Data, Stats and Daily Numbers started 5 December 2021

[JanglyBeads]

Welcome to the DATA thread.

Our preference is for actual, data driven and analytical contributions.
Please try to keep discussion focused on these

Our links below probably need a refresh ready for the festive season,. so all reasonable suggestions 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/ includes R estimates
PHE 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/

boys those increased rates at the start of November for older age groups, was that triggered by half term mixing?

@Firefliess

Really good thread from James Ward on Twitter here twitter.com/JamesWard73/status/1467628403553615885?t=MOlL3dtuZSIWEQ-mQ0vnzQ&s=19

Basically saying that even if milder (quite a big if I think at present) the faster spread of Omicron will concentrate a very large number of hospital admissions into a short space of time - similar to January this year.

Very sharp wave predicted there. He's good at balanced views James Ward, and really clear about how the level of uncertainty is huge with this. The timeline is seriously tight to find anything out before the wave hits; it's a tough call on extra mitigations, the impact on hospitality businesses is huge even without official closures.

@Firefliess

Really good thread from James Ward on Twitter here twitter.com/JamesWard73/status/1467628403553615885?t=MOlL3dtuZSIWEQ-mQ0vnzQ&s=19

Basically saying that even if milder (quite a big if I think at present) the faster spread of Omicron will concentrate a very large number of hospital admissions into a short space of time - similar to January this year.

From what I’ve seen he’s been pretty good at being reasonable

I’ve heard of a few companies switching to wfh from next week. Probably to protect Christmas without isolation but behaviour change is happening.

@Firefliess

I think the idea that we can "keep children safe" via bubbles, masks or ventilation is looking more and more unlikely. If they're going to catch it at some point, does it really matter if it's now or later on? Vaccinating first might have been a good idea, but infection followed by vaccination seems to give the best protection possible, so I can't see why it matters much what speed they catch it at.

I take it you don't have a vulnerable child then.

@herecomesthesun. I don't, no. If I had a very vulnerable 5-12 year old I'd be bloody cross that the government for not giving them a vaccine right now!

Fun facts on how waves move around - So Guildford was top 10 in the country a week or so ago, here are some stats:

24/11 - 05/09 year olds - 3053 per 100k (peak)
30/11 - 05/09 year olds - 2079 per 100k (most recent)

24/11 - 40/44 year olds - 1470 per 100k (peak)
30/11 - 40/44 year olds - 1231 per 100k (most recent)

Other age groups rose and fell, 45/49 just tipped in the 1,000's per 100k, but all have been falling since.

Guildford continues to fall and I have my booster this afternoon .

I don't get how the immunity breakthrough against vaccination being so (relatively) low is standing up against the super spreader anecdotes, how does the vaccine immunity having 80% success tally with events reported where over 50% of the people present caught omicron?

Is everyone purely basing it on the Israeli doctor's estimate?

@sirfredfredgeorge

I don't get how the immunity breakthrough against vaccination being so (relatively) low is standing up against the super spreader anecdotes, how does the vaccine immunity having 80% success tally with events reported where over 50% of the people present caught omicron?

Is everyone purely basing it on the Israeli doctor's estimate?

Isn't the 80/90% "success" rate being reported for boosters, only for serious illness and hospitalisations though? So, you can still become infected, bad, but you're not going to end up in hospital, good.

The James Ward thread seemed to be using 80% for infection too, I'm not saying it's obviously wrong or anything, and it could of course be possible, but I don't see any reason to decide on that number over any other number? And the anecdotes from Belgium / Somerset / Norway all have way higher breakthrough rates with the super spreader events.

I believe vaccine effectiveness is based on reduced chance of being infected per exposure as opposed to being individual if you're susceptible, is there data on that being the same with omicron too?

Its a numbers game. If the booster is 90% effective, then 10% are still affected. This variant seems to be very infectious. So if lots of people get it, 10% can still be a lot of people.

@sirfredfredgeorge

I don't get how the immunity breakthrough against vaccination being so (relatively) low is standing up against the super spreader anecdotes, how does the vaccine immunity having 80% success tally with events reported where over 50% of the people present caught omicron?

Is everyone purely basing it on the Israeli doctor's estimate?

