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Daily numbers, graphs, analysis thread 20

970 replies

BigChocFrenzy · 22/09/2020 22:46

Welcome to thread 20 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 reports & LA Local Watchlist Maps by LSOA
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 GB test positivity etc, DIY country graphs
FT DIY graphs compare deaths, cases, raw / million pop
Alama Personal COVID risk assessment
Local Mobility Reports for countries
UK Highstreet Tracker for cities & large towns Footfall, spend index, workers, visitors, economic recovery

Our STUDIES Corner

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

Request to posters giving a link:
Please do so in full, so people can see in advance what they are clicking
Also at least a brief title so we know what the link is about

OP posts:
Thread gallery
82
BigChocFrenzy · 23/09/2020 08:29

[quote Eyewhisker]github.com/dmcalli2/covid19_yll_final/blob/master/Scripts/Addendum.md[/quote]
....
Executive summary:

•	<span class="italic">Following additional analyses, using a range of national life tables in addition to the Global Burden of Disease (GBD) 2010 life tables which we used previously, the average years of life lost (YLL) due to COVID-19 remained above 10, even after adjusting for the number of long-term conditions</span>

•	The number and type of long-term conditions has a large impact on YLL for individual patients, but a minimal impact on the overall average YLL

•	<span class="italic">The comparatively small average overall impact is largely due to the fact that long-term conditions in general and multimorbidity in particular (the presence of two or more long-term conditions) are common in the older general adult population, not just among people who died with COVID-19</span>
OP posts:
BigChocFrenzy · 23/09/2020 08:33

....
Since inclusion in the Welsh dataset simply required having been being registered with a participating general practice (GP),
and since all care home residents in the UK are registered with a local GP, people resident in care homes will have been included in our survival models.

Moreover, although the comorbidity prevalence data from the ISS reports was based solely on hospitalised patients, the age-sex distribution from the ISS reports included anyone who died from COVID-19 provided they had tested positive for SARS CoV2.
Therefore, care home residents will have contributed to the average YLL in the estimates we produced.

Nonetheless, we strongly agree that care home residents, are a special population, in whom more severe disease, multimorbidity and frailty are likely to be commoner.
We also agree that there are good biological reasons for suspecting that care home residents may be over-represented among COVID-19 deaths compared to other causes of death (because it is an infectious disease and people in care homes are in a communal residence),
and that the inclusion of more care home residents would likely have lowered the YLL in our analyses.

Therefore, we would argue that the best approach for determining life expectancy in this group would be to estimate it using data which includes care home residency status.

OP posts:
RedToothBrush · 23/09/2020 08:37

This is an overall national tracker for the positivity rate.

You can see how the increase started around week ending 24th Aug

Daily numbers, graphs, analysis thread 20
RedToothBrush · 23/09/2020 08:47

Going back to the PHE surveillance report from Friday, I've picked up another couple of graphs worth posting - my circles on the chart:

The chart on outbreaks in institutions, doesn't show significantly more cases for the previous four weeks in educational settings in the NW compared to other regions. I think it worth keeping an eye on the numbers on this.

The place that is showing the biggest problem with most institutions affected is worrying as its care homes. But these are the most heavily monitored place so perhaps thats also a good sign.

The other thing that I find noticable in this chart is the NW has a higher number of outbreaks than anywhere else linked to food outlets / restuarants.

Daily numbers, graphs, analysis thread 20
Oldbutstillgotit · 23/09/2020 08:48

Thank you for the new thread . I don’t really contribute but I appreciate the calmness here . I am in Scotland and our new restrictions are a bit stricter than England.

Castiel07 · 23/09/2020 08:49

Do you think the new measures will help keep the virus down (England)?
I honestly don't think it will, and we will end up with more restrictions in the coming weeks.
My mum is in a care home she is only in her 60s but due to MS she is practically bedbound.
They had covid in May and it was rife In there, luckily she didn't catch it.
I know a few people who work in care homes also and the turn around for testing is taking far to long.
I'm in a low virus area (was in an enhanced support area though a few weeks back).
And people are finding it extremely hard to get a test, so are our numbers down because they just are or is it because people just can not get a test?

RedToothBrush · 23/09/2020 08:58

But if you look at where most people are picking up the virus, (do read the blurb above the graph as it excludes certain things from this graph) it does seem to exclude travel as a significant driver.

