Data, Stats and Daily Numbers started 6th April 2021

[boys3]

UK govt pressers Slides & data www.gov.uk/government/collections/slides-and-datasets-to-accompany-coronavirus-press-conferences#history
Data Dashboard coronavirus.data.gov.uk/
Covid 19 Genomics www.cogconsortium.uk/tools-analysis/public-data-analysis-2/
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 MSAO Map English deaths www.england.nhs.uk/statistics/statistical-work-areas/covid-19-daily-deaths/
CovidMessenger live update by council area in England www.covidmessenger.com/
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/

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I don’t think they existed then?
.... only a twinkle in Dominic Cummings’ eye at that stage! Operation Moonshot not announced til early September.

Thanks boys3 Yes my personal thoughts were going in the direction ceeveebee has said there.

Much more and regular testing along with the surge testing in places I feel it's more positive than last summer. Although good to have a comparison, thanks

Worth remembering though that last summer there was much less testing (and no lateral flow testing at all

And they still haven't managed to remove any false positives in over 3 weeks, so unless there are huge coincidences, so real rates are even better - however specifically on the suppressed cases it's less likely to make much difference unless the false positive reasons are linked to other viruses etc. and all happen in the same places.

Interestingly there were a handful of cases removed from my borough today so I wondered whether there had been any false positives removed today. But not sure how to tell as haven’t been downloading the PCR/LFD split recently

I haven't actually checked todays, only been doing every few days explicitly and eyeballing the other dates to see if there are big changes, so maybe they have started, but the eyeballing still looks as I remember.

From looking at today’s I’m pretty sure they haven’t yet

Teachers on MN wonder if the 100 cases in a secondary school indicate the scale of infections that might have been picked up in the autumn in a few schools if we’d been using LFTs then......

@lonelyplanet

The B1.617.2 (a subset of the Indian variant) looks to be increasing fast. Last week was the first time it was mentioned on the dashboard: 202 total cases were reported (time frame not clear). On the COG website today it is reporting a total of 753. That's a big jump in a week. Also now accounting for over 3% of sequenced cases. I don't understand why surge testing wasn't carried out.

sars2.cvr.gla.ac.uk/cog-uk/

See table 3.

Surge testing works if there is suspected community spread in a particular area. If those cases are linked with enhanced testing of contacts and known travellers then surge testing would be pointless, OR if they are spread with 700 across 200 MSOA then surge testing would be too widespread. B.1.617.2 doesn't have the E484Q, so of the 3 it's least threatening. We need more info!

@lonelyplanet

The B1.617.2 (a subset of the Indian variant) looks to be increasing fast. Last week was the first time it was mentioned on the dashboard: 202 total cases were reported (time frame not clear). On the COG website today it is reporting a total of 753. That's a big jump in a week. Also now accounting for over 3% of sequenced cases. I don't understand why surge testing wasn't carried out.

sars2.cvr.gla.ac.uk/cog-uk/

See table 3.

I believe there is no surge testing unless it’s a “variant of concern” rather than “variant of interest”. However I believe it is to be “upgraded” as of tomorrow. Surge testing will be happening in Bolton and I’m expect other places.

Deepti Gurdasani has some interesting comments.

"Currently B.1.617.2 appears to be doubling every wk, so it may become dominant in some parts of the UK in 2-4 weeks"

mobile.twitter.com/dgurdasani1/status/1390390386854612997

www.theguardian.com/world/2021/may/06/new-concerns-indian-covid-variant-clusters-found-across-england-ongoing-risk-high?fbclid=IwAR3pkPXv4hD13rxkOXQJ2-dTKQxL65orLmWBYsfnggyytgQF0kYwW_6Qdt0

At least one of the variants likely to be upgraded to VOC tomorrow.

www.manchestereveningnews.co.uk/news/surge-testing-rolled-out-bolton-20539149
Does anyone have any thoughts on what is happening in Bolton. It is near me and I am worried by it.

MRex
Can’t remember where I read it now, perhaps it was on the Christina Pagel thread on twitter or someone summarising Gupta lab results, but I think it is to early to make this conclusion

“ B.1.617.2 doesn't have the E484Q, so of the 3 it's least threatening. ”

It has been shown that there is no difference in binding and neutralisation between the .2 subtype and those with E484Q

I.e. E484Q is a bit of a red herring and unlikely to be contributing to the effect of the so called “Indian variant”

As an aside, this mutation is a change from an E (glutamic acid, positively charged) to a Q (glutamine, neutral). Whereas the mutation in some other VOCs was to a K (lysine, negatively charged).

The E484K was significant structurally as the charge difference is critical for neutralising antibody binding and has some effects on other sites in close proximity in the tertiary structure.

It wasn’t certain, but turns out a smaller change in charge from positive to neutral has not had such an effect.

EducatingArti

Google UK 1.617 maps Sanger.
My phone is having trouble with the Sanger website right now but I think many newspapers are now showing their maps.

My guess is Bolton has a rise in the so called “Indian variant” but check the maps.

boys3 is there anything in your datasets that you can glean about the Indian variant?

As the numbers are relatively small, I’m guessing it is completely hidden in the much larger numbers of the Kent variant and may be in areas with suppressed figures?

@everythingthelighttouches - you're starting to go way beyond my knowledge, I love it. Thank you. I hadn't understood the likely E / Q / K difference.

According to the MEN article I linked, Bolton now has 82.8 cases per 100,000 which seems alarming high all of a sudden.

I think Bolton’s gone up even more since then - for the week to 4 May (which is not yet complete) there are 282 cases which gives a rate of about 98.

After today’s update, Bolton is now showing 339 cases in the week to the 5 May, a rate of 118 (and those days won’t be fully complete yet). That’s nearly doubled in a week.

Oh sorry I should say - 2490 cases / 15 deaths (if we still do that!)

It's like an advert for vaccines, the inverse relationship between vaccinated population and number of cases in Bolton: www.theboltonnews.co.uk/news/19273779.amp/.

Sadly I think there will be more like this, viruses find a way in.

Here's a breakdown of where cases of B1.617.2 have been found.

I've updated this graph from today's data. The B1.617.2 seems to be doubling weekly, which is a big worry.

I forgot to add a link to the numbers.
www.gov.uk/government/publications/covid-19-variants-genomically-confirmed-case-numbers/variants-distribution-of-cases-data

This is from the Guardian about Bolton.

"According to data from the Wellcome Sanger Institute’s Covid-19 genomic surveillance, about 24% of Covid genomes in Bolton sequenced in the two weeks around 17 April relate to the three India variants, although the actual number of sequences per week was low and scientists warn the data can be “noisy”."

www.theguardian.com/world/2021/may/07/indian-covid-variant-is-variant-of-concern-says-public-health-england