Pure data thread #1: Daily numbers, graphs, focused analyses

[BigChocFrenzy]

This is pure data, NOT for the "worried about Corona"

We welcome calm factual, data-driven contributions
Please try to keep discussion focused on these and avoid emotional venting or politics
📈 📉 📊 👍

Resource links

UK:
Uk dashboard R, deaths, cases, hospitals, tests - by postcode, 4 nations, English regions, LAs
Interactive 7-day rolling cases map click on map or by postcode
UK govt pressers Slides & data
SAGE Table Interventions with impacts and R
Imperial UK weekly tables & extrapolations LAs, cases / 100k, table, map, hotspots
School statistics Attendance - Tuesdays
ICNRC Intensive Care National Audit & Research reports
UK testing and NHS England track & trace - Thursdays
ONS Roundup deaths, infections & economic reports
ONS England, Wales & NI Infection surveillance report - Fridays
ONS Datasets for surveillance reports
Our World in Data UK test positivity
R estimates & daily growth UK & English regions - Fridays
Modelling real number of UK infections February in first wave

England:
NHS England Hospital activity
NHS England Daily deaths
PHE COVID Clinical Risk Factors Non-respiratory by region, area, district etc
Cases Tracker England Local Government
PHE surveillance reports Covid, flu, respiratory diseases - Thursdays
CovidMessenger live update by council district in England

Scotland, Wales, NI:
Scot gov Daily data
Scotland TravellingTabby LAs, care homes, hospitals, tests, t&t
PH Wales LAs, tests, ONS deaths
NI Dashboard

COVID-19 Risk Factors
Alama Personal COVID risk assessment
PHE Clinical RFs - summary & social vulnerability indicators
PHE Clinical RFs - respiratory disease
PHE Clinical RFs - non-respiratory - CVD,T1, T2, obesity, flu jab coverage
PHE Non-Clinical RFs - deprivation, demography, economic inactivity, ethnicity
PHE Non-Clinical RFs - Vulnerable Groups (1): care / nursing home, MH, visual disabilities
PHE Non-Clinical RFs - homeless, children in care, ESL

Miscell:
Zoe Uk data
ECDC rolling 14-day incidence EEA & UK
Worldometer UK page
FT DIY graphs compare deaths, cases, raw / million pop
Local Mobility Reports for countries
UK Highstreet Tracker for cities & large towns Footfall, spend index, workers, visitors, economic recovery
NHS Triage Dashboard Pathways - triages of symptoms
NHS Triage Dashboard Progression - # people pillar 1&2, # triages

⏭ Our STUDIES Corner ⏮

tried to load the government website and the virus checker tells me it's unsafe because it has PUPs. Anyone else getting that?

Annoying that one of the graphs quoted upthread has american style dates on it - the government is outsourcing graph production now?

21,242 cases today. which is a bit of a relief after yesterday. 19th still looking quite an anomaly at 20k by specimen date - vs 11k on the 18th - maybe a weekend backlog issue of people not being able to get appts on Sat/Sun?

189 deaths.

@NeurotrashWarrior

Thanks for all your info fingon. What age are they wearing masks from and how does that work in lessons?

Hi Neurotrash. Masks are compulsory from age 11 in general, but about one third of year 7 is only 10 at the start of the academic year. So it’s a blanket «everyone in secondary schools». All teachers in primary and maternelle are required to wear them (transparent for nursery up to year 2 to help with speech). Pupils are allowed to wear them if they want. You also have to wear a mask within 100m of a school, even if you’re just walking past.

In lessons it’s absolutely fine. Occasionally I have to ask them to repeat and/or wander down the classroom to get closer so I can hear them. But I teach mfl and a lack of confidence/ mispronunciation works against us. Colleagues in other subjects have less issue. They have no problems hearing us, most teachers have loud voices . Absolutely no problems with discipline, they learned very quickly that despite the masks we can still see them chewing gum and can identify who is chatting (most of the time...). But we’ve been doing it since 18th May, and everyone’s got used to it.

Very occasionally if there is a different sound to make, I stand right away from them, take off the mask and show them what it looks like. That happens less than once a week though.

