COVID-19

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Re: COVID-19

Post by shpalman » Sun Aug 15, 2021 7:01 am

shpalman wrote:
Sat Aug 14, 2021 6:53 am
England’s R number between 0.8 and 1.0 based on last week when cases were coming down, which means that cases were coming down, except of course that they're obviously slowly going up again now as you can see by just looking at the data without needing to do any fancy analysis apart from assuming the testing rate is roughly constant.
There's already "Weekly number of people receiving a PCR test and positivity" at the Testing in England page.

It's now more than 8% whereas in early May it was about 0.8%.* You can see that the number of people tested does vaguely follow the number of new positives, but then the positive rate also follows the number of new positives. So when there are more cases, more tests get done and a greater proportion of them come back positive. So it's not that you seem to have more cases because you're doing more tests, but rather the increasing number of suspected cases means more testing is required but testing capacity can't vary exponentially across orders of magnitude in the way that case numbers can.

* - this metric peaked at around 40% during the first wave and 18% in the second wave.
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Re: COVID-19

Post by Woodchopper » Wed Aug 18, 2021 8:15 pm

A third COVID-19 vaccine shot markedly boosts neutralizing antibody potency and breadth

COVID-19 (coronavirus disease 2019) vaccines have been rapidly developed and deployed globally as a measure to combat the disease. These vaccines have been demonstrated to confer significant protection, but there have been reports of temporal decay in antibody titer. Furthermore, several variants have been identified with variable degrees of antibody resistance. These two factors suggest that a booster vaccination may be worthy of consideration. While such a booster dose has been studied as a series of three homologous vaccines in healthy individuals, to our knowledge, information on a heterologous regimen remains unreported, despite the practical benefits of such a scheme. Here, in this observational study, we investigated the serological profile of four healthy individuals who received two doses of the BNT162b2 vaccine, followed by a third booster dose with the Ad26.COV2.S vaccine. We found that while all individuals had spike-binding antibodies at each of the timepoints tested, there was an appreciable drop in titer by four months following the second vaccination. The third vaccine dose robustly increased titers beyond that of two vaccinations, and these elicited antibodies had neutralizing capability against all SARS-CoV-2 strains tested in both a recombinant vesicular stomatitis virus-based pseudovirus assay and an authentic SARS-CoV-2 assay, except for one individual against B.1.351 in the latter assay. Thus, a third COVID-19 vaccine dose in healthy individuals promoted not just neutralizing antibody potency, but also induced breadth against dominant SARS-CoV-2 variants.
https://www.medrxiv.org/content/10.1101 ... 21261670v1

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Re: COVID-19

Post by shpalman » Thu Aug 19, 2021 6:07 am

shpalman wrote:
Sun Aug 01, 2021 8:34 pm
Not-reviewed-yet preprint on virological and serological kinetics of SARS-CoV-2 Delta variant vaccine-breakthrough infections.

Image

So for the first few days it's the same* but then in vaccinated subjects it decreases faster.

(Ct is the cycle threshold, so the y-axis is basically a logarithmic scale of how much DNA there is with lower numbers meaning more.)

* - vaccinated people would be less likely to catch it in the first place of course.
Jabbed adults infected with Delta ‘can match virus levels of unvaccinated’ which we knew already (see above) but the level doesn't stay the same for more than a couple of days.
... for example, they may have high levels of virus for shorter periods of time”
Well, when it's published you can cite the literature properly.
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Re: COVID-19

Post by shpalman » Thu Aug 19, 2021 6:57 am

Nah, scratch that. Jabbed adults infected with Delta don't match the virus levels of unvaccinated. The Guardian reckons they do based on some preprint they think they've seen but they're just saying it without citing it so it's worthless. I don't care how many quotes from the press release they paste in to make it seem like the journalist has actually spoken to the researchers involved and I don't give a f.cking c.nt of a sh.t what the f.cking expert reaction to it is.

‘Impact of Delta on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK’ by Koen B. Pouwels et al. is some sh.t which we've seen and you haven't, because f.ck you.
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Re: COVID-19

Post by shpalman » Thu Aug 19, 2021 9:12 am

Meanwhile the BBC goes with Covid vaccines still effective against Delta variant... and gives this link which links to the same study that the Guardian failed to: finalfinalcombinedve20210816.pdf.
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Re: COVID-19

Post by Brightonian » Thu Aug 19, 2021 9:29 am

shpalman wrote:
Thu Aug 19, 2021 9:12 am
Meanwhile the BBC goes with Covid vaccines still effective against Delta variant... and gives this link which links to the same study that the Guardian failed to: finalfinalcombinedve20210816.pdf.
Not doubting its contents, but something with "finalfinal" in its name doesn't say much for their document version control.

