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/

@Firefliess

The BBC are also reporting plans to drop the recommendation for confirmatory PCRs. I don't think there's any suggestion of not recording LFTs - I think people would be encouraged to report them and consider a positive test correct. This seems a good thing to me - with prevalence as high as it is, it's far more likely that someone with a positive LFT and negative PCR is in fact positive (ie a false negative PCR).

The sensible thing to do would be to retain the confirmatory PCR for anyone who's traveled abroad in the last fortnight in order to keep track of new variants. They're discussing the rules about traveling testing too today, so might do this.

LFT have low specificity so can show positive for other colds etc. that's why the negative PCR overrides it (high specificity for Covid)

Firefliess
"The BBC are also reporting plans to drop the recommendation for confirmatory PCRs. I don't think there's any suggestion of not recording LFTs - I think people would be encouraged to report them and consider a positive test correct. This seems a good thing to me - with prevalence as high as it is, it's far more likely that someone with a positive LFT and negative PCR is in fact positive (ie a false negative PCR).

The sensible thing to do would be to retain the confirmatory PCR for anyone who's traveled abroad in the last fortnight in order to keep track of new variants. They're discussing the rules about traveling testing too today, so might do this."

Sky News reporting similar and that PCRs will only be retained for people with symptoms. This is surely going to be a disaster unless they update the official symptoms list?

I think it is happening listening this am

David Spiegelhalter discussing it too, saying in high prevalence it makes more sense due to false positive falling

www.theguardian.com/world/2022/jan/04/non-urgent-surgery-and-appointments-paused-across-greater-manchester
All the hospitals in Greater Manchester have paused non urgent surgery and appointments because of Covid.

Re PCR I can see all sorts of confusion re that. People just doing l f t for example even when they should get confirmation from the other test - and that will affect the figures as who will bother to report the results ? Or am I missing something?

The not bothering to report the result/failing too because it's not an easy process is worrying. Mind you slightly less onerous than booking a PCR.

As long as that isn't a big issue, it may increase the number of reported positives precisely because of the number of false negative PCRs previously?

My worry is that it will serve to enforce the public's mistaken belief that all LFT results, including negatives, are 100% reliable.

Again, reports indicate this is for asymptomatic people only. My concern is that people will consider themselves asymptomatic if they don't have the official symptoms and millions with actual covid will be happily spreading away.

I do wonder how accuratly all this is being reported though. A few outlets saying the reason is to reduce the extra days isolation caused by waiting for PCR results but you could just take two days off to achieve the same? They're good at causing confusion aren't they

Whereas I'm hugely relieved, because PCRs will be rapidly available for the symptomful more vulnerable individuals who might benefit from the prophylactic drugs which are available.

England has been detecting a much higher percentage of cases than other countries without any obvious reduction in death rates, suggesting that detecting every case is not helpful. This rationing of PCR's is considerably less rationing than other countries are doing, especially as few other countries have "unlimited" free LFT's if they have any free LFTs available at all.

millions with actual covid will be happily spreading away

If the detection rate is 50%, (which is the best suggested really) and people are infectious for 1-2 days before a test, then there are already lots of people spreading it, the testing is not an NPI that reduces cases in the way hoped other than in the scenario where cases are already rare, when testing and contact tracing works.

Operation Moonshot hasn't been a great success, has it?

And I don't get the "to reduce time spent isolating ("unnecessarily")" - unless you answer the "when did your symptoms start?" PCR booking question wrongly, or fail to register your LFT positive, it doesn't!

Operation Moonshot hasn't been a great success, has it?

If it's prevented lots of people visiting vulnerable people when infectious, then it could still have, also it was likely more effective when transmissibility was lower and vaccine breakthrough much rarer - the mistake is surely believing that it's an effective strategy to prevent omicron, it's not, omicron is too transmissible, but then as I suggested above, PCR testing is equally poor at preventing omicron.

I'm not "hugely relieved" that we aren't backing up positive LFTs with PCRs, as we certainly don't want even more people spreading covid (possibly leading to a larger peak in the surge).

But I'm sure that a lot of care has gone into cost / benefit analysis, at least by the scientists and doctors and that they are trying very hard to find the least bad option to get us through this.

I guess if we don't have enough PCRs available, we have to plan according to the reality of what we have to hand.

Are there enough LFTs for all this?

@JanglyBeads

My worry is that it will serve to enforce the public's mistaken belief that all LFT results, including negatives, are 100% reliable.

This is my concern although i think this is a positive step and should free up capacity that is needed. Messaging is key.

Germany, Austria also now looking like more reliably increasing cases, increasing the evidence for European lockdowns not being sufficient for R to go below 1 against omicron.

Well, do they necessarily want omicron below 1, as opposed to decreasing the burden on healthcare services in the immediate weeks ahead, which lockdown will surely be doing anyway?

That is, decreasing the immediate burden and stress on healthcare services compared to what it would have been without a lockdown?

