COVID-19

Covid-19 discussion, bring your own statistics
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shpalman
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Re: COVID-19

Post by shpalman » Sun Aug 29, 2021 5:53 pm

Covid cases in England are 26 times higher than a year ago says the Office for downloading the National Statistics off the website.

I mean, just dividing the most recent valid 7-day case average by the equivalent figure for a year ago gives 25.4, so, well, it's good that whatever the ONS is doing agrees with the obvious data.

Deaths are 10 times higher than a year ago, using the same method, but of course they would rather talk about how high they were last time we had a similar level of cases and how they're not that high now, without accounting for the lag between cases and deaths.
The fact that deaths and hospital admissions from Covid-19 are a fraction of their levels at the height of the outbreak in Britain demonstrates the protective power of the vaccines – more than 60% of the UK population has had two jabs.
Well, you haven't reached the height of this outbreak yet.
“The last time infections were at their current level in England was late January,” said Kevin McConway, emeritus professor of applied statistics at the Open University. “There were around 2,300 daily hospital admissions and 1,100 deaths a day then. By contrast, the most recent daily figures for England are about 770 hospital admissions and about 80 deaths.”
“Of course,” added some old guy who knows about numbers or sommat, “I'm looking at when we were on our way down off a wave, not on the way up, which would have been mid December, when there were 1800 hospital admissions and 400 deaths per day, because I actually know f.ck all about any of this. Oh and it's actually about 800 hospital admissions and 100 deaths per day in England now.”
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Re: COVID-19

Post by Herainestold » Mon Aug 30, 2021 9:28 pm

New paper in Science on aerosol transmission.
Despite the emerging recognition of airborne transmission of respiratory viruses, numerous issues require further exploration. For example, direct measurements are needed of the concentration of virus in aerosols and droplets as a function of size and their potential to initiate a new infection. The lifetime of viruses in aerosols of varying size requires systematic investigation. More studies are needed to quantify the relationship between viral dose delivered by aerosols and droplets and severity of infection; this relationship likely varies considerably for different viruses. It is also important to investigate whether the severity of disease correlates with the size and number of aerosols and the location in which they are deposited in the respiratory tract. Although more studies are needed, unequivocal evidence indicates that airborne transmission is a major pathway for the spread of SARS-CoV-2 and many other respiratory viruses. Additional precautionary measures must be implemented for mitigating aerosol transmission at both short and long ranges, with a major focus on ventilation, airflows, air filtration, UV disinfection, and mask fit. These interventions are critical strategies for helping end the current pandemic and preventing future outbreaks. It is important to note that these proposed measures to improve indoor air quality will lead to long overdue improvements that have health benefits extending well beyond the COVID-19 pandemic.
https://science.sciencemag.org/content/ ... d9149.full
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Re: COVID-19

Post by Herainestold » Mon Aug 30, 2021 9:36 pm

Twitter thread elaborating on above paper:

https://twitter.com/denise_dewald/statu ... 0377857025
Denise Dewald, MD Statue of liberty
@denise_dewald
·
22h
Eat lunch outside or in your car. Avoid being downwind of other people. Maintain at least 6’ distance outside.

Do not eat inside. It is too hard to know if the inside air is truly safe.

We need to break the chain of transmission. 16/n
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Re: COVID-19

Post by jimbob » Tue Aug 31, 2021 2:26 pm

shpalman wrote:
Sun Aug 29, 2021 5:53 pm
Covid cases in England are 26 times higher than a year ago says the Office for downloading the National Statistics off the website.

I mean, just dividing the most recent valid 7-day case average by the equivalent figure for a year ago gives 25.4, so, well, it's good that whatever the ONS is doing agrees with the obvious data.

Deaths are 10 times higher than a year ago, using the same method, but of course they would rather talk about how high they were last time we had a similar level of cases and how they're not that high now, without accounting for the lag between cases and deaths.
The fact that deaths and hospital admissions from Covid-19 are a fraction of their levels at the height of the outbreak in Britain demonstrates the protective power of the vaccines – more than 60% of the UK population has had two jabs.
Well, you haven't reached the height of this outbreak yet.
“The last time infections were at their current level in England was late January,” said Kevin McConway, emeritus professor of applied statistics at the Open University. “There were around 2,300 daily hospital admissions and 1,100 deaths a day then. By contrast, the most recent daily figures for England are about 770 hospital admissions and about 80 deaths.”
“Of course,” added some old guy who knows about numbers or sommat, “I'm looking at when we were on our way down off a wave, not on the way up, which would have been mid December, when there were 1800 hospital admissions and 400 deaths per day, because I actually know f.ck all about any of this. Oh and it's actually about 800 hospital admissions and 100 deaths per day in England now.”
We do have about December 2020's cases with October 2020's hospitalisations so I don't think lag is that important. Image

Image
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Re: COVID-19

Post by shpalman » Tue Aug 31, 2021 3:57 pm

He said “The last time infections were at their current level in England was late January, there were around 2,300 daily hospital admissions and 1,100 deaths a day then.”

