Data, Stats and Daily Numbers started 18th January 2022

[boys3]

Welcome to another instalment of the DATA thread.

Our preference is for factual, data driven and analytical contributions.
Please try to keep discussion focused on these

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/

Interesting graphs, thank you boys.

This thread has a discussion on the age breakdown of rising cases and also on gender. It appears that females currently have higher rates than males.

mobile.twitter.com/VictimOfMaths/status/1484590929138929665

Being more optimistic where are some of the councils is the regions excluded earlier.

These the five councils in the East Mids with the highest rates in the region on 4th January. Big falls all round although Blaby flattened and showing a slight upward move.

North East councils - again big falls, some slowing but most still gently falling, although with current in several instances similar to the peak rates seen in some of those earlier graphs.

One of the Cheshires always of interest, can't recollect which so both on this graph with an eclectic mis of other NW councils. Big falls both pretty flat from 15th onward.

inner London councils

[quote lonelyplanet]Interesting graphs, thank you boys.

This thread has a discussion on the age breakdown of rising cases and also on gender. It appears that females currently have higher rates than males.

mobile.twitter.com/VictimOfMaths/status/1484590929138929665[/quote]
They're have been fewer male cases reported throughout the pandemic, except for children and the oldest age groups. This isn't seen in the ONS data. I don't think it's plausible that more men get seriously ill from covid (which we've long known to be the case) and also that more are asymptomatic. Much more likely that the male tendancy to avoid dealing with health issues also means they don't test so much except when properly ill (the oldest age groups) or their mothers make them (children) There one exception to the female bias in case rates was after the Euros, which likely did reflect an actual difference in infections.

Much more likely that the male tendancy to avoid dealing with health issues also means they don't test so much except when properly ill (the oldest age groups) or their mothers make them (children)

Or they work in a profession where they come into contact with vulnerable or even just members of the public so test asymptotically more.

It would be interesting to know in the CASE rates, what the symptoms were, with over 40% overall being no-symptoms.

Or they work in a profession where they come into contact with vulnerable or even just members of the public so test asymptotically more.

I imagine this has a lot to do with it. I think what's interesting is the change in behaviour. In the thread Colin Angus noted that the age bracket is different from Autumn, when it was women up to about 40 that had higher cases. This pattern is now being seen in older age groups. I wonder what has changed.

The periods with the strongest bias towards female cases clearly coincide with the times when most children have been catching it - you can see a bit of a dip over the Christmas holidays. Likely a mixture of mothers testing themselves more when they do their children and being more likely than fathers to catch covid from their children due to closer contact.

There does seem to be a bigger divide opening up in the 45-65 age group very recently too - greater use of LFTs meaning women test more? Or more men working from home? It's the Omicron period when we know infections were less likely to result in hospital admission, so likely more people with no symptoms or very minor symptoms, and could be women more likely than men to test just to be sure, or routinely due to work, meaning the men's infections are more likely to be missed.

I do think it's mainly about testing rather than infections though - o don't think the ONS study has ever shown up much of a gender difference has it?

Just had a look myself at what the ONS infection study says on gender. www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/bulletins/coronaviruscovid19infectionsurveycharacteristicsofpeopletestingpositiveforcovid19uk/19january2022#characteristics-associated-with-testing-positive-uk

It says females areless likely than males to test positive. I guess there could be an impact in there is of women getting milder cases so not testing positive for as long (which the ONS methodology would struggle to distinguish from fewer women catching it) But does support the view that the bias in reported cases is due to men being less likely to test (or to report a positive test)

Omicron in Eastern Europe, anyone have any details on Czech Republic / Estonia etc. who had a big delta wave that had peaked and was sharply dropping has returned again - similar pattern to Germany / Netherlands etc. but the Eastern countries weren't in lockdown to get the delta wave dropped (just very strict covid passes like Estonia where you couldn't even go essentially shopping without one)

Do any of the countries provide re-infection details, is this omicron wave really just through vaccinated, or are there others?

From the government website news:
"Omicron sub-lineage BA.2 designated as a variant under investigation (VUI)

The Omicron variant sub-lineage known as BA.2 has been designated a variant under investigation (VUI-22JAN-01) by the UK Health Security Agency (UKHSA).

Overall, the original Omicron lineage, BA.1, is dominant in the UK and the proportion of BA.2 cases is currently low. The designation was made on the basis of increasing numbers of BA.2 sequences identified both domestically and internationally. There is still uncertainty around the significance of the changes to the viral genome, and further analyses will now be undertaken.

