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Watsisname
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Coronavirus (COVID-19) Thread

14 Dec 2021 02:41

That sounds good, provided that antibody levels correlate with infection risk.
They do. It's not the only factor, since it depends on the type of antibody and how specific that antibody is against the variant it encounters, but as long as they have some neutralization ability then the antibody levels correlate to infection risk.
What to make of the numbers from Denmark?
I think that's not unexpected if boosters give 70% efficacy against symptomatic infection by Omicron, and 35% efficacy from two doses. Even when the mRNA vaccines were around 90% effective against symptomatic infection with the virus dominated by the earliest variants, we would see some breakthrough cases. Back then I said that being vaccinated should be a reason to feel safer, but not a guarantee against getting sick. 

I'm boosted but still being thoughtful about what I do -- avoiding crowds, wearing a mask in indoor public spaces, not getting together with multiple households simultaneously, etc. As always it is the case rates and their trends in my area that determine how I behave, and not so much my vaccination status, which I view more as like a safety net. Right now my county is around 26 cases per day per 100k people (barely into "very high risk" by the CovidActNow metric), and relatively flat over the last 3 months (if we smooth the squiggles due to holidays). We've been having a death every couple of days on average, with a population size of 229,000. Most of them were unvaccinated people. 

Expecting to see a big wave of Omicron here before long. Have had 1 known case in the county so far, but there are bound to be many.
 
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Coronavirus (COVID-19) Thread

14 Dec 2021 04:37

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.
Wouldn't that be ironic? I wonder how long it would take though?  So, say, by 2050 this particular coronavirus could be no more dangerous than the common cold?  Conversely, how long ago was it that the common cold was killing people left and right like this virus is doing now?
 
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Coronavirus (COVID-19) Thread

14 Dec 2021 04:41

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?
Maybe there could be a way to program a kill switch into the virus?  It's ironic we talk about this like a computer virus and we could use a computer to try to predict its next moves, but the idea of programming a kill switch that will cause the virus to self destruct after it does its job could actually be possible.
I got this idea from seeing how genetically modified HIV is used to kill brain cancer cells and is harmless to normal cells.  It's almost like basic level computer programming being done on viruses.
 
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Coronavirus (COVID-19) Thread

14 Dec 2021 04:53

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.) 

Image
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.
Wat, you anticipated my next question, which was going to be, if we create a booster shot specifically tailored to Omicron would that result in reduced effectiveness against Delta or maybe even other earlier variants?  Or would a modified shot contain a library of sorts of information on (and thus very good protection from) all the variants?
 
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Coronavirus (COVID-19) Thread

14 Dec 2021 07:40

Expecting to see a big wave of Omicron here before long. Have had 1 known case in the county so far, but there are bound to be many.
Omicron is now assumed to be the dominant variant in London.  Given the speed it spread, it's safe to assume that will be everywhere, and that the current vaccination will make no dent in the exponential spread.  Norway is already in a wave greater than all previous waves put together.  Covid now mainly spreads through schoolchildren and their vaccinated parents.  At this rate herd immunity could be reached in weeks.  Schools are still open as normal, mostly.  One nearby school here decided to close today after about 18% of the pupils and 24% of the teachers/administration got infected in the past two weeks.  It's pretty bad in our local school as well.  I think most of our youngest child's classmates have been through it since the pandemic was declared a thing of the past.
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Coronavirus (COVID-19) Thread

15 Dec 2021 04:56

Early sequencing data for Omicron here in Washington. Yeah, that looks pretty exponential...

Image 

These are out of between about 160 and 360 sequenced samples each day from across the state, which isn't a whole lot of data, but the trend is pretty telling and consistent with what is being reported elsewhere with doubling times as little as 2 to 3 days. At this rate there's pretty much no doubt Omicron will make up nearly 100% of new cases by the end of the year in most areas. And we thought Delta took over impressively fast...

Looking back at this post, Omicron says "hello". Too early to say it's better or worse, though. Some hints that it might be milder, but even if it's somewhat milder, such rapid spread can still easily crush the health care system.

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Coronavirus (COVID-19) Thread

15 Dec 2021 05:35

I heard something tonight which sounds concerning....scientists were talking about how Delta and Omicron could both infect the same person and swap genetic material to mutate even faster? Is this possible and if so how would it happen?  It almost sounds like some kind of asexual reproduction?

Also, about this rate of mutation, if we were to create a genetically modified virus, could be engineer it in such a way where it would be exceptionally stable and thus have a very low rate of mutation?  Is there a way to engineer a virus like that?

Wat some of the stuff I have been reading is that it's only milder for vaccinated people....for the unvaccinated it may be more deadly.
 
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Coronavirus (COVID-19) Thread

15 Dec 2021 06:52

I heard something tonight which sounds concerning....scientists were talking about how Delta and Omicron could both infect the same person and swap genetic material to mutate even faster? Is this possible and if so how would it happen?
Hadn't heard that, so I did a quick Google search and it appears it was mentioned in an interview with Dr. Burton at Moderna. Yes, that kind of viral evolution by co-infection of a cell is possible and can be an important -- though less common -- way in which viruses change.

