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/

Delurking - the only children’s hospital I know much about is GOSH (via work) - and they take in a lot of children because of the ICU capacity which may not be available in other areas. Not just the particularly specialist or long term cases. It’s hard to extrapolate to any understanding of what is going on generally as many have said.

First figures of the new year for Scotland, 20,217 positive results. Test positivity 34.9%.

@Perihelion

First figures of the new year for Scotland, 20,217 positive results. Test positivity 34.9%.

Is that three days' worth of cases though? If so it's not too bad, as they were up to 16k in a day on the 30th. Positivity very high! But I really do suspect a lot of people are using LFTs for minor cold symptoms, getting a PCR if positive and assuming they're ok if negative.....

@Perihelion

First figures of the new year for Scotland, 20,217 positive results. Test positivity 34.9%.

Scotland's last reporting date was 31 December though, so how many of those cases are catch-up?

The link below says the following for Scotland thus far:

"Looking at the data they've had high numbers for the previous 2 days too!
1st - 17,065 (27.1% positivity)
2nd - 14,080 (31% positivity)
3rd - 20,217 (34.9% positivity)"

and fewer tests done on the 2nd.

twitter.com/gamccormack/status/1478010459513049088?s=21

@ToofFairy

Asking here as I'd like an answer backed up by some facts.

Theoretically can coronavirus mutate into something much worse? I've seen a few things being said about this, either:

• No, it will only mutate into something milder and eventually be like the common cold.

• Yes, it has the potential to mutate into something significantly worse.

• It has some limited potential to mutate and it might be worse, but only in a mild/moderate way.

The direction of travel with Alpha and Delta has been towards more immune escape and/or more transmissibility because they both give the virus an advantage in that they help the virus to spread.

Severity has no effect either way on the virus's ability to spread.

There's no advantage for the virus to become milder.

There's no advantage for the virus to become more severe.

(Because the illness part happens after spreading has already happened.)

Mutations are random and they only become dominant if they have an advantage over the current dominant strain.

So, the next variant is likely to be more transmissible and have more ability to evade immune escape than Omicron...

But the severity is a dice throw, a coin toss.

It could go either way.

It just depends what mutations that relate to severity happen to be on the variant that has enough transmissibility and immune escape to trounce Omicron.

There is absolutely no evidence anywhere that the SARS Cov2 virus is on a path of becoming intrinsically milder.

Apologies, that should read evade immunity

But the severity is a dice throw, a coin toss

This isn't really true, because transmissibility is related to severity, if a virus is so debilitating to its host that the host can no longer move around, then transmissibility goes down.

If HIV killed in weeks (higher severity) it would be way less prevalent than it is. With a respiratory virus we certainly don't have the more obvious severity limitations seen with other types, however transmissibility is not fully independent to severity.

@sirfredfredgeorge

But the severity is a dice throw, a coin toss

This isn't really true, because transmissibility is related to severity, if a virus is so debilitating to its host that the host can no longer move around, then transmissibility goes down.

If HIV killed in weeks (higher severity) it would be way less prevalent than it is. With a respiratory virus we certainly don't have the more obvious severity limitations seen with other types, however transmissibility is not fully independent to severity.

When the transmission happens before any signs of severity occur - as it always has so far with covid - the two factors are independent from each other.

HIV does this very well.

With SARS 2 it's a matter of days with HIV it's decades.

But that's because you need close contact with bodily fluids to catch HIV so transmission is one person at a time.

You can infect multiple people with SARS 2 just from breathing.

The infected person doesn't even have to be present to infect multiple people so long as their exhaled air is still floating about the room/lift/office/classroom.

When the transmission happens before any signs of severity occur - as it always has so far with covid - the two factors are independent from each other

But "always so far" is irrelevant, it's not independent, it's not as intertwined as with non-respiratory viruses, but it's still not independent - hence at random mutations will not simply be a coin toss - some of the coin toss severity increasing mutations will kill the host the virus mutated in before it has the opportunity to spread. A severity increase mutation which shortened the time period between infection and death will reduce the time walking around to be able to spread it.

