Coronavirus

[bkp_duke]

This annoys me tremendously because I'm having to enter medical facilities these days to get some treatment for my shoulder. It should be a nearly perfectly safe environment at this point (patients are kept well isolated from one another), but it sounds like it's not.

Seems like the third/fourth surge is just beginning. It seems to be coming perhaps a week later than predicted by models (though that could be due to the models providing day of symptoms and the surge being the day of report).

We'll see how bad it is (I expect we'll remain below 100k for the 7-day average, which is quite high but depends on the age distribution). I'm still optimistic that in many states it's going to end up being very mild due to immunity from infection and vaccination. Just have to keep a close eye on those hospitalizations as the cases spike. I expect the surge will be largely cut off and brought to a halt by late April, regardless. At that point there should be just too much immunity to support a massive outbreak.

It's bad news for school reopening, of course. We really want minimal community spread and very low baseline levels for that to avoid having children killing their parents with the virus. The resumption of spread is not going to make successful reopening easier. Still no talk of rapid tests.

It's actually the opposite. Since the beginning of the pandemic, 1 in 6 infections have been healthcare workers or their families. Assuming they know how to use PPE (most do), this really speaks volumes of just how infectious this virus is.

 

[AlanSubie4Life]

It's actually the opposite. Since the beginning of the pandemic, 1 in 6 infections have been healthcare workers or their families. Assuming they know how to use PPE (most do), this really speaks volumes of just how infectious this virus is.

I am not sure what you are referring to being “the opposite”?

There are 20 million healthcare workers in the United States, 1 in 17 people, as far as I can tell (I just look up the numbers; and I do not know whether your infections number applies to that same population definition). So 1 in 6 infections sounds to me about right, given their very high exposure level, and suggests that PPE and their procedures work quite well to reduce spread. (I’d expect ~1 in 2 infections to be in healthcare workers if PPE did not work well, due to ~10x average exposure risk - not only do they get more exposure at work, their immediate community is more likely to be comprised of healthcare workers, and thus they have higher risk outside of work.)
It also means that states that do a good job of vaccinating these people will see a stronger than expected effect on infections since healthcare workers are one nexus of infection, due primarily to their exposure.

 

[Jeff N]

There have been more updates to the Helix sequencing data (they seem to happen at least once a week).

California’s 5-day average is “only” 29% but the ramp looks to hit 40% very soon. Although not shown here, Minnesota (where overall cases are rising) is above 40% and looks to be not far behind Michigan (where overall cases are now rising sharply).

Tableau Public

public.tableau.com

 

[JRP3]

Looks as if Cali is grabbing all the vaccines

 

[AlanSubie4Life]

Looks as if Cali is grabbing all the vaccines

View attachment 646262

California has had 12% of the vaccine supply delivered to them. They have 12% of the US population. (I don't know when the gov't will change the per-capita allocation - probably not for a while though.)

It looks to me like they are making up for their early lag in administration of vaccines now, but they're still behind many states, according to the data published (but I am not sure how accurate the counts are).

Just speculation though, based on zero analysis.

Most likely the differences in new cases from state to state have to do with the B.1.1.7 prevalence, less to do with vaccination levels. But again, pure speculation, haven't looked at any data. Multiple factors at play, plus probably some luck.

 

[AlanSubie4Life]

https://twitter.com/x/status/1367559003534811136

I missed this thread from Prof Crotty. It's a pretty good summary. I'm slightly more optimistic than him about the efficacy of the Pfizer/Moderna vaccines against the variants (it's not clear which specific vaccine he is sketching here, he specifically focuses on J&J though), but he's the immunologist, not me. (But note that his plot does show immunity against B.1.351 in the early going for longer than a natural infection.) A key point for the natural immunity sketch is the massive variation from person to person - which explains some of the reinfections - some people have curves on this plot that are a lot lower. This seems less common (less variation) with vaccination.

 

[AlanSubie4Life]

Did the coronavirus leak from a lab? These scientists say we shouldn’t rule it out.

For many scientists, challenging the idea that SARS-CoV-2 has natural origins is seen as career suicide. But a vocal few say it shouldn't be disregarded or lumped in with conspiracy theories.

www.technologyreview.com

A discussion about the lab leak vs. natural emergence debate.

I am honestly not sure we will ever know. Seems like the only thing we can say with reasonable certainty, based on the distribution of differences over the genome vs. ancestors, is that this virus was not deliberately engineered. It could have evolved in a lab in the presence of human ACE2, though, it sounds like.

