SARS-CoV-2 testing

Covid-19 discussion, bring your own statistics
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Re: SARS-CoV-2 testing

Post by headshot » Thu Aug 06, 2020 11:19 am

Kings College Covid-19 app estimates 2110 new cases per day.

https://covid.joinzoe.com/data#daily-ne ... source=App

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Re: SARS-CoV-2 testing

Post by Bird on a Fire » Thu Aug 06, 2020 12:13 pm

lpm wrote:
Thu Aug 06, 2020 8:28 am
It would be rational for young people to go to pubs - very low risk - but fewer 50 year olds. Social get-togethers are group decisions, so six 20 year old friends might agree to meet up in a pub, but in a group of six 50 year olds two might veto the decision so the entire group goes to a garden BBQ instead.

John Burn-Murdoch has the charts of activity:
https://twitter.com/jburnmurdoch/status ... 1873455110

Image

It would be very useful to see something like this split by age grouping. Anecdotally, it's young people out and about.

Economic factors are also relevant. With the end of the furlough scheme and job losses, millions won't be able to afford shopping and restaurants and pubs. This might shift the mix.
Interesting the way that footfall seems to have plateaued even though spending continues to increase.

Is this because:
a) the UK basically has two populations, only one of which is willing to go out to pubs and restaurants during an ongoing deadly pandemic,
b) the new distancing arrangements mean that everywhere that's open is now operating at maximum capacity, and no further increase in footfall is possible,
or (c) both/neither/something else?
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Re: SARS-CoV-2 testing

Post by Lew Dolby » Thu Aug 06, 2020 1:17 pm

or people are staying longer in pubs and restaurants so footfall stays same but spending increases /theory/
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Re: SARS-CoV-2 testing

Post by lpm » Thu Aug 06, 2020 3:31 pm

If you're drinking out /eating out budget is X per month, you would be having fewer visits but could treat yourself more per visit. Picking the lobster, champagne not prosecco, etc
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Re: SARS-CoV-2 testing

Post by monkey » Thu Aug 06, 2020 3:50 pm

lpm wrote:
Thu Aug 06, 2020 3:31 pm
If you're drinking out /eating out budget is X per month, you would be having fewer visits but could treat yourself more per visit. Picking the lobster, champagne not prosecco, etc
Round my way some places have compensated for reduced capacity/footfall by increasing prices.

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Re: SARS-CoV-2 testing

Post by shpalman » Thu Aug 06, 2020 3:55 pm

lpm wrote:
Thu Aug 06, 2020 3:31 pm
... champagne not prosecco, etc
You mean people would deliberately go for the worse option just because it costs more?
molto tricky

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Re: SARS-CoV-2 testing

Post by shpalman » Thu Aug 06, 2020 5:53 pm

shpalman wrote:
Thu Aug 06, 2020 9:12 am
Fine, the number of cases in the UK isn't increasing. It was always that high but testing was sh.t. Well, it's still sh.t, but getting a bit less sh.t than before. There's no clear idea now of how many swabs have been performed, and the number of people tested was lost track of ages ago. And there's no record of how many people have recovered.

And the UK is still on over 800 cases per day and currently about 400 deaths per week (compared to an ONS death rate of about 8000-9000 per week at this time of year, so maybe 4-5% of all deaths). If you take that death rate and assume an IFR of 2.5-3.5% as the Italian antibody study suggests, you're looking at the order of 2000 cases per day (yeah I know that number applies to two weeks ago or whatever but unless deaths go down significantly in the next two weeks, it's valid now).

Because comparisons with other countries are meaningless,* Italy has a covid-positive death rate of about 50 per week at the moment. (Italy is testing 27,000 cases per day, performing 50,000 swabs, and the fraction of people tested who turn out to be positive is about 1.1% at the moment. Cases per day is going up in Italy because of a few localized outbreaks, for example in Mantova (Lombardy was actually stable at about 60 cases per day until that happened; the nearby regions of Veneto and Emilia-Romagna are increasing but from much lower baselines).

* - Weird how the UK decided comparisons with other nations were meaningless at the point at which it started to obviously do worse than other nations.
Well I plotted the number of swabs and the number of cases per day on axes such that we can see whether cases are really going up because of increased testing. (The lines are 7-day moving averages to smooth out the weekly variation).
UK-cases-vs-tests.png
UK-cases-vs-tests.png (22.82 KiB) Viewed 595 times
I notice that the older swab numbers I just got from coronavirus.data.gov.uk are somewhat lower than the numbers given at the time. For example, I had 10,340,511 on the 4th of July but now the number on that day is 7,985,271.
molto tricky

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Re: SARS-CoV-2 testing

Post by raven » Fri Aug 07, 2020 11:37 am

shpalman wrote:
Tue Aug 04, 2020 4:39 pm
7-day average cases per day has increased from about 600 to about 800 in the UK during July.

