Daily numbers, graphs, analysis thread 19

[BigChocFrenzy]

Daily numbers, graphs, analysis thread 19

Welcome to thread 19 of the daily updates

Resource links:

Welcome to thread 18 of the daily updates

Resource links:

Uk dashboard deaths, cases, hospitals, tests - 4 nations, English regions & LAs
Imperial UK weekly LAs, cases / 100k, table, map, hotspots
Modelling real number of infections February to date
MSAO Map of English cases
Cases Tracker England Local Government
ONS MSAO Map English deaths
CovidMessenger live update by council district in England
Scot gov Daily data
Scotland TravellingTabby LAs, care homes, hospitals, tests, t&t
PH Wales LAs, tests, ONS deaths
NI Dashboard
Zoe Uk data
UK govt pressers Slides & data
ICNRC Intensive Care National Audit & Research reports
NHS t&t England & UK testing Weekly stats
R estimates UK & English regions
PHE Surveillance report infections & watchlists each Thursday
ONS England infection surveillance report each Friday
Datasets for ONS surveillance reports
ONS Roundup deaths, infections & economic reports
ECDC rolling 14-day incidence EEA & UK
Worldometer UK page
Our World in Data test positivity etc, DIY graphs
FT DIY graphs compare deaths, cases, raw / million pop
Covidly.com world summary & graphs
Alama Personal COVID risk assessment

⏭ Our STUDIES Corner ⏮

We welcome factual, data driven, and civil discussions from all contributors 📈 📉 📊 👍

In my borough apparently we are seeing a 1.2 % positivity rate which suggests a lot of unnecessary testing.

4422 cases today for the UK. 27 deaths.

The UK has a policy of regularly testing large numbers of asymptomatics, in hospitals and in care hospitals. According to Dido Harding that will soon compromise 50% of all testing capacity. For that reason I’d expect the positivity rate to be quite low and for it to appear like there’s mistargeted testing, when in reality they want to avoid the virus spreading in healthcare settings again.

I do wonder if Johnson will announce anything after his weekend talks or the media will die down and we’ll carry on with local restrictions.

Thanks for insightful posts on NYC BigChoc and Sunshine

@wintertravel1980 I notice that article doesn't mention any punitive measures for the idiots involved?
There's students in Manchester now isolating after testing positive after the big party they had last week.
If there's no consequences then people will continue being selfish.

This is such a depressing map - the lighter the colour the harder it is to get a test right now. Well done to the times for pulling that data together. Scotland have focussed their tests where they have an outbreak (Glasgow and the west) England appear to be doing the opposite!

@Toomanyapplesinthefruitbowl

This is such a depressing map - the lighter the colour the harder it is to get a test right now. Well done to the times for pulling that data together. Scotland have focussed their tests where they have an outbreak (Glasgow and the west) England appear to be doing the opposite!

No wonder why our positives have gone right down, if this is correct that's very worrying.

Is there still a lag on the reporting of deaths over the weekend like there was before or are they pretty 'up to date' now?

Is there data for how many tests each region has access to?

Just wondering re the map above - clearly they need to get more tests to the areas of higher prevalence but also wondered is it that those areas already have much higher numbers of tests but it’s still nowhere near enough?

@wintertravel1980 - to be clear I wasn’t suggesting the reduction in London’s testing capacity was wrong in anyway.

Anecdota too but I don’t know any ‘worried well’ testing but many families who have been unable to get tests for children who do have the current listed symptoms this week ( particularly those without access to cars).

@BighouseLittlemouse

Is there data for how many tests each region has access to?

Just wondering re the map above - clearly they need to get more tests to the areas of higher prevalence but also wondered is it that those areas already have much higher numbers of tests but it’s still nowhere near enough?

That would be the kind of useful data that you’d hope Dido Harding would be able to provide, but I’m not holding out much hope given they can’t even tell how many people want a test but can’t get one

This thread has moved really fast!

Back at the start of the pandemic there was a lovely animation which basically showed that the virus spread less rapidly when more people were immune (whether from infection or vaccination). That is why even exponential growth eventually slows. That did assume that you couldnt carry infection in those scenarios and I dont think we're 100% sure on that.

So I do expect areas hit hard to have slower rises this time than they would otherwise have had. It helps that many of those most likely to spread the infection (those who have lots of contacts) are more likely to have been infected in the first wave.

NHS staff had a really hard time in the first wave and are in some cases suffering PTSD. They arent always thinking as clearly as usual.

The second wave - and it's certainly started in the north - is by no means uniform. Personally I think businesses in the South West should be pretty annoyed if the government applies the same restrictions to them as to Bolton. If the chancellor is stupid enough to go along with it again he is not doing his job.

I'm a bit shocked by your comments! Are you implying that NHS staff have been so traumatized by the first wave of Covid that they can't do accurate modelling/planning/ decision making?
I'm also unconvinced that the level of immunity is anywhere near high enough to make much difference to the speed of spread, even in London.

If the chancellor is stupid enough to go along with it again he is not doing his job.

Unfortunately, the person in charge is Boris. I am not sure the chancellor will be able to override him.

