Data, Stats & Daily Numbers started 23rd JULY

[boys3]

This is the DATA thread. We welcome factual, data driven and analytical contributions
Please try to keep discussion focused on these

UK govt press conferences slides & data www.gov.uk/government/collections/slides-and-datasets-to-accompany-coronavirus-press-conferences#history
PHE Variants of Concern Technical Briefings www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201
PHE Vaccine efficacy www.gov.uk/government/publications/phe-monitoring-of-the-effectiveness-of-covid-19-vaccination
SAGE : Minutes and Models www.gov.uk/government/collections/scientific-evidence-supporting-the-government-response-to-coronavirus-covid-19
Data Dashboard coronavirus.data.gov.uk/
Dashboard Vaccine Map to MSOA level coronavirus.data.gov.uk/details/interactive-map/vaccinations
Covid 19 Genomics www.cogconsortium.uk/tools-analysis/public-data-analysis-2/
Sanger Genome Maps & Data covid19.sanger.ac.uk/lineages/raw
UCL Virus Watch ucl-virus-watch.net/
NHS Vaccination data www.england.nhs.uk/statistics/statistical-work-areas/covid-19-vaccinations/
Global vaccination data ourworldindata.org/covid-vaccinations
R estimates UK & English regions www.gov.uk/guidance/the-r-number-in-the-uk
Imperial UK weekly LAs, cases / 100k, table, map, hotspots statistics imperialcollegelondon.github.io/covid19local/#map
NHS England Hospital activity www.england.nhs.uk/statistics/statistical-work-areas/covid-19-hospital-activity/
NHS England Daily deaths www.england.nhs.uk/statistics/statistical-work-areas/covid-19-daily-deaths/
Cases Tracker England Local Government lginform.local.gov.uk/reports/view/lga-research/covid-19-case-tracker
ONS MSOA Map English deaths www.england.nhs.uk/statistics/statistical-work-areas/covid-19-daily-deaths/

Scot gov Daily data www.gov.scot/publications/coronavirus-covid-19-daily-data-for-scotland/
Scotland TravellingTabby LAs, care homes, hospitals, tests, t&t www.travellingtabby.com/scotland-coronavirus-tracker/
PH Wales LAs, cases, tests, deaths Dashboard public.tableau.com/profile/public.health.wales.health.protection#!/vizhome/RapidCOVID-19virology-Public/Headlinesummary
ICNRC Intensive Care National Audit & Research reports www.icnarc.org/Our-Audit/Audits/Cmp/Reports
NHS t&t England & UK testing Weekly stats www.gov.uk/government/collections/nhs-test-and-trace-statistics-england-weekly-reports
PHE Surveillance reports & LA Local Watchlist Maps by LSOA (from last summer) www.gov.uk/government/collections/nhs-test-and-trace-statistics-england-weekly-reports
ONS England infection surveillance report each Friday www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/bulletins/coronaviruscovid19infectionsurveypilot/previousReleases
Datasets for ONS surveillance reports www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/datasets/coronaviruscovid19infectionsurveydata/2020
ONS Roundup deaths, infections & economic reports www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/articles/coronaviruscovid19roundup/2020-03-26
Zoe UK data covid.joinzoe.com/data#interactive-map
ECDC (European Centre for Disease Control rolling 14-day incidence EEA & UK www.ecdc.europa.eu/en/cases-2019-ncov-eueea

Worldometer UK page www.worldometers.info/coronavirus/country/uk/
Our World in Data GB test positivity etc, DIY country graphs ourworldindata.org/coronavirus/country/united-kingdom?country=~GBR
FT DIY graphs compare deaths, cases, raw / million pop ig.ft.com/coronavirus-chart/?areas=eur&areas=usa&areas=bra&areas=gbr&areas=cze&areas=hun&areasRegional=usny&areasRegional=usnj&areasRegional=usaz&areasRegional=usca&areasRegional=usnd&areasRegional=ussd&cumulative=0&logScale=0&per100K=1&startDate=2020-09-01&values=deaths

