Daily numbers, graphs, analysis thread 23

[BigChocFrenzy]

Welcome to thread 23 of the daily updates

Resource links:

Uk dashboard deaths, cases, hospitals, tests - 4 nations, English regions & LAs
UK govt pressers Slides & data
R estimates UK & English regions
Imperial UK weekly LAs, cases / 100k, table, map, hotspots
School statistics Attendance
Modelling real number of UK infections February to date
NHS England Hospital activity
NHs England Daily deaths
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
ICNRC Intensive Care National Audit & Research reports
NHS t&t England & UK testing Weekly stats
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
Zoe Uk data
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 analytical contributions
Please try to keep discussion focused on these
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Agree @littlestpogo. The title is clear; if we don't close work nor educational settings, what's the transmission like for other settings; it is not misleading because there is no small print nor omissions, the title states what's left out. For all anybody knows, the slide before it included work and educational settings.

I don't know why it's being considered surprising in any event, given that it's the same data and roughly the same distribution I've seen on the T&T report every week.

Adam Kucharski@AdamJKucharski

Stages of epidemic normalisation:

"It won't happen"
"It's not happening"
"It's happening but it's not a big deal"

You cant just turf everyone currently in a hospital bed out on to the street, it takes time to empty out other wards. We all remember what happened last time hospitals needed to free up beds in a hurry. And the more people you cram in the more difficult infection control becomes, the more you exhaust your staff.

Rapid tests are expensive and the one I've heard about requires machines that only do a very limited number per day. So they have been trialled in some hospitals but they arent yet available in the numbers needed for mass testing.

Dont see any alternative to some strict local lockdowns and I think they need more than 3 levels. If I was in Liverpool I would be tempted by that hazmat suit.

John Roberts @john_actuary
compares hospital occupancy for the English regions compared to the April peak

also estimates occupancy for possible future scenarios of increased cases

BCF that looks about what the local news were talking about though in a slightly different format.

John Roberts @john_actuary
^I think the other tweets in that thread are really important too.
A 3rd example starts at a higher level, the 208 seen earlier this week, but is flat. You can see the occupancy soon levels off as discharges match admissions. So it's continued growth that causes the problem, not the current rate. Any time when R>1 we will see continued growth.^

This is all very mathematical, and as the CSO has found out, example projections can be open to criticism. But the message is that in the North we are not that far off from April's peak, unless we can rapidly bring R down to 1 and keep it there.

Finally, even at April's levels, we would expect deaths to be much lower (maybe by two thirds), as treatments have improved. But over-peak capacity in hospitals will start to give secondary issues, which themselves will have a negative influence on outcomes. ENDS

Given what I'm seeing and hearing both in terms of data and the acedotal mood on the ground, I've got to be honest in questioning whether it will be possible to get the R down to 1 in places like Liverpool and Knowsley. The positivity rates being so high mean the situation isn't under control and thats ultimately the problem.

Thank you for comments on lack of data for local %age positives. It’s frustrating not to know this!

Rapid tests are expensive and the one I've heard about requires machines that only do a very limited number per day.

Rapid reliable tests are expensive. Rapid less reliable tests appear to be cheaper and are widely used in some countries, e.g. Italy, US:

www.thelocal.it/20200929/covid-19-italy-plans-to-use-rapid-airport-tests-in-schools

These are the tests being used for mass screening of passengers at airports, stations and ferry terminals in Italy, but it’s important to know that they are less accurate than a PCR test.

My thinking is that while we may not want to rely on rapid tests in care homes, they might be completely fit for purpose for lower risk environments.

Latest Liverpool data:

Coronavirus cases by area
Report published 9th October 2020
Cases data from week 30th September - 6th October 2020

Data extracted covering testing up to 6th October 2020 show that the total number of confirmed cases for the last 7 days is 2987, an increase of 900 cases on the previous week. The latest weekly rate of Covid-19 in Liverpool is 599.7 per 100,000 population and the latest positivity testing rate* is 24.7%.

Of those cases where ethnicity was given, 87% people were recorded as White British and 13% people were from a Black and Minority Ethnic background. The majority of cases (61%) were in those aged under 40 years, whereas 24% cases were in those aged 40-59 yrs. Of all the confirmed cases in the last seven days 55% were female and 45% were male.

Yesterday was 24.8% so this is ever so slightly down.

I do think the ultimate problem is that until you can start getting the positivity rates under control you can't get the R number below one.

For instance, it would be a no brainer to use rapid tests to regularly test university students or older school children or employees at meat processing factories to identify potential clusters / super spreading events. We only need to pick up a few positive cases to know that there is a cluster to "bust" (using Atlantic / Japan terminology). It is not an issue if we miss even 50% of positives as long as we identify the remaining 50% and request that everyone in the cluster isolates (even if they have been tested negative).

inaccurate tests are fine outside medical settings if your infection rate is low, not much use when it's spreading rapidly. So I'd be happy to see them in use for, say, attending schools or planning a wedding in the south west but not for restaurant staff in Liverpool if I was thinking of eating out.

