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)
Some points they made:
"It's a variant. It's not a strain. A strain is a virus with a new biological property. There have been no new properties ascribed to this isolate other than sequence differences, which is not enough to make a strain.. nor have we seen any other new strains of SARS-CoV-2 that anybody's demonstrated to be biologically different. None. It hasn't happened yet. I'm not saying it couldn't but it hasn't."
"Nobody's done any experiments to determine the effects of these changes on any property of the virus. Yet when a journalist calls up a scientist and say "What do you think?" and the scientist says "These could have an effect on virulence or transmission or antibody neutralization," somehow that gets translated in to "It's making the virus more virulent" and that's what's circulated and a dozen people this week said to me "What do you think about these mutations in the UK that make the virus more virulent, more transmissible, more resistant to neutralization by antibodies?" None of that has been shown, folks! It's speculation. There's no paper on any of this."
[1] - Starting at about 54 minutes in to episode 696: https://www.microbe.tv/twiv/twiv-696/
This has been an incredibly large issue for almost a year now and it's ridiculous. Journalists not understanding the way scientists speak was vaguely understandable ten months ago, but after a year straight of science being the number one news maker in the world it's obvious that the media is just use it as an excuse to scare-monger and increase their clicks.
Literally every day in the last few weeks I've had to explain to someone that vaccines will almost certainly have a profound impact on if people can transmit the virus because the news articles keep taking the "We don't have data yet on how it impacts transmission" and reporting that as the worst case scenario, when in all likelihood it will profoundly diminish people's ability to transmit the virus.
Commercial news media is so far from critical analysis that it's dangerous that we allow it anywhere near our decision making processes.
The only definitively factual statement he makes is in the first tweet:
"One of the key questions about the new variant (B.1.1.7) is whether there is conclusive evidence that it is more transmissible. I don't think we are absolutely certain yet"
Everything else is speculation. He says that founder effect is not likely because the virus is spreading widely, nationwide: this is a hypothesis, not a statement of fact. He says that there are reasons to believe that the mutations are associated with structural regions known to be important to transmission: this is a hypothesis, not a statement of fact.
He then says that because of these two unproven hypotheses (which he implicitly believes), one should "change your priors" on how likely it is that this strain is selectively advantaged. Certainly, one can "change their priors" based on personal opinion, but that doesn't mean that other informed scientists don't have different opinions.
What this guy is doing is citing the (limited, non-definitive) evidence that we know, and then saying he has an opinion about what it all means. That doesn't make it factual.
Without well-controlled cell-culture or animal studies that show that this strain is out-competing other strains in vivo, we don't have solid evidence either way. Trying to predict the organism-level impact of point mutations is a fun parlor game, but no more or less definitive than asking a sports fan which team is going to win on Sunday.
Also, I doubt twitter is the place where that information should live long-term anyway.
https://twitter.com/DrEricDing/status/1340913688992165888
> "14) “In the lab, Gupta’s group found that virus carrying the two mutations was less susceptible to convalescent plasma from several donors than the wildtype (common strain) virus. That suggests it can evade antibodies targeting the wildtype virus”!!"
Could that mean that the "herd immunity strategy" by letting relatively healthy people being infected by the virus might fail utterly because the immunity they acquire does not help very much against the new variant?
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.
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.
Let's hope it's nothing but I'm glad that measures have been taken now.
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...
However, this does not explains away that it appears to have much higher transmission.
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.
So I would think we're really only concerned with mutations in active regions that impact viability. We don't really care about mutations that decrease viability, since they'll generally be overcome by more viable versions of the virus naturally.
The question with this particular mutation is whether it's a variant or a strain. I.e. is this new variant more infectious? Which would make it a strain, not a variant.
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).
However, this is only true in the LONG RUN, when different variants have played out for a while.
