Pfizer vaccine appears effective against mutation in new coronavirus variants
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cbc.ca
[1]: https://www.biorxiv.org/content/10.1101/2021.01.07.425740v1
[2]: https://www.biorxiv.org/content/10.1101/2020.12.31.425021v1
This is effectively impossible as the virus is dependent on a functioning spike protein in order to infect cells, and the machinery involved with the mechanics of the spike are extremely delicate. Errant mutations that would cause compositional changes to the shape of the protein are almost guaranteed to cause functional failure. Using terminology, this is what we call a highly conserved area.
In both cases for the South African or UK strain, if you take a look at the areas where mutations have occurred, you’ll see that the code responsible for generating the spike protein is basically completely unaffected. This will generally hold true for any successive future strains.
This generally happens when a virus from another animal (and thus with a slightly different version of the receptor) adapts to humans.
Basically, a gradient descent from a very different starting point ending up in a different local minima.
The question is, is the spike protein at a local minima (very probably quite close to it), and could it jump to another local minima then? Most likely not.
It's possible it will evolve to make our antibodies slightly less effective, likely as a trade off for infectiousness, but incredibly unlikely the spike protein would evolve to be unrecognizable to our immune systems. Historically, this doesn't happen all that often, except for viruses with chronic infections over years that can do a deeper search over the gradient, but even then it generally takes years to decades.
Generally though, within the context of machine learning, one of the benefits of gradient descent, especially when stochastic, is that we can get past those local minima humps. Does this hold less true with respect to the process of sequence mutation that viruses go through?
The ancestors of this virus were bouncing around between a relatively small set of humans and animals for a while before becoming SARS-CoV-2.
Now with a significant portion of the world infected, it does not seem unreasonable that it would mutate. Although at that point it probably would not be considered the same virus anymore.
No vaccine is training the body on the exact antibody to raise, it’s training it to (hopefully, because sometimes the stochastic process missed) recognise particular epitopes.
Important to also note that generally (and particularly during early infection) there will be many antibodies that recognise parts of an antigen.
Affinity Maturation through somatic hypermutation is one of the most amazing processes the body does - look it up or for a very brief summary look at my notes on page 32 (or the whole mechanism of adaptive immunity from 27) with a little diagram on page 28
https://www.dropbox.com/s/4ldgs4v9y99anm8/BCHM%203072%20Note...
Still, at this day my hope is that we'll be able to do the body's work even better at some point using computer designed antibodies (or similar) at least for therapies. There are some notable bottlenecks in the adaptive system where antigen fragments have to be broken down and shown to potential antibodies and this is a bit different between humans etc. The human antibody molecule is also very large and it's particular design doesn't fit some epitopes you'd want to hit (not an expert on it but I remember one of the HIV proteins having an area you'd want to train on but that can't accommodate the antibody variable fragments well).
Could you please explain in simpler terms what this means?
Also another scenario: say that we get yearly Covid shots that contain the latest strains, would these accumulate over the years and start interacting with each other?
The first is mostly a question of how similar they are. Best case original vaccine covers all strains without modification, worst case you need 50 different vaccines. But the most likely combination is a mix where you might need say 5 vaccines, each of which over an overlapping subset of the 50 strains to various degrees of effectiveness.
That said the immune system is extremely complex, but here is a simplified version, which gives a reasonable overview: https://microbenotes.com/cells-of-the-immune-system/
what does this mean in plain words? this SA variant has a totally new evasion system?
what exactly are we dealing with here? what causes it to rapidly mutate like this?
An E to K mutation converts a surface negative charge to a surface positive charge. So if your antibodies were expecting a negative charge and therefore putting positive charges near that place when they attach to the virus, the polarity on the mutant has now shifted and the antibodies will be repelled from the mutant virus.
It's really not typical. Even in all of the human cold coronaviruses, only one seems to be evolving its spike protein, and it does so quite slowly.
If it was typical, we wouldn't see the amazing efficacy of vaccines against endemic diseases.
It warms to see that the similarities of some aspects of biological life to the current AI/ML terms has entered the lexicon, well at least on HN crowd. The fact that it makes a lot of sense to use those terms hints that we might indeed be on the right track to building AGI and understnding the life itself in general.
Note that this process is NOT backpropagation.
