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/

There I have been severe shortages of tests in parts of the country. The government is changing the period of isolation to allow more infectious people out spreading the virus around. T cells should be protecting the 20-29s who have been vaccinated and boosted but they dont work as well in the elderly. So with waning antibodies there could be another wave, smaller but still bad for anyone needing health care.

The study trialling vitamin D as a preventive still has not been released, maybe it is being delayed until they can tell us all to get out and save aviation.

Saw this mentioned on another forum and thought I'd bring it here for the MN sleuths to investigate. Seem that the Omicron BA2 variant is increasing in Denmark even with BA1 already dominant. It's not necessarily a problem, I just think it's interesting since many thought nothing could outcompete BA1.

Yes a future summer/autumn wave was being talked about as a possibility due to waning immunity. Seems a bit unlikely to me that everyone's immunity would suddenly wane at the same time - more likely that case rates will bump along at some reasonably stable level where waning immunity is roughly balancing newly acquired immunity from infections.

The thing that looks more likely to cause a big future wave would be a new variant with significant ability to evade previous immunity from vaccines and/or infection. There's no telling when that might happen next.

So, if we are having a fall now, does anyone know if there is an actual rationale for why another wave is predicted in early summer?

Because this is how respiratory viruses work, even more so where so much of the immunity is from the low quality vaccine and not infection - vaccine immunity wanes more consistently than infection immunity because everyone got pretty much the same "dose", whereas some people with infection immunity would've been larger/smaller etc.

So once the amount of immunity in the population falls low enough to support exponential spread, then the virus starts spreading exponentially again.

Normally this coincides with environmental conditions that give a boost to the infectiousness of the virus, but with the more novel virus with lower immunity and more from the vaccine boosters which will have waned by the summer, we'll probably get it in the summer.

They are currently saying we have just passed the peak

We cannot have both "passed the peak" and have an R of 1 - unless the generation time has also extended significantly, otherwise we'd remain at the peak. R must be below 1 (or the generation time growing in a way that isn't really feasible with covid because you recover too quickly)

Seems a bit unlikely to me that everyone's immunity would suddenly wane at the same time

It doesn't need to be everyone's, just enough to bring those individuals who failed to catch it so far back into contention for infection too.

And booster immunity will likely wane at similar times other than people who already got infected as well, just as double dose was waning pretty effectively against delta before omicron came along.

We cannot have both "passed the peak" and have an R of 1 - unless the generation time has also extended significantly, otherwise we'd remain at the peak.

No but I guess although cases are beginning to come down they are still growing in some age groups and some regions so we are at a point of fine balance.

@containsnuts

Saw this mentioned on another forum and thought I'd bring it here for the MN sleuths to investigate. Seem that the Omicron BA2 variant is increasing in Denmark even with BA1 already dominant. It's not necessarily a problem, I just think it's interesting since many thought nothing could outcompete BA1.

I'm interested in this too. Meaghan Kall briefly discusses it here:

mobile.twitter.com/kallmemeg/status/1482025425635352579

One to watch I think but hopefully won't take off here.

These are the areas that the BA.2 has been found. Map from Sanger.

Sorry I should have stressed very small numbers.

Austria joining Germany and Netherlands with lockdown but cases still rising extremely fast.

Italy's deaths seem to be growing faster than elsewhere too proportionate to cases, anyone know if they have a different definition or heard of different variant of concern?

Yes I'd seen that re Italy, but no potential explanation.

See this re latest reinfection figures - implies possible 15,000 cases a day more than the current figures state?

But I don't understand the graph, I have to say. Are potential reinfections those more than 90 days after a previous positive or what?

twitter.com/tigressellie/status/1482812248246652930?s=21

The graph seems designed to confuse!

Weekly rate of possible re-infections - why not simply specify it as a percentage of all infections? That's a simple metric, easily understood, (although 16 / 1000 rate which I think the graph says is of course less than 1.6% re-infections which still seems tiny?)

The red line and the shading is of course the same data in different ways which seems strange.

Are potential reinfections those more than 90 days after a previous positive or what?

Or confirmed different genotyping, but I don't imagine that is that many as both would've needed to have been sequenced, vast majority will simply be on the difference. Would probably be interesting to have a 28 day or something cut off too to see if many delta to omicron re-infection.

Here's its source - ONS, pages 18-20.

assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1046284/weekly-flu-and-covid-19-report-week-2-2022.pdf

It's too complicated for me!

