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/

42% of admissions are now infants (compared to 30% previously).

But still suggesting it is very mild.

@lonelyplanet

This risk assessment for omicron has been updated. For the first time there is an extra row at the bottom for children.

Does anyone else find that colour system weird?

Ah no I'm reading it wrong. As you were!

Child band is a little concerning tbh

This graph shows the ons estimated data plotted against the case rolling rate. Is is interesting to see how much it has diverged in the last few weeks.

The previous time case rates were quite a bit higher than ons estimates was in July. I wonder whether there is any significance to the fact that in July and now, the highest number of cases was in the 20 to 29s group. Could it be possible that they are not well represented in the ons study?

@WarriorN

Ah no I'm reading it wrong. As you were!

Child band is a little concerning tbh

This is from today's variant surveillance report:

"The number of paediatric admissions with COVID-19 infection began to rise from 26 December
2021, from an average of 40 admissions per day to 120 per day, a 3-fold rise in 2 weeks.
Further analysis by age group shows that the rise is most rapid among children under 5 years,
and highest in infants aged under 1 year (Figure 9). This data is for all COVID-19 infections
including all variants, but it should be noted that Omicron represented over 90% of sequenced
samples in the UK from end November 2021 (Figure 5). The top 3 complaints on hospital
attendance records for children under 5 remain consistent with respiratory infection."

The numbers are relatively small and I'm sure someone will come along and say these numbers would be expected with the high level of infection in the community. However it doesn't make it right, or a good thing.

Also in the variant briefing report was news of the BA.2 lineage of Omicron . This maybe one to watch as it is dominant in Denmark. It is still in small numbers here but growing and can't be identified through pcr testing.

"SGTF patterns can be used to assess the spread of Omicron lineage BA.1. The number
of COVID-19 cases with S-gene positive/SGTF by day, among those tested in TaqPath labs is
shown in Figure 4. The Omicron lineage BA.2 does not contain the spike deletion and therefore
is S-gene positive (SGTP). By 1 January 2022, BA.2 accounted for 5% of SGTP and this
proportion is increasing. Therefore, SGTF is no longer sufficient to assess the spread of
Omicron as a whole."

The numbers are relatively small

20,000 typical year RSV admissions in under 1's, and that's treated for RSV, on "with RSV" there, almost all in a ~4 month winter period, so that's at a higher rate than covid is now even if all the under 5's cases were in under 1's. So yes, pretty small, especially as we know a non-zero proportion of them are not admitted for covid, unlike all of the RSV admissions.

The elderly groups are much more concerning to me, especially without any evidence that it's not simply correlated to prevalence. prevalence has risen by more than 3-fold, so admissions increased less than expected if it was purely prevalence related.

This maybe one to watch as it is dominant in Denmark. It is still in small numbers here but growing and can't be identified through pcr testing

How do they know it's dominant in Denmark, do they not use PCR testing? And if it's not detectable by PCR's, that must mean Denmark's true rate is over 12% of the population known to be infected - as Denmark's PCR rate is almost 6% and this must be more than double if it's dominant? That's not credible - so what do you mean by not detectable by PCR?

I didn't mean covid isn't detectable but that the variant couldn't be identified because it doesn't have missing spike gene.

There's a noticeable difference there to previous trends lonely.

I'm also aware that parents tend not to test under 5s as lft aren't mandatory, its extremely difficult (I have an under 5) and the previous ph information has been that children are not as at risk and that symptoms were more cold like or asymptomatic.

I know that I certainly can't test my son for every small cold he gets, which is a lot.

mobile.twitter.com/kallmemeg/status/1482025425635352579

This thread has details on the variant report and mentions the fact that the BA.2 is dominant in Denmark.

Thanks Lonely!

Good news for anyone worried about the Aland island outbreak, beginning to look like it's peaked and still no deaths.

Still no complete confidence that Denmark has peaked, but they're re-opening cinemas and theatres (about their only restriction other than covid pass and isolation) but also going 4th booster.