Its hard to argue against where the restrictions are being focused tbh.

I definitely think again its worth looking at this again with the next couple of reports because this is where - if restrictions are working and compliance is ok - you might see a change in the figures (depending on how numbers in areas without restrictions go).

Daily numbers, graphs, analysis thread 20
alreadytaken · 23/09/2020 09:08

Really wish more people understood numbers.

If you start messing around adjusting years of life down because some are care home residents than you also need to adjust UP for the non care home residents - and by quite a lot as average death rates include those in care hours. Yes it will have an impact but I bet the "back of an envelope" calculations didnt do that and the net effect will be small. It is not going to drop from 10 to 7 years.

If you catch Covid from someone in your household where did they get it? I would suggest it's often from a holiday, pub or restaurant. Certainly in my area it's known that rates rose after a family brought it back from abroad.

BigChocFrenzy · 23/09/2020 09:11

It would be useful to have somehow included the % of contacts that are part of a large outbreak at a care home, meat plant etc
currently excluded from that table

Maybe too complicated to calculate in a suitable way to fit that table, but at least useful to know % of cases & contacts

OP posts:
BigChocFrenzy · 23/09/2020 09:15

@alreadytaken

Really wish more people understood numbers.

If you start messing around adjusting years of life down because some are care home residents than you also need to adjust UP for the non care home residents - and by quite a lot as average death rates include those in care hours. Yes it will have an impact but I bet the "back of an envelope" calculations didnt do that and the net effect will be small. It is not going to drop from 10 to 7 years.

If you catch Covid from someone in your household where did they get it? I would suggest it's often from a holiday, pub or restaurant. Certainly in my area it's known that rates rose after a family brought it back from abroad.

.... If we divide deaths into care home and non care home,

then the average care home death would lose considerably < 10 years, considering the average stay in normal times,
while the non care home deaths, which are the (slight) majority would lose > 10 years, as they would exclude most of the frailest victims

OP posts:
RedToothBrush · 23/09/2020 09:16

@Castiel07

Do you think the new measures will help keep the virus down (England)? I honestly don't think it will, and we will end up with more restrictions in the coming weeks. My mum is in a care home she is only in her 60s but due to MS she is practically bedbound. They had covid in May and it was rife In there, luckily she didn't catch it. I know a few people who work in care homes also and the turn around for testing is taking far to long. I'm in a low virus area (was in an enhanced support area though a few weeks back). And people are finding it extremely hard to get a test, so are our numbers down because they just are or is it because people just can not get a test?
One of the things we saw in April/May is once the virus gets into a care setting it keeps the R rate high because so many people also get it in that setting.

So you might see a couple of things happening: the numbers could stay high but the restrictions could still work.

Thats why I'm saying to look at the data relating to WHERE as much as HOW MANY.

As for you question about low numbers but hard to get a test, the answer is in the postivity rate (which I can't get a full break down by all councils atm).

By region the week 37 positivity rate was as follows:
East Midlands 1.4%
East of England 0.8%
London 1.8%
North East 2.4%
North West 3.7%
South East 0.9%
South West 0.6%
West Midlands 1.9%
Yorkshire and Humber 1.5%

(remembering when you see those figures that the NW has 30% of cases but only 15% of testing capacity).

SistemaAddict · 23/09/2020 09:18

It's interesting how rates increased 2/3 weeks after shielding ended and the general population had been on holidays during the summer school holidays. People would have been moving around the UK a lot more during August and then schools and workplaces went back and boom. It will be very interesting to look back on this in years to come and see what the research shows.

BigChocFrenzy · 23/09/2020 09:19

It really needs professional statisticians and actuarial information to calculate average loss in years,
(and it may even make sense to split care home and non care home for theese calculations)

So far, the most informed estimate seems from the govt statisticians and the lost QALYS, which has a different aim

OP posts:
RedToothBrush · 23/09/2020 09:21

Sorry should say thats Pillar 1 only.

Pillar 2 figures are worse:
East Midlands 4%
East of England 2.3%
London 4.6%
North East 4.6%
North West 7.2%
South East 1.9%
South West 1.5%
West Midlands 4.9%
Yorkshire and Humber 6.8%

Anything above 5 should be taken seriously.

The NW does have a clear problem with track and trace imho.

