Data, Stats & Daily Numbers started 5th August 2021

[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

a slightly different picture, although not hugely troubling, when the current week in progress (cases from Monday spec date onwards as reported so far this week; as compared with the same position reported last Saturday afternoon) is considered. The big comparative fall in Lincoln in bottom right corner.

I am not sure if the real issue is people not isolating. In my opinion, this would result in more stable growth across age groups.

If we look at the age profile, the highest increase (lack of drop) is once again happening in the 20-24 age group. These are not parents of school aged children. Some of new cases might be students planning their holidays but the weekly peaks seem to be falling on Tuesdays-Wednesdays which reflects the impact of Friday-Saturday socialisation (gatherings with friends, nightlife, etc):

twitter.com/VictimOfMaths/status/1423612974800023557/photo/1

My hypothesis is we are seeing impact of various super spreading events (like Lincoln) in LAs that have not yet fully come out of the Delta wave. We have still got large numbers of susceptible population. It is plausible we will continue seeing case growth of about 10% week on week. The big question is when it is going to reverse. It did in March when we re-opened schools but 18-29 year olds appear much more efficient spreaders than schoolchildren.

LAs that have not yet fully come out of the Delta wave

It would be useful if we could collate "LA has seen the Pub Wave" type stats so we could see how much further to go, and also pick up if there are multiple waves in each LA. So far we've seen no rebound in any of the very early ones right?

A quick query. Does anyone know what the probability is of a lateral flow test giving a false negative? I'm reading some confusing things on line that seem to say different things

@EducatingArti I believe lfts are far more likely to give false negative than false positive. They aren’t very reliable but are useful for asymptotic

Looking at phe data the highest rates per 10,000 are in students (rising) and secondary aged children (decreasing).
Positivity is highest in secondary aged children by a long way, which probably means they aren't being tested enough (pillar 2 graphs).

The ONS data have more year 7-11s positive than year 12- age 24s (this is 1 - 2 weeks ago, and gets past the problem of secondary school children no longer testing so regularly, to some degree)

Positivity is highest in secondary aged children by a long way, which probably means they aren't being tested enough (pillar 2 graphs)

Or they're less likely to do "precautionary" tests without symptoms (ie none of them work in healthcare, few are entering hospital etc.) they're much more likely to do PCR tests primarily as contacts if asymptomatic etc.

It's not always simple to compare positivity rates if the groups and testing reasons are different.

I keep meaning to ask, how does our widespread (relatively) testing of asymptomatic people, and using LFTs which are less accurate than PCR tests, affect positivity theory?

@sirfredfredgeorge

LAs that have not yet fully come out of the Delta wave

It would be useful if we could collate "LA has seen the Pub Wave" type stats so we could see how much further to go, and also pick up if there are multiple waves in each LA. So far we've seen no rebound in any of the very early ones right?

I think you are correct on that final point / question sirfred

At the moment we (whoever we may be :) ) only have 3 English council areas with a current seven day rate per 100,000, and using a three day lag so as not to underplay anything, higher than the median rate per 100,000 peak in this wave. All three - Exeter, Hull, Lincoln have rates well below the 95th percentile peak rates, with that in Lincoln looking to be now falling back.

The ONS data have more year 7-11s positive than year 12- age 24s (this is 1 - 2 weeks ago, and gets past the problem of secondary school children no longer testing so regularly, to some degree)

Yes, but both the ONS survey and the latest weekly PHE report currently show the view post the Euro 2020 drop. None of these sources tell us about what happened post the first weekend following the July 19 re-opening (infections happening on July 23 and 24 with symptoms appearing on July 28 and 29).

The best source for that is the daily reported cases broken down by date of specimen (boys3 graph) and age group reports from the Covid dashboard (which I believe are 4 days out of date).

Re: ONS survey and cases in school children - the graphs confirm that the first group to experience increases and drops is young adults. It is absolutely true that the latest numbers show the highest prevalence in secondary school children but the % is very similar to where young adults were a week ago. Secondary school children are a lagging group but, of course, they can amplify and prolong the spread.

