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/

Here's another image of Alasdair Grant's, showing London rocketing ahead.

Also found myself looking at the below site. It shows case rate of 1 in 92 in Lewisham as of the 9th Dec, up from 1 in 159 on 1st Dec.

Case rate of 1 in 65 in Central Bedfordshire on the 9th, up from 1 in 76 on 1st Dec.

coronalevel.com/United_Kingdom/England/London/Lewisham/

coronalevel.com/United_Kingdom/England/East_of_England/Central_Bedfordshire/

I think Mumsnet shrank the image but it's here:

twitter.com/AlastairGrant4/status/1469362287291080711

Will we be looking for a proportionate decline in delta numbers as omicron rises to see if it squeezes delta out?

But if as said by pp (piggy or Fred apologies forgot) you can catch delta after omicron, and omicron after delta, how will delta be squeezed out? What happens if you catch both at once?

Hospital admissions up in every area. Biggest increase in the East.

See here for possibility of new restrictions next week, also simple ‘graphic’ apparently showing SAGE projections as to when we need to take measures if we want to avoid X,000 hospitalisations a day….

www.theguardian.com/world/2021/dec/10/stringent-uk-covid-measures-needed-within-a-week-leak-reveals?CMP=Share_iOSApp_Other

Here is the thread about the vaccine effectiveness study:

twitter.com/freja_kirsebom/status/1469350543172771852

@Firefliess

If Omicron can reinfect people who've had Delta and it seems likely to be that Delta will also reinfect people who've had Omicron, so we'll have both going at once with not a lot of out competing going on. Though any measures we take to pull cases down will of course with for both variants

this made my head want to explode like in the film 'scanners'

this is a generally calm and v helpful thread, thanks to all who toil to keep it going

Rank Area Rate R
1 Hackney and City of London 518 1.30
2 Barking and Dagenham 494 1.29
3 Southwark 563 1.29
4 Lewisham 591 1.27
5 Lambeth 591 1.24

If 30% of cases are Omicron, and Delta is an R of 1 - then how are the R rates above so low?

Not as impressed by 75% btw, individuals who have had a booster in the time period are likely to have a different risk profile (although may also do more as they've been boosted, but I think this is less likely due to the easy availability of booster to those who'd do it) and also it's immediately after a booster, let's see what happens in 2 months.

@sirfredfredgeorge

*Rank Area Rate R 1 Hackney and City of London 518 1.30 2 Barking and Dagenham 494 1.29 3 Southwark 563 1.29 4 Lewisham 591 1.27 5 Lambeth 591 1.24*

If 30% of cases are Omicron, and Delta is an R of 1 - then how are the R rates above so low?

Hmm, I think maybe he said the case figures are based on past 3 days figures. But for the R0 rate is from two days earlier.

He mentions it here though talking about another chart:

twitter.com/AlastairGrant4/status/1469360994841513990

My other confusion with the "3 day doubling time" is
www.theguardian.com/world/2021/dec/09/south-african-covid-cases-up-255-in-a-week-as-omicron-spreads

So what's preventing the spread in South Africa to limit it so much? They haven't introduced any restrictions - which means informal are enough to have huge impacts, which doesn't really tie with the "more transmissible, as informal doesn't move the needle against Delta or Europe wouldn't've needed to introduce more restrictions.

Obviously SAs data may not be the best with the very inconsistent data, but the positivity rate hasn't changed?

The 1.3 R in the London boroughs, is an R rate we've seen across most of Europe at various times with Delta over the last couple of months, it's not unusual at all at regional levels.

I do think a vaccine resistant variant is hugely worrying - the low effectiveness of vaccines has always worried me (and why I've consistently thought that we shouldn't be using them in a foolish errand to prevent infection but using them on people who will get sick) but the evidence for the case numbers provided is not in the data provided.

"get really sick"
btw
the low effectiveness of the vaccines don't prevent you getting sick either.

So the R forecasters here:
epiforecasts.io/covid/posts/global/

Have South Africa at an R now 0.78 - 1.9 most likely 1.3, only slightly above Denmark, it has other countries in Southern Africa higher, as it had South Africa itself higher before, but it has SA dropping back from peaking in mid November (peaking in R terms, R is still above 1 so cases still rising, but not at anything like the same doubling rate.)