Absolutely every student wears the mask, all of our SEN students included. There are some medical exemptions possible in France, but on our entire staff and across all our pupils (collège , lycée and 4 primary schools) no one is using one.

Frazzled I think on the whole people do trust what the government is doing. There’s some complaints about being «infantilised» but people are generally very compliant.

@PatriciaHolm

The schools data is case rates per 100,000 population (not actually number of cases), fwiw.

Interestingly showing a drop (or at least a levelling) in all age groups, not just the Uni students.

Yes. And i thought it interesting that this data is only release the week after that started to happen...

Thanks fingon. As you know that's a sore point for primary teachers here. I'm sen and masks would be helpful.

Nicola Sturgeon said at the weekend that 64,000 test results would be delayed due to a Lighthouse lab issue and them being sent elsewhere, perhaps a good chunk of those went in on 19th.

Nice school charts.

@Shitfuckoh - couple of possible reasons. 1) Single staff member or child off but many others others isolating, you need 2 positive cases in an institution to class as an outbreak but could still have a significant closure (e.g. Manager who went in every room). 2) Not made it into the chart if very recent and will next week. 3) Staff covid + other illness and absence left the setting unworkable due to not enough staff even though only one covid case as above. Due only to having a toddler, I've heard of a couple of nurseries temporarily closed last winter from a combination of issues (including scarlet fever), so it does happen anyway from time to time.

Only 59.6 % of close contacts were reached by T and T in w/e October 14th : lowest ever.

Agreed red.

@Shitfuckoh

The nursery part on those figures state 1 (1) with outbreaks in brackets for the North East but I know 3 in my area alone

It's also got 0 for the NE & NW unis?

Outbreaks are where a case has been passed from child to child in the bubble or to or from staff. So there are lots of closed bubbles that aims to break the chain; that graph shows where transmission in the setting has occurred after the bubble closed.

So we had a bubble close due to a case and one case subsequently arising from that first case.

So primary is similar to secondary, but over all there are many more cases in secondary.

(I think, please someone correct me!!)

It looks like it's easier to manage the bubbles in primary than it is in secondary. But actual ability to transmit isn't lower in primary aged individuals??

I'd like to be corrected if I've read all that wrong.

@Piggywaspushed

Only 59.6 % of close contacts were reached by T and T in w/e October 14th : lowest ever.

This feels hard to reverse. The more it’s needed the slower the outcome. Plus it relies on people a lot.

Maybe being pessimistic. Hope so

Bubbles that closed this week or last week won't yet be showing if they've created a cluster

Lighthouse lab delay shouldn't effect specimen date just report date. Suspect a Monday morning effect (people hoping they'll shake off that cough over the weekend but Monday dawns and not allowed in school/work, oh balls better get a test)

Maybe being pessimistic. Hope so

Not really when you consider todays independent lead story which says the capacity for t & t was exceeded so as of yesterday they had to bring in non clinical staff from serco for roles in t & t which require clinical knowledge and skills.

Sage also said the same thst the effectiveness of t & t was likely to decline.

UK today

(previous days in brackets)

Cases 21,242 ..... (26,688 21,331 18,804 16,982 16,171 15,650 18,980 19,724 17,234 13,972, 12,872, 15,166, 13,864)
Deaths 189 ..... (191 241 80 67 150 136 138 137 143 50 65 81 87)

@Littlebelina

Lighthouse lab delay shouldn't effect specimen date just report date. Suspect a Monday morning effect (people hoping they'll shake off that cough over the weekend but Monday dawns and not allowed in school/work, oh balls better get a test)

This makes sense to me. I've been pondering the weird jump on 19th and hadn't twigged it was a Monday.

The curfew in France has just been extended to a further 38 départements. There are now 46 million people under curfew.

The numbers in hospital and on a ventilator have had a massive spike today. Part of me hopes that there is some backdating of figures not reported previously in there.

@sirfredfredgeorge

which suggests around 25% of cases are being picked up via testing

This seems unlikely to me, unless there's a lot of testing of suspected asymptomatic positives, which seems a huge waste of resources, although it would explain a high positivity rate in tests.

Many people will live with enough other people that one of them is likely infected - but they should not be being tested (just isolating) so that should double the infected without a test.

