Data, Stats & Daily Numbers started 11th JULY

[boys3]

This is the DATA thread. We welcome factual, data driven and analytical contributions
Please try to keep discussion focused on these
List of useful data links below. Suggestions for additions, and indeed deletions, always welcome.
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
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

Then looking at the next doubling - extending that graph a little into the future with 3 very simple scenarios: 1%; 3% and 5% daily growth in the seven day average

at 1% 3rd August before 40,000 reached

at 3% 21st July before 40,000 reached

at 5% 18th July sees 40,000 and the next doubling to 80,000 on 1st Aug; and 100,000 reached on 6th August.

[quote EasterIssland]@MRex is Spain higher ?[/quote]
I'm really really sorry, I didn't look at the variants for Spain as I assumed it was still Delta rising.
Spain has Beta suddenly up at 20% of cases.
Can you go to see your mum and then take the quarantine hit?

I don’t suppose anyone is listening to LBC

Trying to hear but tricky with 3 year old around

Talking about hybrid immunity in community being better as Zoe app showing cases rising in vaccinated and down in unvaccinated

Has anyone heard this argument?

Looks like an increase in Beta going on in the EU generally; Greece and Spain as well as France, plus clear rapid increase for Portugal and Finland. It isn't yet clear to be whether Beta or Delta will prove more transmissible, both seen to be taking advantage of cases restrictions to grow. Screenshot attached from here:
covid19-country-overviews.ecdc.europa.eu/#4_Variants_of_concern.

I wonder if Delta provides immunity against Beta

Or how likely it is to get it after having delta

The human challenge trials should give more information. Moderna's trial using Beta in the vaccines was good against all other variants at the time, so that way should work. I suspect from the adjustments in efficacy, including immunity from previous infection, that number of antibodies has a huge impact and that also explains why those variants are more deadly, because people can't produce enough. So original covid needed x, alpha x + a%, beta x + b%, etc.

Is that actual numbers or proportions infected versus total numbers in the two groups?
As more people get vaccinated, the total numbers of vaccinated people still getting Covid will also increase but it doesn't mean that the vaccines aren't giving good protection, just that a tiny proportion of a huge number is still quite big whereas there are fewer and fewer unvaccinated people to catch Covid

I so confused I thought beta came before delta?

Abcd?

What is beta? What was it before it's new name?
Dies this mean delta is still to hit Europe

@EducatingArti

Is that actual numbers or proportions infected versus total numbers in the two groups? As more people get vaccinated, the total numbers of vaccinated people still getting Covid will also increase but it doesn't mean that the vaccines aren't giving good protection, just that a tiny proportion of a huge number is still quite big whereas there are fewer and fewer unvaccinated people to catch Covid

It was hard to hear but the figures I got were 40% up in vaccinated and 20% down In unvaccinated

I was hoping someone else knew more as I can’t confirm if it’s just due to higher numbers vaccinated

@Lemonmelonsun

I so confused I thought beta came before delta?

Abcd?

What is beta? What was it before it's new name?
Dies this mean delta is still to hit Europe

Beta was South Africa variant. Delta is starting to hit some EU countries now.

Afternoon, firstly thanks for the thread. I lurk a lot but don't often post as I don't generally have anything to add.

I just wondered if you could help me with something. I have done a short calculation on hospital admissions compared to the last wave. Its very crude but wondered if it made sense.
12th July there were 717 admissions.
3 weeks before this was the 21 June (I keep seeing 3 weeks as the length between test and admission) cases were 106333. Which means about 6% of people tested positive went on to be admitted.

10 Oct 717 admissions 3 weeks before that is 19 Sept, where there were 4,442 cases which is about 16%. Showing that there has been a drastic fall in the rate of admissions from positive tests.

If the alpha mutation and the delta mutation were similar - and I believe they were? then it's quite likely that alpha infection is going to be better than an original vaccine, assuming that all infections were significant enough to generate a strong immune response.

We also have the fact that younger people - the unvaccinated - would have very possibly had a stronger immune response than the older who are vaccinated no matter how the vaccine was introduced.

Knowing vaccine+alpha or vaccine+original infections would be useful too.