BigChocFrenzy · 23/09/2020 09:23

Why the same measures may not have the same effect on different countries

  • there would be some difference too between regions of a country, e.g. London vs NW

e.g. some countries have more "innate SD",
from low population density both within a country & within the average household

Adam Kucharski @AdamJKucharski

... another feature of Sweden that stands out is household size
- it's smallest average in Europe, with majority single occupant
(ec.europa.eu/eurostat/web/p…).

What effect could this have on transmission? 1/

The estimated risk of transmission per contact is higher within household than outside household
(thelancet.com/journals/lanin…).

This means it can be helpful to think of an epidemic as a series of within-household outbreaks,
linked by between household transmission... 2/

If the average size of an outbreak in a household is H,
and each infected person within a household spreads infection to C other households in community on average,

then we can think of the
'household' reproduction number as equivalent to H x C 3/

So if household size is smaller in a particular location,
we'd expect H to be smaller,
and hence lead to a lower reproduction number,
even if C is the same... 4/

Now, of course, there are many, many other factors that influence transmission
(behaviour, control measures, immunity, perhaps other seasonal effects).

And it's important to compare countries & understand what might be happening
– and what control measures could be adapted... 5/

But before claiming 'what country X is doing would have same effect here',
we need to consider whether there are key differences in population stucture between countries that might change effectiveness if same measures used elsewhere. 6/6

Daily numbers, graphs, analysis thread 20
OP posts:
BigChocFrenzy · 23/09/2020 09:24

Do we have stats on household size for regions and much more locally for areas within e.g. the NW ?

OP posts:
BigChocFrenzy · 23/09/2020 09:32

As well as cases - and deaths - being significantly higher in areas of greater deprivation,
the ONS found a striking difference between urban conurbations and sparsely populated rural regions - which may also have considerable poverty

As with countries, population density is a major factor in how an epidemic progresses within regions and localities

Daily numbers, graphs, analysis thread 20
OP posts:
RedToothBrush · 23/09/2020 10:03

BCF I wonder if there is something in the idea of 'close community' though.

We know that voting at the last election (and going back to 2016) did feed a lot on this idea of the 'death of the local community' and this notion of community spirit dying.

I wonder if places with higher levels of tight community and the importance of community are having more of an issue simply because of people living closer together to family and putting more emphasis on the importance of friends.

I know northern provincial medium sized towns scored particularly highly on this during election time (though I can't for the life of me think where I'd source data to reflect this). And tbh these are areas that seem to be doing poorly at the moment - they have high levels of deprivation so you'd expect more cases anyway - but it could be something to with this too.

It may not be a pure lack of compliance that the problem either. It could be more connectivity even within the rules/guidelines as they stood.

You might see people who have kept to the guideline of 6 throughout (regardless of the law allowing more) - but have done this multiple times with different groups in a short space of time. So a community where everyone knows everyone else you'd expect to be harder hit than a quiet surburban estate where no one ever talks to anyone else and you don't know any of your neighbours at all.

I also know that where I live I can't go out without a very high chance of seeing someone I know. It was very hard even at the height of lockdown to just go for a walk without saying hello to someone you knew and its often quite hard to just nod say hi and carry on without saying a few words to each other because of social convention and the notion of politeness. We tried to keep this to a minimum but it was very hard.

You might also get bigger kick back and unwillingness to comply in areas like this, and greater resentment of restrictions 'from people not like us from London' because of this feeling of the 'death of the community' being driven by London centre politics.

I'm just speculating here. I think its easy to dismiss along stereotypes of the north being deliberately rebellious and having disrespect for the rules but I do think that if this is the case, its a much more complex issue about the way we live and how communities are interconnected. One thats been an issue floating around and no one really has managed to get to grips with properly.

If this is the case, you might want to look at voting patterns elsewhere in Europe to see if you are getting a similar thing with provincial towns having higher levels of rising rates compared to more rural areas and more metropolitian areas. I'm guess that France wouldn't be the worst place to compare with.

RedToothBrush · 23/09/2020 10:11

@BigChocFrenzy

Do we have stats on household size for regions and much more locally for areas within e.g. the NW ?
Hmm. I thought i posted this, but my post seems to have disappeared.

Nope. There doesn't appear to be anything significant in this.

Firstly the data is dominated by the fact that a significant number of households are lone households. And lone households are more common the further north you go.

Secondly the average size of households doesn't seem to shift significantly by region.

