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03 Dec 2021 01:26

What's known about the outbreak here: Two persons had recently been to South Africa attended the event of 120 people.  The company had requested that people should be fully vaccinated AND get a test before attending, but that's something they couldn't enforce.  It's likely that everybody was vaccinated though, and quite certain that those who came from South Africa were (or travel would be difficult).  Whether everybody actually tested themselves, hard to say.  Only one of the 50-60 positive cases has been confirmed as omicron, but the rest are assumed to be the same.  The story broke a few days ago and omicron was assumed, but that was confirmed yesterday.  The participants are described as "young adults" (around 30 years old?) which means that they probably got their second dose a couple of months ago and should have maximum protection.  It's reported today that all have mild symptoms described as headache, sore throat and some cough, like a cold.

I think it's safe to assume that the vaccines do not protect against omicron in any significant way, and neither will boosters.  The problem is that politicians are stuck with their vaccination track and will refuse to realise that boosters and covid passes wont magically make this go away.  This should have been realised months ago after the new wave in Israel, as I've pointed out before. The vaccine now appears mainly to offer the middle aged protection against critical disease for the old variants.  If omicron takes over and can give symptoms worse than the flu, we're basically back to start, perhaps only better prepared to make improved vaccines, drugs and policies.
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Coronavirus (COVID-19) Thread

09 Dec 2021 01:53

Norway October 2021: Nearly everybody fully vaccinated, covid concerns declared a thing of the past:
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Now let's see what omicron will bring.

Official response: boosters!  Of course it will work.  The tide will turn.  But that kind of evidence collection will also prove that sacrificing a goat in front of the parliament every day will also work.  Looks like I will get my booster within a month or so.  But to what end?  To get another one in another few months?  Or if a vaccine updated for omicron becomes available, I can't have it because I just got my booster for delta which has become irrelevant?

I'm concerned that politicians still are stuck on vaccines as the sole strategy.  Hospitals are operating beyond their limits (meaning that surgeries and other things get put on hold) because 300 covid patients have been admitted, of which 50 requiring intensive care, of which 30 need breathing assistance, which frankly isn't that much in a population of 5.4 million people, many of which are old and weak. Nothing has been done to improve the situation.  Rather, Norwegian hospitals rely much on foreign workers, many from Sweden, but these were given intolerable travel restrictions and got fed up by Norwegian authorities and are no longer interested in coming back after the borders reopened.
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Coronavirus (COVID-19) Thread

10 Dec 2021 04:20

I'm concerned that politicians still are stuck on vaccines as the sole strategy. 
Aren't they bringing back some other public health measures, too? A combination of measures is important. As we saw in other countries, even 80% vaccination isn't enough to stop delta if all other measures are dropped, especially as protection against infection wanes over time. But the more important and practical thing is to dampen the wave of hospitalizations.

In the US we're detecting Omicron in more and more states (no surprise), but the delta wave is still going strong (if anything it's intensifying with winter and holiday gatherings). It still makes up more than 99% of new cases and is killing over 1000 people a day. Many ICUs are above 100% capacity.

Some Pfizer data suggests the antibody levels raised by the third dose is about 25 times higher and more durable than after the second dose, which is consistent with expectations (this makes the mRNA vaccines pretty similar to other 3-dose vaccines, but of course it's very likely we'll still need boosters about every year due to ongoing variants). Early data with Omicron suggests it evades the vaccines several times better than Delta. However, the protection provided by the boosters still appears to hold up pretty well against severe illness, so authorities here are advising people to get their third dose (if their second was more than 6 months ago) instead of waiting. A booster specifically tailored for Omicron would be unlikely to be ready for mass distribution by the time Omicron dominates, anyway, and right now Delta is still a big threat.
 
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10 Dec 2021 09:07

Aren't they bringing back some other public health measures, too?
Yes, they had to bring back some restrictions.  Currently, mandated: At most 20 people indoors in private events (50 for funerals), 50 for public events or up to 3*200 for public events without assigned seating.  Face masks in public transport and shops where a distance of 1 meter can't be kept (youths and adults). No alcohol after midnight in restaurants and bars. Registration of guests (who agree).  Test upon arrival in Norway (regardless of vaccination/recovery status). Recommended: Reduce social contact indoors (adults).  School children between 10 and 16 self-test twice a week.  Accept vaccines.  