"The fact that it makes a lot of sense to use those terms hints that we might indeed be on the right track to building AGI and understnding the life itself in general"
Nope, it's a residual of the fact that AI stole ideas from other fields, and ran with the terminology as marketing. Sometimes even to the point of extreme divergence from the original ("neural" nets).
But there is also the danger of false analogies doing damage, by creating the illusion of understanding something because the wording feels familiar.
There are no doubts similarities, but that does not mean, it is the same.
That happened a couple of times already with progess in technology and then simplified applied technical models to biological life.
So sure, I think so too, that we are on the right track, I am just a bit more hesistant.
Essentially, each replication means mutation, and over time, variants emerge. Think of why you need a seasonal flu vaccine and not one flu vaccine.
Think of it like antibiotic resistance - our crappy attempt at lockdown was like not finishing the course. We gave it loads of places to multiply but didn’t finish it off so it just adapted
Even if you could make this fix in a day, it'll take months to get FDA approval, and then you still have to manufacture and distribute it. And by that time the populous will have gotten immunity the old fashion way.
I see no evidence we are doing that.
> works against a key mutation in the highly transmissible new variants of the coronavirus discovered in Britain and South Africa
> The variant in South Africa carries two other mutations in the spike protein (E484K and K417N, among others) which are not present in the U.K. strain
This three day old article also anticipated this study results:
> While scientists believe the U.K. variant is not likely to affect the efficacy of the vaccines currently being rolled out in the West, there is more uncertainty regarding the other strain.
https://www.cnbc.com/2021/01/06/south-africa-covid-strain-a-...
I’m guessing they are both of the same “strain” but of different “variant”. But I don’t know enough about how virus taxonomy works to validate that. Sounds like two levels of mutation...
I have no knowledge of biology whatsoever.
But also not square one because it takes literally a day to redesign mrna vaccines for new variants. Then hopefully they can be approved faster the second go and manufactured/distributed more quickly.
But I’d say all northern hemisphere countries should do their best to focus on local elimination in summer 2021. Most of europe had it in reach summer 2020 but decided to reopen early and keep the virus at a low level.
That was an abject failure. It probably only would have taken another month of heavy restrictions to eliminate.
The mutations we’re seeing in the winter of high case volumes caution against doing another cycle like this.
This isn’t realistic. Fatigue with COVID restrictions has already set in across Europe: people are wearing masks in sloppy ways (not covering the nose, or even just putting the mask over their chin) and returning to socializing or even leisure travel. The authorities know this, and while they can do things like keep restaurants and theatres closed, they appear to feel little democratic mandate for using the police to enforce strict social separation between individuals. And that is in the winter: once the warm weather comes back, expect even more flaunting of restrictions.
1. The virus is seasonal. Substantially less restrictions are needed over the summer. Outdoor socialization really isn’t high risk
2. School is out. This naturally lowers spread
3. A bunch of people will be vaccinated. This will surely make it easier
4. We’ll probably have new rapid tests by the summer. They go a long way to reducing spread without much inconvenience. Michael Mina has been banging his head against the wall for months to get people to listen: these can be as effective as lockdowns and much less burdensome.
5. At least some countries will figure this out, go for elimination, and require a vaccine/negative test for entry and make travel arrangements with other covid zero areas
Now it might be the vaccines work perfectly, no mutant strains escape them, and we won’t have a repeat of this in fall/winter 2021/22.
But if that scenario does seem likely them elimination is overwhelmingly the best option. And society that can’t pull itself together to do that will live in a purgatory.
The “inconvenience” in the USA (besides outright coronavirus deniers and people who flout restrictions in contempt of expert and professional public health officials) is that there is no guaranteed paid sick/isolation leave if one is ordered to go into isolation. Given that 40% of Americans have less than $400 for a “rainy day”, going to work while sick may be necessary. Also, in a lot of cases, no job: no health insurance, which is tragic and consequential during a pandemic.
You also need to have a strong public health system in place well in advance, where citizens already have been following and adhering to prevention programs for a long time, along with trust in the system. The EU countries generally do better with this, in the most general sense, but it depends on the country. For example, there are published reports of what percent of the country’s population washes their hands every time after they use the restroom. Some of the more “eastern” EU countries (which are now westernized) do way better that west/north Europe.