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Re: COVID-19

Post by lpm » Thu Aug 19, 2021 9:36 am

Who among us hasn't got files called finalfinal this is the final version update 2.
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Re: COVID-19

Post by shpalman » Thu Aug 19, 2021 10:00 am

This is Fig. 3A from that, which appears to be what all this fuss is about.
finalfinalcombinedve20210816_Fig3A.png
finalfinalcombinedve20210816_Fig3A.png (39.88 KiB) Viewed 2660 times
The Ct value is how many PCR cycles it takes for the DNA you're looking for to reach some detection threshold, so it's logarithmic (base 2) and lower numbers mean more viral load. The graph in the
helpfully plotted the Ct values the other way up so that the graph was viral load on a log scale.

But anyway I think the point is that the first set of data "1dec20-16may21" is from the period in which Alpha was dominant, while the set in the middle "17may21-13jun2021" is from the beginning of the Delta phase. And they want you to note how Ct doesn't decay to higher values (indicating lower viral load) in quite the same way depending on when they tested positive in relation to when they got (or didn't get) vaccinated with one or both doses (or previously infected). Then in the "14jun21-" set it seems the Ct values are the same no matter what happens.
Viral burden and symptoms in new PCR-positives aged >=18 years

In 12,287 new PCR-positives in the Alpha-dominant period, Ct values (inversely related to viral load) increased strongly with increasing time from first vaccination and number of doses (age/sex-adjusted trend-p<0.0001, Figure 3A). Ct values were highest in those ≥14 days after second vaccination (median (IQR) 33.3 (31.6-34.0) [N=56]); there was no evidence that this differed from those unvaccinated but previously PCR/antibody-positive (32.8 (30.9-34.2) [N=68]; age/sex-adjusted p=0.72), but Ct values were significantly higher than in those unvaccinated and not previously PCR/antibody-positive (28.7 (20.4-32.9) [N=10,853]; age/sex-adjusted p=0.02).
Then they decide to divide the PCR positives into two populations with low- and high- Ct values, which might be justified for all I know, but the point being that there tends to be more people in the low-Ct group (high viral load) now than there was before Delta showed up.
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Re: COVID-19

Post by shpalman » Thu Aug 19, 2021 12:13 pm

Woodchopper wrote:
Wed Jun 30, 2021 7:22 am
[...]

The move comes amid growing confidence that Boris Johnson will press ahead with plans to lift social distancing rules next month despite a surge in Covid cases.

He told the Cabinet yesterday that our vaccination success means Britain will be able to 'live with Covid' because the link between virus cases and hospitalisations has been broken.
Number of Covid-19 hospital patients in England at five-month high

Cases are still slowly rising overall so numbers in hospital are also going to keep rising which is weird considering "the link between virus cases and hospitalisations has been broken" oh wait no it hasn't.
uk-phases-210818.png
uk-phases-210818.png (71.53 KiB) Viewed 2625 times
I still have deaths with a 3 week lag and 0.3% CFR but I've put admissions on a 3-day lag at 3%. Previously I had a two-week lag but 5%.We could imagine that when things really started taking off at the beginning of June to give that peak in mid-July, those were younger people (watching the football?) with slightly lower mortality and lower risk of ending up in hospital. Yeah we could make anything up but I think the general orders of magnitude are about right and you can see that changing the lag by a lot doesn't massively change the percentage.

Numbers in hospital and on mechanical ventilation of course also depend on the rate at which patients leave hospital (which would also probably be an exponential decay) but I have those both on a three-week lag at 25% and 4% of daily new cases respectively.
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Re: COVID-19

Post by lpm » Thu Aug 19, 2021 12:33 pm

The current cases are remarkably concentrated in the 18-30 group. The heat map has failed to spread up the ages across the past three months.

Vaccination is like a rain storm drenching the trees - a raging forest fire in one area simply isn't spreading.

I don't think any of your old equations and lags will work. It's now a disease suffered by people we don't care about - the young who don't experience significant illness and rarely die, plus older people who have repeatedly refused the vaccine.
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Re: COVID-19

Post by shpalman » Thu Aug 19, 2021 12:55 pm

lpm wrote:
Thu Aug 19, 2021 12:33 pm
The current cases are remarkably concentrated in the 18-30 group. The heat map has failed to spread up the ages across the past three months.
Your case rate amongst older age groups is higher than Italy's entire case rate.
lpm wrote:
Thu Aug 19, 2021 12:33 pm
Vaccination is like a rain storm drenching the trees - a raging forest fire in one area simply isn't spreading.
Vaccination rates
Like a storm drenching the trees
Covid does not spread
lpm wrote:
Thu Aug 19, 2021 12:33 pm
I don't think any of your old equations and lags will work. It's now a disease suffered by people we don't care about - the young who don't experience significant illness and rarely die, plus older people who have repeatedly refused the vaccine.
These equations and lags all apply entirely to the past three months, during which relatively little has changed regarding vaccine coverage, and I don't care about any people.
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Re: COVID-19

Post by lpm » Thu Aug 19, 2021 1:28 pm

Each case in under 30s is the equivalent of a vaccine dose.