I wonder whether it just happened to hit an immunocompromised person very early, and underwent rapid evolution to improve ACE2 binding. Not sure how else to explain the decent (but not perfect) match to ACE-2.

 

[AlanSubie4Life]

Bonus: It’s All a Race — Interview With an Immunologist - Voice of San Diego Podcast

This week, Scott Lewis got to talk to Dr. Shane Crotty, an immunologist and vaccine expert who leads the Crotty Lab at the La Jolla Institute for Immunology at UC San Diego. They broke down some of the science of COVID-19 as it tries to thrive in the world — and the race between us and the...

omny.fm

Podcast interview with Prof Shane Crotty (immunologist at La Jolla Institute for Immunology).

Listened to this today while I was swapping to my summer tires (really, I put winter tires on in San Diego, and I even got to use them a couple times). It's really very informative...learned a couple of new things.

 

[JRP3]

Prepare for a post spring break surge in cases https://www.miamiherald.com/news/local/community/miami-dade/miami-beach/article250090249.html

 

[JRP3]

Idaho Legislature halts session until April due to Covid-19 outbreak among lawmakers and staff | CNN Politics

The Idaho Legislature was forced to recess Friday for more than two weeks amid an outbreak of Covid-19 at the state Capitol among lawmakers and staff.

www.cnn.com

"We could have met remotely or worn masks and distanced reliably but no, we go home now and stop doing the peoples business," Democratic state Sen. David Nelson tweeted.
The Idaho Democratic Party placed blame on the state GOP and Republican leadership for refusing to wear masks, adding in a tweet that "recessing won't stop the spread. Masks will."

 

[dfwatt]

Did the coronavirus leak from a lab? These scientists say we shouldn’t rule it out.

For many scientists, challenging the idea that SARS-CoV-2 has natural origins is seen as career suicide. But a vocal few say it shouldn't be disregarded or lumped in with conspiracy theories.

www.technologyreview.com

A discussion about the lab leak vs. natural emergence debate.

I am honestly not sure we will ever know. Seems like the only thing we can say with reasonable certainty, based on the distribution of differences over the genome vs. ancestors, is that this virus was not deliberately engineered. It could have evolved in a lab in the presence of human ACE2, though, it sounds like.

I wonder whether it just happened to hit an immunocompromised person very early, and underwent rapid evolution to improve ACE2 binding. Not sure how else to explain the decent (but not perfect) match to ACE-2.

With large enough firing numbers a randomly pivoting machine gun will hit a small Target through an angle of way under one degree. An interesting subject to Google scholar to maybe begin to see what the science says is papers comparing the S protein on the original SARS1 and the MERS virus with the current S proteins. My understanding is it's not that mutated, but I haven't read this stuff at all closely.

 

[AlanSubie4Life]

Prepare for a post spring break surge in cases https://www.miamiherald.com/news/local/community/miami-dade/miami-beach/article250090249.html

By virtue of their weather (humidity is really helpful to prevent aerosolization), or something, Florida thus far has had a very difficult time sustaining a surge. Seems like only the hottest months when the AC dries out the air and people are forced inside, and the cold months (which may have been driven by imported infections from elsewhere) are enough to really get things going. Should be even harder now of course.

I guess I’d expect a blip and then things to settle out again. B.1.1.7 could complicate it, but has to be weighed against vaccinations at this point - will take a few weeks for a surge in a particular area to gain momentum. Hopefully will be mostly young people getting sick and going to the hospital, in lower numbers. Usually takes about four weeks or so to shift to the older population as I recall. So maybe four to six weeks total for the remaining olds ( ) to get their vaccines and protect themselves?

 

[winfield100]

Prepare for a post spring break surge in cases https://www.miamiherald.com/news/local/community/miami-dade/miami-beach/article250090249.html

@JRP3
Walmart today (Sunday) early grocery run
sign: Masks required
actuality: probably 50% no masks
SW Floriduh, (60 degrees, sunny, high of low 70's later today)
(Finally got our first shots, very organized and in and out in 1 hour, mass vaccinations at RSW airport)

 

[AlanSubie4Life]

My understanding is it's not that mutated, but I haven't read this stuff at all closely.

I guess the furin cleavage site on the spike is a point of interest, since they can’t find that anywhere else. Need to see if they can find it in the wild, probably.

