COVID-19

Covid-19 discussion, bring your own statistics
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Bird on a Fire
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Re: COVID-19

Post by Bird on a Fire » Mon Feb 01, 2021 2:25 pm

If I understand correctly, though, testing positive doesn't necessarily mean somebody is/was infectious. For that I think we need measures of (peak?) viral load rather than just a Boolean, or just look at the case data in a few weeks.

The vaccine might only cause a third reduction in infections, but if those people are more likely to survive and less likely to infect others then I think we can chalk that up as a win for now (until it mutates again).
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Re: COVID-19

Post by jimbob » Mon Feb 01, 2021 3:31 pm

I think it would have to reduce the R number* by at least 30%


*I usually dislike using that but in this case I think it's appropriate.
Have you considered stupidity as an explanation

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jdc
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Re: COVID-19

Post by jdc » Mon Feb 01, 2021 7:06 pm

Millennie Al wrote:
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.
i'm ignoring the 33% figure; it relates to people who'd had their first jab two weeks prior. Leaving aside the point that it's only halfway through the regime, two weeks isn't even long enough to get the full effect of the first shot.
In a preliminary analysis of 200,000 people older than 60 who received the vaccine, compared with a matched group of 200,000 who did not, researchers found that the chances of testing positive for the virus were 33% lower two weeks after the first injection.

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jdc
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Re: COVID-19

Post by jdc » Wed Feb 03, 2021 7:36 pm

European politicians endagering public health with their anti-AZ comments: https://www.theguardian.com/world/live/ ... 7e5846799f
Kent Woods, a former chief of both the UK and European Union medicines regulators, told AFP:

This can only be negative on the vaccine takeup in France, in Germany and others. This is bad for public health. Forget the politics. This is a threat to public health and people in the public eye need to be very cautious in the messages they make.

The key point to make is that the views coming out from politicians in Europe are in striking contrast to the scientific view reached by the European regulator, which has representation from all 27 EU member states. These are politically driven rather than scientifically driven.
Also some comments from some guy called Michael or something;
Michael Head, senior research fellow in global health at the University of Southampton, said Macron’s intervention was “extremely unhelpful, ill-founded and inaccurate”.

It’s not going to encourage the French population to line up in a queue. I assume they’re wrapped up in the recent history of EU-UK politics rather than any real public confidence issues.

They’ll be picked up by the anti-vaxxer groups who do their utmost to undermine public confidence with social media posts and memes.
He knows about memes and that so he's clearly on the ball. I bet he knows all the shortcuts.

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Re: COVID-19

Post by OffTheRock » Wed Feb 03, 2021 9:32 pm

Press conference if anyone's interested Bit long but anything interesting is usually in answers to media questions which starts at 20mins.

Guernsey up to 329 active cases but numbers going in the right direction. Number of new daily cases looks like it's plateaued and more of them are cases in known contacts than 'surprise' cases. Still no word on which strain but the assumption is it's the new UK one.

Couple of bits that might be relevant to the UK. There's definitely increased transmission compared to our last wave. More cases since 22nd Jan than in the whole of the last wave. Also looks like there is a lot more household transmission than in the last outbreak. More cases where the whole household is getting infected that wasn't seen much before with the old strain.

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Re: COVID-19

Post by shpalman » Thu Feb 04, 2021 6:53 pm

Italy is at about 12,000 new cases per day and 400 deaths per day, slowly falling, but the suggestion is that we've finished seeing the benefit of the Christmas lockdown and it's going to start to go up again (driven in part by all the new variants).
molto tricky

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Re: COVID-19

Post by shpalman » Fri Feb 05, 2021 4:26 pm

Seems like there's been some sort of redefinition of what "mechanical ventilation" means in England.
molto tricky

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Re: COVID-19

Post by KAJ » Fri Feb 05, 2021 5:01 pm

shpalman wrote:
Fri Feb 05, 2021 4:26 pm
Seems like there's been some sort of redefinition of what "mechanical ventilation" means in England.
I think they've corrected a blunder. At 4:10 p.m. the number for 4 Feb was 6,847. Now it shows "Last updated on Friday 5 February 2021 at 4:49pm" and the number for 4 Feb is 3,572.

