Data, Stats and Daily Numbers started 17th December

[boys3]

Welcome to the DATA thread.

Best wishes for the festive season to all contributors and lurkers

The preference for this thread is for factual, data driven and analytical contributions.
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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/

Snap nutnuts!

@JanglyBeads

Snap nutnuts!

How did I not see that?!

Morning!

Have we had a chart on London's positivity rate yet?

[quote Firefliess]Good summary of the findings about Omicron severity here twitter.com/jburnmurdoch/status/1473772679425581069?t=R8lOt39mRqf_SkZ7qQrNBQ&s=19[/quote]
Thank you for this, I have wondered about this point that he makes before

“ Though a tricky issue here is that since most prior infections are missed, the inability to properly control for past infection means some of what we see as "intrinsic mildness" is due to Omicron infecting lots of people with immunity via past infection that we don’t know about”

If early signs are that severity is less that's great, but the problem is that delta is still around and was also gradually growing, fuelled by festivities, prior to omnicron.

We have no way of knowing for sure that a positive test is one or the other at ground level unless we happen to be told and the impact on services through isolation is still as bad.

I hope it's not misinterpreted as large scale infection of either is still an issue for services, especially the nhs.

Schools around me (and my own and my children's) were struggling in the last month and that was through delta; omnicron was only just starting to take off in the last week here.

Though a tricky issue here is that since most prior infections are missed, the inability to properly control for past infection means some of what we see as "intrinsic mildness" is due to Omicron infecting lots of people with immunity via past infection that we don’t know about

In what circumstances would prior infection in someone vulnerable enough to require hospitalisation be missed though? How big an impact can that genuinely be? missing past infection in people who have a mild case, loads.

I agree, but it was more about acknowledging that we are talking about “people who have tested positive twice” rather than being able to put a figure on reinfection rates generally. But presumably we can at least compare with eg delta because the calculation of reinfections is based on the same parameters?

Can anyone help explain this tweet which is from the thread summarising the imperial study? At first glance it look like boosters don’t increase protection relative to 2 doses if an mrna vaccine.

That's it yes @applesandpears23 If you are infected, there's no additional protection from a booster (although almost certainly will be if it's a 3rd shot due to immunosuppression, a minority of individuals will be unknown immunocompressed) however it does reduce the chance of being infected - although probably not enough to spend every day in the pub.

Really?

Do you mean, if you're already infected, then the booster doesn't help at all? (I think that's pretty accepted.)

Or do you mean to say that the Gov't campaign to get us all boosted is not in the end supported by the data? (This will be much more controversial.)

I think the aim with the boosters is to slow the spread. The boosted are less likely to catch covid and subsequently pass it on. 2 doses isn't enough to stop the spread, especially with omicron being so transmissible but will still protect against severe illness and death. So boosters are not necessary for most on an individual level but on a population level will help.

I thought the key message had been increased protection on individual level

So is this overturned by data?

@MarshaBradyo

I thought the key message had been increased protection on individual level

So is this overturned by data?

Increased protection for the individual against INFECTION (of course if you're less likely to get infected then you're less likely to have a severe outcome) but most are still protected against severe illness and death from 2 doses, unless you're over 80 or have no immune system.

For a few months boosters will reduce the chance of infection, between something like 50-70% based on various studies. But that protection will wane (demonstrated by Israel, hence their move to 4th doses). Once you’re infected the Imperial data suggests you are just as likely as someone with two vaccines to end up in hospital.

@sirfredfredgeorge

That's it yes *@applesandpears23* If you are infected, there's no additional protection from a booster (although almost certainly will be if it's a 3rd shot due to immunosuppression, a minority of individuals will be unknown immunocompressed) however it does reduce the chance of being infected - although probably not enough to spend every day in the pub.

Thank you!

Although I wonder if that stat is a bit compromised by the fact that those having a breakthrough case and ending up in hospital now after such a recent booster are likely to be more intrinsically vulnerable. I thought it was odd that the hazard ratio was actually slightly worse for those with 3 mRNA vaccines versus 2 mRNA vaccines.

So this still stands..

‘However, when boosted with a dose of Pfizer vaccine, there was around 70% protection against symptomatic infection for people who initially received AstraZeneca, and around 75% protection for those who received Pfizer.’

IndigoC Yes, and also of course there's potential for individuals boosted the longest ago be more likely to be infected, than more recent boosting, again indicating vulnerability due to the roll out timing. It's very hard to be sure with any of the data, the error bars are large here.

However, I think the general message is still solid. All the (UK) vaccines provide long term protection against severe disease. The booster provides reduction in infection risk, but not massive amounts, it's not a licence to enter high risk situations.

Infection immunity and infection immunity combined with vaccines is even better, however that has the obvious survivor bias, and doesn't completely prevent risk.

Just to add which sounds like it’s better on on an individual level still

Yes, but symptomatic infection is not severe for most after 2 doses. A booster might change the experience from a flu type illness to a cold type illness, for example so it helps in that sense but 2 doses is what prevents you from ending up in hospital.

Please can someone tell me what are the implications for ppl with 2 doses of AZ and no booster? Not me. Family in country with no booster. My brain is broken and I can't read any more scientific papers.

@CaliforniaDrumming

Please can someone tell me what are the implications for ppl with 2 doses of AZ and no booster? Not me. Family in country with no booster. My brain is broken and I can't read any more scientific papers.

Virtually no protection against infection with covid compaired to someone unvaccinated BUT less likely to have a severe illness and very unlikely to die unless over 80 with certain health problems.

Thank you @containsnuts. Hoping the rest of the world gets boosters soon.Some of the family are over 80 :( But being very careful.

@CaliforniaDrumming

Please can someone tell me what are the implications for ppl with 2 doses of AZ and no booster? Not me. Family in country with no booster. My brain is broken and I can't read any more scientific papers.

Presuming they’ve had no prior Covid infection they would have limited to no protection from an Omicron infection but 63% less chance of being hospitalised by it than an unvaccinated infected person who caught Delta.

But this is based on early data with wide-ish confidence intervals, and likely to change considerably, as @sirfredfredgeorge points out.

Is that figure of 63% regardless of how long ago the 2 doses were received @IndigoC? There's so much conflicting data on vaccines and boosters it's hard to keep up.