Daily numbers, graphs, analysis thread 12

[BigChocFrenzy]

Welcome to thread 12 of the daily updates

Resource links:

Slides & data UK govt pressers
UK dashboard sub-national data, local authorities
Beta Uk dashboard deaths, cases, hospitals, tests, partially sub-national
UK stats updated daily by PHE & DHSC
ONS UK statistics for CV related deaths, released weekly each Tuesday
PHE surveillance report infections & deaths released every Thursday with sep. infographic
NHS England stats including breakdown by Hospital Trust
FT Daily updates
HSJ Healthcare updates
Worldometer UK page
Plot FT graphs compare countries deaths, cases / million pop. / log / linear
Covidly.com filter graphs compare countries
Plot COVID Graphs Our World in Data

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

@Firefliess I don't understand why the daily csv file on the dashboard is not presented in a more user friendly format, certainly it is quite easily manipulated if you know a bit about excel, however it would make so much more sense to be keyboard ready

I'm not quite so convinced about the Leicester perceptions. Whilst the peak was certainly earlier looking at June and into July suggests whilst the numbers have come down from those three absolute peak days they are still pretty high, particularly as compared to where Leicester was during the national peak weeks

and same graph since 1st March

Red circles my musings as to what might have transpired if the local PH team could have had access at the time of these earlier spikes.

@boys3 and @Firefliess local cases are now here down to local area - click to the right of United Kingdom

go.mumsnet.com/?xs=1&id=470X1554755&url=coronavirus-staging.data.gov.uk/cases

@alreadytaken

Hospital in Boris's constituency forced to close its a&e because 70 staff are either positive or have to self-isolate. www.ft.com/content/a2cb944b-6f81-4f51-9e65-5d9aa4bb44c6

I dont know why admissions data are so out of date now, almost like the government dont wish us to know what is going on!

It's not - if you change the location to "England", or and NHS region, you get up to date data. Continuing down overall on average.

Immunity and %

Benjamin Meyer@BenjaminMeyer85

1. Since there was a huge discussion about T-cell mediated immunity following the Lancet comment on seroprevalence by @EckerleIsabella and me,

I'd like to share my thoughts on this in the following thread:

1. There are 2 different points that are discussed at the moment:

First, there are some studies, i.e.

Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals
https://tinyurl.com/y8zzf8tw

that show a cross-reactive T-cell response in sample taken before the pandemic,
due to previous infection with common cold coronaviruses.

1. While I do trust these studies, as the authors pointed out themselves, it is in my opinion

quite unclear what this cross-reactive T-cell response means in terms of protection.

We know that despite having this specific T-cell response against common cold CoVs, we do

1. get regularly infected by them (every couple of years).

So it obviously does not prevent infection in the upper respiratory tract and also not transmission of the common cold CoVs,
otherwise they should have died out long time ago.

Therefore, I think it is save to assume that

1. if the specific T-cell response cannot prevent infection and transmission, the cross-reactive response against SARS-CoV-2 cannot prevent it either.

However, the cross-reactive T-cell response might or might not play a role in the protection of patients against severe disease^

1. Yet, as of today we do not know whether this is true or not and we need to investigate it further.

Second, it has been described that people exposed to SARS-CoV-2 only mount a T-cell response but do not produce any antibodies.
^
From this, some people like to conclude that

1. seroprevalence rates are vastly underestimating the true exposure rate and that we are closer to herd immunity that we think.

While I do believe that these patients exist, I don't think that they comprise a large proportion that dramatically changes the exposure rate.

1. In a recent paper from us,

"Validation of a commercially available SARS-CoV-2 serological immunoassay
To validate the diagnostic accuracy of a Euroimmun SARS-CoV-2 IgG and IgA immunoassay for COVID-19."
https://tinyurl.com/yb9388be

we found only 1 out of 44 mild (outpatient) cases after 21 days post onset that did not mount an antibody response.
And all asymptomatic patients in another study

"Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections"
https://tinyurl.com/y9f39twv

^mounted neutralizing antibodies.

9. These findings indicate, that we do not miss many exposed individuals in the current seroprevalence studies.^^
^
In conclusion, I think we should not fall back into wishful thinking that an underestimated T-cell immunity will resolve this pandemic.^

10.^ In the absence of more data on the potential effect of cross-reactive T-cells on the severity of COVID-19,
it is dangerous to lower our guard and loose certain measures such as wearing masks and social distancing.