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Re: COVID-19

Post by OffTheRock » Fri Feb 05, 2021 11:09 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.
Well we've got Covid in a care home now, with both the affected elderly people being 3 weeks after their first vaccine. Not sure about the staff, but they should have had the vaccine by now.

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shpalman
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Re: COVID-19

Post by shpalman » Sun Feb 07, 2021 8:19 am

molto tricky

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shpalman
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Re: COVID-19

Post by shpalman » Sun Feb 07, 2021 9:33 am

molto tricky

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Re: COVID-19

Post by headshot » Sun Feb 07, 2021 11:31 am

But then that means you aren’t saving as many life years. #torylogic

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Re: COVID-19

Post by shpalman » Sun Feb 07, 2021 11:39 am

headshot wrote:
Sun Feb 07, 2021 11:31 am
But then that means you aren’t saving as many life years. #torylogic
It means you aren't helping the economic recovery as much #torylogic

Letizia Moratti (Lombardy health accessory) caused a bit of a fuss last month by suggesting that priority for the vaccine should also be based on the local GDP of a region. (Lombardy already gets the most vaccines because it's the most populous region, and to be fair while it was slow getting started, it's now able to administer the doses as fast as it gets them.)
molto tricky

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Re: COVID-19

Post by KAJ » Mon Feb 08, 2021 7:18 pm

KAJ wrote:
Wed Dec 30, 2020 6:58 pm
shpalman wrote:
Wed Dec 30, 2020 5:39 pm
<snip>
So whatever the correct definition of "by date reported", they are correcting previous numbers. They quietly moved 43 deaths from yesterday's total to Christmas day, and one from yesterday to the 27th. During the holidays things were probably a bit disorganized.

Of course if nobody actually gave those numbers in here at the time we don't have proof of that, I could always have typed the wrong daily total into my spreadsheet (but I do always check that it matches the new daily increment). So I can only hope to actually catch it happening over New Year.
Yes, as I said above I'm not particularly interested in deaths by report date. But storing that data is only a few lines...

Code: Select all

local({
Published <- max(aDF$date) # current data publication date
temp <- aDF[,c("date", "PubDeaths")]  # current PubDeaths data
aggDF <- readRDS("cPDeaths.rds")  # read PubDeaths aggregate
if(Published > max(aggDF$Published)) { # if new data
  temp$Published <- Published # Published col
  aggDF <- rbind(aggDF, na.omit(temp)) # append to aggregate
  saveRDS(aggDF, "cPDeaths.rds") # save PubDeaths aggregate
  print(paste0("Added PubDeaths: ", Published))
  }
  }) 
... in the R Markdown notebook I run every day, so I'll have it in future if you want.
Just a followup on this. Since then I've been storing the published "Deaths by date reported". In that period there arere only two "..by date reported" dates with differing numbers on different publication dates, 1 and 3 Jan 2021. Here the 'date' column is "..by date reported" .

Code: Select all

subset(getcData("cPDeaths.rds", maxlag = 100, mincount = 1)$DF, PubDeaths < max)[,1:5]

            date PubDeaths  Published count max
14939 2021-01-01       613 2021-01-01    39 656
14940 2021-01-01       613 2021-01-02    39 656
14934 2021-01-01       613 2021-01-03    39 656
14924 2021-01-01       613 2021-01-04    39 656

15035 2021-01-03       454 2021-01-03    37 455
15025 2021-01-03       454 2021-01-04    37 455
It's zero effort to collect this data so I'll carry on, but I don't think there's anything interesting there.

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Woodchopper
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Re: COVID-19

Post by Woodchopper » Wed Feb 10, 2021 8:26 pm

Remember Singapore? Looks like there mass testing was key to keeping deaths at a minimum
https://jamanetwork.com/journals/jama/a ... ct/2776190

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Re: COVID-19

Post by Woodchopper » Wed Feb 10, 2021 8:47 pm

Does Prior Exposure to Coronaviruses Protect You?
https://blogs.sciencemag.org/pipeline/a ... rotect-you
The authors looked at 431 pre-pandemic blood samples, and compared them to 251 samples from people who have been infected in the current outbreak and recovered, as well as analyzing antibody profiles in people who are currently hospitalized. What they’ve found is first, that most people have indeed been infected with one or more of the “garden-variety” coronaviruses. The pre-pandemic samples show plenty of antibody responses to these. Second, about 20% of these patients raised antibodies that do cross-reaction with the Spike or nucleocapsid proteins of the current pandemic coronavirus. And what’s more, levels of such antibodies are elevated when a person in this group gets infected with SARS-Cov2: the immune system memory (as present in these patients’ B cells) responds by increasing production of the antibodies to the previous coronaviruses.