If a member of the household gets a positive test, adults regardless of covid status must go into quarantine (going outdoors ok, but no indoor socialising or shopping that is not strictly necessary) until tested negative which has to be repeated up to 7 days (only recommended for those under 18).  10 days for omicron.  Isolation for 5 days is still required if you test positive (7 days for omicron).  A good thing now is that the vaccinated/recovered get few exemptions.

Omicron has been confirmed everywhere, but delta still most common and also spreading amongst vaccinated.  There is a clear pattern how it spreads besides through members of the same household: Where people gather and use their lungs: So restaurants, bars, concerts where people have to speak loudly, choires, brass music, and so on.  Also classrooms, but rarely as superspreader events.  In our children's classes the rate seems to be a steady 1-2 new cases in every classroom per week (the youngest, unvaccinated), or per month (the older, vaccinated), so it's a slow spread amongst the schoolchildren.  This is clearly the intended, but not in no way admitted strategy.

Simply put, volume is a good indicator of infection risk.
Some Pfizer data suggests the antibody levels raised by the third dose is about 25 times higher and more durable than after the second dose
Of course they do what they can to find such data.
which is consistent with expectations
Precisely.

The trouble is, the effects don't last long enough to beat the virus.  And whilst we are "flattening the curve", we are also buying the virus time to adapt.  So this could be a long fight.  Maybe we need a infectious, but relatively harmless variant which is let loose to move through the population so fast that it runs out of hosts before it can change.
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Coronavirus (COVID-19) Thread

10 Dec 2021 16:21

Of course they do what they can to find such data.
I think you're suggesting that we're just seeing confirmation bias? In that case, can you explain why their experimental design is biased towards these results, and could not conceivably produce results pointing to a different conclusion?

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The trouble is, the effects don't last long enough to beat the virus.  And whilst we are "flattening the curve", we are also buying the virus time to adapt. And whilst we are "flattening the curve", we are also buying the virus time to adapt. So this could be a long fight.
Yes, unless the entire world is vaccinated very quickly and keeps a reasonable level of public health measures during that time, then the virus is likely to stay with us. (Edit: and even if we did manage to eradicate it from humans, now that it is establishing itself in new animal reservoirs like white-tail deer, we can't rule out mutated variants getting reintroduced.) But with vaccines and more effective treatments, that future can look more like a nuisance than a doom.
Maybe we need a infectious, but relatively harmless variant which is let loose to move through the population so fast that it runs out of hosts before it can change.
Even if we set aside the ethical issues, and the possibility of reintroduction from animal reservoirs, this probably would not work.

The problem is that mutations are not a function of time, but of transmissions. The number of mutations is proportional to the number of transmissions, because the probability of a mutation is constant with each replication. So a virus running through the population faster is changing faster. It would generate about as many new variants in the course of its spread if it took a few weeks as it would if it took years. The selective pressure on variants that are more transmissible would be reduced (which then wouldn't matter), but selective pressure for variants that evade immunity would be about the same. We would have to hope that the immune protection from all the variants produced overlaps enough to stop the spread of all of them, which isn't realistic. (This is why Omicron is spreading so well.)
 
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Coronavirus (COVID-19) Thread

11 Dec 2021 14:03

I think you're suggesting that we're just seeing confirmation bias?
We don't know that, and probably not "just seeing".  It's too soon.  Peer review might raise relevant questions.  I don't think it's likely that the data collected is much corrupted by bias, but I think the selection of data, what is investigated, easily gets influenced by bias,  If you think that your hypothesis is correct, it is so tempting to focus on verifying what you expect, not so much looking for data suggesting that there are problems.  Even if a booster is efficient against omicron, it's not worth much if it only last a couple of months, and we haven't sufficient data yet to know.

