COVID-19

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

Post by shpalman » Thu Jan 28, 2021 9:55 am

shpalman wrote:
Sun Jan 24, 2021 2:18 pm
Well, he does argue for a "Zero-COVID" strategy, instead of the idea that you could somehow run with an "acceptable" number of deaths.
16 reasons why all countries should pursue a Covid-19 elimination strategy
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Re: COVID-19

Post by Woodchopper » Thu Jan 28, 2021 10:11 am

Bird on a Fire wrote:
Thu Jan 28, 2021 1:00 am
If the United Kingdom had adopted South Korean-style controls in response to the coronavirus pandemic, it would have saved about 65,000 lives through October 2020 and averted its worst economic decline in more than three centuries, according to a new study that modeled the countries’ coronavirus policies.

The authors argued that their paper, which is forthcoming in the February 2021 issue of the Journal of Public Economics, demonstrates that there is not a tradeoff between gross domestic product and public health. Rather, the two are inextricably linked.
https://academictimes.com/south-korean- ... ves-in-uk/
And here's a link to the paper: https://www.sciencedirect.com/science/a ... cid=author

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Re: COVID-19

Post by KAJ » Thu Jan 28, 2021 4:22 pm

KAJ wrote:
Wed Jan 27, 2021 9:12 pm
Anyone know why today's coronavirus.data.gov.uk/details/deaths has "Deaths within 28 days of positive test by date of death" not for UK, but only for "By nation", and that is missing Wales?
Today that page still doesn't show UK "Deaths within 28 days of positive test by date of death" but that data can be downloaded - it couldn't yesterday.
If anyone is interested, here's my analysis of that data. (I've zero-weighted "Data for the period ending 5 days before the date when the website was last updated..." which .data.gov.uk flags as "incomplete". I reckon a few more are also incomplete.)
DateDeaths.png
DateDeaths.png (10.85 KiB) Viewed 788 times

Code: Select all

At 27/01 fit = 1158.7 with halving time = 61.4 days. That time halving in 2.7 days 

Coefficients:
               Estimate Std. Error t value Pr(>|t|)    
(Intercept)     6.88594    0.01365 504.516  < 2e-16 ***
poly(date, 2)1  1.17602    0.09535  12.334 3.98e-12 ***
poly(date, 2)2 -0.49214    0.09241  -5.325 1.61e-05 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 0.06123 on 25 degrees of freedom
Multiple R-squared:  0.938

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Re: COVID-19

Post by Woodchopper » Thu Jan 28, 2021 4:45 pm

Thanks for that KAJ. Its looking like tested cases peaked at around 1 January, hospital admissions peaked about 9 days later, and deaths seem to have peaked about 10 days after that. ETA Best case is if the deaths decline as fats as the case numbers. But so far there hasn't been a steep decline in hospital admissions.

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Re: COVID-19

Post by KAJ » Thu Jan 28, 2021 5:26 pm

Woodchopper wrote:
Thu Jan 28, 2021 4:45 pm
Thanks for that KAJ. Its looking like tested cases peaked at around 1 January, hospital admissions peaked about 9 days later, and deaths seem to have peaked about 10 days after that. ETA Best case is if the deaths decline as fats as the case numbers. But so far there hasn't been a steep decline in hospital admissions.
I tried attaching my complete analyses as .mhtml and .pdf but couldn't make it work.
For interest, here are my processings of:
Cases by specimen date
Hospital admissions
Mechanical ventilation beds
SpecCases.png
SpecCases.png (14.72 KiB) Viewed 762 times
Admits.png
Admits.png (16.28 KiB) Viewed 762 times
MVbeds.png
MVbeds.png (11.41 KiB) Viewed 762 times

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Re: COVID-19

Post by jdc » Fri Jan 29, 2021 1:01 am

lancet infectious diseases, as you'd expect, has some papers on covid.

non-pharma interventions and r https://www.thelancet.com/journals/lani ... 4/fulltext
decreasing trend over time in the R ratio was found following the introduction of school closure, workplace closure, public events ban, requirements to stay at home, and internal movement limits; the reduction in R ranged from 3% to 24% on day 28 following the introduction compared with the last day before introduction, although the reduction was significant only for public events ban (R ratio 0·76, 95% CI 0·58–1·00); for all other NPIs, the upper bound of the 95% CI was above 1.

An increasing trend over time in the R ratio was found following the relaxation of school closure, bans on public events, bans on public gatherings of more than ten people, requirements to stay at home, and internal movement limits; the increase in R ranged from 11% to 25% on day 28 following the relaxation compared with the last day before relaxation, although the increase was significant only for school reopening (R ratio 1·24, 95% CI 1·00–1·52) and lifting bans on public gatherings of more than ten people (1·25, 1·03–1·51); for all other NPIs, the lower bound of the 95% CI was below 1.