But here’s the key part: “cross-react” does not mean “neutralize” and it does not mean “provide protection from”. These antibodies may or may not have been neutralizing against the other coronaviruses, but they don’t seem to have any such effect on the current one. And in keeping with that, having such cross-reactive antibodies seems to provide no protection against catching SARS-Cov2 or against being hospitalized with it if you do. There’s no difference in the infection/hospitalization rates of the people who had cross-reactive coronavirus serum antibodies ready to go versus those who didn’t. They’re basically useless.

Now, you can still make an argument that the T cell component of immunity might provide some protection after a previous coronavirus infection. The current study didn’t address this directly, but after these results, it’s at least less likely that that’s happening. The authors make a note of this, and also note that pre-existing mucosal antibodies might exert a protective effect (which this study didn’t examine, either). But prior circulating human coronavirus antibodies, even ones that can bind to the current one – those it looks like we can rule out. Which is too bad.

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Woodchopper
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Re: COVID-19

Post by Woodchopper » Wed Feb 10, 2021 9:07 pm

The World Mortality Dataset: Tracking excess mortality across countries during the COVID-19 pandemic

Comparing the impact of the COVID-19 pandemic between countries or across time is difficult because the reported numbers of cases and deaths can be strongly affected by testing capacity and reporting policy. Excess mortality, defined as the increase in all-cause mortality relative to the recent average, is widely considered as a more objective indicator of the COVID-19 death toll. However, there has been no central, frequently-updated repository of the all-cause mortality data across countries. To fill this gap, we have collected weekly, monthly, or quarterly all-cause mortality data from 77 countries, openly available as the regularly-updated World Mortality Dataset. We used this dataset to compute the excess mortality in each country during the COVID-19 pandemic. We found that in the worst-affected countries the annual mortality increased by over 50%, while in several other countries it decreased by over 5%, presumably due to lockdown measures decreasing the non-COVID mortality. Moreover, we found that while some countries have been reporting the COVID-19 deaths very accurately, many countries have been underreporting their COVID-19 deaths by an order of magnitude or more. Averaging across the entire dataset suggests that the world’s COVID-19 death toll may be at least 1.6 times higher than the reported number of confirmed deaths.
Contains a summary for each country

https://www.medrxiv.org/content/10.1101 ... 21250604v1

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Re: COVID-19

Post by badger » Thu Feb 11, 2021 11:03 am

Woodchopper wrote:
Wed Feb 10, 2021 9:07 pm
The World Mortality Dataset: Tracking excess mortality across countries during the COVID-19 pandemic

Comparing the impact of the COVID-19 pandemic between countries or across time is difficult because the reported numbers of cases and deaths can be strongly affected by testing capacity and reporting policy. Excess mortality, defined as the increase in all-cause mortality relative to the recent average, is widely considered as a more objective indicator of the COVID-19 death toll. However, there has been no central, frequently-updated repository of the all-cause mortality data across countries. To fill this gap, we have collected weekly, monthly, or quarterly all-cause mortality data from 77 countries, openly available as the regularly-updated World Mortality Dataset. We used this dataset to compute the excess mortality in each country during the COVID-19 pandemic. We found that in the worst-affected countries the annual mortality increased by over 50%, while in several other countries it decreased by over 5%, presumably due to lockdown measures decreasing the non-COVID mortality. Moreover, we found that while some countries have been reporting the COVID-19 deaths very accurately, many countries have been underreporting their COVID-19 deaths by an order of magnitude or more. Averaging across the entire dataset suggests that the world’s COVID-19 death toll may be at least 1.6 times higher than the reported number of confirmed deaths.
Contains a summary for each country

https://www.medrxiv.org/content/10.1101 ... 21250604v1
fascinating - thanks as ever for posting this and various other papers.