I think you are correct on that final point / question sirfred

to back that assertion up to some extent slightly messy spaghetti type graphics for our previously higher case rate areas (North East, North West, to a lesser extent Yorks & Humber and parts of the South West); and a couple of areas (Norfolk and Lincolnshire) where some rises have seen subsequent to the overall peak in England, although a mixed picture in both.

To quote a classic series, presumably available on Brit Box, Our Friends in the North (East)

Lancashire districts; flattening in several over recent days, a couple with showing a slight upward drift (from a relatively low base); but all significantly lower that the position on the 19th.

North West upper tier councils; whilst Blackpool does have one of the higher rates in England, and the highest of those in the graphic; its rate has still fallen considerably.

South West - big falls in Bristol, South West Gloucestershire for example; BCP largely where it was on 19th ; no significant decline, bur rather just bumping along (technical term)

Yorks and Humber; all still above the median level in England but all down, and in the main well down, on their 19th July position.

then the first of two counties which have not seen particularly significant levels of Covid in any wave. Lincolnshire. Lincoln and North Kesteven showing a clear rise but likely to have peaked; but Boston looks to have continued down, and the rest are much of a muchness.

then Norfolk , a county of contrasts; only Great Yarmouth had a rate well above the median on July 19th ; but has come down very considerably; Norwich does have one of the current higher rates in England; but again is at a level still below the median in England on 19th July; Breckland has seen an increasing rate but still remains below the current median level in England. Kings Lynn and West Norfolk doing the opposite and continuing to move down.

I don't see, looking at the PHE graph below, that secondary students have necessarily been "lagging" all the way through? Mostly they have been either fairly similar to the next age group up or, week 10 -20 have had a higher infection rate?

@herecomesthsun

I don't see, looking at the PHE graph below, that secondary students have necessarily been "lagging" all the way through? Mostly they have been either fairly similar to the next age group up or, week 10 -20 have had a higher infection rate?

This is the England bestial, but there's similar drilling down per area. It isn't always consistent of course, but generally waves of cases so far have been led by the 20-24 age group, with 15-19 and 25-29 following, then spreading from there. I think that's what she meant by "lagging".

Bestial = heatmap. My auto-incorrect has gone mad.

Thanks @boys3 good graphs looking at that, seeing a rise in any of those past rise ones will indicate that it's temporary measures (isolation etc.) that was mostly limited spread this time, but if there's no rise, then it confirms that it's antibodies. Looking promising for the latter so far.

It isn't always consistent of course, but generally waves of cases so far have been led by the 20-24 age group, with 15-19 and 25-29 following, then spreading from there.

Yes, exactly. I meant that the waves seem to nearly always start in the 20-24 group who then infect younger and older population (starting with 15-19 and 25-29s and going up age groups).

Cases in 20-24s went down sharply post July 15 which is captured by the latest ONS survey but they are now going back up. We will not see in ONS until a couple of weeks later.

The March mini-wave that started with school re-opening died down very quickly which seems to suggest that the spread at schools is not as efficient as spread in pubs/at parties.

I wonder how much the masks/ testing/ isolating/ bubbles helped in March? Given that kids are about to go back without any of that.

@herecomesthsun

I wonder how much the masks/ testing/ isolating/ bubbles helped in March? Given that kids are about to go back without any of that.

I think it will be hard (partly due to very poor data collection) to compare ‘in school’ effects in March and coming up in September. As ‘number of contacts’ is a key metric for transmission, it is worth noting for primary/younger secondary in particular that extra-curricular activities opened much later than schools in March, but will open at the same time as schools in September. So in March, a primary child may have had 30 close contacts in school, and say 4 in their household. In September, not only will that 30 rise significantly through the removal of bubbles, but they may also have 20+ extra per day due to extra-curricular activities / clubs. For a child doing a couple of activities a week, plus a household mixing more widely, their ‘outside school’ close contacts could easily go up from 4 in March to 50 in September.