Data, Stats Thread June 11

[PatriciaHolm]

UK govt pressers Slides & data

www.gov.uk/government/collections/slides-and-datasets-to-accompany-coronavirus-press-conferences#history

Data Dashboard coronavirus.data.gov.uk/
Covid 19 Genomics www.cogconsortium.uk/tools-analysis/public-data-analysis-2/
Covid 19 Variant Mapping Sanger Institute covid19.sanger.ac.uk/lineages/raw
NHS Vaccination data www.england.nhs.uk/statistics/statistical-work-areas/covid-19-vaccinations/
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 MSAO Map English deaths www.england.nhs.uk/statistics/statistical-work-areas/covid-19-daily-deaths/
CovidMessenger live update by council area in England www.covidmessenger.com/
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/

⏭ Our STUDIES Corner ⏮ www.mumsnet.com/Talk/coronavirus/3869571-Studies-corner?msgid=99913434

We welcome factual, data driven and analytical contributions
Please try to keep discussion focused on these

I guess it is again due to the k-factor.

A few superspreaders will have numerous "close contacts" and will transmit easily in the right settings:

• Hospitality
• Entertainment
• Workplace

and, unfortunately

• Educational settings (although ONS suggests primary schools are still relatively safe - prevalence appears flat).

A few superspreaders will have numerous "close contacts" and will transmit easily in the right settings

But they'd need hundreds! The close contacts test & trace catch up to appear to have 7.5 close contacts, but they need double that - so that means the super spreaders need hundreds - how do you get hundreds of close contacts even with pubs open?

If the close contact rates are really so low transmission, and the majority of transmission is an entirely distinct group of super spreaders, then it shows up even more the harm to kids from isolating when they are very unlikely to have it.

Especially as 6.6% of close contacts means even longer to go throughout a primary school class of 30.

@wintertravel1980

It is not scientific proof but it may be useful to compare two different views.

1. ONS study on Covid prevalence in the community. The latest numbers seem to indicate that our current levels are close to mid-April.

1. Graph from the Covid dashboard with actual Covid cases (which suggests that the numbers have gone up by a factor of 2 or 3).

We may be getting better at testing but are we, really?

Previously we have also seen that ONS numbers (based on PRR testing) were very slow to drop in January even though all other indicators suggested numbers were going down very rapidly.

We know ONS now tests most of the people once a month (rather than once a week). It appears likely that PCR tests might indeed be picking up old infections (cases with "low viral load") and, as a result, underestimate the speed of cases increasing/dropping.

But that's not remotely "proof" - it's one possible hypothesis!

I kind of feel that PCR false +ve's were something dreamed up by Heneghan when we was trying to argue that the second wave wasn't really happening. There probably ARE false +ve's but I think the "old virus" hypothesis is unlikely - contamination more likely. Either way, I don't think they occur enough to affect the numbers.

As far as the slow fall in January goes, it doesn't make sense that that was due to old infections since these would have been in the figures all along, pumping ALL the results up. They'd also be in the PHE figures!

So cross about all the govt messaging and MSM headlines saying the ERP events produced on a handful of positives. One of the BBC articles does say

But the ERP report states there was low uptake of PCR testing before and after events, which meant it was "challenging to determine" whether direct transmission of coronavirus had occurred at the events.

but I don’t think that’s what people (especially those with a stake in further opening up, eg the night time industries guy) are going to remember.

Challenging to determine. What a great euphemism for impossible.

The articles also point out that there was low prevalence when the events took place.

A lot are likely keeping lft to use when they have symptoms. Sigh.
2 separate people said this week it's not covid after lft

Yup. I hate all the media saying “they need to show a negative test to do X, Y or Z” and it turns out it’s LFTs. They should have been called something without the word “test” in - because most people don’t understand that they are nowhere near as good as the PCR tests. They are a different thing.

Guilty here for having LFTs and not using them

I have done a couple and registered them. I work from home and haven't really been socialising.

I should do them because of the kids though!

assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/961291/Stay_at_home_illustration_Feb_2021.pdf

Just to answer my question this morning, I was right and the guidance re when to end your isolation when a further household member tests positive still stands. They’ve made the graphic a little easier to understand too, IMO.

As far as the slow fall in January goes, it doesn't make sense that that was due to old infections since these would have been in the figures all along, pumping ALL the results up. They'd also be in the PHE figures!

Back in January PHE (PCR) numbers primarily included people with symptoms (as a general rule, with newly developed symptoms). As we know, PHE cases peaked at the end of December and started dropping rapidly throughout January.

However - ONS survey (random testing across the whole population, including asymptomatic individuals) was showing something completely different:

www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/bulletins/coronaviruscovid19infectionsurveypilot/29january2021

1. The prevalence numbers were dropping very slowly (much slower than what was reported by PHE). Of course, it was causing anxiety among zero Covid proponents who were arguing that "restrictions were not tough enough".

However

1. The variant analysis of positive PCR tests included in the same ONS study showed ever increasing percentage of "unidentifiable" cases (the blue line in the second attachment). Later ONS reports clarified that these cases represent positives with very low viral load (potentially - old cases). It was the only "variant" / case type that kept growing throughout January offsetting the fast drop in both Alpha and wild type Covid.

