Continuation The One Covid-19 Science and Medicine Thread Part 3

[Puppycow]

Originally Posted by Lplus

I was under the impression that mask wearing in crowded spaces was already common practice in Japan (and china come to that), or am I mistaken?

It was sort of a thing even pre-pandemic, but hardly universal. It was considered polite to do if you had a cold, and also some people wore them for their pollen allergies.

[Lplus]

Originally Posted by Ulf Nereng

No, not at all mistaken. Here's an article about it:

http://www.internationalskeptics.com...ply&p=13445816

"....Millions of masks continued to be manufactured for personal use in Japan, with demand stoked by an emerging culture of mask-wearing being linked with being a good family member, neighbour and citizen."


ETA: I'm not sure about China, though. I think their mask-wearing was more about protection from the highly polluted air in many cities.

Originally Posted by Puppycow

It was sort of a thing even pre-pandemic, but hardly universal. It was considered polite to do if you had a cold, and also some people wore them for their pollen allergies.

I guess it's a lot easier to mandate something that people area lready doing voluntarily.

[Puppycow]

Originally Posted by Lplus

I guess it's a lot easier to mandate something that people area lready doing voluntarily.

The funny thing is, I don't think there's even a legal mandate here. I think it's mostly just social pressure.

[Planigale]

Just when you thought it was all over!

The UK modelling suggests a further wave of infections in late summer / early autumn (fall). This will be a combination of time and easing of lockdown, waning of immunity, strains that have mutated to infect vaccinated / previously infected (e.g. P1) and that vaccines are less than 100% effective. The magnitude of the wave could be comparable to the recent winter wave or the first 2020 spring wave. So everyone, have a good summer, because Autumn / Winter 2021 is going to be another lockdown. Australia and New Zealand will continue to seep out of existence, becoming little more real than Atlantis.

[The Atheist]

Originally Posted by Planigale

The UK modelling suggests a further wave of infections in late summer / early autumn.

Could just be wrong, too.

Israel's infections are 2% of where they were two months ago, so it certainly seems that if you get people vaccinated, things are fine.

[Puppycow]

Yeah, the models have been pretty consistently wrong. By late summer shouldn't most people in the UK have been vaccinated already? And what is the basis for factoring in "waning of immunity"? Where does that come from?

I agree with The Atheist that the numbers in Israel suggest that once you get a certain critical mass of people vaccinated (about 60%ish it seems) that it pretty much crushes new infections. Probably at least 70% there have some sort of immunity, either from the vaccine or from having been infected already.

[Dr.Sid]

Well UK is next big country to reach significant vaccination levels, so we'll see.

[Meadmaker]

Originally Posted by The Atheist

Could just be wrong, too.

Israel's infections are 2% of where they were two months ago, so it certainly seems that if you get people vaccinated, things are fine.

Unless you are in the 2%. But yes.

I was greatly distraught at a headline I saw today saying that there have been 250 cases of people in Michigan who were fully vaccinated, even waiting two weeks after their second dose, who tested positive. Three of those people died.

The story, which I only read in part, did say that the symptoms were generally less, and that 250 is a fairly small number, but it's still quite disconcerting.

I very much want lockdowns, restrictions, work at home orders, and all the lot to end. This seems to me to be a case where reality sucks.

And, knowing that a small number of people who are vaccinated will still get sick, it just makes me more ticked off at the people who will refuse the vaccine. I get how that works, and why those people are dangerous to the rest of us. If the vaccine were perfect, I could say, "Who cares?" because it's their own fault if they get it, but knowing they can spread it, too, not getting the vaccine is just so irresponsible.

[zooterkin]

Originally Posted by zooterkin

David Spiegelhalter is a great communicator of statistics and risk. He's a regular on More or Less on BBC Radio, and I've seen him speak at Skeptics in the Pub.

And he's speaking at Skeptics in the Pub Online in a couple of weeks. All welcome.