@MarshaBradyo

I wonder if Delta provides immunity against Beta

Or how likely it is to get it after having delta

Delta would probably be less protective against beta than the original strain. Here's a phylogeny of covid variants. The original variant (which the vaccines are based on) is at the base of the phylogeny at the bottom left, delta is green, beta is dark blue. To measure the genetic distance between two sequences you need to look at the horizontal distance on the phylogeny (ignore the vertical distance entirely. So the distance from beta to the original variant is pretty much just the branch length for beta as the original variant doesn't have much of a branch and it's the same for the delta variant and the original. The distance from beta to gamma is beta's branch length plus Delta's branch length. You can see here that they're almost twice as different from each other as they are from the original variant.

Hope that makes sense.

@sirfredfredgeorge

If the alpha mutation and the delta mutation were similar - and I believe they were? then it's quite likely that alpha infection is going to be better than an original vaccine, assuming that all infections were significant enough to generate a strong immune response.

We also have the fact that younger people - the unvaccinated - would have very possibly had a stronger immune response than the older who are vaccinated no matter how the vaccine was introduced.

Knowing vaccine+alpha or vaccine+original infections would be useful too.

What I said above also stands for alpha and delta - they're much less similar to each other than they are to the original variant.

@LivinLaVidaLoki

Afternoon, firstly thanks for the thread. I lurk a lot but don't often post as I don't generally have anything to add.

I just wondered if you could help me with something. I have done a short calculation on hospital admissions compared to the last wave. Its very crude but wondered if it made sense.
12th July there were 717 admissions.
3 weeks before this was the 21 June (I keep seeing 3 weeks as the length between test and admission) cases were 106333. Which means about 6% of people tested positive went on to be admitted.

10 Oct 717 admissions 3 weeks before that is 19 Sept, where there were 4,442 cases which is about 16%. Showing that there has been a drastic fall in the rate of admissions from positive tests.

Using 10 days as the gap the ratio of positive tests to admissions is 2.4%

they're much less similar to each other than they are to the original variant

Genetic distance isn't the key thing though is it, it's similarity to the neutralizing antibodies? So two could be more different, but if there's no difference in the proteins that the antibodies bind too, then they're still more similar?

ie Beta immunity escape worry is because of the change? And that worry is not there with alpha / delta?

@sirfredfredgeorge

they're much less similar to each other than they are to the original variant

Genetic distance isn't the key thing though is it, it's similarity to the neutralizing antibodies? So two could be more different, but if there's no difference in the proteins that the antibodies bind too, then they're still more similar?

That would require them to both to still be very similar to the original strain in those areas as there was almost zero sequence evolution before alpha, beta and delta diverged. We know that's not the case for beta as there is considerable vaccine escape. There will be some convergent evolution as there are some mutations that confer a significant transmission advantage but this will be on a background of neutral, mildly deleterious and mildly advantageous mutations, resulting in larger differences overall.

Ok thanks Queen I think I get that even after a long afternoon of picnicking and wine.

I’m still thinking about this hybrid immunity thing. I’m so pro pro everyone vaccinated I’m surprised I’m wondering if there was a point. Not everyone vaccinated but those who can provide natural immunity. Has anyone encountered this?

I presume it comes back to those vaccinated can transmit.

www.bbc.co.uk/news/uk-57876608

All adults have been offered a vaccine, says the government. (So that’ll be “all” adults we have on record?) 88% have received a first dose. Presumably a small proportion of the “all” have been offered and have an appointment booked, but have not actually received first does yet?

Been offered doesn't mean the same as taking up the offer!

Anyone could have booked for weeks, I presume this must mean contacted by GP surgeries, or at least letters sent.

There may be quite a few who are having to miss appts due to self isolation. Or others who have had Covid and need to wait a few weeks. That goes for 1st & 2nd doses.

My 41 yr old sister only got her second jab a few days ago, it's going to be a couple of months or more before the over 18s have had their first let alone second.

@WarriorN

My 41 yr old sister only got her second jab a few days ago, it's going to be a couple of months or more before the over 18s have had their first let alone second.

I don't know any 18+ who hasn't been able to get their first jab, there are walk-ins everywhere and loads of advertising by the council to get them. DNs in another part of the country than me and all their uni friends in various locations are all done. Where do you live that has no appointments?