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/

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

We welcome factual, data driven and analytical contributions
Please try to keep discussion focused on these

BMJ - Historical perspective in U.K. deaths

www.bmj.com/content/373/bmj.n896

I have been reading on Medtwitter that B1.617 regularly returns negative PCR, despite the patient presenting clinically with covid (even when severe e.g. cytokine storm).

Does anyone have more info in this? I wonder if they are using the same kits as us?

Remember how incredibly fortunate we were that B1.117 caused an S-gene drop out in the Thermo kits (caused by 69-70 deletion)?? Enabling us to use this proxy and detect its frequency without full sequence.

I had a quick look at the mutations throughout B1.617 but haven’t read what exactly might cause full PCR failure (I think there’s 3 genes amplified?)

Presumably on if the major PCR kit suppliers is developing a kit with modified primers??

Could be some other technical reason...

@everythingthelighttouches - interested in what you've read about immune escape.

The E484Q mutation is similar to E484K, a mutation found in Kent B.1.1.7 and South Africa B.1.351 variants. I don't think it's correct when this is referred to as "immune escape" because it appears to only very occasionally evade natural immunity antibodies but not vaccine immunity; we know AZ, Pfizer, Moderna, Novovax and Janssen are all fine against Kent strain.

The L452R mutation has been found in California B.1.427 and B.1.429. It is more transmissible because of how the spike proteins bind with ACE2 receptors. Again, this is not considered to be a problem for any of the vaccines based on early April research.

So, why is there so much additional concern about the India variant? I think it's purely because vaccination rates globally are still very low, I don't think it's to do with vaccine issues.

This article suggests initially getting a negative PCR test and eventually getting a positive, also stating PCR sensitivity of only 70%. In the UK we run a lot of cycles and the RT-PCR sensitivity is 94-95%. I don't know if they have a different test or run fewer cycles, but I think the issue is the test.
news.abplive.com/news/india/new-double-mutant-strain-desi-indian-variant-could-causing-the-rapid-spread-of-covid-19-in-second-wave-1453359/amp.
When I say think though, I mean literally I'm guessing based on reading one article, so could be wrong!

Hi MRex no the “Kent” variant doesn’t have E484K.

Only “South Africa “ and “Brazil” variants and it is thought to be linked to the reduced Efficacy in the SA trial they halted.

The second mutation is right next door to it and I’m waiting to see what the structural studies show this does to tertiary structure.

You’re right there’s no escape, more like Reduction n antibody binding.

Here is a table.

Also, thought you lot would appreciate this, apparently SAGE didnt Publish their minutes this week due to DoE funeral......

@everythingthelighttouches

Hi MRex no the “Kent” variant doesn’t have E484K.

Only “South Africa “ and “Brazil” variants and it is thought to be linked to the reduced Efficacy in the SA trial they halted.

The second mutation is right next door to it and I’m waiting to see what the structural studies show this does to tertiary structure.

You’re right there’s no escape, more like Reduction n antibody binding.

Sorry I meant to say "with", there have been about 50 cases of Kent with E484K, but they died off. SA has N501Y that makes it particularly contagious in addition, which I thought was the main issue with it. I don't mean to underplay that there could be some efficacy reduction overall, just that it isn't necessarily disastrous on its own.

1882 / 10

Wales don't look to have reported anything today either, but thats still very low.

Nice weather and first weekend of freedom meaning fewer going for tests, or..?

Sorry, that should say N501Y AND K417N (I went to find the reference and hit send instead), I think it's the combo that's thought to be the big antibody issue:
www.biorxiv.org/content/10.1101/2020.12.23.424283v2

Oh, wait. Wales have reported today - was looking at the wrong section!

From what I can see some some 44,000 p2 PCR tests in Lambeth and Wandsworth in the three days up to and including last Friday. Not unexpectedly a few extra positives being identified, but low numbers relative to the number of tests being carried out.

Good falls in the likes of Mansfield and Corby, both now around the 55 per 100,000 mark, so not far off a 50% reduction compared with a week ago. Still relatively high compared with most English council areas - just 19 with rates over 50; and 50 with a single digit rate - but moving in the right direction. Let’s hope that is maintained with the school holidays ending.

In terms of spec dates for cases added in England.

Saturday 17th

388 added of which

• PCR 55
• LFD 328
• LFD with a confirmed PCR 5

Friday 16th

725 added, taking overall 2 day total to 1267, of those added

• PCR 678
• LFD (26) eg reduction
• LFD with a confirmed PCR 73

Thursday 15th

242 added, taking overall 3 day total to 1701, of those added

• PCR 244
• LFD (140)
• LFD with a confirmed PCR 138

Wednesday 14th

70 added, taking overall 4 day total to 1902, of those added today

• PCR 68
• LFD (153)
• LFD with a confirmed PCR 155

Tuesday 13th

50 added, taking overall 5 day total to 1910, of those added today

• PCR 49
• LFD (40)
• LFD with a confirmed PCR 41

Rest of April

Just 36 more cases, with 10 dating Monday 12th

• PCR 36
• LFD (40)
• LFD with a confirmed PCR 40

March

An upward adjustment of just 6 cases for the entire month

Corby schools went back on Monday, FYI

@JanFebAnyMonth

Corby schools went back on Monday, FYI

Even better news then - although only a few days in of course.

All back tomorrow where I am. The number of LFT tests taken today will be interesting to see.

Really wish gp could be more flexible with 2nd jabs. They keep saulying how patients are annoying them by going on holiday when their second is due. But not allowing for

• people cant choose the date/time of first really
• holidays carried over from last year
• we are now hittibg 2nd doses being over the 5w school holiday for 40yo so unsurprisingly there will be loads who will be away when second dose is due.

We dont really want to delay first dose to avoid this. As with kids at school higher chance of catching it. Maybe have to check hub first as there is possibility more flexibility. Also from thread on mn its clear many gp are not doing the full 12w wait so patirnts couldnt really know when to avoid booking for

I don't know anyone who's been invited by GPs with more than a week's notice, so it does sound unfair to moan.

MRex You’re right about transmission of variants with 501Y (which increases ACE2 binding) and B1.617 doesn’t have it.

Just read this excellent thread, which points out a tiny tiny proportion of cases have been sequenced and a really skewed geographical distribution of samples.

mobile.twitter.com/jcbarret/status/1383872820724174854

Ooh, he’s on Radio4 now!

Thank you, let us know what he says.
I love the site he links at the end, having a dig about now: outbreak.info/situation-reports?pango=B.1.617&loc=IND&loc=GBR&loc=USA&selected=IND

Yes, that site is great and Lonelyplanet linked to that site too.

Ah, I thought I'd seen it before but I hadn't looked properly. Thanks both of you

Could I get some quick advice (if anyone is around) from this logical lot of ppl? :)
which has the bigger risk
A) flying (2.5hrs) and staying with parents who have been to multiple doctors appointments in the past days. but: get the recommended vaccine. repeat in 4 weeks
B) drive 20+ hours, stay with parents who have been to multiple doctors appointments in the past days. but: get the recommended vaccine. repeat in 4 weeks
C) stay here and hope that sooner rather than later I can get the rec. vax?

I need to decide in the next hour, so any thoughts welcome.

C) seems by far the safest option IMO. A) the riskiest.