Coronavirus

[heltok]

 

[AlanSubie4Life]

Their epi chart shows a lot of daily variation.

You should ignore daily variation after November 18th or so, for now, because none of that data is complete yet. If you look prior to that, of course there is daily variation, but it looks like it's bounded by about 10% of the average around that point, roughly. We'll need to wait until after New Year's to see where the December 10th/11th data settles.

We'll see what happens. It looks horrible to me. But not as horrible as the US. Tegnell may be right about that "plateau" that is possibly sloping slightly upwards - lol, what a ridiculous thing to say - when it comes to deaths occurring right now. But that's little solace.

Can look at the nowcast (which currently looks a little broken - the actual model projection doesn't seem to be working...), for a little bit of a different way to look at the reported data:

Reported Covid-19 deaths in Sweden

 

[MXLRplus]

If your goal is to slow down the spread of C19 in California (and many other states), you need to inoculate the Hispanic population. They are still nearly 60% of the cases and nearly 50% of the deaths. There are not even much Spanish language Covid signage.

Data on Racial Demographics

Identity politics, not science, is the #1 factor for triage. The majority of Nursing Home staff are ________ . You get one guess. But we've known that since April...

 

[SMAlset]

Pfizer’s and Moderna’s vaccines contain the excipient Polyethylene glycol (PEG) which researchers think might be linked to anaphylactic reactions in a few people so far.

So what is known about Polyethylene glycol and the allergies?

From Reuters today:
FDA investigating five allergic reactions after Pfizer shot in U.S

Peer reviewed paper:
https://onlinelibrary.wiley.com/doi/pdf/10.1111/all.14711

I’m aware PEG is used in everything from medicines, stool softeners, cosmetics and food. They’re saying in the news that people with severe allergies should not get the vaccines. What more can you guys tell us? Do typical yearly flu shot contain PEG?

 

[SMAlset]

As a healthcare worker, received my first dose of the Pfizer vaccine. The sticky note documents the time of administration as 15 minutes observation required prior to leaving the room. This is a great start to the end of COVID-19! View attachment 618584

I’m curious on the 15-minute wait for reaction time. Allergy offices at least in my area of the country use to make you wait for 15-20 minutes after a shot before leaving but a few years ago made it a 30-minute mandatory wait after an injection in case of an anaphylactic reaction. Surprised with these injections still being so new to a whole population that a longer observation period isn’t recommended.

 

[HVM]

 

[MXLRplus]

Pfizer’s and Moderna’s vaccines contain the excipient Polyethylene glycol (PEG) which researchers think might be linked to anaphylactic reactions in a few people so far.

So what is known about Polyethylene glycol and the allergies?

From Reuters today:
FDA investigating five allergic reactions after Pfizer shot in U.S

Peer reviewed paper:
https://onlinelibrary.wiley.com/doi/pdf/10.1111/all.14711

I’m aware PEG is used in everything from medicines, stool softeners, cosmetics and food. They’re saying in the news that people with severe allergies should not get the vaccines. What more can you guys tell us? Do typical yearly flu shot contain PEG?

PEG is an over-the-counter drug. It has been in use for 70 years. The paper you are quoting appears to be an editorial. No statement of conflicts is attached; interested party could have wrote it.

Anaphylaxis caused by flu vaccines is 1.31 : 1,000,000.

It is my understanding as a layman that PEG is used in influenza vaccine to clump the virions together which enhances its effectiveness.

 

[EVCollies]

I’m curious on the 15-minute wait for reaction time. Allergy offices at least in my area of the country use to make you wait for 15-20 minutes after a shot before leaving but a few years ago made it a 30-minute mandatory wait after an injection in case of an anaphylactic reaction. Surprised with these injections still being so new to a whole population that a longer observation period isn’t recommended.

I believe the wait time is carried over from the studies, I know the AZ trial also uses 15 min waiting time. For patients with history of allergic reactions, they must wait 30 minutes before leaving the waiting room.

PEG is an over-the-counter drug. It has been in use for 70 years. The paper you are quoting appears to be an editorial. No statement of conflicts is attached; interested party could have wrote it.

Anaphylaxis caused by flu vaccines is 1.31 : 1,000,000.

It is my understanding as a layman that PEG is used in influenza vaccine to clump the virions together which enhances its effectiveness.

That is correct, the mRNA construct is PEGylated, this protects them from destruction before entering a cell that can translate the mRNA into the protein to be targeted by the immune system.

 

[Doggydogworld]

You should ignore daily variation after November 18th or so, for now, because none of that data is complete yet.

It's complete enough to see large daily variation. Numbers from one week ago vs. today for the first week or so after November 18th:
11/19 - 45 vs 45
11/20 - 45 vs 45
11/21 - 51 vs 50
11/22 - 57 vs 59
11/23 - 54 vs 54
11/24 - 68 vs 67
11/25 - 67 vs 70
11/26 - 57 vs 59

Very little change in the past week, I expect almost zero next week. Even if lag times are lengthening, and I'm not convinced they are on a percentage basis, three week old data just doesn't change much.