Yes, it is only a hypothesis but it fits into the fact pattern. The January ONS results were over pessimistic - they understated the speed of the drop. The most recent ONS results might be over optimistic by understating the pace of growth.

@HSHorror

A lot are likely keeping lft to use when they have symptoms. Sigh. 2 separate people said this week it's not covid after lft

while that is obviously wrong I don't blame people for doing this. I feel a bit off, I might as well do an LFT, oh its negative, I'll just carry on then. A lot easier than dragging yourself off to do a PCR.

Either way, I don't think they occur enough to affect the numbers.

I do not think they materially affect Covid PHE numbers reported on a daily basis.

However, I am seeing some people (outside of this forum) getting excited about positive ONS published today. I am generally an optimist but I suggest that in this particular case we exercise caution. There is some risk that ONS may underestimate the speed of growth in community cases.

Whilst past infection in 4 week tested individuals would delay the fall. What's the mechanism for delaying the rise? They're including tests taken a long time ago in their analysis or something?

What's the mechanism for delaying the rise? They're including tests taken a long time ago in their analysis or something?

ONS numbers reported today are generally comparable with the ONS numbers mid-April. On the surface of it, its great news - we were doing very well in April.

However, if we assume that the April comparable might have included historic positives from 4 weeks ago, the relative picture is less rosy. The current prevalence does not change but the increase over past 2 months (from April to June) might be higher than what is being reported by ONS.

In any case, this is just my intuition. I cannot fully substantiate it by data.

ONS data is picked up throughout the month, it lags so it's lower when cases are rising and higher when cases are falling.

bylinetimes.com/2021/06/24/the-ghost-of-herd-immunity-still-haunts-boris-johnsons-roadmap-out-of-lockdown/?fbclid=IwAR1ei_abS8lUZPPr7xMtJQCBXuHv2P3D0UVbY79-WYguN6aeFxU3Rg9ERAg

• more than a ghost, from what this article uncovers.

Interesting thread from an intensive care doctor about what's going on in hospitals.

mobile.twitter.com/rupert_pearse/status/1408674929831198721

@JanFebAnyMonth

bylinetimes.com/2021/06/24/the-ghost-of-herd-immunity-still-haunts-boris-johnsons-roadmap-out-of-lockdown/?fbclid=IwAR1ei_abS8lUZPPr7xMtJQCBXuHv2P3D0UVbY79-WYguN6aeFxU3Rg9ERAg

• more than a ghost, from what this article uncovers.

That article is just anti-government spin; its "evidence" is that Sage had infection immunity included in the models by Warwick and Imperial, and that there was a decision to remove masks on schools. It even includes that they have been specifically told by the UK government that this is not the plan!

[quote lonelyplanet]Interesting thread from an intensive care doctor about what's going on in hospitals.

mobile.twitter.com/rupert_pearse/status/1408674929831198721[/quote]
Interesting that he's so clear these are still mostly unvaccinated people, and reassuring that they get released quickly. Even CPAP would indicate a very long recovery though.

I agree, I think it sounded fairly positive with a little bit of we'll have to wait and see.

@JanFebAnyMonth

bylinetimes.com/2021/06/24/the-ghost-of-herd-immunity-still-haunts-boris-johnsons-roadmap-out-of-lockdown/?fbclid=IwAR1ei_abS8lUZPPr7xMtJQCBXuHv2P3D0UVbY79-WYguN6aeFxU3Rg9ERAg

• more than a ghost, from what this article uncovers.

It certainly feels at the moment that this is what is happening, either deliberately or through incompetence. I'm inclined to think incompetence and that they're just not interested in young people.

Anecdotal - in schools locally there have been very few cases throughout. The primary school I work in has got more children isolating now, by far, than we've had before - 150 children sent home this week.

As there seems to be no plan to vaccinate children, the only way herd immunity can be created for everyone is for children to achieve herd immunity through infection.

Without that, given the unvaccinated are collected together daily in an unsafe manner before returning to their homes, there can be no herd immunity for anyone.

@cantkeepawayforever

As there seems to be no plan to vaccinate children, the only way herd immunity can be created for everyone is for children to achieve herd immunity through infection.

Without that, given the unvaccinated are collected together daily in an unsafe manner before returning to their homes, there can be no herd immunity for anyone.

but if they keep getting sent to self isolate it won't happen.

I just don't get it tbh because you need 80% of the population vaccinated to get herd immunity and we won't get it otherwise.

The only thing i can think of is that perhaps it is the plan but with supply limited until the autumn they can't put a date on it. And it is very difficult politically to either say they are exempt from vaccination if going abroad or that they can't go abroad (because the vaccination not available to them). So they might as well just say and no nothing for now.

Over 18k cases today and 23 deaths. I’m losing optimism now... is there any way of finding out the age or location breakdown?

@lonelyplanet we have 150 positive covid cases (last 7 days) within a population of around 150,000 . And probably around 1000 school children isolating this week with some schools having multiple years off

Secret there was a delay at one if the labs yesterday and Scottish figures were lower than expected.

It doesn't say though if they have now been added. So I suspect that it is 18k cases and in a day or so an extra 1k will be added for Scotland.