That's not to say that it's not possible for a mutation to be both more severe and more transmissible, it's just that severity and transmissibility are not the independent variables you claim so it's not simply a coin toss.

We have many kids who are 2 now catching their 1st bugs so I am not sure this is really unexpected - not Covid per se, but paediatric admissions.

I do think this needs to be taken into account. I've been in hospital with my son this winter for other (not Covid) respiratory viruses and they (they being multiple different HCPs) have told me they were expecting an increase in childrens admissions this year due to the lack of mixing last year. I don't think this has been totally unexpected, or at least that was the impression I got from the doctors and nurses I spoke to in our local children's hospital.

This year being 2021 and last year being 2020 (I'm still not with it in terms of it being 2022 now 🤦‍♀️)

157k cases, but that doesn't include NI or Wales.

@sirfredfredgeorge

When the transmission happens before any signs of severity occur - as it always has so far with covid - the two factors are independent from each other

But "always so far" is irrelevant, it's not independent, it's not as intertwined as with non-respiratory viruses, but it's still not independent - hence at random mutations will not simply be a coin toss - some of the coin toss severity increasing mutations will kill the host the virus mutated in before it has the opportunity to spread. A severity increase mutation which shortened the time period between infection and death will reduce the time walking around to be able to spread it.

That's not to say that it's not possible for a mutation to be both more severe and more transmissible, it's just that severity and transmissibility are not the independent variables you claim so it's not simply a coin toss.

mutations that will kill the host the virus mutated in before it has the opportunity to spread don't become globally dominant, and would die out pretty fast if they couldn't spread, wouldn't they?

It is my understanding that there is no inherent trade off between transmissibility and severity with SARS 2. Or with viruses in general.

@pussycatunpickingcrossesagain

157k cases, but that doesn't include NI or Wales.

Noticed it doesn't include the catch-up figures that JanglyBeads linked to either. I thought when cases were reported late they were added into one final figure, so Scotland's figures for 1st and 2nd would be added to those reported on the 3rd? Just checked and I am wrong on this, they are retrospectively added to the day they should have been reported. Is this a new change?

[quote JanglyBeads]The link below says the following for Scotland thus far:

"Looking at the data they've had high numbers for the previous 2 days too!
1st - 17,065 (27.1% positivity)
2nd - 14,080 (31% positivity)
3rd - 20,217 (34.9% positivity)"

and fewer tests done on the 2nd.

twitter.com/gamccormack/status/1478010459513049088?s=21[/quote]
And there's still catch-up cases to add. Then there will be the New Year numbers and schools going back in a few days on top.

"And there's still catch-up cases to add. Then there will be the New Year numbers and schools going back in a few days on top."

My prediction for London was for a 4th peak on Tuesday or Wednesday this week, based on spreading on NYE (matching previous peaks a few days after the weekends before christmas and after christmas day, and I thought we'd see the first stirrings in LFD's today in London with an increase, but it hasn't happened. Maybe shortage of tests still, maybe my prediction was wrong and the size of the peak will be lower than I thought. Or maybe it just is a squeeze too early for the LFD's to be positive and the previous time it was down to mixing on christmas eve / thursday etc. If not though, then I think we can be pretty sure London has exhausted the easy to infect with omicron.

104 increase in hospital today in London, so not as good a pattern as the weekend, but I don't know if bank holiday could've impacted that, admissions today fell again, but we knew that was likely from the small increase in in-patients over the weekend.

Like London for the whole of England back to just over 1000 increase in in-patients after a lower weekend, still no appreciable rise in mechanical ventilation (lower than any period since August other than a few weeks in late september / early october)

health metrics in England.

These are admissions - 2020; 2021 and now start of 2022

plus comparisons for just December - January on a seven day average basis and actual daily numbers.

hospitalisations using the same three graph formats

deaths within 28 days by date of death full year and the seven day average for the Dec-Jan period. 7 day average up to 28th December

admissions and hospitalisations for each NHS England region. These cover just Nov-Jan (with 2020/21 comparison). Each graph shows both the 7 day average and the daily number for the current and previous time periods.

Starting with the East of England

London

Midlands

North East and Yorkshire, one of the most dramatic increases