THURSDAY, 22 APRIL 2021 FROM 18:45 UTC+01-21:00 UTC+01

Communicating statistics to the media: highs and lows during the pandemic - Sir David Speigelhalter

[Filippo Lippi]

Originally Posted by zooterkin

And he's speaking at Skeptics in the Pub Online in a couple of weeks. All welcome.

THURSDAY, 22 APRIL 2021 FROM 18:45 UTC+01-21:00 UTC+01

Communicating statistics to the media: highs and lows during the pandemic - Sir David Speigelhalter

Noted, ta

[Pixel42]

Originally Posted by zooterkin

THURSDAY, 22 APRIL 2021 FROM 18:45 UTC+01-21:00 UTC+01

Communicating statistics to the media: highs and lows during the pandemic - Sir David Speigelhalter

For some reason that link is blocked for me.

Here's one that worked, for anyone else who has the same problem:

https://sitp.online/shows/

[zooterkin]

Originally Posted by Pixel42

For some reason that link is blocked for me.

Here's one that worked, for anyone else who has the same problem:

https://sitp.online/shows/

I screwed up the link. I’ll fix it (it’s to the Facebook event, so yours is a useful alternative).

[Lplus]

Originally Posted by Planigale

Just when you thought it was all over!

The UK modelling suggests a further wave of infections in late summer / early autumn (fall). This will be a combination of time and easing of lockdown, waning of immunity, strains that have mutated to infect vaccinated / previously infected (e.g. P1) and that vaccines are less than 100% effective. The magnitude of the wave could be comparable to the recent winter wave or the first 2020 spring wave. So everyone, have a good summer, because Autumn / Winter 2021 is going to be another lockdown. Australia and New Zealand will continue to seep out of existence, becoming little more real than Atlantis.

Does it take into account the booster vaccinations for the variants which were suggested would start in the late summer?

[The Atheist]

Originally Posted by Meadmaker

I was greatly distraught at a headline I saw today saying that there have been 250 cases of people in Michigan who were fully vaccinated, even waiting two weeks after their second dose, who tested positive. Three of those people died.

Don't be too disheartened, it's not even clear cut that they did have the disease 14 days after vaccination.

Quote:

Some of the 246 people may ultimately be excluded from the state's tally of vaccine breakthrough cases because they may have had earlier coronavirus infections and still tested positive two weeks post-immunization.

https://www.freep.com/story/news/loc...us/7101678002/

With 1.8 million fully vaccinated people, 3 deaths is well within the range of fails from the most efficacious vaccine results you could hope to achieve.

With a death rate for oldies of maybe 3 or 4% cutting it to 0.00003% looks pretty good to me. I'll take those odds any day.

[Puppycow]

Uh-oh.
‘Double mutant’ COVID strain discovered in California

One place where Covid is really spiking right now is India, and this strain or a similar one is getting more common there at the same time.

[Rolfe]

Originally Posted by Meadmaker

Unless you are in the 2%. But yes.

I was greatly distraught at a headline I saw today saying that there have been 250 cases of people in Michigan who were fully vaccinated, even waiting two weeks after their second dose, who tested positive. Three of those people died.

The story, which I only read in part, did say that the symptoms were generally less, and that 250 is a fairly small number, but it's still quite disconcerting.

I very much want lockdowns, restrictions, work at home orders, and all the lot to end. This seems to me to be a case where reality sucks.

And, knowing that a small number of people who are vaccinated will still get sick, it just makes me more ticked off at the people who will refuse the vaccine. I get how that works, and why those people are dangerous to the rest of us. If the vaccine were perfect, I could say, "Who cares?" because it's their own fault if they get it, but knowing they can spread it, too, not getting the vaccine is just so irresponsible.

This is your regularly scheduled reminder that the purpose of a vaccination campaign is not primarily to protect individual people, although obviously that's a very welcome part of it, it's to allow community spread of the virus to be eliminated. The idea is not that everyone will be going out into a miasma of virus particles, but it will be fine because everyone is vaccinated - except of course for those people who didn't mount a protective immune response too bad.