The git I used for the numbers isn't updating anymore.
Probably because the gov.uk page has completely changed. Again. (This one: https://coronavirus.data.gov.uk/cases)

Before they changed it you could download the whole data set for UK, the 4 nations,Upper tier & Lower tier local authorities, the whole shebang. I was using it to look at cases in local areas. Now if you download the data you seem to only get the UK figures.

But there's a drop down menu at the top of the page that you can use to pick a local area and it'll show you the local figures in a nice graph, which is pretty handy and a lot less effort for me. Plus it's nice to see figures for hospital occupancy, which Scotland have been doing for ages.

ETA: Ah-ha. You can get local figures by date if you switch to a local area first, and download the graph data. But only one local area at a time.

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Re: SARS-CoV-2 testing

Post by Woodchopper » Tue Sep 01, 2020 10:02 pm

Seroprevalence of SARS-CoV-2 in slums and non-slums of Mumbai, India, during June 29-July 19, 2020
https://www.medrxiv.org/content/10.1101 ... 20182741v1
Results: The positive test rate was 54.1% (95% CI: 52.7 to 55.6) and 16.1% (95% CI: 14.9 to 17.4) in slums and non-slums, respectively, a difference of 38 percentage points (P < 0.001). Accounting for imperfect accuracy of tests (e.g., sensitivity, 0.90; specificity 1.00), seroprevalence was as high as 58.4% (95% CI: 56.8 to 59.9) and 17.3% (95% CI: 16 to 18.7) in slums and non-slums, respectively.

Conclusions: The high seroprevalence in slums implies a moderate infection fatality rate. The stark difference in seroprevalence across slums and non-slums has implications for the efficacy of social distancing, the level of herd immunity, and equity. It underlines the importance of geographic specificity and urban structure in modeling SARS-CoV-2.
Prevalence as high as 58% would argue against the modeling which suggested that herd immunity could be achieved with as low as 20% infected.

The low IFR could be more evidence that people whose immune systems encounter a lot of infections are much better able to fight off Covid without getting very ill. Or maybe the slum dwellers are all young.

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Re: SARS-CoV-2 testing

Post by Millennie Al » Thu Sep 03, 2020 3:15 am

Woodchopper wrote:
Tue Sep 01, 2020 10:02 pm
The low IFR could be more evidence that people whose immune systems encounter a lot of infections are much better able to fight off Covid without getting very ill. Or maybe the slum dwellers are all young.
Or it could be evidence that if you don't have a strong immune system then living in a slum will have killed you long before Covid-19 came along to try.
Covid-19 - Don't catch it: don't spread it.

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Re: SARS-CoV-2 testing

Post by Woodchopper » Thu Sep 03, 2020 3:18 am

Poop tests stop COVID-19 outbreak at University of Arizona
https://www.sciencemag.org/news/2020/08 ... ty-arizona

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Re: SARS-CoV-2 testing

Post by Woodchopper » Thu Sep 03, 2020 3:18 am

Millennie Al wrote:
Thu Sep 03, 2020 3:15 am
Woodchopper wrote:
Tue Sep 01, 2020 10:02 pm
The low IFR could be more evidence that people whose immune systems encounter a lot of infections are much better able to fight off Covid without getting very ill. Or maybe the slum dwellers are all young.
Or it could be evidence that if you don't have a strong immune system then living in a slum will have killed you long before Covid-19 came along to try.
Yes, that too.

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Re: SARS-CoV-2 testing

Post by AMS » Thu Sep 03, 2020 6:31 am

Woodchopper wrote:
Thu Sep 03, 2020 3:18 am
Millennie Al wrote:
Thu Sep 03, 2020 3:15 am
Woodchopper wrote:
Tue Sep 01, 2020 10:02 pm
The low IFR could be more evidence that people whose immune systems encounter a lot of infections are much better able to fight off Covid without getting very ill. Or maybe the slum dwellers are all young.
Or it could be evidence that if you don't have a strong immune system then living in a slum will have killed you long before Covid-19 came along to try.
Yes, that too.
Slum residents are less likely to be obese or diabetic?