It looks like Boris has been convinced all along he can deal with the pandemic by just "following the science". If only life had been that simple... All the science UK had been relying on prior to the March first wave was based on flu research and some of the early recommendations made by SAGE turned out plain wrong. Banning mass gatherings earlier would have made a big difference (non-locked down Sweden did it on March 11!), closing borders would have also helped, etc.

Now Boris seems to be terrified of repeating the mistake of not acting early and might follow the most conservative advice without due considerations for the economy. However, since he is in charge, he cannot listen to only one side (epidemiologists) - he has to balance risks. If I remember correctly (BigChoc will probably know better), Merkel had to override her medical advisor on school opening. He was advising against it back in spring - she went ahead. It was a risk based decision.

Boris, however, will not have the guts to go against his scientific advisors so if they strongly recommend a national lockdown ("because it's the only thing that works"), he is likely to go with the flow.

People in South West will have all the rights to be furious.

Chancellor's can always resign - might be a good move for someone who clearly has his eye on the top job one day.

The news today reported on a university that is screening all its students, using it's own lab. There were comments about how they work with the NHS, it's the sort of capacity the government would have drawn on if it wasn't dogmatically bent on giving contracts to its chums.

@Shitfuckoh

Is there still a lag on the reporting of deaths over the weekend like there was before or are they pretty 'up to date' now?

Yes there is still a lag in deaths (although not as dramatic as before as overall figures are lower) but the lag is in the figures published on sunday and Monday (which are the deaths reported on sat and Sunday respectively). The figures published on a Saturday are those reported on Friday so these don't lag (death reporting is more efficient on a weekday basically)

"If I remember correctly (BigChoc will probably know better), Merkel had to override her medical advisor on school opening. He was advising against it back in spring - she went ahead. It was a risk based decision."

That was the leading virologist Drosten, recommending in May that Merkel try to get R down to about 0.2 or 0.3

I don't think he had a problem schools reopening pt on 4 May, as that was all that was reopening for 2 weeks.
What he advised against was then reopening shops, gyms and outdoor restaurants from 16-18 May

Merkel took the correct decision then imo,
both to reduce economic damage and because lowering R further always seemed impractical as Germany has 9 land borders and hence can't possibly be sealed off like NZ

Drosten said she understands the science very well
However, Merkel, like any leader, also has to consider the economy, education etc whereas public health experts focus on their subject

Current policy seems to be accepting that cases will slowly rise, in exchange for keeping the economy roaring back.
That is a gamble, but not as much as it would be in the UK, as the German health system has huge spare capacity even in normal times.

Another leading virologist here, Hendrik Streeck (who ran the Gangelt study) has been calling for a new approach
and for scientists to be allowed to take risks and make mistakes

He wasn't specific, but I gather he wants to relax SD further, or at least not tighten it up unless deaths start to rocket again.
However, some scientists may naturally be afraid of the consequences if they are wrong and a lot of deaths results; hence his wish for allowing mistakes.
Hmm, good luck with that

Graph by @UKCovid19Stats showing what the positive trend would be if we were still testing the same way as April.

We've never picked up more than half of all the infections based on the surveillance studies. My estimate of cases at peak epidemic is around 100,000. So I think they have the bars too high in the early days.

My estimate of peak UK cases around end March is 200,000

calculating not just test positivity and cases then,
but also using the 22 days of deaths > 1,000 and the 1,445 peak on 8 April.

However, I may be using a rather optimistically low IFR - for the UK, at least -
considering the figure then of only 33% being discharged alive from NHS ICU (it's now 54% according to ICNARC)

I see the different models in OurWorld estimate 100k - 180k, which illustrates the degree of uncertainty

That graph is great BCF however - and please correct me where needed! - it seems to show we haven't shown signs of exponential growth but rather rumbling for 4-5 weeks. It doesn't seem to show we are or even may get that sudden exponential growth again?

I obviously know it's possible but I'm wondering if there's anyway of predicting or plotting based on previous data?

Execellent, informative thread about NHS knowledge gained and plans from an ICU doctor in London's East End:

threadreaderapp.com/thread/1307242471789912065.html

Just had a notification for Greater Manchester. Such dire numbers.

@itsgettingweird

That graph is great BCF however - and please correct me where needed! - it seems to show we haven't shown signs of exponential growth but rather rumbling for 4-5 weeks. It doesn't seem to show we are or even may get that sudden exponential growth again?

I obviously know it's possible but I'm wondering if there's anyway of predicting or plotting based on previous data?

... The graph illustrates the relative scale of where we are now compared to then

In March-April we had a genuine emergency that needed the drastic measures of lockdown

atm, we have a situation potentially serious, because of the risk of exponential growth taking off,
but not looking serious in the immediate future

However, to analyse current trends in more detail,
I prefer to plot the 7-day rolling average of cases / million population,
switch to log scale and erase the earlier part of the curves, see attached

@alreadytaken I don't know if they are the only ones, but Cambridge University is testing all students in college accommodation each week using their own labs - www.cam.ac.uk/coronavirus/stay-safe-cambridge-uni/get-tested

To achieve it, they are pooling students samples and batch testing them so that they only need about 2000 tests a week. If a batch tests positive they then test individually. They are batching students who live together as they'd all have to self isolate if one tested positive anyway. I don't know if there's a good reason the rest of the country can't batch up households too to use testing capacity more efficiently?