Can look at the nowcast (which currently looks a little broken - the actual model projection doesn't seem to be working...), for a little bit of a different way to look at the reported data:

Reported Covid-19 deaths in Sweden

Yes, I use this page and also his raw data (github link at bottom of page). The 7 day average line from Worldometers (below) shows Tegnell's "plateau" slowly rising from 60 on November 27 to 63 on December 6. I'm confident that December 6 number will increase and ruin his plateau. But IMHO the flattish stretch from 11/27-12/4 won't change much. And my guess is the slope after December 4th will not be nearly as steep as it was prior to November 27.

 

[AlanSubie4Life]

Very little change in the past week, I expect almost zero next week. Even if lag times are lengthening, and I'm not convinced they are on a percentage basis, three week old data just doesn't change much

Yeah, I was giving a safe date where things are well settled (based directly on above chart). Some of these other dates are close, but certainly not final. You had mentioned a comparison to the 28th-29th to measure variation, which definitely is not complete. That is all; was not saying there are going to be huge changes there.

I agree that the rise in deaths is very likely slowing. Gotta love that second derivative. That is what happened with cases so is as expected.

And yes, there does seem that there will be a lull in the curve where you mentioned. It will change, but not too much, probably.

 

[NikolaACDC]

New strain of Covid-19: Boris Johnson backtracks on relaxing Christmas rules - CNN

"The hopes of millions of Britons that Covid-19 restrictions would be eased over Christmas were dashed on Saturday, after scientists warned a new strain of the virus is spreading more quickly than others.
...
"The spread is being driven by the new variant of the virus," Johnson said in a hastily called press conference. "It appears to spread more easily and may be up to 70% more transmissable than the earlier strain.
...
As with other new variants or strains of Covid-19, this one carries a genetic fingerprint that makes it easy to track, and it happens to be one that is now common. That does not mean the mutation has made it spread more easily, nor does it not necessarily mean this variation is more dangerous.
Multiple experts in the genetics and epidemiology of viruses are noting that this one could be just a "lucky" strain that's been amplified because of a superspreader event; it could be the mutation somehow makes it spread more easily without causing more serious illness; or it could just be by chance."

 

[AlanSubie4Life]

Related discussion of emerging variants:

https://twitter.com/trvrb/status/1340409968818671616?s=21

All the more reason to bring down case counts, to minimize genetic diversity. Also, the more people who have been infected, the greater the evolutionary advantage of the emerging variants.

We’ll probably be getting boosters (not really a booster since it will be modified) in future years, it seems.

But, it is TBD whether reinfection, or infection after vaccination, due to antigenic drift, will still result in severe disease. It may not, and we probably won’t know for a while. But will probably know before the time when a booster with a new spike protein encoding is needed.

 

[NikolaACDC]

An open letter from European scientists, calling for aggressive measures to keep infections low
:
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)32625-8/fulltext

"First, low case numbers save lives, and fewer people will die or suffer from long-term effects of COVID-19.
...
Second, low case numbers save jobs and businesses.
...
Third, the control of the spread is most effective at low case numbers.
...
Fourth, contact tracing and quarantine is not feasible at high infection prevalence.
...
Fifth, aiming for naturally acquired population immunity is not an option."

--------------------
Basically spelling out what is pretty obvious even for (informed) laypeople.
Their main reason for spelling it out is to call for a Europe-wide synchronized approach instead of the each-country-for-themselves that has happened so far.

 

[dhanson865]

new record high of 724 new cases locally

 

[dhanson865]

update from the ghoul pool.

wisdom of the crowds for the win, 320,845 + about 3,000 per day gets us to the 11 voters for 0.1% to 0.2% by about Christmas eve/day. Then on to about 350,000 by new years.

 

[wdolson]

If your goal is to slow down the spread of C19 in California (and many other states), you need to inoculate the Hispanic population. They are still nearly 60% of the cases and nearly 50% of the deaths. There are not even much Spanish language Covid signage.

Data on Racial Demographics

Identity politics, not science, is the #1 factor for triage. The majority of Nursing Home staff are ________ . You get one guess. But we've known that since April...

When California had its first spike in the spring I watched it grow in the Imperial Valley, then spread across Southern California, then up the central valley as migrant farm workers first visited family in the cities after the spring crops were in and then spread it in the Valley as they went to work on summer crops there.

My partner is Mexican and I grew up in East LA (though I'm not Hispanic) and Hispanic culture is more social and family focused than white culture. My partner is a bit concerned for her family who live in San Jose. They all live close to one another and are used to seeing each other very often. All her cousins are well educated and do take every precaution but her last aunt is around 95 and her kids take turns staying at her house to help take care of her.

My partner's family were "haves" in Mexico. They came here in the 30s during a peasant uprising that made it too dangerous where they lived. Before leaving they had the best education money could buy, so they were unusual among Hispanic immigrants. For those without money the education system in most Hispanic countries is poor and people don't get educated about hygiene and the concept of invisible things that could kill you and how to prevent their spread seems like strange stories the Gringos make up.

