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/

Fred I'm not sure what you mean. As omicron has grown delta has declined in most countries. The graphs are from the GISAID data. I guess some countries aren't sampling variants much so numbers may be low.
outbreak.info/location-reports

@lonely, Estonia still showing 80% delta, 20% omicron right?

But During October (so 100% delta on the graph) Estonia dropped from ~1600 to ~500 in late december then it started growing to ~4000, if it's 80% delta still, then ignoring the omicron portion delta would've had to have grown faster than it ever did previously, it would still be double the peak that was seen in October - that started falling back without lockdown or anything, so with no NPI's changing, I can't see how it makes sense.

Much more logical that almost all the growth since mid December is omicron, explains the growth, explains the no change in deaths, just the sequencing graphs aren't up to date., perhaps they sequence weeks in arrears or something and the data is that old?

Well we do try to respect each others' opinions and ability to research on this long-running series of threads @Ohsofedupwiththis.

There is this in the current guidance
"You can end your self-isolation on the sixth day of self-isolation following 5 full days isolating and 2 negative rapid lateral flow test tests taken on consecutive days." which does seem quite clear....

but also this:
"You can take an LFD test from 5 days after the day your symptoms started (or the day your test was taken if you did not have symptoms), and another LFD test on the following day. If both these test results are negative, and you do not have a high temperature, you may end your self-isolation after the second negative test result"

and the examples below which is what really left me wondering - far right column, says self isolate at the top of the last beige box for Day 7, the 'end isolation' blue box is near Day 8?

And am sure when this change was first reported they said you had to wait until
midnight on the 6th day.

The graphs show the percentage of variants from the cases that have been sequenced. So if 100 cases were sequenced 80 would be delta and 20 omicron. They don't show numbers of cases.

Yes lonely, but 4000 cases, assuming they sequence a representative percentage is the 3200 delta - but 3200 doesn't match the other data (growing faster than delta has before, no increase in deaths etc.) So it's much more likely that it's not 80% delta, than delta itself has changed how it works in Estonia, between October and Late December

There is more information here:
outbreak.info/location-reports?loc=EST

In Estonia the number of cases sampled looks to be very small, so I guess may not be representative, but I think the data source is reliable.

Jangly indeed! I posted 2 replies trying to he helpful and you weren't satisfied. I don't have any links that are not available to everyone I'm afraid.

I apologise if I got a bit fed up. As I thought I was being very clear and helpful.

Jangly but the 2 things above say the exact same thing?

And the diagram also says the same thing?

If you are positive on day 5 you have to still isolate on day 6. If you do get a negative result on day 6 and then negative on day 7 you no longer have to isolate.

Basically as soon as you have 2 clear days (post 5 days) you stop isolating, or you stop isolationg after 10 full days even if negative.

My gut feeling has been that cases have actually been rising in certain parts of the country for the last couple of weeks as localised outbreaks follow the main wave (kind of like ripples behind an initial wave). But you have to really drill down into the stats to see it.

Daily cases nationally have remained almost level for the last week. But looking at the interactive case map, some areas are seeing rising case numbers again. And the data on the maps is a) 5 days behind (so today only includes data up to last Monday), and b) they only show the the trend based on a 7 day average, which introduces an even larger lag.

I think what's going to emerge in the next few days is significantly rising case numbers in school age kids, which is based upon the return to school at the beginning of the month. And then increasing number is their parent's age groups. A lot of people seem to overlook/underestimate the lagging nature of the stats.

So my prediction is case numbers continuing around 80-100k a day for some time. That sounds like a high number, but the really scary thing is that even if it continues to spread rate (which it probably won't) it'd still take 2 years before the whole population has had it.

@altmember might I assume you missed all the graphs I posted yesterday evening?

[quote boys3]@altmember might I assume you missed all the graphs I posted yesterday evening?[/quote]
I've just looked at your graphs, what are saying about them? Why isn't Cornwall on any of the SW charts?

But seems to be pockets of infections have flared up (particularly in/around primary schools). The more data you lump together, then more the finer detail gets smoothed out and missed. Even regional data isn't that useful when looking at a large regions.

You need to remember that the actual number of cases in the community is far higher than 80-100k, it will be bigger by a factor of 2 or 3, see the ONS stats.

About 1 in 25 people was positive for covid a week ago.

That is a lot of people.

Also, spread is erratic, depending on local prevalence and risk-taking behaviour.

I think considerations also come into play like variations in temperature in different areas, and population density. The South West broadly speaking, tends to be less hard hit and the North rather worse hit, is my perception.

So I'd expect spread to be very lumpy and bumpy (technical term) and to lurch on in fits and starts.

@JanglyBeads I found this helpful (if my attachment works); basically, as @Ohsofedupwiththis says, you isolate until midnight on day 10, but can end isolation early if you test negative on 2 tests, taken 24 hours apart, from day 5 onwards. In that situation, isolation ends immediately after the second negative test.

@altmember

So my prediction is case numbers continuing around 80-100k a day for some time. That sounds like a high number, but the really scary thing is that even if it continues to spread rate (which it probably won't) it'd still take 2 years before the whole population has had it.

Those are confirmed cases, not actual numbers... The ONS estimated that 3.3 million people had Covid in the week ending 15 January (1 in 20) down from 4.3 million the week before. In total c. 15 million are estimated to have had Covid since the omicron wave really got going in mid-December.... That's getting on for 1/4 of the population!

And that's not counting those since 15 January (as these aren't in the ONS analysis yet).

I saw a really useful graphic on twitter a few days ago, comparing population level immunity, and type of immunity, by age (eg 1 vaccine, 1 vaccine plus infection) in the UK and US. I foolishly didn't save it and now can't find it. Can anyone link to it? Would really like to see it again.

BA.2 is currently doubling every 4 days.

.

@lonely I don't know the source of the data, or exactly what it is, but on what is written on the graph itself it is percentage of omicron that is BA2, and whilst it's showing that it's growing, it's not showing that BA2 is doubling every day, on a simplistic assumption that all reported cases are omicron, then we have ~980 cases of BA2 on the 4th of Jan, ~500 cases on the 8th of Jan and ~1200 cases on the 14th of Jan, 2330 cases on the 16th Jan.

So whilst the absolute number is certainly growing between the 14th and 16th, and quite fast, it hadn't grown at all between the 4th and the 12th, so I don't see how we can really claim too much about how it's growing.

The proportion of BA.2 out of the total omicron cases is growing. Last week on 8th January when variants were updated on the Sanger website it accounted for 0.2% of cases. It is now approximately 2.75% of cases.

The proportion of BA.2 out of the total omicron cases is growing

Yes, but with cases dropping, that does not mean BA2 is doubling as fast as you claim.

It entirely depends which regions it is growing in and whether the BA.1 is dropping at the same speed that the BA.2 is growing. Sanger will update tomorrow and we will find out more then.

A thread on hospital situation in London:

twitter.com/rupert_pearse/status/1484811524246024194

Health metric graphs for England and its constituent NHS regions for patients in hospital and admissions. Short term comparator graphs extended out to include February - still start from December so now three months rather than two, although a mid December start point is probably the next move.

These first ones the complete years seven day average for patients in hospital and admissions for England.

shorter terms graphs for England with both seven day average and daily figures shown. All the regional graphs follow this format.