Also, some countries routinely issue self-isolation orders for 14 days, and the police will check, multiple times. In some countries these fines are over $1,200 for the first offense, and for the second offense, it’s $20,000. Both of these fines are unaffordable for the majority of the population.
Anyways, my point is that rapid self tests do work, but it requires a properly functioning government, with a strong public health system, and a cooperative public that trusts their officials and adheres to public health recommendations well before a pandemic occurs.
So over the long run there’s much more turmoil of the type you speak of. But I agree the US needs a better system for letting the contagious stay home.
Perfect needn’t be the enemy of the good though. If, say, 45% of people could isolate, then having them know they’re positive could help too.
I agree. Everywhere should've pursued elimination strategy like Australia and New Zealand, and even at this late stage would be the best option.
Australia and New Zealand were very unusual in having that possibility, not everyone could have followed such a strategy. The EU had to move thousands and thousands of migrant agricultural workers from Eastern Europe to Western Europe for the harvests, otherwise there would have been scarcities of common foodstuffs. Also goods move through Europe largely through freight trucks that mean drivers moving about, not container shipping like the two island nations you mention.
We have freight trucks from the US too! A lot of obstacles are not, in fact, insurmountable. The actual issue is that most places weren’t aiming at elimination.
As you might remember, there was a shortage of tests the first time that the EU needed to move its agricultural workers en masse (which happened already in the spring – harvests in Spain are more or less continuous, unlike Atlantic Canada where it is much more restricted seasonally). Also, many of those agricultural laborers live in precarious working conditions that the state has little insight into, and arranging any kind of isolation on short notice was not possible.
The EU was not aiming at total elimination because the virus had already spread throughout the bloc practically before the authorities were even aware of it and again, these are not island nations.
You could have kept internal border controls except for essential work. We did that in Atlantic Canada. Australian states did that. We’re just as integrated as the EU is! We never had a border at any point in our history. So we set one up.
There are non islands that more or less eliminated it. China, vietnam for example.
Harder in the EU? More complicated? Absolutely. But the policy the EU pursued was an abject failure, so merely saying “there would have been difficulties” doesn’t show that elimination would have been worse. The places that reduced covid better generally saw better economic results too.
Lack of internal borders in the EU is one of the most important features of the bloc, both in terms of maintaining close integration that could prevent more intra-European wars and in terms of mere everyday convenience. I would gladly sacrifice the demographic most at risk of COVID (about half of all deaths in the EU so far have been in care homes) in order to avoid internal borders.
Also, China has been able to eliminate COVID (and even that is subject to doubt) only through civil-rights violations that the West would not tolerate. Pointing to China and saying "They did it, so the EU could too" misses the point. Vietnam was able to avoid a surge in COVID cases only because they hadn’t yet got the huge number of cases that the EU had first without even being aware of it; of course if somewhere else is already suffering, and you aren’t, you can close the borders and avoid the problems from the start.
I can’t see a human trial being able to show this, and contact tracing is overall so poor how long will we have to wait to not see a case that can be tracked back to a vaccinated individual before we are willing to agree that the vaccine is highly effective at stopping transmission?
For example, by Feb 1 we will have millions of people who are effectively protected at least from symptoms due to vaccine. So e.g. by March 1, if we have no, or single digit, reported cases of 2-week post-jab transmission?
The corollary is how durable is the effect?
To fully reopen the economy you need some kind of consensus on where the truth lies to these two questions.
I wonder if public health agencies will never really admit, but just the case count will start to dwindle and mitigations will start to lessen, without ever really coming out and admitting vaccinated people don’t need mitigations 2-weeks-post-jab.
Similar to how we’ve never really admitted that people who’ve had COVID are immune and can no longer spread it.
I think fundamentally gov’t is too afraid of having two classes of citizens, and mainly, that one class (the antibody negative class) lying that they are actually the other.
It’s not just a political choice.
But I agree this can depend on the community. I even specified neighborhood rather than city because I'd imagine this is different in other neighborhoods in my own city.
Public health, economic, liberty, community cohesion?
As far as pressures on healthcare systems though, once over 65s have been vaccinated (and the northern winter ends) the pressures pretty much vanish.
> Similar to how we’ve never really admitted that people who’ve had COVID are immune and can no longer spread it.