IFR estimated for New York https://www.thelancet.com/journals/lani ... 6/fulltext
During the period March 1 to June 6, 2020, 205 639 people had a laboratory-confirmed infection with SARS-CoV-2 and 21 447 confirmed and probable COVID-19-related deaths occurred among residents of New York City. We estimated an overall infection-fatality risk of 1·39% (95% credible interval 1·04–1·77) in New York City. Our estimated infection-fatality risk for the two oldest age groups (65–74 and ≥75 years) was much higher than the younger age groups, with a cumulative estimated infection-fatality risk of 0·116% (0·0729–0·148) for those aged 25–44 years and 0·939% (0·729–1·19) for those aged 45–64 years versus 4·87% (3·37–6·89) for those aged 65–74 years and 14·2% (10·2–18·1) for those aged 75 years and older. In particular, weekly infection-fatality risk was estimated to be as high as 6·72% (5·52–8·01) for those aged 65–74 years and 19·1% (14·7–21·9) for those aged 75 years and older.
coronavac phase i/ii trial https://www.thelancet.com/journals/lani ... 4/fulltext
We found that two doses of CoronaVac at different concentrations and using different dosing schedules were well tolerated and moderately immunogenic in healthy adults aged 18–59 years.

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Re: COVID-19

Post by shpalman » Fri Jan 29, 2021 3:00 pm

It turns out that if you go to Sorveglianza integrata COVID-19: i principali dati nazionali you'll find a presentazione esplicativa del metodo per la stima degli Rt (an explanatory presentation on the method for estimating Rt) and a weekly-updated link to the national data and the R script.

Unfortunately those "open data" links don't seem to be on the English version of the page.
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Re: COVID-19

Post by shpalman » Fri Jan 29, 2021 6:35 pm

shpalman wrote:
Thu Jan 28, 2021 9:55 am
shpalman wrote:
Sun Jan 24, 2021 2:18 pm
Well, he does argue for a "Zero-COVID" strategy, instead of the idea that you could somehow run with an "acceptable" number of deaths.
16 reasons why all countries should pursue a Covid-19 elimination strategy
What sense does it make to say that a zero-covid strategy would be "incredibly risky" because there would be "re-introduction of the disease and that could easily be new variants"?

Without lockdowns and controls on incoming travel, you'll get introduction of the disease that could easily be new variants anyway; why is it therefore a bad thing to try to eliminate your internal contagion as much as possible?
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Re: COVID-19

Post by Sciolus » Fri Jan 29, 2021 8:03 pm

#13 will astonish you! Well, no it won't, because it's exactly the same point I've banged on about loads of times on here.
shpalman wrote:
Fri Jan 29, 2021 6:35 pm
What sense does it make to say that a zero-covid strategy would be "incredibly risky" because there would be "re-introduction of the disease and that could easily be new variants"?

Without lockdowns and controls on incoming travel, you'll get introduction of the disease that could easily be new variants anyway; why is it therefore a bad thing to try to eliminate your internal contagion as much as possible?
f.cked if I know. You may not be able to get to exactly zero cases (although countries have) but that doesn't mean it shouldn't be your target. A higher case rate is always worse than a lower case rate. Maybe he thinks it will be too expensive to get there, but all the evidence is that it is far easier and cheaper to sustain a very low level of infection than to to have constant hokey-cokey lockdowns.

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Re: COVID-19

Post by shpalman » Fri Jan 29, 2021 8:55 pm

The UK's deaths data for the day is in now: 1,245.
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Re: COVID-19

Post by shpalman » Fri Jan 29, 2021 9:09 pm

Sciolus wrote:
Fri Jan 29, 2021 8:03 pm
#13 will astonish you! Well, no it won't, because it's exactly the same point I've banged on about loads of times on here.
shpalman wrote:
Fri Jan 29, 2021 6:35 pm
What sense does it make to say that a zero-covid strategy would be "incredibly risky" because there would be "re-introduction of the disease and that could easily be new variants"?

Without lockdowns and controls on incoming travel, you'll get introduction of the disease that could easily be new variants anyway; why is it therefore a bad thing to try to eliminate your internal contagion as much as possible?
f.cked if I know. You may not be able to get to exactly zero cases (although countries have) but that doesn't mean it shouldn't be your target. A higher case rate is always worse than a lower case rate. Maybe he thinks it will be too expensive to get there, but all the evidence is that it is far easier and cheaper to sustain a very low level of infection than to to have constant hokey-cokey lockdowns.
It's the sort of thing you normally hear from right-wing/populist politicians, not from "A senior member" of a "National Public Health Emergency Team".