My concern, which I've expressed before, is that what we don't know yet is so often neglected when communicating to the public.  There was no time to test how good the vaccines were after 6 months, yet they were rushed out.  Which is fine, if people are told that this is somewhat experimental, but the story has been that the two doses were the way out of the pandemic, which has definitely proven to be false.  This leads to less trust in vaccines and less trust in authorities.
The problem is that mutations are not a function of time, but of transmissions.
The immunity is a function of time, and that is the reason why a virus can be in the lead if we give it time.
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Coronavirus (COVID-19) Thread

12 Dec 2021 02:30

I don't think it's likely that the data collected is much corrupted by bias, but I think the selection of data, what is investigated, easily gets influenced by bias,  If you think that your hypothesis is correct, it is so tempting to focus on verifying what you expect, not so much looking for data suggesting that there are problems.
I don't really think that's the case here. The research question was essentially "how does the immediate antibody response from two and three doses of vaccine against Omicron compare to that produced against Delta and earlier variants?" It's an important question that can be studied early, and the data could have landed toward several different conclusions. They could have found that antibody response from a third dose was significantly less neutralizing against Omicron than Delta, or they could have found that a second dose against Omicron was comparable to a second dose against Delta. These would have very different implications, even if our understanding of the full response over time is incomplete and still being studied (as said even in the press release.)

I easily imagine a skeptic raising doubt about any conclusion by claiming that there was a bias towards finding it. "Of course, the vaccine makers want to show that we need new vaccines -- the previous doses had already been paid for."  Or, "of course, they want to show that the original vaccines still work very well, so that they don't lose shareholder confidence." Or "of course they try to find something in the middle, it's what most people expected." Because someone could spin such a claim for any outcome, I don't find it compelling.
The immunity is a function of time, and that is the reason why a virus can be in the lead if we give it time.
Immunity is a function of both time and variant evolution, and variant evolution is a function of transmissions. We have immune-evading variants now not because the pandemic is slow, but because so many people have been infected. Having the virus spread faster would not guarantee it burns itself out -- we'd be just as likely to see similarly evasive variants as Omicron arise before it burned itself out. Omicron is sufficiently mutated to escape immunity from the earlier variants and vaccines tailored to those variants, even if that immunity was gained recently.

It is often said (and I've said it myself) that immunity wanes over time, but the full story is more complicated. The immune system has memory, and as the initial antibody response to infection declines, there is also a transition to memory cells that can instruct the production of new antibodies upon infection, which can even be more efficient than the original ones. When we say immune response declines, we're really referring to the decline of the initial burst of antibodies, and the emergence of mutated variants that are better at evading them. Much of the decline in vaccine efficacy against transmission, like seen in the Veteran's study earlier, is not just from the first effect, but also from the emergence of Delta.
 
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Coronavirus (COVID-19) Thread

12 Dec 2021 06:33

Wat can we use that info you just mentioned to eventually create a new type of vaccine that will provide permanent protective results for viruses like this one?  Making the transition to memory cells more efficient I mean and keep the original rate of protection?

Also what do you think of NY bringing back full protection laws (mask mandates in addition to vaccine mandates)....we're seeing quite the surge here -- rises in hospitalizations of around 50% not just infection rates.    I've also heard Pfizer talk of a possible second booster shot, so a 4th dose of the vaccine, what are your thoughts on that?  If that happened would that be a further 6 months after the first booster shot?
 
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Coronavirus (COVID-19) Thread

12 Dec 2021 06:40

Aren't they bringing back some other public health measures, too?
Yes, they had to bring back some restrictions.  Currently, mandated: At most 20 people indoors in private events (50 for funerals), 50 for public events or up to 3*200 for public events without assigned seating.  Face masks in public transport and shops where a distance of 1 meter can't be kept (youths and adults). No alcohol after midnight in restaurants and bars. Registration of guests (who agree).  Test upon arrival in Norway (regardless of vaccination/recovery status). Recommended: Reduce social contact indoors (adults).  School children between 10 and 16 self-test twice a week.  Accept vaccines.  

If a member of the household gets a positive test, adults regardless of covid status must go into quarantine (going outdoors ok, but no indoor socialising or shopping that is not strictly necessary) until tested negative which has to be repeated up to 7 days (only recommended for those under 18).  10 days for omicron.  Isolation for 5 days is still required if you test positive (7 days for omicron).  A good thing now is that the vaccinated/recovered get few exemptions.