Well we don't know that. In many cases the virus reproduces and spreads without any symptoms. If the spread occurs before the immune system kicks in you could still be a carrier even though the vaccine makes your symptoms pretty much zero.
We know that asymptomatic people who are not immune can possibly spread the virus. But that’s a slightly different question.
We know that it’s very rare for someone with antibodies to be symptomatically reinfected with COVID. That’s also a slightly different question.
The specific question on the likelihood of someone with natural immunity to be able to later spread COVID without a symptomatic infection;
I’ve never heard of a single confirmed case of this happening. And the point is not that it never happens, the point is it’s a negligible risk. Smaller than, for example, someone who isn’t immune who is wearing a mask.
But from a public policy perspective, we’ll never actually admit this, just because the second order effects — where some people can rightfully walk around without a mask and are rightfully not subject to mitigations and lockdowns - are political untenable.
I have to show my yellow piece of paper with the stamp from my jab when I travel to several countries, most recently Nigeria
Have a look at hcov’s seasonality in figure 2 here: https://www.annualreviews.org/doi/10.1146/annurev-virology-0...
“It’s not seasonal” is one of the mantras health agencies repeated in february, along with “masks aren’t shown to work” and “it doesn’t” spread by aerosol.
My guess is your health agency simply hasn’t re-examined their beliefs as evidence came in.
First wave ended in June in the northern hemisphere and started in the southern hemisphere at about the same time. We are seeing a similar shift in the second wave.
It can be a coincidence but since people are more likely to stay inside when it is cold outside, and transmission is more likely inside, it makes sense.
Since the cold season is usually when it is cold outside, yeah. Might be more than coincidence.
Hopefully it is the case that the 5% are people that have a weak response to the vaccine and the remainder mostly aren't infectious. They can study this by monitoring for asymptomatic infections (I don't know if they are going to or not).
If you gave the vaccine to 1000 people and placebo to 1000 people, and 100 of the placebo and 5 of the treatment group got sick, that's 95% effective, as is if all 1000 in the control group got COVID and only 50 in the treatment group.
I don't think it's reasonable to try to run an open economy for those who are likely immune and a parallel economy for those who are unknown. There's no way anyone can verify any of that in a day to day setting.
I would expect that some international borders might reduce quarantine requirements if you can show evidence of probable immunity, but not right away.
In the scenario where only the old accept to get vaccinated, and the vaccine doesn't reach the required threshold to stomp the virus. The virus become manageable, the economy reopen but the virus run rampant in the asymptotic population slowly mutating over-time until it finds a variant that is resistant to the vaccine by successfully infecting a vaccinated person.
And it just needs for this to happen in a large population cluster where the vaccination doesn't reach the threshold, either because they do not have access to the vaccine yet or because some fraction of the population decide to not get vaccinated, for everyone to get screwed-up again.
Then we get a new vaccine every year.
But the current situation where we simultaneously have a high number of active case and high number of vaccinated people over a sufficiently long time because of slow vaccination schedule, is a recipe for creating vaccine resistant variants.
As soon as we start vaccinating we are giving the virus opportunities to pressure-select against the vaccine. The more active case we have and the longer it takes the better for the virus.
I'm no epidemiologist, but with the apparition in a short amount of time of 2 variants which affects the spike protein, it seems the current level of active case we are entering a red-zone, where the virus is given too many opportunities to mutate. And we should try to contain it via the current measures (masks, tracking and lock-downs), before sabotaging our best card.
Once we are done with COVID, will the new vaccine methods enable us to develop vaccines for virus that we couldn't do before. E.g. maybe HIV?
The number of mutations is proportional to the number of people currently infected. The faster the virus spreads the more variants will be created. The fact that the N501 variant spreads faster seems to imply that the rate of mutations is already in the process of accelerating.
It may make more sense to use evolutionary modeling and analysis of existing SARS-type viruses to create antigens robust to all expected mutations. Here’s one such bit of research: https://www.biorxiv.org/content/10.1101/2020.11.17.387092v2
From https://en.wikipedia.org/wiki/BioNTech:
It develops pharmaceutical candidates based on messenger ribonucleic acid (mRNA) for use as individualized cancer immunotherapies, as vaccines against infectious diseases and as protein replacement therapies for rare diseases, and also engineered cell therapy, novel antibodies and small molecule immunomodulators as treatment options for cancer.