And it can't be about the cost because he "chairs the government's epidemiological modelling advisory group" and it's therefore not his job to do the cost/benefit of analysis (but rather just explain the benefit) or the f.cking "lockdown fatigue" b.llsh.t for that matter.

"It's risky to try to eliminate a disease because it might come back" makes no sense.
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Re: COVID-19

Post by OffTheRock » Fri Jan 29, 2021 10:01 pm

It’s about the same level of sense as it being too late to start an elimination strategy because we have too many cases. Ditto being too late for border controls.

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Re: COVID-19

Post by shpalman » Fri Jan 29, 2021 10:09 pm

OffTheRock wrote:
Fri Jan 29, 2021 10:01 pm
It’s about the same level of sense as it being too late to start an elimination strategy because we have too many cases. Ditto being too late for border controls.
Or too early to order a lockdown.
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Re: COVID-19

Post by Woodchopper » Sat Jan 30, 2021 9:07 am

Sciolus wrote:
Fri Jan 29, 2021 8:03 pm
#13 will astonish you! Well, no it won't, because it's exactly the same point I've banged on about loads of times on here.
shpalman wrote:
Fri Jan 29, 2021 6:35 pm
What sense does it make to say that a zero-covid strategy would be "incredibly risky" because there would be "re-introduction of the disease and that could easily be new variants"?

Without lockdowns and controls on incoming travel, you'll get introduction of the disease that could easily be new variants anyway; why is it therefore a bad thing to try to eliminate your internal contagion as much as possible?
f.cked if I know. You may not be able to get to exactly zero cases (although countries have) but that doesn't mean it shouldn't be your target. A higher case rate is always worse than a lower case rate. Maybe he thinks it will be too expensive to get there, but all the evidence is that it is far easier and cheaper to sustain a very low level of infection than to to have constant hokey-cokey lockdowns.
There’s a summary of the remarks here.
https://twitter.com/gavreilly/status/13 ... 54112?s=21

It looks like he’s disagreeing with two things. First that a zero Covid strategy is possible. Unlike New Zealand, Ireland has an open border with a heavily infected neighbour. Trying to seal the border with the UK would not be possible.

Secondly, against the notion that a zero Covid strategy would involve a New Zealand like normality eg packed rugby stadiums. He seems to suggest that even if there were zero cases in Ireland, there would still need to be restrictions on everyday life as it would be inevitable that new outbreaks would occur after people crossed the border.

He does though seem to want to get cases as low as possible.

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Re: COVID-19

Post by shpalman » Sat Jan 30, 2021 9:13 am

The quarantine restrictions are also intended to apply to those who arrive into the State via Northern Ireland (good luck with that).

It may not be possible or sustainable to achieve zero-Covid but it's still something to strive for.

So the "risky" part would be assuming you actually had zero Covid, and acting accordingly, not necessarily the measures to achieve it themselves?
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Re: COVID-19

Post by basementer » Sun Jan 31, 2021 5:16 am

Perth is locking down. One case in the community, premier announces five day close down starting today.
https://7news.com.au/lifestyle/health-w ... -c-2064693
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Re: COVID-19

Post by Martin_B » Sun Jan 31, 2021 10:49 am

basementer wrote:
Sun Jan 31, 2021 5:16 am
Perth is locking down. One case in the community, premier announces five day close down starting today.
https://7news.com.au/lifestyle/health-w ... -c-2064693
Decisive leadership.
Yep, we got 5 hours notice of a 5 day lockdown. Fortunately I usually keep about a week's food in the apartment. I've checked my inventory and I have 160 teabags. Should be enough.
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Re: COVID-19

Post by shpalman » Sun Jan 31, 2021 11:56 am

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Re: COVID-19

Post by OffTheRock » Sun Jan 31, 2021 1:51 pm

shpalman wrote:
Sat Jan 30, 2021 9:13 am
The quarantine restrictions are also intended to apply to those who arrive into the State via Northern Ireland (good luck with that).

It may not be possible or sustainable to achieve zero-Covid but it's still something to strive for.

So the "risky" part would be assuming you actually had zero Covid, and acting accordingly, not necessarily the measures to achieve it themselves?
Similar logic applies to the not zero covid policy, just with more Covid, more deaths and more long term health issues. If it's not going away and can still be brought in then you are just tying yourself into the next lockdown when cases start to rise and then get too high. And it's not like there aren't going to need to be some level of measures between the lockdowns anyway.