The idea is that having sufficient vaccinated people reduces the R value quite spectacularly so that test and trace is able to keep up with new clusters and stamp them out, until community transmission is no more and it's only re-introductions that have to be addressed. Once that is achieved then it's safe to go out and mix. It sounds as if Israel has got there already. But even if I were fully vaccinated I wouldn't be mixing indoors in a location where I knew that community transfer was still a thing. Nobody is safe until everybody is safe.

(Ironically, although I personally have had only one dose and don't consider myself protected, community transfer has indeed been halted where I live and the only danger is re-introduction. But since we're still officially in lockdown I stay isolated. Also, nobody is taking any steps to avoid people breaking lockdown and re-introducing the virus.)

[The Atheist]

Originally Posted by Puppycow

Uh-oh.
‘Double mutant’ COVID strain discovered in California

One place where Covid is really spiking right now is India, and this strain or a similar one is getting more common there at the same time.

Spiking isn't even strong enough to describe what's happening in India - or Brazil. India's cases have gone from a seven-day average of 16,000 to 93,000 in just one month.
________________

And just to add more misery to the wildfire, Lancet (so take with a pinch of salt until verified) is reporting:

Quote:

Among 236 379 patients diagnosed with COVID-19, the estimated incidence of a neurological or psychiatric diagnosis in the following 6 months was 33·62% (95% CI 33·17–34·07), with 12·84% (12·36–13·33) receiving their first such diagnosis.

https://www.thelancet.com/journals/l...084-5/fulltext

[Skeptic Ginger]

Reading this I had a thought: NPR: CDC Says More Virulent British Strain Of Coronavirus Now Dominant In U.S.

When we look back I wonder if we'll find new variants were as much a contributor to the second and third waves (and now the 4th) as anything else such as climate.

[Planigale]

Originally Posted by Skeptic Ginger

Reading this I had a thought: NPR: CDC Says More Virulent British Strain Of Coronavirus Now Dominant In U.S.

When we look back I wonder if we'll find new variants were as much a contributor to the second and third waves (and now the 4th) as anything else such as climate.

I think you are correct. It is certainly thought that the B.1.1.17 strain (Kent British) is the driver for the UK wave pre Christmas and the current European third wave. The P1 variant is thought to be the driver of the current Brazilian wave. The early Chinese strain was less infectious than the strain that infected Europe / USA in early 2020, the far more infectious and perhaps more deadly strains in South America and Europe and Africa currently circulating are less easy to control. Both the South African and Brazilian strains appear to be able to re-infect people who have been infected by the earlier strains and some vaccines.

[The Atheist]

Originally Posted by Planigale

It is certainly thought that the B.1.1.17 strain (Kent British) is the driver for the UK wave pre Christmas and the current European third wave. The P1 variant is thought to be the driver of the current Brazilian wave.

And christ knows what's driving India's current surge, because it's off the charts, with growth of 500% in cases in the past one month.

In a complete lack of surprise, India isn't doing anywhere near enough testing to know what's happening, but we know for sure there's a "double variant: version on the loose there.

Given the shape of the pandemic to date, it seems highly likely India's managed to brew a newer, even more-contagious breed of the virus than Brazil, UK, or South Africa. Did the damned virus read The Stand?

[angrysoba]

Quote:

A woman in Japan has become the world's first Covid patient to receive a living donor lung transplant.
The patient received lung segments from her son and husband after her organs failed because of damage caused by the coronavirus.
Doctors in Kyoto hope she will make a complete recovery within months.
Waiting lists for full lung transplants - where the organ is provided by donors who have died - are very long in Japan and elsewhere.

Covid patient receives world's first living donor lung transplant https://www.bbc.co.uk/news/world-asia-56684073

[Puppycow]

Originally Posted by Puppycow

Oxford-AstraZeneca Vaccine Safety

Article by Steve Novella of the Skeptic's Guide podcast about the blood clotting question.

