Data, Stats and Daily Numbers started 18th January 2022

[boys3]

Welcome to another instalment of the DATA thread.

Our preference is for 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
UKHSA Variants of Concern Technical Briefings www.gov.uk/government/publications/investigation-of-sars-cov-2-variants-technical-briefing
UKHSA Vaccine efficacy www.gov.uk/guidance/monitoring-reports-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/ includes R estimates
UKHSA Weekly Flu & Covid Surveiilance Reports 2021-22 Season www.gov.uk/government/statistics/national-flu-and-covid-19-surveillance-reports-2021-to-2022-season
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/
Sewage www.gov.uk/government/publications/wastewater-testing-coverage-data-for-19-may-2021-emhp-programme/wastewater-testing-coverage-data-for-the-environmental-monitoring-for-health-protection-emhp-programme.
Sewage reports www.gov.uk/government/publications/monitoring-of-sars-cov-2-rna-in-england-wastewater-monthly-statistics-june-2021
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/

1 in 45 is all ages 1 in 45 is pretty roughly the 7 day positive tests in school age children, rough because that's not an actual age band in the cases data, and isolation periods aren't 7 day etc. it could be maybe 1 in 30 if the overlapping bands and every kid needed 10 days not 7 etc., but still 1 in 30 and 1 in 8 is a huge difference.

However as Jangly now shows, it's not 1 in 8 at all, in fact you're more likely to be off because of something other than covid, than off because of covid.

The 3.9% with covid doesn't meet the published stats either, are many of the kids who are "off with covid" not registering with PHE? making up the positive but not registering the fake one? 'cos that should tally much closer shouldn't it?

Its certainly spreading thru local shools. 10 in in one class, been sent home messages to please lft from school where lots in our year. At least one table is off in my daughters class.

I wonder if people are lft and not reporting them as they only need an lft now?

BBC are reporting this morning that the React study found two thirds of Omicron cases in January were reinfections

The new ones due to be shown in the dashboard from the 31st won't be quite that high as that because React knows about all previous infections (unless in early 2020 before they started) rather than just previous reported cases, but still suggests we're quite significantly under reporting cases currently

Here's the link to the BBC article about all these reinfections www.bbc.co.uk/news/health-60132096

But I've also looked at the React study of itself, which is here www.imperial.ac.uk/medicine/research-and-impact/groups/react-study/real-time-assessment-of-community-transmission-findings/
And I can't seem to see this 65% at all. The BBC is saying it's self reported previously having had a positive test, and unclear whether this could include having already been tested for their current infection. But I can find no mention of any of this in React's headline article nor a skim and search of the full report. Can anyone explain this?

Among the 3,582 swab-positive individuals reporting whether or not they had had previous COVID-19, 2,315 (64.6%) reported confirmed previous COVID-19 and 267 (7.5%) reported suspected previous COVID-19

It is there, although it doesn't scale to 65% with the adjustments for overall prevalence of 4.5%, but still interesting, I am a little suspicious of REACT though based on that, as the number doesn't match anything else on re-infections, so are they over-represented in healthcare etc. ?

Page 9 of
spiral.imperial.ac.uk/bitstream/10044/1/93887/2/R17_preprint.pdf

Ah, just realised that the definition of re-infection could be different and it's re-infection within the last month (ie had covid in December and January) which would not then mismatch other stats, but would be new news that I thought they might mention.

Thanks @sirfredfredgeorge. I should have thought to try a text search for 64 when 65 proved unproductive!
Sounds like about 1000 positive people didn't provide data on whether they'd had a previous infection. But it's still very high and out of line with estimates I've heard quoted from other sources. I think they try to get a cross section of people in React, and rates of infection amongst healthcare workers aren't high compared to others lately anyway so don't think that explains it. More interest in taking part in React if you've had covid maybe? Do they test your antibodies or something that might be of interest?

Out of the 5-10 people I know of with covid currently/very recently only one is a reinfection.

@sirfredfredgeorge

Ah, just realised that the definition of re-infection could be different and it's re-infection within the last month (ie had covid in December and January) which would not then mismatch other stats, but would be new news that I thought they might mention.