PHE local health data fingertips.phe.org.uk/profile/health-profiles
Alama Personal COVID risk assessment alama.org.uk/covid-19-medical-risk-assessment/
Local Mobility Reports for countries www.google.com/covid19/mobility/
UK Highstreet Tracker for cities & large towns Footfall, spend index, workers, visitors, economic recovery www.centreforcities.org/data/high-streets-recovery-tracker/

⏭ Our STUDIES Corner ⏮ www.mumsnet.com/Talk/coronavirus/3869571-Studies-corner?msgid=99913434

If the data covers the whole of the UK, then Scottish schools finished at the end of June though. Plus there were a huge number of children self isolating in the last few weeks of the English school term.
Then there was the "keep them out of school for the last week so as not to risk the family holiday being cancelled" syndrome.
If you combine all of these I think it would give a noticeable reduction in contact levels.

We told 10_15% postive covid cases are genome sequenced. How much of this is airport's if any as assume airport testing private not state.
Genome test focus when it's restricted is on travellers and hospitals, so a fair amount of it is sequenced.

Are postive tourists currently included within the postive stats or just UK residents?
Covid-19 is a notifiable disease, therefore legally they must be included.

Once again, because people just ignore the question, why would cases start dropping evenly across 20-29 but continue rising in kids during that period if every infection in the country is to be blamed on children? Why would child cases consistently rise with a lag after adult cases if they are the source of all infections? Why would socialising NOT be the cause of most infections when it's consistently shown to be the cause?

I do think teenagers (and younger when that's confirmed to be safe) deserve the right to choose if they are to be vaccinated or not, to prevent them from getting unwell. I don't think there should be restrictions like for adults for the kids who choose not to. I really wish people would look at the actual data though.

@EducatingArti

If the data covers the whole of the UK, then Scottish schools finished at the end of June though. Plus there were a huge number of children self isolating in the last few weeks of the English school term. Then there was the "keep them out of school for the last week so as not to risk the family holiday being cancelled" syndrome. If you combine all of these I think it would give a noticeable reduction in contact levels.

The data is broken down into the four nations and takes account of isolations and absences.

"Mean contacts by age across the four nations reflect to some extent the different school holidays, with contacts for 5-17 years old reducing earlier in Northern Ireland and Scotland than England and Wales (Figure 4)."

This heatmap of contacts for England only is interesting.

@MRex

Once again, because people just ignore the question, why would cases start dropping evenly across 20-29 but continue rising in kids during that period if every infection in the country is to be blamed on children? Why would child cases consistently rise with a lag after adult cases if they are the source of all infections? Why would socialising NOT be the cause of most infections when it's consistently shown to be the cause?

I do think teenagers (and younger when that's confirmed to be safe) deserve the right to choose if they are to be vaccinated or not, to prevent them from getting unwell. I don't think there should be restrictions like for adults for the kids who choose not to. I really wish people would look at the actual data though.

Problem is we not being consistent with kids.

In Wales and Scotland kids were not counted in the rule of 6.
In England they are either they risk of transmission or they not.
The phe surveillance report although not seen in a while like they used to show education and hospitals bigger spread than hospitality that was 5% last September.
Education i feel drove the 2nd wave more so than eat out to help out.
June July was very bad for my local schools j don't know 1 school that did not have cases 147 schools related outbreaks within Bristol in 1 week.
Our primary was so bad they said keep siblings in other bubbles off to reduce spread.
I know so many people who thought they got it from their kids.
Personally I'm currently sahm mum with a toddler and family a distance away.
I seldom go to pub, restaurant, cafe.
No toddler groups running
Haven't seen freinds that much or been in anyones houses in ages.
My husband is customer facing retail role and have 3 school age kids 10 12 and 15.
I think if I got it school would be most likely source .

I do think jabs should be offered to teens but optional as that would increase amount vaccinated within total population as whole.
This mantra every jab matters unless you under 18.
MHRA have approved it and lots other counties are offering it to 12 to 15.