Omicron has been confirmed everywhere, but delta still most common and also spreading amongst vaccinated.  There is a clear pattern how it spreads besides through members of the same household: Where people gather and use their lungs: So restaurants, bars, concerts where people have to speak loudly, choires, brass music, and so on.  Also classrooms, but rarely as superspreader events.  In our children's classes the rate seems to be a steady 1-2 new cases in every classroom per week (the youngest, unvaccinated), or per month (the older, vaccinated), so it's a slow spread amongst the schoolchildren.  This is clearly the intended, but not in no way admitted strategy.

Simply put, volume is a good indicator of infection risk.
Some Pfizer data suggests the antibody levels raised by the third dose is about 25 times higher and more durable than after the second dose
Of course they do what they can to find such data.
which is consistent with expectations
Precisely.

The trouble is, the effects don't last long enough to beat the virus.  And whilst we are "flattening the curve", we are also buying the virus time to adapt.  So this could be a long fight.  Maybe we need a infectious, but relatively harmless variant which is let loose to move through the population so fast that it runs out of hosts before it can change.
I think this is something you might have mentioned before, but moral issues aside is there any way we could "guide" future mutations or evolution of the virus towards better outcomes for us (for example a lower infection rate) through genetic engineering or through some other method?  I know there are dangers with this kind of tweaking but do you see this is something that might be possible in the future and with computer simulations that had some predictive accuracy we could actually have a chance to change the course of evolution of the virus towards something less impactful for us?
 
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Coronavirus (COVID-19) Thread

12 Dec 2021 12:08

Because someone could spin such a claim for any outcome, I don't find it compelling.
What results do you think will go to the public more quickly: the good news or the bad news?  Or rather, what kind of results would be checked and rechecked the most before going public - the good or the bad?  If a company has bad news about their product, I easily see how they would delay to publish it before they are absolutely sure, but with good news, they can publish and stress that the results are preliminary and they're good.  This is significant bias.  It would be naive to think that this is not normal.
Omicron is sufficiently mutated to escape immunity from the earlier variants and vaccines tailored to those variants, even if that immunity was gained recently.
Do we know that?  Over here the distribution of the boosters tailored to those earlier variants has been accellerated to beat omicron.  So the working hypothesis seems to be that escape is much more difficult with recently gained immunity.
It is often said (and I've said it myself) that immunity wanes over time, but the full story is more complicated.
That is reasonable.  I have been wondering about what the reason for covid apparently causing much milder symptoms here in Scandinavia is.  Here the common cold, often caused by some kind of coronavirus, is, well, very common.  Pre-school children have the cold pretty much continuously (and their parents), but the symptoms are mild.  This could lead to two things: the frequent immunity response could lead to a better defense.  And/or it could go into the genes.  Until 250 years ago the child mortality was about 40%, so a weak defense against coronaviruses would selected away.
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12 Dec 2021 12:16

is there any way we could "guide" future mutations or evolution of the virus towards better outcomes for us (for example a lower infection rate) through genetic engineering or through some other method?
Even if we get good at doing this, I think the danger lies in foreseeing the virus' next moves.  If we make a suicide virus, how can we be sure that it can't become something much worse several generations down the line?
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13 Dec 2021 02:57

Some early data from Denmark on omicron:
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For comparison, the latest vaccination status in Denmark:
One dose: 79% of the population
Two doses: 76% of the population
Three doses: 20% of the population

That doesn't look too encouraging.  It probably means that omicron will dominate by Christmas in many countries and that the current idea that vaccines are an efficient tool against infection has to be given up, but rather the vaccines can at best be seen as a means to reduce the risk of serious illness.  It certainly does not weaken my opinion that covid passes and mandatory vaccination policies are clearly pointless, and will only increase distrust in public advice and vaccination and thereby worsen the pandemic.