HIV, like other retroviruses, embedds itself in the cell DNA.
Some cells remain dormant for weeks and then start producing virions.
So the other problem with HIV, even if it didn't attack immune cells, is the hidden virus reservoir, I guess, just like other incurable viruses, like herpes and some hepatitis.
https://www.globenewswire.com/news-release/2019/11/18/194889...
If you take antiretrovirals you're very unlikely to become infected with HIV, even if you take it after initial exposure (but do your own research on that), but as soon as you stop, you lose that protection -- same with antibodies (not sure how a vaccine would help T-cell immunity if HIV infects T-cells).
This is both true for natural infection and first generation vacines.
Later generation vaccines avoid this by not presenting certain proteins.
My point is, you can't just include hundreds of protein variants without a lot of trials.
In the optimal case you would attempt the 100+ cocktail and don't have any unreasonable side effects from them. Of course if there is a single variant in there that causes side effects you would need a ton of trials to triangulate which one causes them, but there is no guarantee that that is necessary or that you wouldn't run into that variant when you just adding 5 new variants in an iteration.
So ultimately we may not achieve herd immunity except with mandatory vaccination campaigns.
I know several families in my town who have gotten COVID. All of these families had 2 or more kids and in 3 of the families there was at least one kid who never had any symptoms and never tested positive despite being PCR tested repeatedly.
It’s theorized that there is some cross-immunity that some people have from other coronaviruses.
Coronavirus is a generic term for a type of virus.
For example, a few of the more common strains of the common cold, representing perhaps 15% of cases, are coronavirus - but they have no real relation to _the_ coronavirus, as term is typically used.
How long will the mod-RNA express the spike proteins? (where is the actual 'protein expression'/time plot?)
The poly(A) tail isn't just A (which would give a mechanic answer to my first question?), there is also a 10-nucleotide linker (GCAΨAΨGACΨ). I wonder if this could be there to trigger some sort of self-amplification. Can someone point me to the relevant paper?
Anyone know how long it would take AstraZeneca with a more traditional vaccine?
If we enter a cycle of new variants every 9-6 months that require new vacines, simply because the volume of people infect allows the virus to have enough diversity, then it's pointless.
It's basically a "weird flex" from Pfizer, because what they should say is: even though we can make a new vaccine easily, we will have nowhere near the production capacity to make a difference, so global governments need to get their shit together.
Longer-term, if we need a new vaccine every 9 months, that doesn't sound like a huge manufacturing problem. We manufacture many high-tech things on a scale of 1 per person per year, like the flu vaccine. The difficulty is ramping up fast (especially when you think that demand may only last a year).
I wonder if, under some potential circumstances (eg. the virus turns out to escape current vaccine & be much more contagious) exceptions will be made.
Or is it simply genetic drift?
https://www.who.int/csr/don/21-december-2020-sars-cov2-varia...
There is certainly something going on in the UK and Ireland, but it's not a randomized controlled study designed to measure the infectiousness of the variants that have recently been sampled there.
(because it's exponential, higher infectiousness can be quite a lot worse than higher lethality)
Look here for how one of the lines is not like the others. (UK)
https://ourworldindata.org/coronavirus-data-explorer?zoomToS...
Not to mention a similar uptick in serious cases and even just more people presenting to the hospital. Imagine the current situation, where some cities are already at 0% capacity, but 70% worse...
Just something worth noting when we say that a new strain is _just_ more infectious.
That's wrong if this virus, like many other viruses, is mutating to become simultaneously more infectious and less lethal.
https://www.reuters.com/article/us-health-coronavirus-mutati...
You could halve the death rate in that scenario and still have 10x the number of deaths or more.
Run two exponential series: one at 1.1x, one at 1.7x. Start at 1,000 cases each. Death rate 1% for the first, 0.5% for the second. Assume doubling in a week. Check new cases and thus new deaths after eight weeks.
2143 new cases on week eight fir the second one, 21.4 deaths.
110,199 new cases on week eight for second one, resulting in 550.5 deaths.
20x worse. And unfortunately the new strain doesn’t seem to be less deadly, so it would be 40x worse if death rate the same.
