Coronavirus

[NikolaACDC]

Some newer (not yet peer-reviewed) studies referenced and linked to in this article:

Your Case of Omicron Might Have Super-Boosted Your Immunity—If You Were Vaccinated


"SARS-CoV-2 Omicron sublineages carry distinct spike mutations and represent an antigenic shift resulting in escape from antibodies induced by previous infection or vaccination. We show that hybrid immunity or vaccine boosters result in potent plasma neutralizing activity against Omicron BA.1 and BA.2 and that breakthrough infections, but not vaccination-only, induce neutralizing activity in the nasal mucosa. Consistent with immunological imprinting, most antibodies derived from memory B cells or plasma cells of Omicron breakthrough cases cross-react with the Wuhan-Hu-1, BA.1 and BA.2 receptor-binding domains whereas Omicron primary infections elicit B cells of narrow specificity.
While most clinical antibodies have reduced neutralization of Omicron, we identified an ultrapotent pan-variant antibody, that is unaffected by any Omicron lineage spike mutations and is a strong candidate for clinical development."
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"Omicron is the evolutionarily most distinct SARS-CoV-2 variant (VOC) to date and displays multiple amino acid alterations located in neutralizing antibody sites of the spike (S) protein. We report here that Omicron breakthrough infection in BNT162b2 vaccinated individuals results in strong neutralizing activity not only against Omicron, but also broadly against previous SARS-CoV-2 VOCs and against SARS-CoV-1. We found that Omicron breakthrough infection mediates a robust B cell recall response, and primarily expands preformed memory B cells that recognize epitopes shared broadly by different variants, rather than inducing new B cells against strictly Omicron-specific epitopes. Our data suggest that, despite imprinting of the immune response by previous vaccination, the preformed B cell memory pool has sufficient plasticity for being refocused and quantitatively remodeled by exposure to heterologous S protein, thus allowing effective neutralization of variants that evade a previously established neutralizing antibody response.
One Sentence Summary: Breakthrough infection in individuals double- and triple-vaccinated with BNT162b2 drives cross-variant neutralization and memory B cell formation."

 

[AlanSubie4Life]

I think I’ve seen other papers, not mentioned in the article, that also implied better immune protection against BA.2 from combining vaccination with an Omicron (BA.1) infection than unvaccinated with only a prior BA.1 infection.

Yes, I have as well. Would be nice to see the actual data at a community level, carefully gathered and studied, before someone writes an article like this.

Finally, all of these variants are behaving similarly to the other 4 Coronaviruses that give people “common cold” symptoms in that you can be reinfected with the same variant after about 6 to 9 months.

Meanwhile, the article suggests every 3-6 months.

I just think it's a poorly supported article. It may be that the article is correct - I think the push from the virologists here is that people shouldn't just assume they're done after getting infected. But need actual data to understand the immunity landscape and how it impacts outcomes.

Some newer (not yet peer-reviewed) studies referenced and linked to in this article:

Your Case of Omicron Might Have Super-Boosted Your Immunity—If You Were Vaccinated


"SARS-CoV-2 Omicron sublineages carry distinct spike mutations and represent an antigenic shift resulting in escape from antibodies induced by previous infection or vaccination. We show that hybrid immunity or vaccine boosters result in potent plasma neutralizing activity against Omicron BA.1 and BA.2 and that breakthrough infections, but not vaccination-only, induce neutralizing activity in the nasal mucosa. Consistent with immunological imprinting, most antibodies derived from memory B cells or plasma cells of Omicron breakthrough cases cross-react with the Wuhan-Hu-1, BA.1 and BA.2 receptor-binding domains whereas Omicron primary infections elicit B cells of narrow specificity.
While most clinical antibodies have reduced neutralization of Omicron, we identified an ultrapotent pan-variant antibody, that is unaffected by any Omicron lineage spike mutations and is a strong candidate for clinical development."
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The first paper here is the one discussed in this Tweet thread, above: Coronavirus

It is interesting. It doesn't really answer the question of how long lasting and effective the neutralizing antibodies are against Omicron and its minor variants. It seems like if you're lucky enough to get some of that pan-variant antibody S2X324 you could be in good shape.

 

[wdolson]

I think the point that was being made is that vaccination status does not increase risk of autism. Whether acetaminophen use does is another question which seems worth investigating to see whether the data support it.

You mentioned an “interaction with one of the vaccines.” I didn’t read the paper. But anyway such an interaction would mean that rates would be higher in vaccinated children. But sounds like it’s not, after controlling for acetaminophen use. So nothing to do with the vaccine. That’s not an interaction. Using acetaminophen to reduce fever, caused by vaccination, is not caused by vaccination! It is correlated, presumably.