He has a new post about it now, reflecting new information:

Update on AstraZeneca Vaccine and Blood Clots

Quote:

Amidst this uncertainty, however, the EMA has signaled it will officially report today or tomorrow that they are now ready to conclude that there is a link between the AstraZeneca vaccine and an increased risk of CVST in people under 55. However, they also stress that the benefits of getting the vaccine (the risk of not getting it) is greater than this risk of rare blood clots. That is turning out to be a hard sell, and many people are forgoing the vaccine because of this possible risk.

There are a few points worth emphasizing here. First, we do not know what the ultimate answer is, in terms of if there a genuine increased risk, in which populations, and due to what specific mechanism? Each step of the way scientists are giving the best answer possible based on the currently available evidence, which includes a wide range of uncertainty.

In normal times, the precautionary principle would prevail in such cases. However, during a pandemic the risk of delaying the vaccine will definitely lead to otherwise preventable deaths. If you are dead, it doesn’t matter if you were killed by COVID or a rare vaccine side effect. So we should take whichever course leads to the fewest deaths, which is clearly on the side of getting the vaccine, even in the worst-case scenario in terms of risk of CVST.

An obvious question is – can’t people just take other vaccines that don’t have this risk? Again, in normal times that might be the case, but not in the middle of a pandemic. In Europe COVID is experiencing another surge, likely caused in part by the emergence of new variants, and perhaps also by prematurely relaxing preventive measures and pandemic fatigue. The AstraZeneca vaccine is a critical part of Europe’s strategy to vaccinate its population as quickly as possible. It is also cheaper and easier to administer than other vaccines, and so is critically important to poorer countries. You can also argue that worldwide we are in a race against the emergence of new and deadlier variants, and any delay in vaccination can have significant repercussions. A global risk vs benefit approach is needed here.

Some countries are compromising, and not giving the vaccine to those under 55 or 50, while still giving it to older populations who apparently do not have the higher risk. If the risk is truly only higher in women, than the excluded population can be narrowed further. This still may not optimize risk vs benefit, but it is better than a global ban.

What we need now is more research to learn as much about this possible link as we can, mitigate if possible, and maximize benefit to risk in the face of a still-raging deadly pandemic.

[DevilsAdvocate]

Originally Posted by The Atheist

And christ knows what's driving India's current surge, because it's off the charts, with growth of 500% in cases in the past one month.

In a complete lack of surprise, India isn't doing anywhere near enough testing to know what's happening, but we know for sure there's a "double variant: version on the loose there.

Given the shape of the pandemic to date, it seems highly likely India's managed to brew a newer, even more-contagious breed of the virus than Brazil, UK, or South Africa. Did the damned virus read The Stand?

Is this a regional thing? At one time I saw a map of cases in India over time. We have gotten to a point of information overload where there is so much covid stuff that it is hard to sort through to find the good stuff. So I can't find the map now.

That map had shown that covid was mostly in the big cities in the south, west, and southeast. It hadn't hit the big populations in the northeast. Is this a case where it has finally broken through into the northeast causing a second bigger wave?

[Vixen]

Originally Posted by Planigale

I think you are correct. It is certainly thought that the B.1.1.17 strain (Kent British) is the driver for the UK wave pre Christmas and the current European third wave. The P1 variant is thought to be the driver of the current Brazilian wave. The early Chinese strain was less infectious than the strain that infected Europe / USA in early 2020, the far more infectious and perhaps more deadly strains in South America and Europe and Africa currently circulating are less easy to control. Both the South African and Brazilian strains appear to be able to re-infect people who have been infected by the earlier strains and some vaccines.

B.1.1.7

[The Atheist]

Originally Posted by DevilsAdvocate

That map had shown that covid was mostly in the big cities in the south, west, and southeast. It hadn't hit the big populations in the northeast. Is this a case where it has finally broken through into the northeast causing a second bigger wave?

Could be that, but it's impossible to tell with India - their data has been dodgy from the start.