We spent months tracking daily vaccine numbers, celebrating milestones achieved. Now we get to celebrate cases in the same way. If 300,000 under 30s get partial immunity in a week that's another step closer to herd immunity. But if it's 200,000 via infection and 100,000 via vaccination then everyone gets agitated about the 200,000 figure. It's even worse on twitter than it is on here - people unbelievably slow to adapt to the new climate and still trotting out 2020 presumptions.

For example, hospitalisations are about three doublings away from being a crisis. In 2020, three doublings wasn't a lot - easily got there in few weeks. But in the 2021 land of the vaccinated it's a huge gulf. We're basically fine for the rest of the year.
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Re: COVID-19

Post by shpalman » Thu Aug 19, 2021 2:21 pm

lpm wrote:
Thu Aug 19, 2021 1:28 pm
Each case in under 30s is the equivalent of a vaccine dose.

We spent months tracking daily vaccine numbers, celebrating milestones achieved. Now we get to celebrate cases in the same way. If 300,000 under 30s get partial immunity in a week that's another step closer to herd immunity. But if it's 200,000 via infection and 100,000 via vaccination then everyone gets agitated about the 200,000 figure. It's even worse on twitter than it is on here - people unbelievably slow to adapt to the new climate and still trotting out 2020 presumptions.

For example, hospitalisations are about three doublings away from being a crisis. In 2020, three doublings wasn't a lot - easily got there in few weeks. But in the 2021 land of the vaccinated it's a huge gulf. We're basically fine for the rest of the year.
At current rates you won't get 200,000 infections without 600 deaths and 6000 people sent to hospital, between unlucky young people and cases leaking into the older age groups, but that's what you already have now (and it's going up with nothing planned to bring it down and it will only get worse in September with schools going back and socializing moving back indoors). You still have about 10% of the adult population without a single vaccine dose* which is 5.5 million so you'll only need to carry until the end of the year like this. But yeah who cares about another 10,000 deaths when you can go to the pub. I just hope continental Europe maintains travel restrictions from the UK. Forever.

* - this number will change today as 16-17 year-olds are added to the denominator
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Re: COVID-19

Post by Herainestold » Thu Aug 19, 2021 3:26 pm

shpalman wrote:
Thu Aug 19, 2021 2:21 pm
But yeah who cares about another 10,000 deaths when you can go to the pub. I just hope continental Europe maintains travel restrictions from the UK. Forever.
A country where the government cared about the welfare of the people would be going into lockdown now, ahead of the autumn spike which will add to the carnage. Europe (and the rest of the planet) would be perfectly justified in imposing permanent travel bans on UK residents.
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Re: COVID-19

Post by lpm » Thu Aug 19, 2021 3:36 pm

shpalman wrote:
Thu Aug 19, 2021 2:21 pm
lpm wrote:
Thu Aug 19, 2021 1:28 pm
Each case in under 30s is the equivalent of a vaccine dose.

We spent months tracking daily vaccine numbers, celebrating milestones achieved. Now we get to celebrate cases in the same way. If 300,000 under 30s get partial immunity in a week that's another step closer to herd immunity. But if it's 200,000 via infection and 100,000 via vaccination then everyone gets agitated about the 200,000 figure. It's even worse on twitter than it is on here - people unbelievably slow to adapt to the new climate and still trotting out 2020 presumptions.

For example, hospitalisations are about three doublings away from being a crisis. In 2020, three doublings wasn't a lot - easily got there in few weeks. But in the 2021 land of the vaccinated it's a huge gulf. We're basically fine for the rest of the year.
At current rates you won't get 200,000 infections without 600 deaths and 6000 people sent to hospital, between unlucky young people and cases leaking into the older age groups, but that's what you already have now (and it's going up with nothing planned to bring it down and it will only get worse in September with schools going back and socializing moving back indoors). You still have about 10% of the adult population without a single vaccine dose* which is 5.5 million so you'll only need to carry until the end of the year like this. But yeah who cares about another 10,000 deaths when you can go to the pub. I just hope continental Europe maintains travel restrictions from the UK. Forever.