The initial study found that childhood autism was much rarer in Europe than the US despite using the same vaccines. When methods were compared, it's routine in the US to give children Tylenol after vaccines, but it is almost never done in Europe. That was the only significant difference which led to a hypothesis that there was an interaction between Tylenol and vaccines.

However it might just be giving Tylenol to children. We don't know for sure yet, but it looks like there is a Tylenol connection to autism.

It’s not that I don’t believe this article - the performance of the Omicron vaccine suggests this could be true, and characteristics of the virus may give this result. However, this story does not provide supporting data for the claims.

I would like to know how well boosting plus prior infection with Omicron protect against infection by Omicron sub variants, as compared to unvaccinated with prior Omicron infection.

Seems like that is the relevant data point. Anyone seen such data? They link a paper in the story which does not provide the relevant information (studies reinfections by Omicron after infection by other variants, showing low efficacy - interesting, suggestive, but not useful!).

https://twitter.com/x/status/1526226681702367232

Has potential to be very disruptive on an ongoing basis if true. Need to figure out exactly what is happening and why. I do mostly trust the virologists here, but there’s not much supporting evidence. And how common will infections by BA.2.12.1/BA.4/BA.5 be? Is it something special about them that allowed them to escape, but after infection you’re protected? Or are all Omicron variants consistently able to escape immunity? No data.

Bkp_duke a while back pointed out that humans don't tend to get long term immunity from respiratory viruses. I think it's even harder with upper respiratory viruses (can't remember for sure). Omicron has shifted from a lower to upper respiratory virus and become milder.

This may have been the progression with the other corona viruses that have been endemic for so long very little research was done on them before this pandemic.

In any case it's normal not to get long lasting immunity from respiratory viruses. That's why people keep getting the common cold once or more a year.

 

[cwerdna]

Re: California, the spike that began March 6th at SARS-CoV-2 Sewage Monitoring Data - Emergency Operations Center - County of Santa Clara is a bit concerning. I wonder if has peaked or it'll continue rising? Will other cities in the Bay Area see that soon too?

https://covid19.sccgov.org/dashboard-wastewater is showing concerning trends for 3 out of the 4 areas if you look under "Timeframe: since tracking started in Oct / Nov 2020".

But, so far, if you Google for us covid deaths and filter by either California or California, Santa Clara County, the 7-day moving average of COVID deaths is pretty low. Will be interesting to see if it picks back up and by how much due to the several week lag between infection and death.

 

[AlanSubie4Life]

We don't know for sure yet, but it looks like there is a Tylenol connection to autism.

Whew! So nothing to do with vaccines. Case closed. Definitely worth looking into acetaminophen!

Omicron has shifted from a lower to upper respiratory virus and become milder.

Citation needed for intrinsic severity. Also, relative to what? Delta? Wuhan? Alpha?

Seems like all the evidence I have seen suggests about the same as the original. Intrinsic, of course. (Which is good, that we are talking about intrinsic severity…) But this distinction is very important for those who are naive!

In any case it's normal not to get long lasting immunity from respiratory viruses.

This does appear to be true, on the order of 9 months though. Seems poorly researched in any case.
What’s not normal is a respiratory virus which seems to have this persistent virulence in non-naive hosts - not clear what the exact level is though. It may be that the immunocompromised are just screwed. It seems worse than influenza, for now - compare to those contracting influenza who are vaccinated against that strain…worse or better?

That's why people keep getting the common cold once or more a year.

Is it from the same virus? Citation needed.

 

[heltok]

I would like to know how well boosting plus prior infection with Omicron protect against infection by Omicron sub variants, as compared to unvaccinated with prior Omicron infection.

Seems like that is the relevant data point. Anyone seen such data? They link a paper in the story which does not provide the relevant information (studies reinfections by Omicron after infection by other variants, showing low efficacy - interesting, suggestive, but not useful!).

How Omicron infection turbo-charges vaccinated people's immunity

Two studies show that this group may be primed to overcome a broad range of coronavirus variants. Read more at straitstimes.com.

www.straitstimes.com

BERLIN (BLOOMBERG) - People who are vaccinated and then get infected with Omicron may be primed to overcome a broad range of coronavirus variants, early research suggests.

A pair of studies showed that infection produced even better immune responses than a booster shot in vaccinated patients. Teams from Covid-19 vaccine maker BioNTech and the University of Washington posted the results on preprint server bioRxiv in recent weeks.

 

[AlanSubie4Life]

How Omicron infection turbo-charges vaccinated people's immunity

Two studies show that this group may be primed to overcome a broad range of coronavirus variants. Read more at straitstimes.com.

www.straitstimes.com

BERLIN (BLOOMBERG) - People who are vaccinated and then get infected with Omicron may be primed to overcome a broad range of coronavirus variants, early research suggests.