@3asAbird the new rules will still require fully vaccinated travellers to do pre-departure testing, and Day 0-2 testing on arrival in the UK, it just removes the requirement to self isolate following amber arrival (it’s essentially the same rules as green list travel).
The Govt website says that if your day 2 test shows a variant of concern all your contacts will be requested to test.

www.gov.uk/guidance/how-to-quarantine-when-you-arrive-in-england

Mean contacts by age

Mean contacts is not particularly useful with covid surely - (or that useful in general anyway) but the high k-factor in covid must particularly make it worse?

What is interesting is a lot of discussions have been focused around the end of term, but actually contacts between children have been reducing for the few weeks before this

But the report that schools isolations were ineffective in stopping spread, suggest it would be irrelevant anyway?

@sirfredfredgeorge

Mean contacts by age

Mean contacts is not particularly useful with covid surely - (or that useful in general anyway) but the high k-factor in covid must particularly make it worse?

The report was written for sage and Spi-m-o so I guess that they must think contacts important. The reason lockdowns worked is because they reduced contacts. Transmission rates are also important but transmission can't happen without contacts.

I'm just surprised that I haven't noticed these reports before as they contain lots of useful information on social interaction and have been written throughout the pandemic. It might be that I've just missed them.

Just been digging around more trying to find how SAGE and it’s members use CoMix, found this Royal Society paper that I hadn’t heard of before, might be of interest to modellers?
royalsociety.org/-/media/policy/projects/set-c/set-covid-19-R-estimates.pdf

@sirfredfredgeorge

What is interesting is a lot of discussions have been focused around the end of term, but actually contacts between children have been reducing for the few weeks before this

But the report that schools isolations were ineffective in stopping spread, suggest it would be irrelevant anyway?

Sorry, I'm not sure I know what you mean. Which report are you referring too. What data are you saying is irrelevant?

The bubbles could have been effective.
But you would need to keep off siblings of contacts too (as children get fewer symptoms).
Our outbreak was 8 children plus at least 2 paarents.
Including at least one pair of siblings.
4 primary year groups. Our bubbles particularly useless as afterschool clubs mix several year groups.
If say pcr is only 80% accurate though then we likely had at least one tested child who had symptoms who was actually positive.

All that recent schools report showed was that if you isolate students they miss school....

It didn’t look at onward transmission FROM contacts.

See this lonely:

“Contacts of individuals under the age of 18 were collected by asking parents to answer on behalf of their child.“

bmcmedicine.biomedcentral.com/articles/10.1186/s12916-021-01924-7

So have SAGE been relying entirely on parental estimates of children’s contacts for the last 15 months? That’s fine for those who are not at school (age/holidays/closures), and those not old enough to go out by themselves, but otherwise, deeply flawed, I would say!

That doesn't surprise me at all, Jan. What is surprising is that despite this, it still shows how high the number of child contacts are compared to adult ones.

That report concludes: "The imposition of various local and national measures in England during the summer and autumn of 2020 has gradually reduced contacts. However, these changes are smaller than the initial lockdown in March. This may partly be because many individuals were already starting from a lower number of contacts"

However if lookin at the graph from the CoMix report, contacts dropped down low again in January when schools were mainly closed again.

@lonelyplanet I think the report @sirfredfredgeorge is referring to is the one published by University of Oxford in relation to a trial in 200 schools where daily tests of contacts was done instead of sending them home to isolate. The report found that daily testing was more effective than sending contacts home.

@MRex

Once again, because people just ignore the question, why would cases start dropping evenly across 20-29 but continue rising in kids during that period if every infection in the country is to be blamed on children? Why would child cases consistently rise with a lag after adult cases if they are the source of all infections? Why would socialising NOT be the cause of most infections when it's consistently shown to be the cause?

I do think teenagers (and younger when that's confirmed to be safe) deserve the right to choose if they are to be vaccinated or not, to prevent them from getting unwell. I don't think there should be restrictions like for adults for the kids who choose not to. I really wish people would look at the actual data though.

I don't think there is an answer that will apply across the board.