How much of the consecutive falls in daily infection figures are due to people not registering positive LFTs, I wonder?

Spiegelhalter warned about this issue when the need for confirmatory PCRs was paused.

@JanglyBeads

Here's its source - ONS, pages 18-20.

assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1046284/weekly-flu-and-covid-19-report-week-2-2022.pdf

It's too complicated for me!

For me too!

This is in the same report:
"Based on provisional figures to 2 January 2022, 315,330 possible reinfections have been
identified in England since the beginning of the pandemic and 11.5 million first positives or
primary infections are included in the figures. There were 106,297 possible reinfections
identified in updated provisional figures for week 52 (ending 02 January 2022), accounting for
9.5% of all first or possible reinfection episodes with SARS-CoV-2 that week."

@JanglyBeads

How much of the consecutive falls in daily infection figures are due to people not registering positive LFTs, I wonder?

Spiegelhalter warned about this issue when the need for confirmatory PCRs was paused.

Would people who previously would have gone to the trouble of ordering a PCR, waiting for the test, then waiting for the result now not just go online and report their positive LFT more-or-less immediately?

I can't get a feel for LFT reporting at all as I have always reported mine and felt guilty on the odd occasion when I've forgotten, assumed most people did the same and was surprised to learn that it's not that common to keep on reporting negatives.

It's clearly more hassle to go and get a PCR than it is to report a LFT online. I guess the issue is whether the change in guidance to say not to bother with a confirmatory PCR has changed people's perception of the value of positive LFTs. If they were previously getting PCRs because they didn't really believe they were positive and wanted to see if they really were that might have been the motivation, rather than being motivated to "do the right thing" which is the motivation required to register a LFT.

However, it doesn't look to me from the data that there's been any big change in behaviour around testing or reporting tests. The numbers of both PCR and positive LFTs have fallen a little in the last week, mirroring the fall in case rates and in positivity rates, like we've seen before when cases fall

@amicissimma I have ordered a pcr before. I wouldn't bother reporting positive lateral flow.

Wouldn't we see 'not reporting pos lft' in positivity rates?

If they were previously getting PCRs because they didn't really believe they were positive and wanted to see if they really were that might have been the motivation,

Wouldn't someone who wanted that confirmation still get a PCR?!

I've never recorded the result of a LFT, but they've always been negative, and I only take them for the peace of mind of the one social group I attend maskless. I get regular PCRs and antibody tests via the ONS study so am reasonably sure that I've never had Covid and have antibodies from immunisation.

Wouldn't we see 'not reporting pos lft' in positivity rates?

Yes, the main problem with that is the dashboard only has 7 day positivity rates on a big lag, so we've not got any data yet.

On the 5th, LFT confirming ones made up almost 20% of the PCR positives, but only 4% of the PCR tests conducted. That would've changed the positivity rate from 22% to 18% alone, but we may have a problem with definitions in the dashboard and dates as when we get positivity. However positivity will decline, and we should see an acceleration in the decline once this appears in the data.

If there is actually more covid around and it's simply not being found, then we'll see an acceleration in Pillar 1 positivity particularly (as there will be a higher chance people seeking care will be positive)

@treeflowercat

If they were previously getting PCRs because they didn't really believe they were positive and wanted to see if they really were that might have been the motivation,

Wouldn't someone who wanted that confirmation still get a PCR?!

Not if they now realise that if you get a positive LFT you almost certainly have covid. The messaging has changed from "some LFTs give false positives so you need a PCR to be sure" to "people with positive LFTs have covid and should isolate"

I'm sure some people might still get PCRs to check, there's nothing stopping you (especially if you've not yet registered your LFT). But it's possible that some people will feel differently about a positive LFT now that we're being told they're to be trusted.

I'm terms of positivity rates, I think there could be a bit of an issue - confirmatory PCRs were nearly all positive, so if these are no longer required you'd expect the positivity rate to fall a bit. So I guess we shouldn't read too much into a fall in the last week or so.

So I guess we shouldn't read too much into a fall in the last week or so

Where would you get the positivity rate change? The dashboard only offers 7 day rates until the 9th, which includes little to none of the changed advice testing. Even the 9th itself (which mostly wouldn't appear on the positivity graph yet as that's specimen date remember and the test positivity is date it took I believe) was over 2/3rds confirmed which is higher than the confirmed ratio on the 29th etc.