Netherlands deaths have dropped properly after their lockdown despite the omicron surge, but Germany still has high deaths (over 350 a day) despite now a long time after the lockdown from delta, I imagine that will make it harder for them to unlock - does it suggest there's more than omicron for the recent spread, or is the lockdown not really worked as well against delta as elsewhere?

I haven’t been on these threads for a long time, but I wondered whether anyone had investigated or discussed the divergence in trends between reported deaths and numbers on ventilators. For most of the pandemic it’s been a clear pattern: higher cases are followed by higher hospital numbers, then higher numbers of seriously ill and finally, higher numbers of deaths (albeit with vaccinations massively reducing numbers seriously ill overall). Over the last month though numbers ventilated have been flat or decreasing, but deaths have risen sharply.

I wondered whether this is a definition problem: people who have tested positive in the last 28 days but where Covid is not the cause of death are being included in the reported figures? This explanation is I think backed by the ONS data where numbers with Covid as cause on a death certificate have also decreased.

Thoughts?

Part of it is an increase in "with covid" coincidental deaths due to the huge percentage of people who have had covid in the last 6 weeks.
See some discussion here
www.bbc.co.uk/news/health-60000391

The other is the deaths from covid now are also more heavily in the vulnerable groups who die when a winter respiratory virus comes along, these groups are mostly too sick to have value in ventilating, ventilation is pretty horrible, I'm sure it's also used less on more marginal cases too as people are talked through the consequences.

But basically, because the vaccines reduce the risk so much, only the very much sicker would tend to die in a way that ventilation was a possibility to help, but it is still covid killing them, even if there's a good chance they might've died in a normal year from the flu - equally their pre-immunity from the flu strains might've given them a few more years.

Another difference on he pattern that is relevant is that admissions peak the same as cases, this is also a good sign that more of the cases are coincidental, as otherwise there would be more of a lag as the people who tested positive X days before deteriorated such that they needed hospitalisation.

Thanks for the link and explanation @sirfredfredgeorge, I’d not seen the BBC article when I posted, but it explains much more clearly the thinking behind my previous post. I 100% agree with the conclusion that death certificate information will increasingly be the only reliable statistic for measuring direct Covid deaths.

I’d also not thought about the very unfortunate “too frail to ventilate” group, so that’s helpful in explaining it too.

" I 100% agree with the conclusion that death certificate information will increasingly be the only reliable statistic for measuring direct Covid deaths."

Unfortunately I don't think this will be particularly reliable. I have heard many complaints from bereaved relatives that Covid was put on their loved one's death certificate although there was no indication at all that the deceased had Covid at all. Early on the in the pandemic it was very common for doctors to put it on death certificates of Care Home residents leading the poor managers to struggle to convince people that there were, and never had been, cases in their Home.

Only a few months ago one of my ILs died having been tested twice weekly while in her Care Home and daily for weeks while declining in hospital, never tested positive and yet the doctor put Covid on the death certificate. Her DD was livid and got it removed, but it took a lot of fight, which most people can't cope with when they've just been bereaved.

It seems to matter a great deal to people that their loved ones' deaths are recorded correctly.

There are going to be many deaths not recorded properly - those who died because they didnt get health care, or got it late, or got substandard care from overworked staff trying to do the work of 2 because colleagues were sick with covid. I doubt those people will be fighting to have covid on the death certificate but it will be what killed them.

At the start of the pandemic, testing was very limited so it’s understandable that whether it was Covid or not was guesswork for doctors.

I agree that most relatives care what goes on the certificate. Also, I think the vast majority of doctors are ethical professionals who are genuinely trying to get it right (no, I’m not a doctor!). So what goes on the death certificate will not be perfect, but in most cases is likely to be pretty reliable and hence the best source of data over time.

I think NE and NW have surpassed Londons rate?!

@boys3

Seen this - R rate falling to 0.6 suddenly???

twitter.com/i_petersen/status/1482467764442914825?s=21

Do we know if they are isolating? Because some might avoid elderly parents but otherwise carry on as normal.

It's still on the up in some areas of the NE so I can't imagine its just behaviour based