Good to see all the countries together, along with the excess death per 100,000 figure (in black, top right of the four on each graph). I know the FT and others were doing similar but haven't seen anything from them for a while.

Image

Also, for the "Lockdowns cause deaths" brigade:
Our data and analysis support the view that excess mortality during an epidemic outbreak can be taken as a proxy for COVID-19 mortality (Beaney et al., 2020). Indeed, countries that implemented stringent lockdown and social distancing measures in the absence of COVID-19 community spread, such as Australia and New Zealand, showed a consistent decrease in all-cause mortality, likely due to reduced influenza transmission (Kung et al., 2020), suggesting that lockdown measures on their own decrease — and not increase — the death rate. This is in agreement with the evidence that lockdowns reduce violent and accidental deaths (Calderon-Anyosa and Kaufman, 2020). Together, this suggests that lockdowns do not contribute to excess mortality. On the other hand, some countries with a severe COVID-19 outbreak reported more COVID-related deaths than the value of excess mortality (e.g. France and Belgium, with undercount ratio below 1), strongly suggesting that most excess deaths even during the local epidemic outbreak are due to COVID-19. In fact, these arguments show that excess mortality may even underestimate the COVID-19 death toll.

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Re: COVID-19

Post by shpalman » Fri Feb 12, 2021 5:09 pm

I wonder what subtle analysis of the case numbers having been consistently falling for the past month leads them to suggest that R is less than 1?

More seriously how do they get that it was more than 1 up until now, despite cases halving roughly every two weeks?
molto tricky

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Re: COVID-19

Post by lpm » Fri Feb 12, 2021 5:47 pm

They repeatedly announce stuff that comes out of their models, without bothering to look out the window and consider if it agrees to the real world. Makes them look stupid, journalists give confused write ups and the public ends up misinformed.
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 bob sterman » Fri Feb 12, 2021 6:47 pm

shpalman wrote:
Fri Feb 12, 2021 5:09 pm
I wonder what subtle analysis of the case numbers having been consistently falling for the past month leads them to suggest that R is less than 1?

More seriously how do they get that it was more than 1 up until now, despite cases halving roughly every two weeks?
It's baffling.

The only way I can think of to calculate a national R value > 1.0 while cases are falling nationally, would be by calculating R as the mean of a load of R values for smaller geographical areas (e.g. counties/regions) - without weighting them according to population.

E.g. if R was < 1.0 in Greater London, West Midlands, Greater Manchester etc but R > 1.0 in Northumberland, Cumbria, Shropshire etc - and these areas were getting weighted equally in the calculation.

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Re: COVID-19

Post by jdc » Fri Feb 12, 2021 7:23 pm

I thought the traditional method was to use 3-week old data for your calculation but not mention that fact when you tell everyone what you reckon R 'is'.

In shpalman's link though they seem to be claiming it's based on relatively up-to-date info (up to 8 Feb) so it's possible they've now switched to the Sterman Method.
Sage based its analysis on the latest data available up to 8 February, including hospital admissions and deaths, as well as symptomatic testing and prevalence studies.

It estimates the R value is below 1 in all NHS regions of England.

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Re: COVID-19

Post by basementer » Sun Feb 14, 2021 6:29 am

Three cases found in the community, so Auckland locks down by two levels, the rest of the country one level, as of midnight tonight. To be reviewed every 24 hours.
I think most people I know would be OK with acting fast and waiting for the all-clear.
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Re: COVID-19

Post by Martin_B » Sun Feb 14, 2021 7:02 am

basementer wrote:
Sun Feb 14, 2021 6:29 am
Three cases found in the community, so Auckland locks down by two levels, the rest of the country one level, as of midnight tonight. To be reviewed every 24 hours.
I think most people I know would be OK with acting fast and waiting for the all-clear.
Good luck with it, basementer. Our 5 day lockdown seemed to work well.
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Re: COVID-19

Post by shpalman » Sun Feb 14, 2021 9:04 am

molto tricky

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