* - this number will change today as 16-17 year-olds are added to the denominator
No that's wrong. A million cases can have zero deaths if it's 100% school children.

Leakage into the old age groups is what matters, and it isn't happening to the degree that leads to hundreds of deaths. The UK has extremely high percentages of over 50s and particularly over 80s fully vaccinated, probably with 3rd boosters on the way across the autumn. Hence only 100 deaths a day.

Case statistics are currently pretty useless for equation building, because such a huge proportion are young people.

Come back in September and it might be different.
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Re: COVID-19

Post by shpalman » Thu Aug 19, 2021 3:42 pm

lpm wrote:
Thu Aug 19, 2021 3:36 pm
shpalman wrote:
Thu Aug 19, 2021 2:21 pm
lpm wrote:
Thu Aug 19, 2021 1:28 pm
Each case in under 30s is the equivalent of a vaccine dose.

We spent months tracking daily vaccine numbers, celebrating milestones achieved. Now we get to celebrate cases in the same way. If 300,000 under 30s get partial immunity in a week that's another step closer to herd immunity. But if it's 200,000 via infection and 100,000 via vaccination then everyone gets agitated about the 200,000 figure. It's even worse on twitter than it is on here - people unbelievably slow to adapt to the new climate and still trotting out 2020 presumptions.

For example, hospitalisations are about three doublings away from being a crisis. In 2020, three doublings wasn't a lot - easily got there in few weeks. But in the 2021 land of the vaccinated it's a huge gulf. We're basically fine for the rest of the year.
At current rates you won't get 200,000 infections without 600 deaths and 6000 people sent to hospital, between unlucky young people and cases leaking into the older age groups, but that's what you already have now (and it's going up with nothing planned to bring it down and it will only get worse in September with schools going back and socializing moving back indoors). You still have about 10% of the adult population without a single vaccine dose* which is 5.5 million so you'll only need to carry until the end of the year like this. But yeah who cares about another 10,000 deaths when you can go to the pub. I just hope continental Europe maintains travel restrictions from the UK. Forever.

* - this number will change today as 16-17 year-olds are added to the denominator
No that's wrong. A million cases can have zero deaths if it's 100% school children.

Leakage into the old age groups is what matters, and it isn't happening to the degree that leads to hundreds of deaths. The UK has extremely high percentages of over 50s and particularly over 80s fully vaccinated, probably with 3rd boosters on the way across the autumn. Hence only 100 deaths a day.

Case statistics are currently pretty useless for equation building, because such a huge proportion are young people.

Come back in September and it might be different.
You have more than 90 deaths per day at the moment, so that's already more than 600 deaths per week. The CFR now is about 0.3%, which is greater than zero.
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Re: COVID-19

Post by Herainestold » Thu Aug 19, 2021 3:43 pm

Interesting piece on the problems facing NZ as they roll out vaccines and look at how they are going to re open to the world.
All that said, there is a widespread acceptance that the borders must open again, that such a move is both just and necessary. And as Skegg notes, Covid-19 is rampant around the world so when we start reopening the borders, the virus will creep in.

“Our allies have let us down. Many countries that could have eliminated Covid-19 either never tried, or threw in the towel,” he says, pointing to the challenge ahead.

The country needs to vaccinate “enough people” (as the government describes it) to allow border opening. The government will not say what “enough people” actually is. New South Wales has signalled it will look to ease lockdowns once 70 per cent of its population is vaccinated.
70% is not near enough. Delta will quickly infect the remaining 30% plus half the vaccinated.
Again, it’s widely accepted the snap Level 4 lockdown currently in place was the right call to slow down Delta. But one overseas expert emailed me on Wednesday morning saying Delta is simply too tough to stop. “If they manage to stop this one spreading, another case will pop up somewhere else. But when you are trying to roll out the vaccine then time is what you need.”
It was quite notable that Ardern has not ruled out using some sort of lockdown even after mass vaccination.

Such a move would be politically challenging, and according to Hunter, it might not even be enough to curb Delta.