Between being a very social, family oriented culture and a large number of people who don't understand hygiene well enough to practice it well that sets up the almost perfect storm for heavy spread.

Related discussion of emerging variants:

https://twitter.com/trvrb/status/1340409968818671616?s=21

All the more reason to bring down case counts, to minimize genetic diversity. Also, the more people who have been infected, the greater the evolutionary advantage of the emerging variants.

We’ll probably be getting boosters (not really a booster since it will be modified) in future years, it seems.

But, it is TBD whether reinfection, or infection after vaccination, due to antigenic drift, will still result in severe disease. It may not, and we probably won’t know for a while. But will probably know before the time when a booster with a new spike protein encoding is needed.

The severe coronaviruses thus far are mostly one and done viruses. A study done on SARS victims from 17 years ago found that they both still had t-cell immunity and they appeared to also be immune to COVID-19.

With some viruses the body is able to generalize from one strain to related strains fairly easily and t-cell immunity to one give you t-cell immunity to the family. That was what was discovered with small pox and cow pox. Infecting people with cow pox which is only a minor illness in humans, gives them immunity to small pox.

I don't think we have very good data on the long term immunity to the nuisance strains of coronaviruses, though it doesn't look like the long term immunity is all that great. The nuisance strains are minor enough problems there wasn't much research on them until a few years ago. Because they cause all the same symptoms of rinoviruses medicine didn't really pay that much attention to the fact that there were two families of viruses that cause the same sort of disease out there until fairly recently.

But the nuisance strains of coronaviruses are like to two major branches of the car family. One branch leads to most of the large cats and the other to house cats. One branch has a species that make good companions for humans and the other, not so much.

It's possible that infection with one strain of COVID, or getting the vaccine for one strain gives most people permanent immunity. Or it may not. We probably won't know for a while. The fact that we're not hearing about very many second infections I lean towards the one and done theory, but I may be wrong and there may be a new strain that comes along to avoid detection by t-cells from an old infection.

We just don't know.

 

[AlanSubie4Life]

I lean towards the one and done theory, but I may be wrong and there may be a new strain that comes along to avoid detection by t-cells from an old infection.

I am not concerned about reinfection in the traditional sense. I am concerned about infection after vaccination by a virus that has evolved to escape the body’s antibody response, and general memory. That seems likely right now though it may take time, and whether t-cell cross reactivity helps is TBD. Maybe won’t be that severe an infection if you have been immunized against something fairly similar - I have no idea how this works. We’ll know more in about 6-9 months is my guess.

 

[wdolson]

I am not concerned about reinfection in the traditional sense. I am concerned about infection after vaccination by a virus that has evolved to escape the body’s antibody response, and general memory. That seems likely right now though it may take time, and whether t-cell cross reactivity helps is TBD. Maybe won’t be that severe an infection if you have been immunized against something fairly similar - I have no idea how this works. We’ll know more in about 6-9 months is my guess.

Soldiers say the bullet you don't hear is the one that gets you. The infectious disease community was focused on flu mutations and while they started to pay some attention to coronaviruses after SARS, few were all that concerned about the next big pandemic to be a coronavirus so not many resources were put on the job.

I always had a feeling that flu viruses were not the big risk. What made the 1918 flu pandemic so bad had a lot of factors we can deal with effectively now. The survival rate for secondary infections from flus is much higher now than it was 100 years ago.

On the backside of this human knowledge about the whole coronavirus family is going to be several orders of magnitude larger than it was at the start of this pandemic.

 

[AlanSubie4Life]

On the backside of this human knowledge about the whole coronavirus family is going to be several orders of magnitude larger than it was at the start of this pandemic.

Yeah previously only bat virologists paid much attention.

Meanwhile the Navajo nation has *known* infections of 11% of their population, meaning probably 30-40% infected so far.

And over 0.4% of their population has died.

745 deaths, 20.8k cases.

CFR 3.5% (will get higher based on where they are on their curve; their cases are starting to decrease).

So that gives a fuzzy idea of what herd immunity would look like. Not that great. I guess they are probably a bit more than halfway there.

I guess if they get a decent vaccine allotment, they will be able to be finished with this more quickly than most places.

 

[SMAlset]

Just saw this CBS News report on CDC recommendations for next two groups of vaccine recipients:

CDC panel recommends older Americans and frontline workers be next in line for COVID-19 vaccine

from CBSNews:
“The first people receiving the vaccine, known as Phase 1A, are healthcare professionals and long-term residents of health care facilities, like nursing homes. The CDC panel recommended Phase 1B* should include Americans 75 and older and frontline workers, and 1C should cover Americans aged 65-74 and people 16-64 with high-risk medical conditions and other essential workers, Kristen Nordlund of the CDC confirmed to CBS News on Sunday.”

*Americans 75 and older and frontline workers — including police, firefighters, teachers and grocery workers.