He should have said “The previous wave reached the current level in England in mid December, there were around 1,800 daily hospital admissions and 400 deaths a day then.”

... and compared that with “the most recent daily figures for England are about 800 hospital admissions and about 100 deaths” (not 770 and 80, respectively).

You may not consider the difference between 2300/770 ~= 3.0 and 1800/800 ~= 2.3 to be particularly significant, but you didn't say anything about the difference between 1100/80 ~= 13.8 and 400/100 ~= 4.0, where the lag certainly is important.
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Re: COVID-19

Post by jimbob » Wed Sep 01, 2021 7:12 pm

https://www.science.org/doi/10.1126/science.abd9149

Abstract
The COVID-19 pandemic has revealed critical knowledge gaps in our understanding of and a need to update the traditional view of transmission pathways for respiratory viruses. The long-standing definitions of droplet and airborne transmission do not account for the mechanisms by which virus-laden respiratory droplets and aerosols travel through the air and lead to infection. In this Review, we discuss current evidence regarding the transmission of respiratory viruses by aerosols—how they are generated, transported, and deposited, as well as the factors affecting the relative contributions of droplet-spray deposition versus aerosol inhalation as modes of transmission. Improved understanding of aerosol transmission brought about by studies of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection requires a reevaluation of the major transmission pathways for other respiratory viruses, which will allow better-informed controls to reduce airborne transmission.
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Re: COVID-19

Post by Herainestold » Wed Sep 01, 2021 8:31 pm

Inescapable” COVID-19 Antibody Discovery – Neutralizes All Known SARS-CoV-2 Strains

This sounds like a click bait headline.
Sotrovimab, the newest antibody therapy, was developed by GlaxoSmithKline and Vir Biotechnology after a large collaborative study by scientists from across the nation discovered a natural antibody (in the blood of a SARS survivor, back in 2003) that has remarkable breadth and efficacy.

Experiments showed that this antibody, called S309, neutralizes all known SARS-CoV-2 strains – including newly emerged mutants that can now “escape” from previous antibody therapies – as well as the closely related original SARS-CoV virus.
https://scitechdaily.com/inescapable-co ... 2-strains/
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Re: COVID-19

Post by jimbob » Thu Sep 02, 2021 5:23 pm

https://www.nbcnews.com/science/science ... 9-rcna1858
A study involving more than 340,000 people in Bangladesh offers some of the strongest real-world evidence yet that mask use can help communities slow the spread of Covid-19.

The research, conducted across 600 villages in rural Bangladesh, is the largest randomized trial to demonstrate the effectiveness of surgical masks, in particular, to curb transmission of the coronavirus. Though previous, smaller studies in laboratories and hospitals have shown that masks can help prevent the spread of Covid, the new findings demonstrate that efficacy in the real world — and on an enormous scale.

"This is really solid data that combines the control of a lab study with real-life actions of people in the world to see if we can get people to wear masks, and if the masks work," said Laura Kwong, an assistant professor of environmental health sciences at the University of California, Berkeley, and one of the co-authors of the study.
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Re: COVID-19

Post by shpalman » Thu Sep 02, 2021 5:24 pm

Sage members sent suspicious packages throughout pandemic

I think they mean that SAGE members were sent suspicious packages.
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Re: COVID-19

Post by basementer » Thu Sep 02, 2021 6:07 pm

shpalman wrote:
Thu Sep 02, 2021 5:24 pm
Sage members sent suspicious packages throughout pandemic

I think they mean that SAGE members were sent suspicious packages.
Maybe they used a grammar checker which told them not to use the passive voice.
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Re: COVID-19

Post by Herainestold » Fri Sep 03, 2021 2:35 am

jimbob wrote:
Thu Sep 02, 2021 5:23 pm
https://www.nbcnews.com/science/science ... 9-rcna1858
A study involving more than 340,000 people in Bangladesh offers some of the strongest real-world evidence yet that mask use can help communities slow the spread of Covid-19.