One case study: Breakthrough infections with SARS-CoV-2 Omicron variant despite booster dose of mRNA vaccine
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Coronavirus (COVID-19) Thread

13 Dec 2021 06:29

Wat can we use that info you just mentioned to eventually create a new type of vaccine that will provide permanent protective results for viruses like this one?  Making the transition to memory cells more efficient I mean and keep the original rate of protection?
Maybe, at least to some degree. There is research being done on trying to create vaccines that improve the generation of T cells, which are part of the enduring immune system response and better at responding to multiple variants.
What results do you think will go to the public more quickly: the good news or the bad news?  Or rather, what kind of results would be checked and rechecked the most before going public - the good or the bad?
I think both tend to go public pretty quickly, especially if the findings are especially good or especially bad. But if the findings are preliminary or come with high uncertainty then I have usually found that well communicated... unless you get the story from politicians or media, where the degree of fact checking, nuance, and bias can vary a lot. Some amount of bias is unavoidable even in "pure" science. But do I see signs of it being a significant factor for the choice of research questions, methods, or interpretation of results announced by those testing the vaccines? Not really. I think they're motivated to understand the effectiveness of their vaccines, whichever direction that might land.
Do we know that?  Over here the distribution of the boosters tailored to those earlier variants has been accellerated to beat omicron.  So the working hypothesis seems to be that escape is much more difficult with recently gained immunity.
Confidently, yes! First, the evasiveness of Omicron compared to Delta against the antibodies produced in response to the original variant (or vaccines tailored to the original variants) has been tested directly. It is several times more evasive. Secondly, we see Omicron infecting people who had their second doses as little as two months ago very frequently. Yet the antibody levels raised by the second dose after two months are still very close to their peak values (the peak happens between about 30 and 60 days and declines slowly thereafter.) 

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Source: Antibody Persistence through 6 Months after the Second Dose of mRNA-1273 Vaccine for Covid-19

The reason boosters help against Omicron is because the antibody levels raised by the third dose are so much higher (about 25 times) than what was raised by the second dose. So even though those antibodies are less effective against Omicron, having more of them helps fight the infection better. Having a vaccine specifically tailored for Omicron would probably help even more (or at least the antibodies would be more efficient), but that's some months away. 

It is hoped and perhaps expected (because it's a general behavior of immune response with evidence from other vaccines) that the third dose also elicits a broader recognition to variants, such as by producing more robust T cells like I described to ALEX. But that remains to be demonstrated directly.
 
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Coronavirus (COVID-19) Thread

14 Dec 2021 02:06

More data coming in, this time from a study of real-world infection data in the UK where Omicron is quickly approaching half of all new sequenced cases and is likely to dominate before the end of December. The study found that two doses of the Pfizer vaccine provided only about 35% protection against symptomatic infection against Omicron, while a third dose increased it to about 70-75%. Two doses of the AstraZeneca vaccine, on the other hand, provided no measurable protection against Omicron after 15 weeks.

A pretty good improvement from the booster. 70% is a higher effectiveness than flu vaccines, though less than the initial mRNA vaccine efficacy against the original virus. We should not be surprised to see many breakthrough Omicron cases even in boosted people, as is already being seen. But boosting should be a useful factor for helping to slow the growth of new cases and hospitalizations compared to having most of the population have two doses, especially if the second dose was a while ago.

This excerpt from the paper's introduction also gives a good summary of the vaccine effectiveness throughout the full evolution of variants thus far:
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Coronavirus (COVID-19) Thread

14 Dec 2021 02:26

 I think they're motivated to understand the effectiveness of their vaccines, whichever direction that might land.
There is no reason to question their motivations, but this is not the only factor.  If they work for a company, they might not be free decide what to publish, or feel pressure (even from themselves, consciously or not, to verify some results more than others.  And I think some degree of confirmation bias is unavoidable to the degree that it also always must be regarded significant.  Confirmation bias doesn't mean that the result will be wrong, though.
The reason boosters help against Omicron is because the antibody levels raised by the third dose are so much higher (about 25 times) than what was raised by the second dose. So even though those antibodies are less effective against Omicron, having more of them helps fight the infection better.
That sounds good, provided that antibody levels correlate with infection risk.  What to make of the numbers from Denmark?  The infection count by vaccination status seems to match the 1, 2 and 3 dose percentages in the population pretty closely.  Of course it's more complicated, since we also need to adjust for age and other factors.  Boosters apparently make an impact for delta, but what help is that really when omicron will dominate well before the boosters get distributed?  I think the real test for the mRNA vaccines now is their promise to be updated quickly for new variants.
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