To date, there have been 426 cases of Omicron BA.2 confirmed by Whole Genome Sequencing (WGS), with the earliest dated 6 December 2021.

The areas with the largest number of confirmed cases are London (146) and the South East (97). Data for the devolved administrations will follow in due course.

Early analyses suggest an increased growth rate compared to BA.1, however, growth rates have a low level of certainty early in the emergence of a variant and further analysis is needed.

In total, 40 countries have uploaded 8,040 BA.2 sequences to GISAID since 17 November 2021. At this point it is not possible to determine where the sublineage may have originated. The first sequences were submitted from the Philippines, and most samples have been uploaded from Denmark (6,411). Other countries that have uploaded more than 100 samples are India (530), Sweden (181), and Singapore (127).

Omicron BA.2 lacks the genetic deletion on the spike protein which produces S-gene target failure (SGTF) in some polymerase chain reaction (PCR) tests, which has been used as a proxy for Omicron cases previously.

Dr Meera Chand, COVID-19 Incident Director atUKHSA, said:

It is the nature of viruses to evolve and mutate, so it’s to be expected that we will continue to see new variants emerge as the pandemic goes on. Our continued genomic surveillance allows us to detect them and assess whether they are significant.

So far, there is insufficient evidence to determine whether BA.2 causes more severe illness than Omicron BA.1, but data is limited andUKHSAcontinues to investigate.

Case rates remain high throughout the UK and we must remain vigilant and take up vaccinations. We should all continue to test regularly withLFDsand take aPCRtest if symptoms develop."

@sirfredfredgeorge

Omicron in Eastern Europe, anyone have any details on Czech Republic / Estonia etc. who had a big delta wave that had peaked and was sharply dropping has returned again - similar pattern to Germany / Netherlands etc. but the Eastern countries weren't in lockdown to get the delta wave dropped (just very strict covid passes like Estonia where you couldn't even go essentially shopping without one)

Do any of the countries provide re-infection details, is this omicron wave really just through vaccinated, or are there others?

In the Czech Republic, omicron has just overtaken delta. Delta still looks at about 20%.

Estonia looks to be further behind with their omicron wave.

Poland

Can anyone post CLEAR guidance as to when you come out of iso if negative on day 5/6... or 6/7? I can't find-any! Need for a colleague.

The NHS coloured diagram of examples- says “self isolate” at top of (eg) day 7 but also end isolation if test negative that day.
Was sure I’d read that when they changed 7 to 5 days you couldn’t leave til day 6?
Thanks.

@lonelyplanet re BA.2

en.ssi.dk/news/news/2022/omicron-variant-ba2-accounts-for-almost-half-of-all-danish-omicron-cases

"The subvariant BA.2 accounted for 20% of all covid-19-cases in Denmark in week 52 increasing to approximately 45% in week 2. During the same period, the relative frequency of BA.1 has dropped."

"Initial analysis shows no differences in hospitalisations for BA.2 compared to BA.1. Analyses regarding infectiousness and vaccine efficiency etc. are ongoing, including attempts to cultivate BA.2 in order to perform antibody neutralization studies. It is expected that vaccines also have an effect against severe illness upon BA.2 infection."

Seems to be outcompeting BA.1 in Denmark. Maybe more transmissible but hopefully not more deadly?

*Jangly. You isolate for 5 fulls days. So if test positive today, its day 0. Tomorrow is Day 1 and Thursday day 5. You would take a test on Thurs morning and if that was clear and then Fri morning also clear, you can come out if isolation. Its 10 full days if LFTs positive. So following Wed if 10 days.

Hope that makes sense.

This is the Denmark picture. It may explain why cases in Denmark have continued to rise even though they started their omicron wave at the same time we did.

UK as a comparison.

But my question is do you come out of iso the day you get your second negative or the following morning? Am sure I read something about the latter when this new change was brought in!

So if day 5 is Thurs in example above, you come out on Friday morning. So day 6. If you are still positive you need to isolate until you get to clear tests or completed day 10.

Dd tested positive on 16th. She has to isolate up to and including 26th.

If 2 negative tests She could have left isolation today (she isn't).

Do you have a link to clear guidance Ohso?

@lonely those graphs on delta vs omicron look extremely dubious to me, if it's true, what happened to bring delta to a fraction of their previous rate, but then start growing almost as fast as omicron?

Are they perhaps just missing the recent data?

@JanglyBeads

Do you have a link to clear guidance Ohso?

Google covid isolation and pull up the gov.uk page?

You get told when your las6 full day of isolation is (for 10 days).

You can then easily work back.

To be honest I am not sure what's so difficult?