[quote boys3]@Firefliess I don't understand why the daily csv file on the dashboard is not presented in a more user friendly format, certainly it is quite easily manipulated if you know a bit about excel, however it would make so much more sense to be keyboard ready

I'm not quite so convinced about the Leicester perceptions. Whilst the peak was certainly earlier looking at June and into July suggests whilst the numbers have come down from those three absolute peak days they are still pretty high, particularly as compared to where Leicester was during the national peak weeks[/quote]
Leicester are doing a lot more testing now I think, which (in the immortal words of Donald Trump) leads to more cases. However, I would hope the powers that be have a good handle on % of tests and people that are positive (which we don't know) which will give a better picture....

What is the reason for the sharp increase in Victoria, Australia?

Do they not have social distancing measures in place?

I would hope the powers that be have a good handle on % of tests and people that are positive (which we don't know) which will give a better picture....

I'm just not convinced that is yet the reality for local public health teams. Still they've been let out the deep well, the gag has been removed but the blindfold and one hand tied behind their backs still probably remain.

I think this picks up on the points in some of @BigChocFrenzy's posts today. Germany - federal structure, more localised access to information and decision making, and critically more locally raised cash. We are still largely hugely centralised, Whitehall or rather the Treasury knows best, and c.95%of funding is determined centrally.

@FATEdestiny

What is the reason for the sharp increase in Victoria, Australia?

Do they not have social distancing measures in place?

There appear to have been several main centres of infection; this breaks them down.

"The Victorian premier, Daniel Andrews, has said the outbreaks were largely caused by gatherings of extended families stretching out across multiple households and suburbs, as well as school communities and failures in hotel quarantine management."

"hotel quarantine management" - ah yes. Your security guards having sex with quarantined arrivals counts as a "failure", I think.

There is a big outbreak related to a high school. "The chief health officer has suggested that senior students with a transmission rate closer to that of adults had spread the virus around the school. He suggested that older students may not have been practising proper social distancing."

www.theguardian.com/australia-news/2020/jul/07/coronavirus-victoria-melbourne-covid-19-cases-clusters-hotspot-suburbs-hard-lockdown-family-outbreak-towers-flemington-keilor-downs-albanvale-hallam-coburg-brimbank-wollert-ascot-vale-maribyrnong-fawkner-tullamarine-truganina

Not a stat but a cute story!
I work special ed. Child today had bad stomach. RA is full PPE (mask, shield, apron, gloves and shoe covers) for any illness. Also for any personal care with a stool or if feeding due to coughing.
Non verbal student was fascinated. Trying to clean them up and they are looking right up close through the mask at my face and kept poking the mask on my nose. Think it was the whole transparent thing

Do people think the reason we are seeing cases how 8n tones where they've had no cases for 14+ days is the fact people have travelled to busy beaches etc and lots of mixing? Our cases are low still (1 a day) but that's after 16 days in my town and 18 days in neighbouring town of no cases at all.

@SummerSazz is there a downloadable file on the new dashboard yet, could not see one? The old dashboard still has a daily download file for all english LAs, - just over 48,000 delightful lines today :) and with it going back to 31st January a full timeline for every LA can be determined. That's the one that I have been using.

I see the new dashboard includes council areas in Scotland, Wales & NI now too. However still just the total cumulative case number, and has rate per 100,000 also disappeared.

tbh, I've been surprised how well local control has worked in Germany

I approved of local democracy in principle, but before this pendemic,

I always assumed that in any crisis the UK with its centralised decison-making would be able to move more swiftly
< oops I was wong there >
while Germany would be bogged down with central & regional government logjammed in debate.

Instead, Merkel / federal government has at every stage quickly agreed overall COVID policy with the 16 states,
such as the threshold case level for local lockdowns, masks on public transport etc

while the individual states retain a lot of latitude how - and also how strictly - to implement this

• which makes sense as some states had far fewer infections than others; some have different cultures

The detailled implementation and control of testing, track & trace, hospitals etc is even more locally than state level

• it's controlled in the 401 administrative districts, each averaging about 200k people,

with full local control over budget and in the case of COVID, being able to call on extra budget for measure e.g. agreed with head teachers to enable their schools to reopen.