Now of course they're a model, it's all estimates etc. others could be right, but it just echoes some more that the numbers are not quite matching the narrative anywhere.

Has there been any data if previous infection gives you some immunity against delta?

I am thinking mainly kids, especially the youngest who haven't been vaccinated.

I know reoinfection is higher than Delta, but do we know the percentage of people who may get reinfected?

London didn't have a massive Delta wave? Is this rise due to waning immunity for infection prior to Delta?

@sirfredfredgeorge

So the R forecasters here: epiforecasts.io/covid/posts/global/

Have South Africa at an R now 0.78 - 1.9 most likely 1.3, only slightly above Denmark, it has other countries in Southern Africa higher, as it had South Africa itself higher before, but it has SA dropping back from peaking in mid November (peaking in R terms, R is still above 1 so cases still rising, but not at anything like the same doubling rate.)

Now of course they're a model, it's all estimates etc. others could be right, but it just echoes some more that the numbers are not quite matching the narrative anywhere.

He's posted a bit more. Maybe he's just shooting high then:

"Probable Omicron cases make up 11.4% of the 12.8k COVID samples from 8th December for which SGTF data are available so far.
That would equate to 5600 of the 49k cases in England reported today

Growth since 23rd November indicates R = 5.1 (CI 4.2 - 6.3)
Doubling time of 2.1 days"

twitter.com/AlastairGrant4/status/1469451643167121416

"R for Omicron in England is estimated to be 3.7 (between 3.3 and 4.2).

This means that each person who is infected with Omicron goes on to infect 3.7 more.

Even with a highly vaccinated population (although one where most have not been boosted)."

twitter.com/Dr_D_Robertson/status/1469443206404317186

If four days ago in some part of London you had 70 new Delta cases and 10 Omicron, and now you have 70 new Delta cases and 30 new Omicron, that would give an overall r rate of about 1.3, and the Omicron now at 30% but the Omicron has tripped. In another four days you'll have another 70 Delta (assuming r of exactly 1 for Delta) and now 90 Omicron - r rate now nearly 2 because it's becoming more Omicron.

This from John Burns Murdoch.

Walked past a pub in Southwark on my way to the late night shop, it was rammed! And why not, eh.

Latest predictions from Andrew Lilico.....

mobile.twitter.com/andrew_lilico/status/1469471597052452874

@Ohsofedupwiththis

Has there been any data if previous infection gives you some immunity against delta?

I am thinking mainly kids, especially the youngest who haven't been vaccinated.

I know reoinfection is higher than Delta, but do we know the percentage of people who may get reinfected?

London didn't have a massive Delta wave? Is this rise due to waning immunity for infection prior to Delta?

What I have picked up on this is that reinfection rates are fairly low 1% (I think?) but delta requires high circulating antibodies to resist reinfection and these typically wane quite quickly for coronavirus (hence boosters), I'm assuming that omicron is the same if not more so due to the huger transmissibility, (waning immunity applies also for the unvaccinated who have had wild infection.) Further when we look at cold coronavirus the typical immunity provided is averaging just months, one study IIRC 9 months, but with COVID-19 children are not reliably seroconverting and in addition there are questions around delta providing immunity for omicron. Because covid is still novel and variants are w new erm, variable, we have to watch and wait.

Personally I feel jabs or prior infection should been seen as one layer of protection along with all others available including ventilation, decent masks, testing etc

Walked past a pub in Southwark on my way to the late night shop, it was rammed! And why not, eh.

Loads of people will be blissfully unaware of what is going on nationally, or in their area. MN makes one think everyone is highly engaged in news and information. As a teacher, I am increasingly astounded by what people (in which I include 18 year olds and adult colleagues) don't know.

I’m not sure at this point why the Southwark pub wouldn’t be rammed.

What behaviour change are people expecting?

It may not be lack of awareness either but idea of personal risk - young etc not worried

Or enjoy our freedom whilst we can
Or it's just a mild thing they are over reacting
Or it won't affect me and people who hide away are evil and killing the economy and all that relies on it

There are many different quite logical reasons for a full pub

Tbh I’m not changing my behaviour and I’m fairly aware, many on here will be the same.