They’ve released all the slides from the briefing to northern MPs yesterday - the leaked one looks like it was the final one

assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/925332/Evidence_pack_parliamentary_engagement.pdf

So I'd be happy to see them in use for, say, attending schools or planning a wedding in the south west but not for restaurant staff in Liverpool if I was thinking of eating out.

I would argue that rapid tests would work even in Liverpool as long as they are performed regularly and at scale.

If you only test restaurant staff with the three symptoms, you may want to go for PCR tests to aim for maximum accuracy.

If you test everyone working in a restaurant (e.g. 10 people), rapid tests are very useful. Even if 4 people are infected and you only get 2 positives, this will highlight a cluster. You can then back trace their contacts and request that they self-isolate.

ONS infection survey is out

An estimated 224,400 people within the community population in England had the coronavirus during the most recent week, from 25 September to 1 October 2020, equating to around 1 in 240 people.

The estimate shows the number of infections has increased rapidly in recent weeks.

In recent weeks the highest rates of people testing positive for COVID-19 are among older teenagers and young adults.

There is clear evidence of variation in COVID-19 infection rates across the regions of England, with highest rates seen in the North East, North West, and Yorkshire and The Humber.

During the most recent week we estimate there were around 17,200 new cases per day.

There has been a marked increase in the incidence rate over the last six weeks.

You can swab all staff in a restaurant, process it as one test and ony test individually if you get a positive. Cambridge are doing that for their students. Higher accuracy and cheap and as you are doing fewer tests can be processed promptly. We could also be checking waste water.

Perhaps if we didnt have a private testing service we'd be doing these things.

Thanks for that @ get, what stuck me though was the bit at the end about other countries, that information is not true for France and seems incredible that they cant get that information correct. Bars shut on the 6 october in paris not two weeks ago, and restaurants are not closed. Not sure then if it accurate for other countries.

Yes, you could but both of these methods take time. The first one (if there is a positive) will require at least 2 PCRs. This is exactly the problem with the current approach - everyone still tries to preserve maximum accuracy while in fact in many circumstances it may be a secondary consideration.

The advantage of rapid testing (even if it is less accurate) is that you get results instantly.

I am sure you have already seen the article (it was referenced here by several people including the OP) but one of the "aha moments" for me was that in the trade off between timeliness and accuracy timeliness may be more important:

www.theatlantic.com/health/archive/2020/09/k-overlooked-variable-driving-pandemic/616548/

It is not a universal statement and i do not suggest that we all switch to rapid testing but completely disregarding it (just "because it is much less accurate) is, in my opinion, a big mistake.

@cathyandclare

Some really interesting information in there. Particularly useful that they have split the positive tests by age to now differentiate between primary, secondary and older.

Very clear that older teenagers and young adults are seeing a very significant increase. Based on that it doesn't seem as though there would be much of an argument for any further measures in Primary schools, secondary schools might need to consider some extra measures in high incidence areas.

wintertravel one you have a single positive for a restaurant the rest of the people there should be self isolating until they get a negative result. And if you are doing one swab instead of 8 or 10 you dont have the same processing delays. We have those delays because capacity is not being used well and because the NHS is not allowed to buy in capacity. If you can test accurately and promptly why would you opt for inaccurate and prompt?

Red

I saw that North-West Tonight report yesterday and yes, the peak hospitalisations figure at the first wave was 3065. They estimate it could be the same in 17-22 days from now, and at double that within a month.

I'm in Sefton. Rates bounding up all the time. I have a very vulnerable close relative in hospital. As you can imagine, I'm not sleeping much for worry.

The ONS survey is quite depressing.

South East though looks good. Wales and Northern Ireland seem to be levelling off (even though the samples are very small).

The most interesting - and depressing - part of that briefing is that rates are rising in older age groups. It was to be expected this would happen, especially where grandparents do child care, maybe for those young children.

If you can test accurately and promptly why would you opt for inaccurate and prompt?

As per the article - to identify clusters/super spreading events even more promptly and to add onto the existing capacity.

Even a 24 hour delay with the timely processed PCR tests may slow down "cluster busting".

The rationale behind cluster busting is that identifying two or more positives in the same setting is a much bigger red flag than picking up a single infection. If we know two people in the restaurant are positive, it is a potential super spreading event which will require extra focus (e.g. self-isolating individuals may need to be visited/checked on to ensure compliance with the rules).

Of course, in the ideal world we should always be testing accurately, timely and at scale but no other country is in this scenario. Everyone has to operate within a limited testing capacity and make their own decision on trade offs.

In Italy they are trialling a non invasive saliva test (initially the trial is being used for testing children).
mobile.twitter.com/marklowen/status/1314214810725150722

Report about hospital beds.

https://www.theguardian.com/world/2020/oct/08/hospitals-in-north-of-england-to-run-out-of-covid-beds-within-a-week?CMP=ShareiOSAppp_Other

Does anyone know if it's true that there is now more in hospitals with covid than there was when we went into lockdown in March?

If it is true then doesn't that mean that's pretty much it and now it'll get out of control again since we're doing less restrictions now than we did in March