So that means only two other cases for each identified one, I am very surprised about that, I can't see how that manages to get to an R of 1.2-1.5 so easily - you have to assume the identified 50% (in my model) would have an R well below 1, which means the other 50% would need an R higher than the probably R0 of 3?

.... Maybe down to the low dispersion factor, K, for Covid, ~0.1

~10% of infected people, the "superspreaders" transmit 80-90% of infections
Most people infect 0 or 1 person;
the superspreaders can each infect a great many; highest so far being Patient 31 in Skorea who reportedly infected several hundred and likely up to 5,000

So, the 1 in 10 superspreaders infecting dozens e.g. in the pub, or during sport - superspreader events have infected people much more than 2m away

www.sciencemag.org/news/2020/05/why-do-some-covid-19-patients-infect-many-others-whereas-most-don-t-spread-virus-alll

Deaths have averaged > 200 over the last 3 days

@LivinLaVidaLoki

The numbers in hospital and on a ventilator have had a massive spike today. Part of me hopes that there is some backdating of figures not reported previously in there.

I can't see that - looking at the day by day numbers here

coronavirus-staging.data.gov.uk/details/healthcare

doesn't show any spike.

@BigChocFrenzy

Valance saying 312-362k infected in report for previous week ONS tomorrow (still looking at the past) expected to be higher

Modelling consensus is 53-90k new infections per day

Have I misunderstood anything, or based on the lowest modelling estimate, and a 14 day doubling (which I think is roughly where we are atm), will we not be at March lockdown estimated case levels by bonfire night?

@NeurotrashWarrior - there is very little clarity from research about ability of younger ages to transmit the virus.

1. Fewer younger ones seem to catch it based on any measure of testing, which is good because if you don't have it you can't spread it; thought to be linked to lack of ACE2 receptors so puberty would reduce that protective effect. Great for under 11, helpful under 14, no help at all after 14 or so.
2. Those who catch it may have the similar levels of virus in their nose. Bad for all ages.
3. Younger children who catch it do seem to be asymptomatic or have a milder dose; this is helpful because asymptomatic spread seems to usually be presymptomatic, getting over a virus quickly gives much less time in the infectious stage to transmit it. Good - all ages.
4. Theories about younger ones breathing less air and therefore transmitting less virus. When I see them shouting, I'm less convinced... but anyway, again Good - young, Bad - teens.
5. Superspreaders are responsible for 80-90% of cases; school bubbles restrict the potential spread. For primary. Secondary generally don't seem to have done much to limit the bubble sizes. Where they did, it was under-14s before subject picks. Good for younger, bad for older.
6. Rates started to go up in August, before return to school and uni, that means holiday travel and socialising is what kicked off the increase for young people rather than education itself. University lectures didn't cause that outbreak, it was shared living plus parties. Risk taking may increase when people feel out of control of their risks. With kids socialising, mumsnet was full of people saying sleepover was fine because the kids would all be in class together next week, teachers saying they would see friends because they'll be in a class of 30 next week etc.

From tests with symptoms, from randomised tests, and all over the world - younger ones are least likely to catch it and then mostly from overnight settings (parents, older siblings, family, US camp). That protection runs clearly to about age 11, but of course puberty average age is 11 for girls (8-13) and 12 for boys (9-14) and there seems to be some overhang effect.
After 16 they seem more likely than any other age to catch it, being naturally risk-taking probably doesn't help. That is why the cut-off of where to declare it's an issue depends on community infection rates; if they're high then the rates for 11-16 will get steadily too high to be acceptable in enclosed spaces like classrooms. If they're low, then it's much safer.

@BigChocFrenzy

Deaths have averaged > 200 over the last 3 days

Though 150 a day for the past week by day reported, and 132 by actual date of death (ignoring 21st). The spike of 241 on the 20th brings the last 3 days average up, but of course that was a Tuesday number so is normally higher because of the weekend PHE drop.

UK today

Cases 21,242
Deaths 189

Richard@RP131 chart shows where the 189 deaths came from
and also overlays with 10-day death doubling since 17 deaths on 15 Sept,
which fits well for date of death

England
17,354 cases
160 deaths

Scotland
1,712 cases
17 deaths

Wales
1,134 cases
7 deaths

NI
1,042 cases
5 deaths