A pair of studies showed that infection produced even better immune responses than a booster shot in vaccinated patients. Teams from Covid-19 vaccine maker BioNTech and the University of Washington posted the results on preprint server bioRxiv in recent weeks.

Exactly, as I posted last week with one of these studies. Would be good to see what the actual population-level benefit is though. I suspect we’ll find out in a month or two! I hope it is robust protection - it greatly impacts the size of this wave.

 

[dhanson865]

fwiw the moving average for deaths in the US is now lower than at any time on the chart since the March 2020 (when the first wave hadn't even ramped up yet). Now lower than the minimum in Summer 2021 which used to be the low point.

If it follows last 2 years patterns the uptick will be in the first week of July and then ramp up into Fall. The week of July 4th seems to be a superspreading week.

If we don't see the ramp up this summer/fall I'd be pleasantly surprised.

 

[AlanSubie4Life]

fwiw the moving average for deaths in the US is now lower than at any time on the chart since the March 2020

Yes, as I've mentioned it does seem like this should happen, though I expect it to flatten out soon. Based on the ICU numbers, it should drop below 150, but there's some question about whether those numbers are correct (to be clear, it's only a question because the death numbers weren't making sense...they seem to be starting to come into line after a large bump of old death reports last week). And also if ICU numbers start to ramp up rapidly that'll put an end to things (they have a ways to go before reaching Summer 2021 levels though).

Keep in mind that you can't compare current numbers vs. the numbers last year, until you've waited a couple weeks at least, due to epi-curve reporting by many states which Worldometers now uses. The rolloff is artificial. In a couple weeks, the number of deaths reported for today's date will be higher and likely higher than the Summer 2021 minimum (old datapoints keep increasing over time).

Other counting sites show a less precipitous drop because they are not doing partial date-of-death reporting like Worldometers does. That being said, it seems that deaths are still declining, as one would expect given the ICU numbers.

If we don't see the ramp up this summer/fall I'd be pleasantly surprised.

With the existing variants, I'd be surprised if we exceed a 7-day average of 750 deaths again. There's a lot of reinfection taking place. 750 deaths a day is bad though; even 500 deaths a day is completely ridiculous and unnecessary.

Of course with the withdrawal of support for free testing for the uninsured, we probably also have a bit more uncounted death taking place at the moment. We'll have to wait for the excess mortality numbers for that, in several months.

 

[Jeff N]

Covid got the clap.

Eric Clapton catches COVID-19 after calling vaccine efforts a ‘mass psychosis’

Eric Clapton, who has railed against lockdowns and vaccines, has tested positive for COVID-19. The 77-year-old English singer has canceled two upcoming concerts, Tuesday in Zurich and Wednesday in …

www.nydailynews.com

 

[AlanSubie4Life]

To me it looks like this wave is primarily COVID moving through prior uninfected (the majority of whom would be vaccinated):

Also, everyone I know is getting infected. It seems to be moving through the privileged, who have decided to dispense with precautions. I guess it is more convenient to get infected, now that it's easy to test at home.

These are (generally) NOT the typical zip codes showing higher infection rates (it has consistently been more in Southern and Eastern San Diego County, and close to downtown). Coveted 92037 is in here!

Not up to Omicron BA.1 levels yet, but no slowing in sight yet (this can change very rapidly of course). Slope is substantially less than Omicron BA.1, so unless somehow the dynamics change, I don't see this getting anywhere near BA.1 (would take 3 more months at the current rate).

Anyway, the point is from anecdata and actual data that this is at least consistent with infection of vaccinated, who prior to this were uninfected (excluding the unvaccinated here). We'll see if it ends up spilling over, though.

Just a matter of time before it makes it through (around?) my N95 mask. Currently swimming with (poorly matched) antibodies, though.

 

[madodel]

Omicron’s Surprising Anatomy Explains Why It Is Wildly Contagious
Specific mutations hide the COVID-causing variant from the immune system and give it a new route into more cells

Omicron hosts twice as many mutations as other variants of concern, and its BA.2 sublineage may have even more. There are 13 mutations on Omicron’s spike protein that are rarely seen among other variants. Those changes to its anatomy gave it new and surprising abilities. If Delta is the brute-force Hulk variant, think of Omicron as the Flash—masked and wicked fast.​

 

[EVNow]

To me it looks like this wave is primarily COVID moving through prior uninfected (the majority of whom would be vaccinated):

Also, everyone I know is getting infected. It seems to be moving through the privileged, who have decided to dispense with precautions. I guess it is more convenient to get infected, now that it's easy to test at home.