In the short term, there could be a highly transimissible strain with a much higher mortality. It will eventually come to a point when the most common strains in a population are milder strains... but one of the reasons that happens is that hosts with immune systems unable to handle the strain die off... and those who survive do so because they can handle it better. So, at a later stage, it looks like the virus got milder, but:
- it doesn't generally apply to all strains
- the strains look mild later because only those for whom it was mild survive
It further drives me crazy because I am still disconnected from my family because the U.S. still refuses to allow my fiancée to travel back (she lives and works in the U.S.) from the country best dealing with this to to the worst. It's just sickening there's no support for people like us, and now it looks like it can only get worse in the west.
Note that the document appears to imply that WHO’s team will not be allowed to operate on the ground in China to collect evidence (see Phase 1 of Implementation plan, the paragraph about building on existing information and not duplicating existing efforts).
Note that the document does not mention the possibility of lab escape, despite documented evidence of SARS-CoV previously escaping from a lab in Beijing and resulting in at least one death years earlier, and the fact that Wuhan is home to another one of the very few BSL–4 labs.
I am tired of uninformed “who dealt it” finger-pointing as much as the next guy. First, we currently lack information. Second, even if we had that information, we should accept that mistakes happen (human factor and so on).
The only valid grounds for finger-pointing, as far as I’m concerned, is if someone attempts to undermine an effort aimed to make humanity better equipped to deal with a similar scenario in future.
[0] https://www.who.int/publications/m/item/who-convened-global-...
I heard this quote on a podcast recently, and somehow stuck with me, because it's quite amazing how we think that we can control somehow such a force of nature like a new virus: “Man cannot control the current of events. He can only float with them and steer.” Otto Von Bismarck.
Where was that suggested?
The most alarming thing to me is the public appetite for authoritarian policies.
Secondly, why is this an excuse to totally fail at handling the pandemic and to let the economy fail?
https://nextstrain.org/groups/neherlab/ncov/S.N501?c=gt-S_50...
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.
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?
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'.
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.
The impression that I get from my country (The Netherlands) is that we are doing a bit better than the UK for reasons that nobody quite understands yet. The best I can guess is that we ultimately make 'bigger' choices comparatively, even though compared to many other EU countries we're not doing particularly well despite being one of the richer ones.
The way I see it, our country is run by technocrats who are faced with something very different and new. Like with projects I've worked on as a programmer, the best solution often involved going way off course. And like with projects I've worked on, this usually didn't happen.
Solutions were conservative, even if something more drastic seemed prudent to almost everyone involved. It's really fucking hard to rewrite some of the core code. So instead we address things further away from that core with all sorts of special cases.
If anything, the pandemic has shown that our current way of doing things isn't quite equipped to deal with big upsets, and considering the future this is something we should probably prioritize dealing with somehow.
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.
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.
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.
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.
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.
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).
Yes. If the new variant is duplicating every week even under medium lock-down measures, as it appears, it will be very difficult to contain it, and impossible with the current set of measures. It would require a very strict lock-down at least. And the vaccinenes would not yet help - they will help later but probably not before late Summer, while the new variant will very likely be all over Europe until March.
Thinking about what we know, what appears very likely, and the conclusions of it, the first half of the year will be far away from normal, even catastrophic.
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?).
I think extreme lockdown measures could, but they'd almost have to be indefinite, and there's no appetite for that.
Honestly, that doesn't sound like a real lockdown at all.
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.
They said the same thing about overnight vote counts in Fulton County, GA... turns out it was nothing.
Is this correct?
UK has a widespread ongoing outbreak and is the first nation to deliver vaccinations at a big scale.
Yes, we are getting into it but something like 300K first jabs for a two jab vacc in two weeks is not going to set the world on fire. The logistics behind delivering the jab are absolutely breathtaking.
Here in the UK we are rich and have the science etc. We are a small, comparatively, densely populated place. We have a country funded health service and a fairly well funded military with experience and gear and man power. I think the UK represents one of the best possible case studies for mass vaccination.
60M people at 300K per week is 200 weeks or nearly four years - this is a very artificial example and only an illustration. To get 60M people jabbed, twice, in a few months is going to need a few resources!
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.