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Re: SARS-CoV-2 testing

Post by Woodchopper » Thu Sep 03, 2020 7:37 am

AMS wrote:
Thu Sep 03, 2020 6:31 am
Woodchopper wrote:
Thu Sep 03, 2020 3:18 am
Millennie Al wrote:
Thu Sep 03, 2020 3:15 am


Or it could be evidence that if you don't have a strong immune system then living in a slum will have killed you long before Covid-19 came along to try.
Yes, that too.
Slum residents are less likely to be obese or diabetic?
That's likely. Though I wouldn't go as far as saying that slums in India or Africa have fewer people with co-morbidity. They are pretty unhealthy places, but as Millennia Al suggests, maybe sick people die before they get old.


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Re: SARS-CoV-2 testing

Post by Bird on a Fire » Thu Sep 03, 2020 12:01 pm

That seems quite a reasonable hypothesis, and I'm not sure there's much in your link that undermines it - especially if it's a particular coronavirus lineage endemic to Africa that contributes to immunity.
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Re: SARS-CoV-2 testing

Post by Tessa K » Fri Sep 04, 2020 11:06 am

I started feeling ill so I thought I'd be a responsible citizen and order a Covid test kit. There are none available. None. And no appointments at the only test centre I can get to (I'm in London, apparently there is only one). I really hope it's just a cold.

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Re: SARS-CoV-2 testing

Post by lpm » Fri Sep 04, 2020 11:17 am

Yep, they increased quantity at the expense of quality, then redirected capacity to the hotspots up north.

The stats for the south east and south west are so low they probably decided it's not worth bothering with much testing. But London is higher and seems to be rising.

Out of interest, what is the nearest test centre you could get to in a car?
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Re: SARS-CoV-2 testing

Post by headshot » Fri Sep 04, 2020 11:33 am

I wonder how many test kits are sitting in people's homes, unused.

Back in May/June/July the number for tests sent out were much higher than the actual number of tests being processed.

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Re: SARS-CoV-2 testing

Post by Tessa K » Fri Sep 04, 2020 11:46 am

lpm wrote:
Fri Sep 04, 2020 11:17 am
Yep, they increased quantity at the expense of quality, then redirected capacity to the hotspots up north.

The stats for the south east and south west are so low they probably decided it's not worth bothering with much testing. But London is higher and seems to be rising.

Out of interest, what is the nearest test centre you could get to in a car?
I have no idea, they don't give you that option unless you start again. I have now managed to order one, maybe they were overloaded with requests earlier. It's supposed to come within 48 hours but as that will be Sunday, it will be longer than that and then I have to book a courier to return it. So it could be a lengthy process.

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Re: SARS-CoV-2 testing

Post by lpm » Fri Sep 04, 2020 11:57 am

I'll miss him after he's died in the pandemic

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Re: SARS-CoV-2 testing

Post by lpm » Fri Sep 04, 2020 1:38 pm

Here's a chart showing "quantity up but quality down". 3.5 days median for Tessa's home test

https://twitter.com/jneill/status/1301494759383539712

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Re: SARS-CoV-2 testing

Post by Bird on a Fire » Fri Sep 04, 2020 4:38 pm

Tessa K wrote:
Fri Sep 04, 2020 11:46 am
lpm wrote:
Fri Sep 04, 2020 11:17 am
Yep, they increased quantity at the expense of quality, then redirected capacity to the hotspots up north.

The stats for the south east and south west are so low they probably decided it's not worth bothering with much testing. But London is higher and seems to be rising.

Out of interest, what is the nearest test centre you could get to in a car?
I have no idea, they don't give you that option unless you start again. I have now managed to order one, maybe they were overloaded with requests earlier. It's supposed to come within 48 hours but as that will be Sunday, it will be longer than that and then I have to book a courier to return it. So it could be a lengthy process.
This is just so weird to me. Most people here get their results in under 24 hours - you just turn up, take a test and then they call you back. If you get tested in the morning you'll often hear by the end of the day.

How has the UK not sorted this in almost 6 months? They are running a more tests - Portugal is currently running about 16,000 daily tests, so 1.6 per thousand people. compared with about 2.6 per thousand in the UK - but still.
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Re: SARS-CoV-2 testing

Post by JQH » Fri Sep 04, 2020 10:59 pm

I'm going with "gross incompetence" as the explanation.
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Re: SARS-CoV-2 testing

Post by headshot » Sat Sep 05, 2020 12:05 pm

I’ll take “corrupt privatisation of public services” please Bob.

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