These are (generally) NOT the typical zip codes showing higher infection rates (it has consistently been more in Southern and Eastern San Diego County, and close to downtown). Coveted 92037 is in here!

Thats my take as well.

In our case we just got tired of keeping kids away from their friends all this time. They started going back to the local park to play with friends - and Inslee removed mask mandates. So, even though they wear N95 masks, didn't matter.

So, Covid is now sweeping what has been a fairly safe school district. We are getting pleading texts from the school to keep children at home if they have any symptoms, "even if they are from allergy".

The numbers don't tell the whole story since most just test and home and I guess a lot of them don't report.

 

[EVNow]

Interesting note about the forgotten pandemic from 1918 that killed 50 to 100 million people (!).

Crosby's book "probes the curious loss of national memory of this cataclysmic event." The 1918 pandemic killed between 50 - 100 million people in two years. Encyclopedia Britannica's 1924 history of the 20th century so far didn't even mention it once. 2/​

https://twitter.com/x/status/1526617195987587072

 

[bkp_duke]

Our 3rd grader was sent home today, had a cough that she's had for a few days. Tested COVID negative last week with the cough . . . now tested COVID positive.

Guess we get to babysit.

Other than the cough, ZERO symptoms. And by cough standards, it's a pretty mild cough.

Annoyed I get to babysit till at least Monday, but happy that it looks like things are morphing along the projected "endemic" pattern.

 

[EVNow]

Our 3rd grader was sent home today, had a cough that she's had for a few days. Tested COVID negative last week with the cough . . . now tested COVID positive.

Guess we get to babysit.

Other than the cough, ZERO symptoms. And by cough standards, it's a pretty mild cough.

Annoyed I get to babysit till at least Monday, but happy that it looks like things are morphing along the projected "endemic" pattern.

Second time ?

BTW, I think one of the other reasons for a wave now (among the "more careful") is that immunity from boosters and vaccines for kids has sufficiently waned now.

 

[bkp_duke]

Second time ?

Kids have never had a positive COVID test, just clinical suspicion by me.

First confirmed test in the household since the pandemic started (although I really do believe we had a false negative about 2 months ago).

 

[Jeff N]

Our 3rd grader was sent home today, had a cough that she's had for a few days. Tested COVID negative last week with the cough . . . now tested COVID positive.

Anecdotally, it seems like I’m hearing about more people testing positive now (people I know personally and that I read about online) even though the official stats are only modestly high. Good luck with it and all the best to your family.

 

[AlanSubie4Life]

It’s sort of amusing that after all this talk about seasonality, and weather-induced waves, that the virus is now surging in the US at a time of year when it has never surged before. (In 2020 and 2021, this time corresponded to just a couple weeks before local minimum case numbers.) “It’s seasonal!”

Does this mean we’re really in trouble for this summer, when we’ve always had surges? I don’t know. But I don’t think so. Though it is true that the South is largely biding their time, and will rise (in cases) again, perhaps. Maybe we’ll just end up sort of flat at a high level as the wave breaks elsewhere and rises in the south? It’s possible that nearly everyone there already got Omicron, but lower vaccination rates means more potential.

I've had symptoms for about a week, very mild (head cold basically), and today I lost my sense of smell. Otherwise fine, but I'm assuming I have it. Not going to waste a test to confirm, as at this point it doesn't matter, testing would not change anything.

First confirmed test in the household since the pandemic started (although I really do believe we had a false negative about 2 months ago).

Not sure if you ever ended up testing but I guess not? Anyway will be interesting to see if you get reinfected. I would suspect not but then of course you won’t know 100% if it’s reinfection.

Best of luck anyway. Everyone I know who has had it and been vaccinated has been just fine - vaccines work of course. One person who has lung issues is taking Paxlovid on a precautionary basis even though boosted.

Everyone at work is coughing. Not supposed to come to work if you don’t feel well. I guess that is subjective. Sigh…the great N95 experiment continues.

Anyway…

New rounds of antigen tests (8) available, easy to get for you or people you know. If you have not done both prior rounds (this is the third round) you can do two separate orders (I think for a total of 12, or 16 including all three rounds).

COVID-19 Testing

Every home in the U.S. is eligible to order an additional 4 free at-⁠home tests beginning November 20. If you did not order tests this fall, you may place two orders for a total of 8 tests.

www.covid.gov

 

[bkp_duke]

Kid stayed home today. Logged into school via her chromebook, finished her reading "diagnostic test", reading assignments, math, and everything else in 2.5 hours. Made me wonder how much time the public education system is wasting annually for my children and how much more work could have been completed. . .

She's barely had a cough all day.

Tested her sister X2 (asymptomatic) with two different kits, negative. Sent her butt to school.