Well, do they necessarily want omicron below 1, as opposed to decreasing the burden on healthcare services in the immediate weeks ahead, which lockdown will surely be doing anyway?

An R of 1 from todays prevalence does almost nothing to reduce healthcare load, prevalence is already very high - and exponential growth is exponential as we keep being told. So if you need to reduce healthcare load, then a lockdown equivalent to the European countries with one would not appear to be successful.

However it could be pre-existing immunity would now be sufficient in the places well into the omicron wave, of course if the pre-existing immunity is that high, then again it points to no reduction in healthcare load as that must mean already a very high proportion have caught it.

I think even decreasing the burden on healthcare services with a lockdown is a question, it seems a big issue is staff absences and realistically in lockdown omicron would still spread amongst non locked down sectors, including healthcare. So a lockdown may prevent me picking it up at the pub but if one nurse gets it in a hospital then they can still bring down the whole shift and the fact that I am sitting healthy at home will do little to help that (since I cannot just become a nurse). The high transmissibility just means this is more likely she previously the nurse gave it to one other but not the whole team. I know our local library has shut because eight staff got it, it’s that taking down whole teams which is a problem and will remain a problem in open parts of society. Obviously you might bring down some of the burden of covid patients with a lockdown but the staffing problem seems a big one. I don’t know what the answer is but as I said I don’t think balance for isn’t falling in favour of a lockdown in very many place - Spain had over 100,000 cases yesterday, they had one of the strictest lockdowns in the world last time yet have vowed to do whatever they can to stay open this wave. It seems few are convinced you can achieve much against omicron re lockdown (Netherlands abs Austria the lockdowns are actually to deal with their delta wave not specifically to deal with omicron)

@sirfredfredgeorge

Well, do they necessarily want omicron below 1, as opposed to decreasing the burden on healthcare services in the immediate weeks ahead, which lockdown will surely be doing anyway?

An R of 1 from todays prevalence does almost nothing to reduce healthcare load, prevalence is already very high - and exponential growth is exponential as we keep being told. So if you need to reduce healthcare load, then a lockdown equivalent to the European countries with one would not appear to be successful.

However it could be pre-existing immunity would now be sufficient in the places well into the omicron wave, of course if the pre-existing immunity is that high, then again it points to no reduction in healthcare load as that must mean already a very high proportion have caught it.

Well, in terms of the European countries you were talking about, their lockdown started earlier in the wave; they would surely have had a far higher number of cases if they hadn't locked down; to some extent they have protected their population and their healthcare from the worst of the surge.

So if that was their goal, that wasn't unreasonable.

I haven't argued that we should have necessarily locked down here; if lockdown was an option that the UK had wanted, now would not be the optimum time, in terms of getting the best outcome

That is different to saying that the previous decisions in other countries had no useful effect, because their cases are rising to some extent.

The countries all locked down for DELTA, not omicron, they all had little to no omicron when they locked down (Netherlands reportedly locked down from fear of omicron on top of their delta, Germany / Austria locked down before omicron) And no, I was making no judgement about their lockdowns at all, just translating what their data shows to any other country who needs to lockdown against omicron, pointing out that the typical European measures are unlikely to stop exponential growth on their evidence.

I don't understand how people think that removing the requirements for a confirmatory PCR would lead to people going round spreading covid. The only people it affects are those who would have received a negative PCR and so are now going to be isolating, but would previously have been told (quite possibly incorrectly) that their positive LFT was an error and gone around spreading it! Seems a small improvement in terms of reducing spread to me, plus an obvious cost saving and hopefully meaning PCRs can be faster for those who need them - which is especially important now that there are drugs that can be given to the most vulnerable to help keep them out of hospital but only once diagnosed.

Fireflies I think the fear they have is that by increasing the "authority" of the LFT test, people will just use them instead of getting a PCR and the higher false negative rate of those will lead to more people out and about.

I can see the concern, I don't particularly buy it as a concern, but then I don't particularly buy the value of mass testing now anyway, too many people are already walking around spreading it completely innocently (pre-testing spread, and those where it's not detected at all)

Focused testing, mandatory masks or indoor bans if you can't mask for anyone with any respiratory illness symptoms is where I'd go now, could even be more effective (depending on the efficacy of masks) and a lot cheaper and more equitable.

It depends what stage lockdown is introduced and what you want to achieve with it. In the UK it's purpose has been to ease strain on the health service. Too late for that now. Millions are already infected so locking down will do nothing to prevent the subsequent hospitalisations. Jenny Harries mentioned a week back that restrictions could be used for purposes other than to reduce hospitalisations but to manage worforce crisis in other areas. Obviously a very unpopular suggestion and I've never seen it mentioned since.

LFT have low specificity so can show positive for other colds etc. that's why the negative PCR overrides it (high specificity for Covid)

@FrazzledCareerWoman Can you please link to any research that backs this up? I can only find papers that conclude high specificity, and no evidence that they pick up 'other colds'.