[Puppycow]

Variants are spreading in Japan now. The country just came out of a state of emergency 2 weeks ago and is now declaring another one, as new cases are rising sharply again.

Coronavirus variant cases grew 14-fold in a single month

That's much faster than the overall rate of growth during the same month, which suggests that the variants are more contagious.

Quote:

Mutant strains of the novel coronavirus are spreading so rapidly that experts are calling for immediate measures to discourage people in hotspot areas from going on unnecessary outings.
Between the end of February and the end of March, cases of coronavirus variants increased by about 14-fold across Japan, new data shows.
There were only 56 cases of variant infections reported in the last week of February, but the figure grew at a rapid clip until it reached 767 by the week of March 22 to 28.
While the problem is especially prominent now in prefectures in western Japan, experts warn the Tokyo area could see a major increase in variant cases over the next month.
The variant first discovered in Britain in December is believed to be the main one spreading like wildfire in Osaka and Hyogo. Evidence points to the strain not only being more infectious, but also posing a higher risk of patients developing serious symptoms and dying.
The average number of people a single COVID-19 patient will infect, known as the effective reproduction number, is much higher for the variant strain. The average figure for the period between Feb. 1 and March 22 was 1.32-fold higher for the variant strain compared to the original virus.
Testing found variants made up 75 percent of the cases in Hyogo Prefecture and 54 percent of the cases for Osaka Prefecture.
The corresponding figure was much lower for Tokyo, at just 3 percent. But experts warn if variant cases increase at the current rate, they could make up about 70 percent of new infections by May 1.

And if you look at the data by prefecture, the prefectures with the greater proportion of variants are also the ones where the rate of new infections is increasing fastest. The effective reproduction number is significantly higher:

https://toyokeizai.net/sp/visual/tko/covid19/en.html

[Bob001]

More bad news:

Quote:

An astonishing study found that roughly one out of three COVID-19 survivors were diagnosed with either a brain or psychiatric disorder within six months of contracting COVID-19.

The shockingly high proportion of brain and psychiatric disorders in COVID-19 patients suggests that 10 million Americans (out of the 30 million who have contracted COVID-19) could suffer mental health repercussions in the coming years. That prophesies an impending social crisis for which American society is unprepared.

https://www.salon.com/2021/04/08/mon...ric-disorders/
https://www.thelancet.com/journals/l...084-5/fulltext

[Dr.Sid]

Originally Posted by Puppycow

Variants are spreading in Japan now. The country just came out of a state of emergency 2 weeks ago and is now declaring another one, as new cases are rising sharply again.

Coronavirus variant cases grew 14-fold in a single month

That's much faster than the overall rate of growth during the same month, which suggests that the variants are more contagious.



And if you look at the data by prefecture, the prefectures with the greater proportion of variants are also the ones where the rate of new infections is increasing fastest. The effective reproduction number is significantly higher:

https://toyokeizai.net/sp/visual/tko/covid19/en.html

Indeed. It's too late already, and on national level, they do nothing. Fall for the old "so far it seems ok" after so many countries did that before you is just stupid.
Well .. time to wave Olympics bai bai.

[The Atheist]

Originally Posted by Bob001

More bad news

Ninjad 10 posts before yours.

Originally Posted by Dr.Sid

Well .. time to wave Olympics bai bai.

I'm just off to the Olympics thread to suggest that likelihood has just increased considerably.

[rjh01]

Originally Posted by The Atheist

And just to add more misery to the wildfire, Lancet (so take with a pinch of salt until verified) is reporting:

Quote:

Among 236 379 patients diagnosed with COVID-19, the estimated incidence of a neurological or psychiatric diagnosis in the following 6 months was 33·62% (95% CI 33·17–34·07), with 12·84% (12·36–13·33) receiving their first such diagnosis.

https://www.thelancet.com/journals/l...084-5/fulltext

Looking at the details I suggest that most of these people will be able to function normally with treatment. I also wonder if they controlled for age? Older people are more likely to be admitted to hospital for Covid 19 and they are more likely to suffer from one of these conditions.