This puzzles me too. I guess it's possible that we only hear about the super spreader events that were exceptional - so we're not hearing about the ones where much lower numbers were infected. But vaccine protection from just two doses against Delta infection was recently estimated to be only around 50% (hence the need for boosters and value in rolling them out to younger people too) so I can't see how 80% protection against Omicron is possible. James Ward is usually very good with taking reasonable estimates so that makes me think maybe I've not followed what he was doing property - or maybe he IS factoring in boosters in the UK context?

Superspreading events may have involved people who were vaccinated but didn't have a booster yet, possibly?

The Somerset anecdote from Tim Spector

*On Sunday, Mr Spector revealed that a 60th birthday party in Somerset turned into a super spreader event.

All guests at the party, which was attended by a Zoe study contributor, were vaccinated, some had received boosters, and produced negative results from lateral flow tests taken 24 hours beforehand, but 14 out of the 18 guests later tested positive for Omicron*

All vaccinated and some boosted, although we don't know the details obviously and it's just an anecdote.

Though the 80-90% was for hospitilisation/death, not infection...

*Thought not though

@Firefliess about children and timing of infection. I feel cautious although my children are not CEV, we do not know what makes some kids susceptible to long covid and as time goes by hopefully this will become clearer. Last month a study identified a gene common in people with south Asian heritage doubling their risk of covid death. Also hopefully a more robust vaccine for children will come along and other effective treatments.

[quote Lelivre]@Firefliess about children and timing of infection. I feel cautious although my children are not CEV, we do not know what makes some kids susceptible to long covid and as time goes by hopefully this will become clearer. Last month a study identified a gene common in people with south Asian heritage doubling their risk of covid death. Also hopefully a more robust vaccine for children will come along and other effective treatments.[/quote]
It's possible that by delaying when they catch it they'll be better treatments. But it's also possible that as the virus mutates it becomes more virulent - people who've had previous strains may have more protection and get less ill, but those who've avoided catching it and also not had vaccines could be at higher risk than ever. Fortunately it appears that the vast, vast majority of children are at very low risk. A doubling of a very, very low risk would still be very low. But I don't think it's obvious that the best strategy is just mitigation to try to slow down the rate of spread.

Has it been discounted that this new variant could be our way out of a serious situation? Or is that still a vague hope? Eg if this is a milder variant and more infectious could we welcome its dominance once we know the long term effects?

Placemarking again

@julieca

Its a numbers game. If the booster is 90% effective, then 10% are still affected. This variant seems to be very infectious. So if lots of people get it, 10% can still be a lot of people.

I just found a thing that shows how many people have had the booster in your area Under 40% near me of adults have had it

A milder variant is only useful if there's cross immunity anyway - if there's no cross immunity from Omicron to Delta, then everyone catching omicron even if completely harmless does little to prevent subsequent waves other than by reducing delta by virtue of the extra isolation caused by your omicron infection.

We currently have no knowledge on the cross immunity conferred by omicron to delta etc.

@Notmulan

Has it been discounted that this new variant could be our way out of a serious situation? Or is that still a vague hope? Eg if this is a milder variant and more infectious could we welcome its dominance once we know the long term effects?

Certainly lots of people desperately hoping that's the case! Biologists seem to be saying though that it's unlikely to be less severe per se - it gives people a higher vital load so lots of reason to think people who've not yet caught covid or has a vaccine may get sicker with Omicron than if they caught the original strain (Delta - in between in level of mutations - was estimated to be twice as likely to cause a hospital admission in the immune naive) But it may be less severe in most countries where most of the people infected have already either had a previous strain or a vaccination - it's that partial protection that helps them, not that it's mutated into a virus that's innately less severe.

@sirfredfredgeorge

A milder variant is only useful if there's cross immunity anyway - if there's no cross immunity from Omicron to Delta, then everyone catching omicron even if completely harmless does little to prevent subsequent waves other than by reducing delta by virtue of the extra isolation caused by your omicron infection.

We currently have no knowledge on the cross immunity conferred by omicron to delta etc.

The view of biologists in this appears to be that it's very likely (pretty much certain) that they'll be some cross strain immunity. It's not a new virus so your immune system will recognise it and fight it off quicker after vaccination/ previous infection than it would otherwise. But yes, noone really knows how much cross strain immunity there is, nor whether that differs between prior infection strain or vaccination.

51,459 infections and 41 deaths.

Larger increase than recently - will be interesting to see the geographic distribution