In terms of the 'risk' of assuming you were zero covid, keep an eye on the Guernsey outbreak. 4 cases last Friday is now 189 active cases, despite the lockdown occurring less than 24hrs after the cases but there are already early signs the lockdown is having an effect so I'd imagine that number will start to fall fairly soon.

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Re: COVID-19

Post by lpm » Sun Jan 31, 2021 2:10 pm

Except if the vaccines prevent most transmissions. Then everything changes.

It would be worth vaccinating all of Guernsey and none of Jersey. Then send in Dominic Cummings to spread the virus on both islands. See how many cases each has a month later. If Guernsey has the same but mostly asymptomatic then the world is f.cked.

It's so ridiculous we don't have any info on this yet. No way to plan or strategise without this fundamental piece on knowledge.
What ever happened to that Trump guy, you know, the one who was president for a bit?

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Re: COVID-19

Post by shpalman » Sun Jan 31, 2021 2:16 pm

lpm wrote:
Sun Jan 31, 2021 2:10 pm
Except if the vaccines prevent most transmissions. Then everything changes.

It would be worth vaccinating all of Guernsey and none of Jersey. Then send in Dominic Cummings to spread the virus on both islands. See how many cases each has a month later. If Guernsey has the same but mostly asymptomatic then the world is f.cked...
Depends on what happens to the IFR. If nobody* dies on Guernsey then, meh, once everyone is vaccinated let everyone get asymptomatic covid. You just wouldn't be able to rely on herd immunity, but then that's the difference between having to vaccinate all the population, and having to vaccinate almost all of the population. It doesn't change the rollout logistics by an order of magnitude.
lpm wrote:
Sun Jan 31, 2021 2:10 pm
It's so ridiculous we don't have any info on this yet. No way to plan or strategise without this fundamental piece on knowledge.
We are learning by doing.
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Re: COVID-19

Post by OffTheRock » Sun Jan 31, 2021 2:32 pm

lpm wrote:
Sun Jan 31, 2021 2:10 pm
Except if the vaccines prevent most transmissions. Then everything changes.

It would be worth vaccinating all of Guernsey and none of Jersey. Then send in Dominic Cummings to spread the virus on both islands. See how many cases each has a month later. If Guernsey has the same but mostly asymptomatic then the world is f.cked.

It's so ridiculous we don't have any info on this yet. No way to plan or strategise without this fundamental piece on knowledge.
I'm not sure they'd agree. They've already run the zero covid vs not zero covid experiment. Not really having had any community spread since last April I don't think Guernsey would be happy to deliberately try to spread it. OTOH we could quarantine DC for at least a couple of weeks. If he breaks it he can have a nice big fine or some jail time.

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Re: COVID-19

Post by jimbob » Sun Jan 31, 2021 5:07 pm

lpm wrote:
Sun Jan 31, 2021 2:10 pm
Except if the vaccines prevent most transmissions. Then everything changes.

It would be worth vaccinating all of Guernsey and none of Jersey. Then send in Dominic Cummings to spread the virus on both islands. See how many cases each has a month later. If Guernsey has the same but mostly asymptomatic then the world is f.cked.

It's so ridiculous we don't have any info on this yet. No way to plan or strategise without this fundamental piece on knowledge.
We have good early indications from Israel

https://www.nature.com/articles/d41586-021-00140-w
As countries worldwide roll out COVID-19 vaccines, researchers are eagerly watching for early signs that they are having an impact on the pandemic. Last week, researchers in Israel reported preliminary figures suggesting that people vaccinated there were about one-third less likely to test positive for SARS-CoV-2 than people who had not received a shot. But scientists say that population-wide effects of immunization will take time to become clear.
That's hopeful
Have you considered stupidity as an explanation

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Re: COVID-19

Post by shpalman » Sun Jan 31, 2021 6:11 pm

Brit wishes he'd stayed in Wuhan
"They lied to us," he says of the UK authorities. "We're being told to get out of Wuhan, 'come back to England, you'll be safe here'.

"We would have been safer and much more freer if we stayed in China.

"They tackled it short and sharp and locked down the cities and it was the right thing to do."
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Re: COVID-19

Post by Millennie Al » Mon Feb 01, 2021 3:16 am

jimbob wrote:
Sun Jan 31, 2021 5:07 pm

We have good early indications from Israel

https://www.nature.com/articles/d41586-021-00140-w
people vaccinated there were about one-third less likely to test positive for SARS-CoV-2 than people who had not received a shot.
That's hopeful
Yes, but not very. 33% effectiveness is much too low to stop the disease - it needs to be at least twice that.
Covid-19 - Don't catch it: don't spread it.

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