The research, conducted across 600 villages in rural Bangladesh, is the largest randomized trial to demonstrate the effectiveness of surgical masks, in particular, to curb transmission of the coronavirus. Though previous, smaller studies in laboratories and hospitals have shown that masks can help prevent the spread of Covid, the new findings demonstrate that efficacy in the real world — and on an enormous scale.

"This is really solid data that combines the control of a lab study with real-life actions of people in the world to see if we can get people to wear masks, and if the masks work," said Laura Kwong, an assistant professor of environmental health sciences at the University of California, Berkeley, and one of the co-authors of the study.
Cloth masks had no effect, the effect was seen in older adults with surgical masks.

I would like to see them test double masking.
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Re: COVID-19

Post by lpm » Fri Sep 03, 2021 7:37 am

Doesn't sound ethical? Extra people will have died in the experiment's control group.
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Re: COVID-19

Post by Woodchopper » Fri Sep 03, 2021 7:50 am

lpm wrote:
Fri Sep 03, 2021 7:37 am
Doesn't sound ethical? Extra people will have died in the experiment's control group.
As I understand it, it wouldn't be unethical if they only had enough masks for half the population in the study, and then distributed them randomly (and followed-up with monitoring). IMHO it would have been a ethical problem if they could have given masks to everyone but decided to restrict them form half the population.

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Re: COVID-19

Post by shpalman » Fri Sep 03, 2021 7:58 am

Woodchopper wrote:
Fri Sep 03, 2021 7:50 am
lpm wrote:
Fri Sep 03, 2021 7:37 am
Doesn't sound ethical? Extra people will have died in the experiment's control group.
As I understand it, it wouldn't be unethical if they only had enough masks for half the population in the study, and then distributed them randomly (and followed-up with monitoring). IMHO it would have been a ethical problem if they could have given masks to everyone but decided to restrict them form half the population.
https://www.poverty-action.org/sites/de ... 083121.pdf
All intervention arms received free masks, information on the importance of masking, role modeling by community leaders, and in-person reminders for 8 weeks. The control group did not receive any interventions.
They didn't prevent the control group from wearing masks just like they didn't force the intervention group to wear them. They just didn't give them free ones. They didn't even get some moron telling them that masks lead to a false sense of security or lead you to touch your face more or whatever.
The intervention increased proper mask-wearing from 13.3% in control villages (N=806,547 observations) to 42.3% in treatment villages (N=797,715 observations) (adjusted percentage point difference = 0.29 [0.27, 0.31]). This tripling of mask usage was sustained during the intervention period and two weeks after.
The proportion of individuals with COVID-like symptoms was 7.62% (N=13,273) in the intervention arm and 8.62% (N=13,893) in the control arm. Blood samples were collected from N=10,952 consenting, symptomatic individuals. Adjusting for baseline covariates, the intervention reduced symptomatic seroprevalence by 9.3% (adjusted prevalence ratio (aPR) = 0.91 [0.82, 1.00]; control prevalence 0.76%; treatment prevalence 0.68%). In villages randomized to surgical masks (n = 200), the relative reduction was 11.2% overall (aPR = 0.89 [0.78, 1.00]) and 34.7% among individuals 60+ (aPR = 0.65 [0.46, 0.85]). No adverse events were reported.
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Re: COVID-19

Post by PeteB » Fri Sep 03, 2021 12:08 pm

In England, the Covid epidemic has de-facto ended

I know it's a bit overblown, but isn't his central point valid : We have reached the point where the number of vaccinated and recovered have effectively hit the herd immunity threshold given current behaviour. Because R0 is so high for delta any change in R will have limited effect (see linked graph), When schools return & over winter when more people indoors, any increase in numbers will soon take us over the herd immunity threshold again ?

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Re: COVID-19

Post by Martin_B » Fri Sep 03, 2021 1:35 pm

PeteB wrote:
Fri Sep 03, 2021 12:08 pm
In England, the Covid epidemic has de-facto ended

I know it's a bit overblown, but isn't his central point valid : We have reached the point where the number of vaccinated and recovered have effectively hit the herd immunity threshold given current behaviour. Because R0 is so high for delta any change in R will have limited effect (see linked graph), When schools return & over winter when more people indoors, any increase in numbers will soon take us over the herd immunity threshold again ?
Doesn't herd immunity imply, though, that people who have had either the vaccine or the disease can't get it again? What I (and I think many people would think, although we may be wrong) is that herd immunity means that the disease will die out due to immunity throughout the population (herd) and it can't be passed along and survive.

But from what has been reported, the Delta version can infect people who have already had the disease, so there isn't "immunity", there's a reduced infection severity and some reduced infectivity.