Also, your numbers are arbitrarily picked. Why don't you pick 1.8x and 1% vs. 1.9x and 0.999%?
>You are wrong on principle because you stopped thinking after you calculated the death rate after week eight. The virus doesn't stop spreading in either of the hypothetical cases and the population is a finite number. Keep calculating!
This only applies if the plan was to let literally everyone get infected. That wasn’t the plan. We have vaccines now. It should be possible to end things by the end of summer, so excess deaths now are needless deaths.
Also you’re ignoring speed. 200,000 hospitalizations in a week is much much worse than 200,000 in a year. Get too many people needing to be hospitalized at once and the death rate goes up because you can’t treat them as well. You also get more deaths from other conditions as hospitals can no longer serve cancer patients, heart attack victims past a certain point etc.
It's well known that harmless viruses exist, they infect a lot of people and kill nobody (or almost nobody). Claiming that more infectious = generally more lethal is just not based on facts. If Covid-19 mutates into a mostly harmless variant, we will easily treat the few more severe infections and nobody will die.
These variables are the ones that are relevant to deaths and have been talked about since the beginning of the pandemic: hospital overwhelm, total percent of populace infected, etc
To refuse to deal with the complexities of the situation doesn’t make them go away. I didn’t introduce any factors apart from the common ones.
> It's well known that harmless viruses exist, they infect a lot of people and kill nobody (or almost nobody).
We’re not talking about those viruses though. Most viruses that we don’t have a vaccine for are either orders of magnitude less lethal or substantially less contagious.
> Claiming that more infectious = generally more lethal is just not based on facts.
I didn’t say that. I said that at the level of lethality coronavirus is at, an increase in contagiousness is worse than an increase in lethality. Very different claim.
> If Covid-19 mutates into a mostly harmless variant, we will easily treat the few more severe infections and nobody will die.
This would be true if it mutated into something maybe 100x less contagious. An entirely theoretical possibility. That’s how much more lethal covid is compared to stuff like the cold.
On the other hand, spreading more easily means higher reproductive fitness under any circumstance. And not taking measures to reduce spread probably just means more infections faster, which is more opportunity for reproduction and mutation, which means you probably get higher fitness variations sooner.
Also I'm trying to think of anywhere in US/UK society for which "incessant lockdown" could possibly be an accurate description of policy much less behavior.
Say you have two variants, variant S-spreader and variant L-lethal. S kills 1 in 100 people and has a doubling time of 3.5 days L kills 2 in 100 people and has a doubling time of a week.
First week L kills twice as many people of S. Week 2 they kill the same number of people. Week 3 S kills twice as many people as L Week 4 S kills 4x as many people as L.
It's very important, specifically in the UK, to put N501Y in the context of political decisions that impact the R index.
People were sharing on a Facebook and tweeting that the new strain was being spread through touching surfaces and farts and that masks no longer work.
Big Tech is poison and many thousands would still be alive today if they had never logged on. These companies are no longer defensible.
A massive percentage of the public has decided to give up on safety protocols and if Thanksgiving and Christmas didn't change any minds, why would this?
What good did terrorizing the people who are already following the rules with this variant panic do? "THE VACCINE MIGHT NOT WORK NOW!" only scares people who want the vaccine. The media frenzy around the variant did absolutely no good.
I've got several acquaintances who work in both areas and what I'm hearing that there are challenges: not ones that have to do with "rules", but actual supply and logistics. Still, among these are people who've received their first dose.
That is the consensus, and even within medical community misinformation about the vaccine has footing.
That’s good news at least.
For the nation's without a vaccine, the leaders there likely would be quite motivated to act and enjoy a great deal of support at home.
The genome was shared. At least four competitors in global economic terms (China, Russia, the EU and the USA) all developed vaccines.
This is not like pre-hydrogen bomb information hoarding. The techniques behind mRNA are taught worldwide. Most medicines come from India, which was a leading non-aligned economy for years and years.
The above does leave room for bad armies. Some tiny insignificant nation might do this. China isn't insignificant, and not stupid. Even in an all out war they would still share virus and vaccine information with their enemies as there is nothing to lose and goodwill to gain.
They still not letting WHO scientists into Wuhan to study it's origins and we are being told to take CCP's word at face value.