In short this is not as bad as it looks.

[marting]

It appears the CDC has increased its IFR estimate according to a piece in reason.com. Interesting because Reason is a libertarian oriented site that has consistently published pieces with lower estimates of IFR.

https://reason.com/2021/04/02/new-cd...ously-thought/

They look at the CDC's new age IFR estimates, which are higher than previously published and suggest the IFR in the USA is probably around .8% perhaps due to the new variants. Lots of links to various CDC sites one of which I found fascinating. The CDC started collecting serological data from blood drawn for unrelated purposes across the states back in mid 2020.

https://covid.cdc.gov/covid-data-tracker/#national-lab

This is a truly interesting site because you can see the evolution of antibody prevalence over time in each state along with Covid-19 case rates. And if you pick a state and two week period you get a breakdown of antibody positives by percentage in age/sex groups.

Two things stand out.

1. The decline of antibody positive percent over time in a few places like New York which was hard hit last spring. It's now at 13% v Texas as nearly 30%. The difference is that most infections in NY occurred early last year though it's been trending up in recent months. Hence, because of the time decay in antibody levels, one can't use serologic data to determine percent previously infected. It's much higher in NY than the current 13% would indicate. How immune previously infected people who no longer express detectable antibodies remain, perhaps depending on T memory cells, is an interesting question.

2. The surprisingly high antibody positive levels in the 0-17 and 18-49 y/o groups compared to the older, 65+ group in most states (not NY). Especially Texas, Florida, and California where the 65+ group's antibody+ percents are 2 to 3 times lower. The elderly in these states appear to be taking better precautions. Good for them.

[Skeptic Ginger]

Originally Posted by marting

... Hence, because of the time decay in antibody levels, one can't use serologic data to determine percent previously infected. ....

But why does it matter to count these cases if past infected persons no longer have protective antibodies? We can measure how many people were previously infected in NY vs in TX using other means.

Testing seroprevalence is going to be useful if it is determined those persons are indeed susceptible again.

It may turn out new commercial testing will be developed that allows us to detect past infections even in people whose protective antibodies have disappeared.


I'm going to have to look at that data more closely to see if it is really saying people over 65 were more careful or if they no longer show seroprevalence for the antibodies tested.

[The Atheist]

Ugly numbers coming out this week, and will probably be uglier next week.

Highest number of cases since early January, and a 50% increase in 7-day average in the past month.

The only positive is that Israel is under 200 cases in a day for the first time since June last year, so the vaccines look pretty good.

Now, if only there were a way to lower the infection rate prior to vaccinations...

[Rolfe]

Why wouldn't people be depending on B memory cells? If antibody is the important means of combating the virus then it would be the B memory cells that would be important rather than the T ones. It's only if CMI is the important thing in combating the virus that the T memory cells would be the important ones.

I didn't think we were far enough advanced in our understanding of the disease to have a proper handle on this yet.

[marting]

Originally Posted by Skeptic Ginger

I'm going to have to look at that data more closely to see if it is really saying people over 65 were more careful or if they no longer show seroprevalence for the antibodies tested.

That's a good point. Here in Calif. they record the age groups of new cases over time. Initially, the old has cases that were consistent with middle aged. By May, that had shifted with the old case rate cutting in half. Fairly consistent with the subsequent sero data. Also consistent with NY v FL where NY has fairly similar sero+ across age groups in comparison to FL. Also consistent with the higher NY fatality rate.

I mentioned the declining sero+ over time because it has been used to estimate percent previously infected by some and it has gotten much less useful for that purpose. Especially for states hit hard early.

[RecoveringYuppy]

Link describing a "pancoronavirus" vaccine that would target spike proteins and possibly provide immunity against a wide range of coronaviruses.

https://www.advisory.com/en/daily-br...single-vaccine

I came across while wondering a recombination event with other coronaviruses, such as the common cold, could lead to a vaccine resistant variant.