[I write this from somewhere where there's so little Covid, and from that a lack of urgency in getting vaccinated, that when we do open our borders there will be a wave which we aren't prepared for.]
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Re: COVID-19

Post by PeteB » Fri Sep 03, 2021 2:12 pm

Yes, people can catch it twice (although that really is very small numbers) and yes you can catch it and be infectious after being vaccinated so yes the actual number of people immunised and recovered has to be greater than the "theoretical" HIT. But the virus has to find people to infect and despite very few formal restrictions now it seems to be struggling. But looking at the graph the 'theoretical' herd immunity threshold is so high because R for delta is so high and if it increases more because of schools, universities, winter, etc then that only makes a few % difference to the HIT even if that is quite a big increase in R - so I think if numbers increase we are likely to hit that threshold pretty quickly and it will start decreasing again

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Re: COVID-19

Post by shpalman » Fri Sep 03, 2021 2:39 pm

What do I know, some weeks it looks like it's going up (and morons like me write that we'll have 100,000 cases per day 10,000 deaths per week in a couple of weeks!) and then some weeks it looks like it's going down and morons like that write that it's all over.
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Re: COVID-19

Post by shpalman » Fri Sep 03, 2021 3:25 pm

shpalman wrote:
Fri Sep 03, 2021 2:39 pm
What do I know, some weeks it looks like it's going up (and morons like me write that we'll have 100,000 cases per day 10,000 deaths per week in a couple of weeks!) and then some weeks it looks like it's going down and morons like that write that it's all over.
And as today's relatively high number reminds us, you shouldn't base any conclusions on what's happening "now and for over a week", especially if it's been a week with a bank holiday in it.
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Re: COVID-19

Post by jdc » Fri Sep 03, 2021 4:21 pm

PeteB wrote:
Fri Sep 03, 2021 2:12 pm
Yes, people can catch it twice (although that really is very small numbers) and yes you can catch it and be infectious after being vaccinated so yes the actual number of people immunised and recovered has to be greater than the "theoretical" HIT. But the virus has to find people to infect and despite very few formal restrictions now it seems to be struggling. But looking at the graph the 'theoretical' herd immunity threshold is so high because R for delta is so high and if it increases more because of schools, universities, winter, etc then that only makes a few % difference to the HIT even if that is quite a big increase in R - so I think if numbers increase we are likely to hit that threshold pretty quickly and it will start decreasing again
The theoretical HIT is ~85% which is higher than the VE for current vaccines against current variants so we'd need to vaccinate more than 100% of the population to reach that level.

(The theoretical HIT doesn't account for Nonrandom Mixing or Nonrandom Vaccination. Not a clue how much effect they're likely to have, I'm afraid.)

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Re: COVID-19

Post by Herainestold » Fri Sep 03, 2021 6:13 pm

jdc wrote:
Fri Sep 03, 2021 4:21 pm
PeteB wrote:
Fri Sep 03, 2021 2:12 pm
Yes, people can catch it twice (although that really is very small numbers) and yes you can catch it and be infectious after being vaccinated so yes the actual number of people immunised and recovered has to be greater than the "theoretical" HIT. But the virus has to find people to infect and despite very few formal restrictions now it seems to be struggling. But looking at the graph the 'theoretical' herd immunity threshold is so high because R for delta is so high and if it increases more because of schools, universities, winter, etc then that only makes a few % difference to the HIT even if that is quite a big increase in R - so I think if numbers increase we are likely to hit that threshold pretty quickly and it will start decreasing again
The theoretical HIT is ~85% which is higher than the VE for current vaccines against current variants so we'd need to vaccinate more than 100% of the population to reach that level.

(The theoretical HIT doesn't account for Nonrandom Mixing or Nonrandom Vaccination. Not a clue how much effect they're likely to have, I'm afraid.)
So basically what we are going to see is a series of waves above a high baseline. It should diminish once everybody has either been vaccinated or infected. It will never disappear entirely as the virus is perfectly capable of infecting the vaccinated and reinfecting the previously infected. We need to get used to the idea that our hospitals are going to see permanent high numbers of Covid patients, and it will kill a certain number of people every year, just like cancers, heart attacks, strokes etc.
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Re: COVID-19

