Data, Stats and Daily Numbers started 1st January 2022

[boys3]

Whilst I'd love to say all is quiet on New Years Day the reality is:

Welcome to yet another DATA thread.

Our preference is - still - for factual, data driven and analytical contributions.

Please try to keep discussion focused on these.

All the usual links below; New for '22 suggestions always welcome, and there may well be some that just need to go.

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/

North West

South East

South West

Just so I understand @boys3 Are your using the term hospitalisation to mean the number of hospital beds occupied?
(I'd always understood it to mean the number of people hospitalised, which is synonymous with admissions, but clearly I'm missing something as your charts show two different measures)

Now I find those admission figures worrisome, whilst obviously much better than 2020, in the beginning of 2021 we headed for lockdown hence the flattening of the curve. If we continue as we are with plan B, what will flatten the curve?

Additional note, am very stressed, just had confirmed staff for tomorrow, years 8,9 will not be having any specialist teachers as we try to cover years 10 and above and that depends on staff movement within the MAT.

@Firefliess

Just so I understand *@boys3* Are your using the term hospitalisation to mean the number of hospital beds occupied? (I'd always understood it to mean the number of people hospitalised, which is synonymous with admissions, but clearly I'm missing something as your charts show two different measures)

@Firefliess patients in hospital as per the dashboard. Would have been easier if I had called the graph that to avoid confusion. :)

@Regulus

Now I find those admission figures worrisome, whilst obviously much better than 2020, in the beginning of 2021 we headed for lockdown hence the flattening of the curve. If we continue as we are with plan B, what will flatten the curve?

Additional note, am very stressed, just had confirmed staff for tomorrow, years 8,9 will not be having any specialist teachers as we try to cover years 10 and above and that depends on staff movement within the MAT.

Herd immunity from both vaccination and past infection will flatten it eventually, as it's already done so in London, and then make it fall gradually. Hospital admissions are a lot lower per case than they were last year, so it's viable to let that happen this year. I think it's the only realistic way forward as anything the government can do to lockdown will just spread the pain out over longer (as well as causing additional hardship via the lockdown measures themselves) But it is going to mean a rough next few weeks for a lot of people. Hope you manage to sort your staffing difficulties out.

Thanks firefliess I do hope you are right, my thoughts generally are skewed by work, but then our area is on the upward trajectory.

Netherlands certainly looks like cases are rising and not an artifact of holiday testing - anyone know what's happening with their lockdown?

Germany up slightly again, but not the same turn around - should maybe look at regional data there to see if there's omicron spiking against their lockdown some places?

Denmark, France, Spain, Aland islands all going up faster than here it seems (testing differences so who knows for sure) and to a higher probable level - the delta wave over the summer and autumn putting more of a brake on things here?

I thought that previous delta infection wasn't very protective against omicron?

www.imperial.ac.uk/news/232698/omicron-largely-evades-immunity-from-past/

So it does still offer some protection.

We also had higher vaccine uptake than many European countries and were well ahead on boosters going into Omicron.

Regarding the trade-off between transmissibility and severity referred to by NutNuts and others, there is actually a link for omicron. Just not related to an evolutionary model. Omicron infects and multiplies much more easily in the upper respiratory tract which confers its greater transmissibility. However the lower respiratory tract (ie the lungs) are relatively spared which results in less severe disease.

Not sure that study is peer reviewed yet but, to add, this is also the suggestion as to why nose only swabs might not be great at detecting omicron - was in an article posted quite a bit upthread.

@Quartz2208

www.imperial.ac.uk/news/232698/omicron-largely-evades-immunity-from-past/

So it does still offer some protection.

That article is titled "Omicron largely evades immunity from past infection or two vaccine doses"

"protection against reinfection by Omicron afforded by past infection may be as low as 19%"

So very little protection?

We also had higher vaccine uptake than many European countries and were well ahead on boosters going into Omicron

Not Denmark for sure, on either level, although boosters is an interesting one, as boosters are very much waning for protection against symptomatic omicron, so being early on boosters may not be an advantage in spread, but Denmark is on about 105% doses, to our 100% doses and is doing it twice as fast currently.

On protection from past infection - we don't have reliable data because we still don't have re-infections published in London particularly where it would be useful - However, we do have re-infections included in the welsh data, if re-infections were significant, we'd see Welsh data being much higher than England. (Unless of course the different NPI's in Wales happened to reverse it, despite those same NPI's doing nothing in European countries)

The imperial estimate particularly looks dubiously ineffective, given other estimates in other countries data too but we don't know.

Front page of the i today:

"PM admits NHS will come under considerable pressure in the coming weeks but suggests Covid-related shortages can be solved by moving NHS workers around the country"

Anyone have any ideas why this might not work? 🤔
🤦‍♀️

On protection from past infection - we don't have reliable data because we still don't have re-infections published in London particularly where it would be useful - However, we do have re-infections included in the welsh data, if re-infections were significant, we'd see Welsh data being much higher than England.

Fred - Cases in the last 7 days per 100,000 from the dashboard. Wales is significantly higher.

The do publish the reinfection data in the weekly reports. I think the vaccine minister was saying in Twitter it was about 7% of all cases currently - so you're right, not a huge impact on overall trends.

Re NHS staff being moved around. I don't think there are any plans to move people around the country (for obvious reasons!) But there are certainly plans to move them around between roles - eg to redeploy staff from outpatient roles into covid wards as happened last year. My nurse friend is less worried about this this year as she says she now knows what she's doing on an ICU ward - she didn't last year and found it a rough and steep learning curve.

lonely snapshot of timing of waves there though I think, NI doesn't have re-infections and it's even higher, so you first need to control for those things - so you need to look at the total infections in a corresponding part of the wave in a reasonably similar area.

London still higher than Wales despite dropping now - obviously having an England rate that includes London but also all the people in Torridge with their low rates is no good for the comparison.

Cardiff might be similar to London? But Cardiff rates are lower than London still too, and a lot lower than London's peak - but I don't think Cardiff is likely to have reached its peak yet, or any of Wales, particularly as we've not had data for awhile.

Going back to protection why was it mentioned as a benefit that SA had high infection previously?

Delta included but proportion compared to beta?

lonely snapshot of timing of waves there though I think, NI doesn't have re-infections and it's even higher, so you first need to control for those things - so you need to look at the total infections in a corresponding part of the wave in a reasonably similar area.

Fred you are absolutely correct, which is why your statement about Wales was nonsensical.

which is why your statement about Wales was nonsensical

How was it nonsensical, just because you can't see it in a single snapshot at the time, doesn't mean that the data difference of reinfections included vs not included will not be able to be identified in the data. You just need to do the work to control for that wave timing - as soon as we have peaks it won't even be a hugely difficult control (area under the curve between start and peak will go a long way to doing it) and if re-infections are significant (ie previous infection provides little or no protection) then it would obvious. All you can't do is look at a snapshot.

There is no evidence in the data that I could find that re-infections are significant. Which would give the conclusion that past infection still gives better protection than vaccine against omicron, despite imperials claim.

Is there a better study than Imperial looking at reinfection rates, in your opinion?

There has been some chat on Twitter about a new variant B16402 - worrying because it sounds more severe than omicron. Wondered if knowledgeable data people on this thread had any thoughts about whether it could/would replace omicron? Perhaps less infectious? see eg twitter.com/OAlexanderDK/status/1477767585202647040

(apologies if already discussed, I dip in and out of this thread and find it very helpful)