Another risk of coinfection by Delta and Omicron, or one or both with the flu, is that they likely result in higher chance of hospitalization and death. We could see a lot of that this winter. Last winter there was not so much flu, but this winter could be different. And there is certainly a lot of Delta, and for a short window, a lot of Omicron at the same time.
 
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Coronavirus (COVID-19) Thread

15 Dec 2021 13:55

Wat, you anticipated my next question, which was going to be, if we create a booster shot specifically tailored to Omicron would that result in reduced effectiveness against Delta or maybe even other earlier variants? 
Sorry, missed this question earlier. I don't think it would matter. My intuition says to expect an Omicron-specific booster to improve protection most dramatically for Omicron, offer a smaller protective boost against Delta, and continued diminishing returns for earlier variants like Beta and Alpha (but those variants have effectively died out anyway). By the time an Omicron booster would be ready to distribute, it's likely that Delta will have diminished away, too. 

Actually, I would not be very surprised if by the time that booster is ready, Omicron has been or is starting to be outcompeted by whatever variants come after it. But like using previous boosters to help fight Omicron, an Omicron booster would likely still be of some use for variants after Omicron for a little while. Again, not too different from how flu vaccines work. They are in a sense trying to predict the properties of the strains next season based on the previous one, which isn't perfect and is one of the key factors that limits their effectiveness.
 
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Coronavirus (COVID-19) Thread

16 Dec 2021 00:40

Yes, this is looking more and more like a race like with flu.  Flu vaccines don't stop the virus, we still have the flu season, but they protect those who take them against serious illness, sometimes well, sometimes not so well.  Many pointed this out already a year ago, but it has been much disregarded out of fear that such talk wouldn't be compelling enough to make everybody take the vaccine.  Sometimes the flu season is mild and the reason could both be that the vaccines that year were effective, or that the variant that year was relatively kind.  Or even both.  These possibilities all seem plausible for the winter and omicron so far.  It would also mean that covid vaccines, like the flu vaccines, will no longer be strongly recommended for young, healthy people.

One HK study: Omicron SARS-CoV-2 can infect faster and better than Delta in human bronchus but with less severe infection in lung.

So more like a regular cold, that is.  Which hopefully is real, good news, and not just wishful thinking. 
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Coronavirus (COVID-19) Thread

16 Dec 2021 09:44

Outbreak caused by the SARS-CoV-2 Omicron variant in Norway, November to December 2021

In total, 111 out of 117 attendees (95%) participated in the interviews. Respondents had an average age of 39 years (SD: 9.2; median: 38; range: 26–68) and 48 (43%) of them were women. Most respondents (n = 107; 96%) were fully vaccinated. Eighty-nine percent of the respondents (n = 99) had received two doses of mRNA vaccines. None reported having received a booster dose. All respondents reported having a negative rapid antigen self-test taken at home or PCR within 1–2 days before attending the event. Eight (7%) respondents had previously had COVID-19, but none in the previous 4 months, according to information gathered through the interviews.

Of the 111 respondents, 66 (59%) were confirmed cases (26 based on WGS and 40 based on PCR VOC screening) and 15 (14%) were probable cases (PCR-positive only). One PCR-positive attendee was confirmed to be infected with SARS-CoV-2 Delta variant (Pango lineage B.1.617.2), and subsequently excluded from further analysis. The total attack rate for the Omicron variant was 74% (81/110) (Figure). The cases had an average age of 38 years (SD: 8.6; median 36, range: 26–61) and 35 (43%) were women. The remaining 29 attendees did not have a positive PCR result by 13 December 2021.
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Coronavirus (COVID-19) Thread

17 Dec 2021 01:10

I heard something tonight which sounds concerning....scientists were talking about how Delta and Omicron could both infect the same person and swap genetic material to mutate even faster? Is this possible and if so how would it happen?
Hadn't heard that, so I did a quick Google search and it appears it was mentioned in an interview with Dr. Burton at Moderna. Yes, that kind of viral evolution by co-infection of a cell is possible and can be an important -- though less common -- way in which viruses change.

Another risk of coinfection by Delta and Omicron, or one or both with the flu, is that they likely result in higher chance of hospitalization and death. We could see a lot of that this winter. Last winter there was not so much flu, but this winter could be different. And there is certainly a lot of Delta, and for a short window, a lot of Omicron at the same time.
Thanks I see we're learning something new every day which is fascinating with how quickly the science is evolving and it makes me wonder if the pandemic actually gave virology a seismic boost and advance (necessity is the mother of invention.)
In the other post you mentioned what might come after Omicron, this is going to be a bit speculative but bear with me....successful variants, where do they come from, other successful variants?  So whatever came after Omicron, is it more likely that it would evolve from Omicron? Or from a different variant, perhaps Delta or some other?  But since Omicron seems to be so much more successful than Delta and represents the greatest genetic change between variants, wouldn't that make it more likely that whatever comes after Omicron would most likely evolve from Omicron?  And if that is true, would it make more likely that any booster specifically tailored to Omicron would also offer added effectiveness to whatever came after it?
 