• There is body of kids/parents, where schools play a big part, and we know the reasons for the drop in that group.
• There are a body of football wankers who have had their out-out occasion for the year, and crawled home to watch sky sports, who can be accounted for.
• There are a body of sociable 20-30yos, who are doing something different. I don't know many people in that group, and can only guess that they are all outdoors drinking strawberry cider in the park instead of at the pub, but actually have no idea.

It seems equally odd that all these groups are seeing drops at the same time, as that all regions are seeing it. But I just can't see a single factor that can apply to all of them.

Thank you, Patrick. I'm not sure that is what that report showed; that was the what the headlines wanted us to believe.
mobile.twitter.com/chrischirp/status/1418919282256318467

But I just can't see a single factor that can apply to all of them

All groups are sociable enough that delta can rapidly move through the entire susceptible community, but the community is simply not as susceptible as we thought it was (perhaps some people deal with it extremely quickly due to similarity to previous infections and antibodies drop below detectable almost immediately, or they're not receptive for some other reason around nose/throat)

It's been consistent with other countries, so an artifact of testing/restrictions that are specific to the UK would be weird too.

The Colin Davies tweet linked yesterday concluded (tentatively) that there was no one factor, apart from the Euros. They were included in a general mix of behavioural changes to do with rules loosening but people responding to the rising case numbers.

[quote JanFebAnyMonth]Just been digging around more trying to find how SAGE and it’s members use CoMix, found this Royal Society paper that I hadn’t heard of before, might be of interest to modellers?
royalsociety.org/-/media/policy/projects/set-c/set-covid-19-R-estimates.pdf[/quote]
Ooh thanks for finding that paper. Now I can just direct people to it instead of having to explain all the maths myself.

Though I guess it's useful to note that it was published BD (Before Delta).

@JanFebAnyMonth

See this lonely:

“Contacts of individuals under the age of 18 were collected by asking parents to answer on behalf of their child.“

bmcmedicine.biomedcentral.com/articles/10.1186/s12916-021-01924-7

So have SAGE been relying entirely on parental estimates of children’s contacts for the last 15 months? That’s fine for those who are not at school (age/holidays/closures), and those not old enough to go out by themselves, but otherwise, deeply flawed, I would say!

Who knows. I'm not a hugely scientific person but I'm fairly logical and try to look at whats reported in a logical unbiased way and so many contradictions and holes that I can see.

Let's not forget the now chief of bio security dr jenny harries seemed know very little about kids and said they don't generally share lunch.
That they had more chance being run over by a bus than covid.
That they don't get ill see 4 people in 10 to 19 age group died this week I don't know if they died of other things and caught covid in hospital or they had poor health previously catching infection.

We had Boris saying schools are not dangerous but the journey school is.
Shut schools down after 1 day back in jan.
My eldest takes public bus but jack then they distanced the seats and worse masks.
They dident pack 30 unmasked kids u vaccinated in small badly ventilated space.
We told message although messages change
Hand face space ventilation none of these applied to schools.

I think the arrival of delta did mean more cases in children and education summer term.
As my sons school had no covid all year until June..

I think combination bad cases in school parents off work plus pindemic which is actually caused by increase in cases.

If I was a behaviour scientist I would say some people fed up restrictions and isolating so they liked idea of close contact not isolating and pretending covid is gone.

Others maybe don't trust the figures as they don't trust the government.
If scientists don't know why there's reason for fall and tim spectator of zoe is also skeptical.
Suppression of education data the unions asked for , losing so many cases off excel and allegations that phe is no longer independent government meddling makes me distrust what could be postive figures.

As for independent sage regardless political persuasion they are more qualified than me so interested in what they have to say.
I think even whitty is struggling with uk being a outlier and freedom day which is why van tan appeared.

I thought this was another clear and interesting way of thinking about the shape of the curve just now:
mobile.twitter.com/ConversationUK/status/1420648189611454465

I thought the Colin Davis thread was good but I’m not convinced he has appreciated that the dreaded “herd immunity” isn’t a static number - he didn’t make that clear.