Post by Millennie Al » Sat Sep 04, 2021 3:15 am

Herainestold wrote:
Fri Sep 03, 2021 2:35 am
Cloth masks had no effect, the effect was seen in older adults with surgical masks.
I don't think that's what the study found. From the study (downloadable from https://www.poverty-action.org/publicat ... bangladesh p.22):
We find clear evidence that surgical masks lead to a relative reduction in symptomatic seroprevalence of 11.2% (aPR = 0.89 [0.78,1.00]; control prevalence = 0.80%; treatment prevalence = 0.71%). For cloth masks, we find an imprecise zero, although the confidence interval includes the point estimate for surgical masks (aPR = 0.95 [0.79,1.11]; control prevalence 0.67%; treatment prevalence 0.62%).
I think the figures in square brackets are the 95% confidence interval, but didn't see that being explicitly stated in my quick read through. As such it seems the CI for surgical masks includes them having no effect. However, if we assume good luck such that the estimate of the effect is very good, it's still only about 10%, which is fairly useless for something as infectious as Covid.
I would like to see them test double masking.
I would like to see them test masking properly - using a blinded study. This would involve giving out masks of two types - one designed to be a standard type of mask, such as a surgical mask, and the other designed to be ineffective but hard to tell apart from the effective one. This study also found physical distancing was greater in the intervention group than the control group, so either that, or some other unobserved difference, might have caused the difference in infection rate.
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Re: COVID-19

Post by Herainestold » Sat Sep 04, 2021 3:37 am

Millennie Al wrote:
Sat Sep 04, 2021 3:15 am
Herainestold wrote:
Fri Sep 03, 2021 2:35 am
Cloth masks had no effect, the effect was seen in older adults with surgical masks.
I don't think that's what the study found. From the study (downloadable from https://www.poverty-action.org/publicat ... bangladesh p.22):
We find clear evidence that surgical masks lead to a relative reduction in symptomatic seroprevalence of 11.2% (aPR = 0.89 [0.78,1.00]; control prevalence = 0.80%; treatment prevalence = 0.71%). For cloth masks, we find an imprecise zero, although the confidence interval includes the point estimate for surgical masks (aPR = 0.95 [0.79,1.11]; control prevalence 0.67%; treatment prevalence 0.62%).
I think the figures in square brackets are the 95% confidence interval, but didn't see that being explicitly stated in my quick read through. As such it seems the CI for surgical masks includes them having no effect. However, if we assume good luck such that the estimate of the effect is very good, it's still only about 10%, which is fairly useless for something as infectious as Covid.
I would like to see them test double masking.
I would like to see them test masking properly - using a blinded study. This would involve giving out masks of two types - one designed to be a standard type of mask, such as a surgical mask, and the other designed to be ineffective but hard to tell apart from the effective one. This study also found physical distancing was greater in the intervention group than the control group, so either that, or some other unobserved difference, might have caused the difference in infection rate.
That would definitely be unethical.

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Re: COVID-19

Post by Millennie Al » Sun Sep 05, 2021 1:04 am

Herainestold wrote:
Sat Sep 04, 2021 3:37 am
Millennie Al wrote:
Sat Sep 04, 2021 3:15 am
I would like to see them test masking properly - using a blinded study. This would involve giving out masks of two types - one designed to be a standard type of mask, such as a surgical mask, and the other designed to be ineffective but hard to tell apart from the effective one.
That would definitely be unethical.
Not nearly as unethical as advocating an unproven treatment. And it wouldn't be unethical at all if done with informed consent.
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Re: COVID-19

Post by lpm » Sun Sep 05, 2021 8:29 am

PeteB wrote:
Fri Sep 03, 2021 12:08 pm
In England, the Covid epidemic has de-facto ended

I know it's a bit overblown, but isn't his central point valid : We have reached the point where the number of vaccinated and recovered have effectively hit the herd immunity threshold given current behaviour. Because R0 is so high for delta any change in R will have limited effect (see linked graph), When schools return & over winter when more people indoors, any increase in numbers will soon take us over the herd immunity threshold again ?
There's nothing wrong with the mechanics of this. England is clearly close to R=1 under current lockdownicity and that's due to the huge quantity of protection from injection and infection.

The only problem with the article it's over sciency and has exaggerated precision, pretending a model will be right and charts provide certainty. I think we can expect the coming transition from epidemic to endemic to be pretty unpredictable. The next few months could easily see things we can't readily explain.

But the article reiterates what I've been saying for months - infection is similar to injection in young people, so we should add case numbers to vaccination numbers. And that it will be very hard to build a wave. But also that we're in an uncomfortable position of high case numbers while doing a major piece of unlockdowning - reopening England and Wales schools and universities about to restart. The position at the end of September should give an indication of how bad the stress on the NHS will be for the rest of the year.

I'm still of the position that the govt is racing down a foggy motorway but could well get away with it.
What ever happened to that Trump guy, you know, the one who was president for a bit?

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