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Coronavirus (COVID-19) Thread

17 Dec 2021 04:04

So whatever came after Omicron, is it more likely that it would evolve from Omicron? Or from a different variant, perhaps Delta or some other?  But since Omicron seems to be so much more successful than Delta and represents the greatest genetic change between variants, wouldn't that make it more likely that whatever comes after Omicron would most likely evolve from Omicron?  And if that is true, would it make more likely that any booster specifically tailored to Omicron would also offer added effectiveness to whatever came after it?
Yep, all of that is good reasoning. The more infections there are by a particular variant, the more chances there are for a new variant to diverge from it. At the moment there are a lot of chances by both Delta and Omicron, but it's pushing more toward Omicron very rapidly.
One HK study: Omicron SARS-CoV-2 can infect faster and better than Delta in human bronchus but with less severe infection in lung.

So more like a regular cold, that is.  Which hopefully is real, good news, and not just wishful thinking. 
Yes, good news if true. There was also a study of recent cases in South Africa finding that Omicron has about a 30% less chance of resulting in hospitalization than Delta. (I haven't tracked down and read their methods though so I'm not sure how they account for factors such as varying levels of immunity and time since infection.) But it's another hopeful indicator.

Despite these hopeful signs, societies must be careful not to relax, because even if Omicron has less risk of hospitalization per person, the rapidity can mean a huge number of people requiring hospitalization at the same time. If a lot of people who need it are unable to get care, mortality rate would increase. So we really need to be back into a "flatten the curve" mentality with this wave -- both the cases curve with social distancing, and the severe cases curve with boosters.


Edit: speaking of rapidity, the case trends in areas dominated by Omicron are astounding:
► Show Spoiler
 
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Coronavirus (COVID-19) Thread

17 Dec 2021 04:31

So whatever came after Omicron, is it more likely that it would evolve from Omicron? Or from a different variant, perhaps Delta or some other?  But since Omicron seems to be so much more successful than Delta and represents the greatest genetic change between variants, wouldn't that make it more likely that whatever comes after Omicron would most likely evolve from Omicron?  And if that is true, would it make more likely that any booster specifically tailored to Omicron would also offer added effectiveness to whatever came after it?
Yep, all of that is good reasoning. The more infections there are by a particular variant, the more chances there are for a new variant to diverge from it. At the moment there are a lot of chances by both Delta and Omicron, but it's pushing more toward Omicron very rapidly.
One HK study: Omicron SARS-CoV-2 can infect faster and better than Delta in human bronchus but with less severe infection in lung.

So more like a regular cold, that is.  Which hopefully is real, good news, and not just wishful thinking. 
Yes, good news if true. There was also a study of recent cases in South Africa finding that Omicron has about a 30% less chance of resulting in hospitalization than Delta. (I haven't tracked down and read their methods though so I'm not sure how they account for factors such as varying levels of immunity and time since infection.) But it's another hopeful indicator.

Despite these hopeful signs, societies must be careful not to relax, because even if Omicron has less risk of hospitalization per person, the rapidity can mean a huge number of people requiring hospitalization at the same time. If a lot of people who need it are unable to get care, mortality rate would increase. So we really need to be back into a "flatten the curve" mentality with this wave -- both the cases curve with social distancing, and the severe cases curve with boosters.


Edit: speaking of rapidity, the case trends in areas dominated by Omicron are astounding:
► Show Spoiler
The less serious nature of it is a bit calming but there is a very bad vibe in NYC right now (I know that doesn't sound scientific) hospitalizations have tripled over the past 3 days and everything is starting to get shut down again.  It feels like Spring 2020 again but hopefully this surge going on doesn't last that long.  Maybe just a week or two.  I hope that's good reasoning too, considering we seem to have had a Thanksgiving surge and this seems to be mostly Delta related (although there are about 13% Omicron cases from what I remember.)
 
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Coronavirus (COVID-19) Thread

17 Dec 2021 04:38

New York’s omicron situation is changing by the hour / Twitter

They changed their thinking

New York’s omicron situation is changing by the hour

What happens during the collision of two variants when the public’s reserve of trust and patience has been exhausted?
Photo via @bopinion

The change of expert opinion was sudden.

Researchers at Harvard Medical School now say the omicron variant, not delta, is likely fueling the current surge in Covid-19 cases in the northeastern U.S.
edit: fixed text formatting -- Wats

Thanks Wats -- I was trying to figure out how to do this right but those weird font symbols never showed up on the edit page.  I was about to can the whole post and try to paste it to notepad first (since that removes all formatting.)

So based on all this new info how long do you think this new surge will last?  The Harvard people think that the surge will be worse here than it was in South Africa because we have both Delta and Omicron at the same time while South Africa was mostly done with Delta when Omicron showed up.  But they didn't give a timeframe for how long this surge might be.  They did say that cases are doubling throughout the Northeast every 4 days and no computer system they use can keep up with that and Omicron has traveled the world in two weeks?  They also said that if the cases keep increasing like this that even if the number of people who get hospitalized is small the sheer numbers will still overwhelm the hospital system?  All elective procedures are canceled here, we are back mask mandates and theatres have shut down.
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