Our immune systems are general enough to face a wide variety of viruses, infections and strains.
When one is vaccinated, it gets prepared for that particular strain of a particular virus. The cost is that it could become more vulnerable to other infections... it's the cost/benefit of specialization vs generalization. Reference: https://pubmed.ncbi.nlm.nih.gov/14970928/
The reason is that the immune system is highly optimized and it is optimized to be flexible enough to save enough individuals for the next generation. It is not optimized to save each and every individual against all possible infections. That is unnecessary, as far as evolution is concerned.
Having said that, vaccines generally don't weaken individuals to a slightly different variant of the same virus. It should rather strengthen it. The immune system expects the virus to mutate so it prepares for the mutations to an extent. In fact, a category of vaccines called live-attenuated vaccines are basically weakened strains of the same virus (these can sometimes mutate into dangerous strains, eg. https://www.the-scientist.com/news-opinion/polio-vaccination..., but that's a different discussion).
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.
I'm getting the sense that there's little public appetite for waiting another 6-9 months for a new vaccine. This might change as more people get the virus, but there's a good chance 10-15% of Americans have already had or currently have the virus, so if that didn't scare people already, I'm not sure if another month of full ICUs will.
> 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.
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.
[1] https://www.cogconsortium.uk/wp-content/uploads/2020/12/Repo...
Yeah but if somebody is shot and you are found with a smoking gun right around the corner, you need to have a pretty good, and also testable explanation.
https://www.cogconsortium.uk/wp-content/uploads/2020/12/Repo...
I'm not saying that the Oxford/Astrazeneca vaccine is bad. This is however very unwise. It would definitely erode trust in vaccines if the Oxford/Astrazeneca were to have significant side effects. Which would erode trust in science in the long term.
This variant does not have any genetic differences in the spike protein targeted by the vaccines. It is unlikely the vaccines will be differently effective.
https://virological.org/t/preliminary-genomic-characterisati...
https://www.telegraph.co.uk/news/2020/12/21/supercharged-cov...
Vaccines target subsequences of amino acids on proteins which both variants most likely have.
Mark my words that this a non story/media sensationalism and will be out of the news in a few weeks.
But most of the population will be immune, so outbreaks will be limited and spread slowly. Ideally that immunity will come via vaccination instead of infection. And yes, it remains possible that if it mutates as rapidly as influenza, that we'll need a yearly "covid shot" to plug the gap.
- 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
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.
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.
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.
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.
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.
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.
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.
"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'
This was probably made worse by politicians because it's their natural instinct, but you'll see regular people trying to bargain like this too. "OK I know it's unsafe to do X, but I really wanted to, and so was extra careful to use hand sanitiser today".
The virus doesn't understand your proposed bargain, it's just (very complicated) chemistry, it is no more able to agree to a "deal" where you can spend Xmas opening presents with the extended family without getting COVID-19 so long as you promise not to stay overnight than a falling rock is able to spare your life because you prayed to Jesus.
One small piece of good news is that to a limited extent, and for some privileged people, technology made it possible to ignore these bad policies and enjoy much of the safety offered by sane policies despite living somewhere that had chosen to ignore them.
Anyway, the idea (which I'm not agreeing with) isn't that Boris knew the old plan (Xmas week doesn't need rules) wouldn't work, and concocted this story to cover for the fact that he'd need to U-turn rather than just never issuing the obviously bad policy, nor that this new strain is the only reason it's out of control and the old policy wouldn't work. Instead the idea is Boris was disappointed to hear that scientists (who've said all along that couldn't work) are right and it's going to drown the NHS in patients, likely resulting in staggering death tolls around New Year - and once he understood that he wanted an excuse to U-turn for which a new strain provides a convenient excuse.
Boris always looks like a fool. It's a big part of how he got elected. British people think he's a charming buffoon. Under current plans he has several years for them to forget he killed their parents or grandparents before they get the chance to kick him out directly, although it's the nature of Tory party politics that Boris isn't likely to survive that long.
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.
