You're right for the short term but (in the hypothetical case
| it becomes deadlier) once we are aware it has becomes
| deadlier, our behaviour will change and reduce transmission.
| Asraelite wrote:
| Is there any data yet on the exact change in deadliness?
| arcturus17 wrote:
| This sounds scientifically rigorous.
| rubyist5eva wrote:
| About as rigorous as the fear mongering in the media right
| now.
| jmnicolas wrote:
| I almost stopped commenting about it on HN, it feels like a
| wall of downvotes if you don't agree with the mainstream
| opinion.
| thatguy0900 wrote:
| We will have some very interesting textbooks about the
| mainstream public response to this in 50 years, I'm sure.
| anonunivgrad wrote:
| Doubtful. The victors write the history. The Church of
| "If It Saves Even One Life" and "Anti-Lockdown and Anti-
| Maskers are Murderers" are clearly the victors in this
| timeline. Your children and grandchildren will be taught
| about the backwards racists who were willing to sacrifice
| old people in the name of money, but how the fascist
| Donald Trump was finally defeated by the forces of
| democracy and justice and health was restored.
| thatguy0900 wrote:
| Well, I agree with you on trump but I feel like the
| people who have to live with the economic reality of all
| the mom and pop stores never reopening in favor of big
| international companies wont be very happy with us
| guscost wrote:
| Based on the precedent of all other endemic human coronaviruses,
| there is reason to guess that the winning mutations will be less
| dangerous. This is also consistent with theory:
|
| https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4873896/
|
| > By far, the most widely studied trade-off involves transmission
| and virulence (Anderson and May, 1982; Frank, 1996; Alizon et al.
| 2009).
| CommieDetector wrote:
| You will obey! You will obey! You will obey! You will obey!
| parliament32 wrote:
| The question I'm most curious about: Does the vaccine(s) we've
| hustled to get developed, produced, and distributed over the last
| few months basically get invalidated because of the new strain?
| cyounkins wrote:
| No. There is a section in the article about that.
| parliament32 wrote:
| That's what I get for just skimming the first half of the
| article.. thanks.
| TazeTSchnitzel wrote:
| https://en.wikipedia.org/wiki/VUI_%E2%80%93_202012/01
| gewa wrote:
| This Report from the COVID-19 Genomics UK Consortium gives a good
| summary of the prevalent genotypes with UK COVID-19 cases. You
| can see how the B.1.1.7 mutations N501Y + D69-70 and N501Y are
| very recent and mostly showed up during the last 28 days.
|
| https://www.cogconsortium.uk/wp-content/uploads/2020/12/Repo...
| throwaway4good wrote:
| My worry is this: If you take a population where a virus is
| widespread and start vaccinating then the likelihood for a
| mutation that escapes the vaccination is much higher, had you
| instead taken a population where the virus not widespread and
| vaccinated there.
|
| Is this correct?
|
| UK has a widespread ongoing outbreak and is the first nation to
| deliver vaccinations at a big scale.
| kace91 wrote:
| I'm not sure I follow.
|
| Why would vaccination increase the likelihood of new mutations,
| or mutations surviving better?
|
| The only way I can see that reasoning working is that the
| mutation was somehow vaccine resistant but not resistant to the
| immune reaction we get after being sick with the comon corona,
| but it is not obvious to me that it would work that way, I
| would assume the opposite.
| Volundr wrote:
| Yeah this is sort of true on it's face, but doesn't really
| change anything. Of course if a virus is widely spread it's
| more likely to have vaccine escaping variants out there. If
| you vaccinate that population those vaccine escaping variants
| become dominant. Obviously this is less likely in a
| population with less cases. But you have to vaccinate that
| high case population eventually and the sooner you do it the
| better. No sense giving the virus more time to mutate.
| saberdancer wrote:
| If "normal" variant is more virulent, it should spread faster
| than other variants and will be dominant. If you vaccinate
| which eradicates "normal" variant than those less virulent
| strain which may be vaccine resistant will get opportunity to
| spread. That is if such variants exist.
|
| Problem is that there is no alternative. You either vaccinate
| or let it run through your population. With IFR of 0.5-1% that
| is really hard choice to make.
___________________________________________________________________
(page generated 2020-12-21 23:01 UTC)