 

[JRP3]

By virtue of their weather (humidity is really helpful to prevent aerosolization), or something, Florida thus far has had a very difficult time sustaining a surge.

My concern is country wide as the breakers return to their home states, and schools. So far the local schools CU and IC have done a good job at limiting spread but we did see a spike in the fall when CU returned to classes while IC was remote. This semester they are both back to in class and we saw an even larger spike in January.

Edit:
I see that neither college is providing a formal spring break. Sanity prevails.

As Wellness Days Replace Spring Break, Students Prepare for a Long Semester - The Cornell Daily Sun

Students express their concerns and thoughts on Cornell's wellness days instead of spring break.

cornellsun.com

For the spring semester, the University is enforcing its travel restrictions by requiring each student to be tested on a Friday, Saturday or Sunday to keep students in Ithaca for the weekend. The weekend testing policy was based on data from the fall that linked many positive tests to travel outside Ithaca.

 

[scottf200]

Sun 21-Mar-2021 ** Andy Slavitt ** White House Senior Advisor, COVID Response
VACCINATION UPDATE: Another 3 million vaccines reported administered today.

81 million people w at least one dose
-32% of adults (17% are fully vaccinated)

38 million seniors w at least one dose
-69% of seniors (42% are fully vaccinated)

 

[AlanSubie4Life]

Sun 21-Mar-2021 ** Andy Slavitt ** White House Senior Advisor, COVID Response
VACCINATION UPDATE: Another 3 million vaccines reported administered today.

81 million people w at least one dose
-32% of adults (17% are fully vaccinated)

38 million seniors w at least one dose
-69% of seniors (42% are fully vaccinated)

2.5 million per day average (about what you'd expect for 17.5 million per week, 9mil Pfizer + ~5 mil Moderna + ~4 mil J&J). Now we just need more vaccine - seem to still be vaccine limited. Pfizer still lagging - they should be providing 4 million more doses per week (13 million) by now which would allow us to get to 3 million per day. Hopefully we can get to 3.7 million per day by early April if Moderna actually follows through on their capacity increase commitment (unlike Pfizer...). Assuming constant output from J&J here, but that hopefully will ramp in April as well. Maybe over 4 million per day (average...peak will be more 5 million per day) is possible sometime in April with more J&J.

Keep on vaccinating!

According to the polling (which seems to mostly agree with these numbers, since the poll says 65+ is 50% already vaccinated, and there's going to be lag in the polling), 82% of all people over 65 want to get vaccinated, with 7% unsure (so could be as high as 89%).

Those people make up 80% of the deaths, so that's great news. By just finishing up that group, we should cut mortality by about 72% (assuming 100% death prevention which it appears is fairly close) from pre-vaccination rates, not even including the improvements from other age groups. Overall I guess I expect about 85% reduction in mortality rates, and hopefully infections will plummet by late April too and protect the holdouts from the consequences of their poor decisions.

Nearly 80% of vulnerable 65+ Republicans also will likely get vaccinated (69% for sure want to be vaccinated).

https://civiqs.com/results/coronavirus_vaccine?annotations=true&uncertainty=true&zoomIn=true

 

[AlanSubie4Life]

https://twitter.com/x/status/1373719118151569408

Turns out the New Zealand case probably wasn't the garbage can after all. Aerosol transmission, not too surprising. Amazing the things you can figure out if you have nearly zero cases.

 

[madodel]

By virtue of their weather (humidity is really helpful to prevent aerosolization), or something, Florida thus far has had a very difficult time sustaining a surge. Seems like only the hottest months when the AC dries out the air and people are forced inside, and the cold months (which may have been driven by imported infections from elsewhere) are enough to really get things going. Should be even harder now of course.

I guess I’d expect a blip and then things to settle out again. B.1.1.7 could complicate it, but has to be weighed against vaccinations at this point - will take a few weeks for a surge in a particular area to gain momentum. Hopefully will be mostly young people getting sick and going to the hospital, in lower numbers. Usually takes about four weeks or so to shift to the older population as I recall. So maybe four to six weeks total for the remaining olds ( ) to get their vaccines and protect themselves?

But these young people in the streets are from all over the country. They will be bringing the virus mutations back to where ever they call home. The stupidity of opening up Florida just for this hurts.

 

[shinytop]

Florida governor is still bragging about our employment and bustling economy. He does not give a *sugar* about lives lost as long as he pleases CPAC.