In terms of multi generational households, these represent only a very small percentage of the number of households:
www.ons.gov.uk/peoplepopulationandcommunity/birthsdeathsandmarriages/families/bulletins/familiesandhouseholds/2019

From ONS data from last year:
Multi-family households (consisting of two or more families) were the fastest growing household type over the last two decades to 2019. They grew by three-quarters from 170,000 in 1999 to 297,000 households in 2019, a statistically significant increase. However, they represented a very small proportion of all household types in 2019 (1.1%)

Families in these households may be unrelated, for example two couples house-sharing alone or one or more couples with other adults, or may be related in some way, for example, a couple with their child and their partner.

The growth in the number of multi-family households could reflect a growth in multigenerational families choosing to live together, or out of necessity because of reasons such as housing affordability, childcare responsibilities and caring for older relatives.

London contained the highest proportion of multi-family households (2.0%), compared with the rest of the UK. Over the last five years up to 2019, the North East of England showed the largest decrease in multi-family households (0.8% to 0.2% in 2019), while the North West showed the largest increase (0.9% to 1.5% in 2019) in this household type.

Hopefully that answers the question you were after.

(This post was SUPPOSED to before my last. Which makes the last one make a little more sense for context!)

Daily numbers, graphs, analysis thread 20
Daily numbers, graphs, analysis thread 20
Daily numbers, graphs, analysis thread 20
Cornettoninja · 23/09/2020 10:12

I came across this on another site and thought it might be of interest to some of you. It’s not peer reviewed but interesting nevertheless.

www.medrxiv.org/content/10.1101/2020.09.16.20194787v1

Here we show that the transmission of SARS-CoV-2 in Manaus, located in the Brazilian Amazon, increased quickly during March and April and declined more slowly from May to September. In June, one month following the epidemic peak, 44% of the population was seropositive for SARS-CoV-2, equating to a cumulative incidence of 52%, after correcting for the false-negative rate of the antibody test. The seroprevalence fell in July and August due to antibody waning. After correcting for this, we estimate a final epidemic size of 66%

MRex · 23/09/2020 10:19

I found a new (to me) data dashboard, which looks interesting: digital.nhs.uk/dashboards/progression#dashboard. Apologies if it's already been posted.

If you click on the bubble chart regions, the table below shows each area. The triage/ cases link by area is also useful. It's Beta and asks for feedback on what we're looking for...

BigChocFrenzy · 23/09/2020 10:20

Thanks for the links on households especially, Red

OP posts:
RedToothBrush · 23/09/2020 10:22

www.birmingham.ac.uk/news/latest/2020/06/community-spirit-dwindling-amongst-British-public-during-lockdown-says-new-poll.aspx
Think this is worth reflecting on too:

A poll undertaken by Populus of 2,088 adults in the UK found that older generations and women have felt a stronger sense of community togetherness recently, compared with younger generations and men, who have not felt this to the same degree.

and

There was a decline in the value placed on the civic character strengths of ‘being of service’ and ‘having community awareness’ in the people around us, compared to the April 2020 poll. Instead, the British public placed greater value on ‘being resilient’; this is suggestive that the public mood has moved to one of self-preservation over community togetherness.

As we moved from this idea of we are all in this together to one of the government 'abandoning us' or not caring about 'people who live in the real world' etc etc you might get kick back.

It would be interesting to see polling on views on this.

BigChocFrenzy · 23/09/2020 10:24

@MRex

I found a new (to me) data dashboard, which looks interesting: digital.nhs.uk/dashboards/progression#dashboard. Apologies if it's already been posted.

If you click on the bubble chart regions, the table below shows each area. The triage/ cases link by area is also useful. It's Beta and asks for feedback on what we're looking for...

.... I can't load the dashboard on iPad Sad

I get "[Tableau loading error]"

I'll send an error report to them
but could you first post a screenshot of what it should look like, pls

OP posts:
RedToothBrush · 23/09/2020 10:26

www.bbc.co.uk/news/uk-scotland-tayside-central-54261668
Covid in Scotland: Hundreds of Dundee students told to isolate

NHS Tayside is investigating a single positive case and a small number of suspected cases linked to Parker House in Dundee.

Close contacts of the positive case, who is a student of Abertay University, are being contacted.

All 500 residents at the accommodation have been asked to self-isolate until contact tracing has been completed.

That sounds like a bloody nightmare to contact trace. Imagine if a contact doesn't isolate and then later tests positive...