However, another factor in this quick reaction has been that public services have been well-maintained for decades:

with large spare capacity in hospitals, spacious schools with plenty of sinks, a large pool of trained contact trackers and other local civil servants to provide extra manpower....

i.e. although services had to be built up quickly, it was from a high base level.

Interesting thread on T cell immunity @BigChocFrenzy thanks

[quote boys3]@SummerSazz is there a downloadable file on the new dashboard yet, could not see one? The old dashboard still has a daily download file for all english LAs, - just over 48,000 delightful lines today :) and with it going back to 31st January a full timeline for every LA can be determined. That's the one that I have been using.

I see the new dashboard includes council areas in Scotland, Wales & NI now too. However still just the total cumulative case number, and has rate per 100,000 also disappeared.[/quote]
You can now download from the dashboard yes, from the arrow in the top right of the graph. You can now download each local area timeline separately as well which makes it much easier to track a local area.

Try this one - you may need to copy and paste

coronavirus-staging.data.gov.uk/cases

Click on the United Kingdom at the top and it will drop down

Numbers and analysis.

Shops to schools in one train of thought.

Just knowledge of how masks are normalised everywhere else.

Mentioned schools as it was mentioned upthread and also I work in one. And yes, it's being discussed a lot in education. So many opinion piece articles include images of children and staff wearing masks.

@BigChocFrenzy

Thank you for your post concerning t-cells immunity, even if the conclusion is a little depressing (i.e. there is low confidence that there are swathes of people who have been infected but did not mount an antibody response, thus meaning we are much closer to herd immunity than serological testing indicates).

I’m thinking that drastically differing levels of infectiousness could be the real reasons we find some people not become infected where a household member has. It would be interesting to know if any studies have been done to assess viral shedding rates of infected people.

www.leicestershire.gov.uk/sites/default/files/field/pdf/2020/7/8/COVID-19-cases-leicesestershire.pdf

I've shamelessly pinched this from another thread. Would be interested to know if other council areas are publishing similar somewhat more detailed data. As far as I can see from their website nothing similar in the UTLA in which I live - although equally we're probably nearer the other end of the cases per 100,000 spectrum. So beyond the various districts in Leicestershire this goes down to MSOA. It only covers a two week period, and presumably largely driven - in terms of making this information public - by the scale of the spike in Leicester itself.

@boys3

www.leicestershire.gov.uk/sites/default/files/field/pdf/2020/7/8/COVID-19-cases-leicesestershire.pdf

I've shamelessly pinched this from another thread. Would be interested to know if other council areas are publishing similar somewhat more detailed data. As far as I can see from their website nothing similar in the UTLA in which I live - although equally we're probably nearer the other end of the cases per 100,000 spectrum. So beyond the various districts in Leicestershire this goes down to MSOA. It only covers a two week period, and presumably largely driven - in terms of making this information public - by the scale of the spike in Leicester itself.

Oh that's very good.

Nothing where I live, but then my county is getting about 10 cases a day now.

UK daily figures:

Daily deaths in all settings = 126
Cumulative deaths = 44,517

Positive daily cases (pillars 1 and 2) = 630
Cumulative positive cases = 286,979

www.gov.uk/guidance/coronavirus-covid-19-information-for-the-public

Derby Also, if I understood some other papers correctly -

T cell immunity does not actually prevent someone becoming infected

• it can only cure the infection after it has occurred.

So that person could infect others before being cured.

Immunity to becoming infected can only happen via antibodies, especially IgA

Can anyone provide me with a link to a graph showing how different underlying conditions contribute to COVID deaths pls? i.e so I can see which underlying conditions most people who have died from COVID actually had?

Many thanks

@botheritagain

Can anyone provide me with a link to a graph showing how different underlying conditions contribute to COVID deaths pls? i.e so I can see which underlying conditions most people who have died from COVID actually had?

Many thanks

This might help - section 8 deals with co-morbidities.

assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/892085/disparities_review.pdf

however, it is very difficult to extract the various interdependences between ethnic groups, jobs and predisposition to illnesses (such as diabetes) so its very difficult to say, for example, diabetes increases your risk; other factors may be more important and the diabetes is just more predominant because of the other factors.