Wouldn't most of those be the existing infection already having been picked up? So 65% of people testing positive at a random point in time are testing for an infection they already know about?

If that's true reinfections within a month, then it would mean that Omicron entirely evades past immunity and also picks on certain people again and again while leaving others alone. That seems unlikely and conflicting with other sources of information. The fact that they've not mentioned this crazy high reinfection figure in their summary also suggests to me that they are dubious about it

Yes, I don't think it makes sense, but the other re-infection sources are all "more than 90 days or multiple negative in between", so it's possibly that the group are less than 90 days and haven't tested, I still don't think it matches the reports, but it's not completely out of the question because of the different definitions.

90 days does seem quite long to class something as a reinfection, especially with Omicron hitting soon after a big Delta wave. But within 30 days seems unlikely for a genuine reinfection, and quite likely to be the same infection.

According to Twitter the React study have now removed the 65% reinfection bit from their report.

Yes, just pulling the preprint entirely, but now at
spiral.imperial.ac.uk/bitstream/10044/1/93887/7/R17_updated_final.pdf

And this is added I think
Our results on reported previous COVID-19 are based on self-reported data and therefore it is uncertain what proportion of these are reinfections or recent infections picked up due to the sensitivity of PCR testing

Which I think says "people said that they had covid before and tested +ve in the REACT PCR swab" but there's nothing to say that wasn't an LFT positive by the individual the week before... So not a re-infection at all.

(pulling pre-prints is bad science btw, don't like that)

You would assume that quite a lot of people testing positive during the React study would already have been tested for the infection that they currently have wouldn't you? 90 days might be too long a gap to cover all reinfections, but you need some kind of a gap!

If you work in a primary school you wouldn't be at all surprised at the suggestion of a high percentage of reinfections. Almost all of my class had covid in the half term before Christmas. This week there are 5 cases all of which are reinfections.

12% with covid. That's approximately 1 in 8.

I posted this on Jan 11th.

I think the numbers are indeed informative.

I remember born plus the refusal of some to see that school acquired infections does drive rates. Rates in school were fine for the first two and a half weeks, then they started growing. Now in school it is exponential- we are week 4.

Re-infections are the worst as they students have already missed large blocks of learning.

Here is the updated REACT data on reinfections. This could mean we're missing huge numbers of cases from the official numbers - even if it is a bit of a high estimate. It will be interesting to see what happens to the dashboard data on Monday.

…plus the refusal of some to see that school acquired infections does drive rates.

I think there is a difference between “driving rates” and “driving pandemic waves”.

What we saw in late December-early January was a pandemic wave. As it was the case with every single pandemic wave before that, it was driven by young adults (18-29 year olds).

What we are seeing now is “back to school” spread (which is similar to what was happening in autumn). There is some spillover into other age groups (parents), however we are not seeing the same exponential growth that we observed in December. The trends are quite different.

Re: REACT - I am a bit sceptical about their conclusions. In the past, they got a couple of big things wrong. It will be interesting to see PHE numbers.

ONS survey should reflect true prevalence and it has generally been in line with reported cases up until very recently:

mobile.twitter.com/PaulMainwood/status/1486352666355720200

I think there is a difference between “driving rates” and “driving pandemic waves”.

In practical terms, what does that mean? And how does it matter?

In practical terms, what does that mean?

A pandemic wave leads to infections quickly spreading across all population groups, reaching vulnerable people and putting significant pressure on healthcare system.

And how does it matter?

It does because increase in cases in school children (with some spillover into parents/teachers/granparents age groups) is highly unlikely to overwhelm NHS. We saw it in Scotland in September. Back then Covid prevalence in schoolchildren also exceeded 10% (based on ONS). Cases went up, peaked and went down.

Seems to me that high and rapidly increasing rates (especially with reinfections and waning immunity from boosters) are more problematic than a “wave passing through” then.

It is certainly a problem for my students. And whilst rates in my MAT are now the second highest they have been since the pandemic began, all masks have been removed including on the buses. Excellent.