“Lockdowns by themselves are unlikely to be enough to control the spread of Delta; it is just too infectious unless they are really, really strict. The virus is just too infectious. Yes, you can manage localised outbreaks for a while but when it has started spreading widely it gets very difficult.”
NZ must keep lockdowns in place as they steadily vaccinate. Will they ever be able to re-open their borders and risk what they have achieved?

https://www.stuff.co.nz/national/health ... e-of-delta
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Re: COVID-19

Post by Herainestold » Thu Aug 19, 2021 3:49 pm

shpalman wrote:
Thu Aug 19, 2021 3:42 pm
You have more than 90 deaths per day at the moment, so that's already more than 600 deaths per week. The CFR now is about 0.3%, which is greater than zero.
The CFR will increase as vaccine efficacy wanes. Some countries have set vaccine expiry dates at 9 months. That means the more vulnerable older people who were first vaccinated around the beginning of the year, will be exposed to the more transmissive and virulent Delta without adequate protection.
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Re: COVID-19

Post by lpm » Thu Aug 19, 2021 3:51 pm

shpalman wrote:
Thu Aug 19, 2021 3:42 pm
You have more than 90 deaths per day at the moment, so that's already more than 600 deaths per week. The CFR now is about 0.3%, which is greater than zero.
And zero of those are children or young people. Not very low. Zero.
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Re: COVID-19

Post by shpalman » Thu Aug 19, 2021 3:59 pm

lpm wrote:
Thu Aug 19, 2021 3:51 pm
shpalman wrote:
Thu Aug 19, 2021 3:42 pm
You have more than 90 deaths per day at the moment, so that's already more than 600 deaths per week. The CFR now is about 0.3%, which is greater than zero.
And zero of those are children or young people. Not very low. Zero.
Well, a non-zero number of children and/or young people have died of covid, but ok fine it's a small number (fewer than 70 deaths under the age of 20 in England). But it will increase if you let covid run rampant - look at the US. And more cases in young people will mean more cases leaking into older people (and more chance of a variant e.g. Alpha), which is why you are currently heading for 100 deaths per day.
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Re: COVID-19

Post by lpm » Thu Aug 19, 2021 4:28 pm

Around 50% of child fatalities are children with severe neurological conditions, about 17% with other life limiting illnesses. The remaining 33% includes other conditions and a few perfectly healthy children.

It sounds callous but Covid is now a disease that only matters to the very elderly and those with very serious conditions, plus those who've rejected vaccines.

For the rest of us it's just one of many serious illnesses and we should worry more about poverty related killers and similar - things where health outcomes can be improved at far far lower cost than mass lockdowns, trashing of education, unemployment, etc
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Re: COVID-19

Post by Herainestold » Thu Aug 19, 2021 4:53 pm

lpm wrote:
Thu Aug 19, 2021 4:28 pm
Around 50% of child fatalities are children with severe neurological conditions, about 17% with other life limiting illnesses. The remaining 33% includes other conditions and a few perfectly healthy children.

It sounds callous but Covid is now a disease that only matters to the very elderly and those with very serious conditions, plus those who've rejected vaccines.

For the rest of us it's just one of many serious illnesses and we should worry more about poverty related killers and similar - things where health outcomes can be improved at far far lower cost than mass lockdowns, trashing of education, unemployment, etc
The question is, as a society, how many excess deaths are we willing to tolerate?
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Re: COVID-19

Post by shpalman » Thu Aug 19, 2021 4:58 pm

200,000 cases per week among young people (0-19) is still going to be 10-15 deaths per week amongst those categories, unless you managed to kill them all already or at least vaccinated the most vulnerable over 12. 33% of that would still be a few per week.
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Re: COVID-19

Post by lpm » Thu Aug 19, 2021 5:29 pm

Herainestold wrote:
Thu Aug 19, 2021 4:53 pm
lpm wrote:
Thu Aug 19, 2021 4:28 pm
Around 50% of child fatalities are children with severe neurological conditions, about 17% with other life limiting illnesses. The remaining 33% includes other conditions and a few perfectly healthy children.

It sounds callous but Covid is now a disease that only matters to the very elderly and those with very serious conditions, plus those who've rejected vaccines.

For the rest of us it's just one of many serious illnesses and we should worry more about poverty related killers and similar - things where health outcomes can be improved at far far lower cost than mass lockdowns, trashing of education, unemployment, etc
The question is, as a society, how many excess deaths are we willing to tolerate?
That's surprisingly easy to answer. Our society is prepared to kill 80,000 smokers a year and still sell cigarettes in every cornershop. Kill 5,000 via suicide and still wreck mental health services through cuts. Kill 2,000 on the roads and still effectively decriminalize speeding. Kill 40,000 through air pollution and still prioritise the road lobby. Kill 30,000 through obesity and refuse to regulate the food industry.

But when I try to kill another 30,000 with Covid y'all get upset and want to trash the economy instead.
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Re: COVID-19

Post by wilsontown » Thu Aug 19, 2021 5:40 pm

Yep, and around 30,000 people die of flu in an average year. We have vaccinations and public health information campaigns but we don't shut the whole nation down.
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