Data, Stats & Daily Numbers started 28th Jan

[TheSunIsStillShining]

UK govt pressers Slides & data www.gov.uk/government/collections/slides-and-datasets-to-accompany-coronavirus-press-conferences#history
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 Attendance explore-education-statistics. service.gov.uk/find-statistics/attendance-in-education-and-early-years-settings-during-the-coronavirus-covid-19-outbreak
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 district 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, tests, ONS deaths Dashboard app.powerbi.com/view?r=eyJrIjoiZGYxNjYzNmUtOTlmZS00ODAxLWE1YTEtMjA0NjZhMzlmN2JmIiwidCI6IjljOWEzMGRlLWQ4ZDctNGFhNC05NjAwLTRiZTc2MjVmZjZjNSIsImMiOjh9
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 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 rolling 14-day incidence EEA & UK read https_www.ecdc.europa.eu/?url=https%3A%2F%2Fwww.ecdc.europa.eu%2Fen%2Fcases-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=gbr&areas=fra&areas=esp&areas=ita&areas=deu&areas=swe&areasRegional=usny&areasRegional=usnj&byDate=1&cumulative=1&logScale=1&per100K=1&values=deaths
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

To boys3 's point - at the moment, I just don't feel the extra day's lag adds much accuracy. So I am happy with 4 days for now.

But this might change and I may need to flip back to 5 days.

In the past, these windows of "increased speed of reporting" have been short lived... but this "feels" different.....

It's been sustained for quite a few weeks now during a very high positive case window (in the past, as the number of positive cases increased nationally, the speed of results being returned fell quite significantly - presumably because labs were overwhelmed with samples in the "queue" for testing). Similarly, on the other hand, when cases were low, results were turned around super fast.

However, things are looking so good at the moment (wrt result turnaround time), it is not inconceivable that we may be able to flip to a 3 day lag.

I just have less confidence that they can maintain the accuracy on a 3 day lag basis. But it looks quite good at the moment - and that certainly was not the case, say 2 months ago.

I suspect they threw a hell of a lot of additional resources at lab testing sites in mid Dec when the transmission implications of the new variant become better understood and the value of speedy results (and isolating cases quickly) became evident.

So, right now, council-level testing data is coming back faster than it ever has since the start of the pandemic.

@nordica

With LFTs - if someone is having symptoms or mild symptoms, and is not diligent enough to go for/get a PCR test delivered are they more likely to get a LFT?

Some people are confused about the different types of test centres, too. Anecdotally, there have been posts in my local area Facebook group from people with symptoms asking where they can get a test and lots of others pointing them in the direction of the local walk in centres (which are actually both LFT centres for asymptomatic people).

Are people asked about symptoms when they attend the test centre I wonder?

Yes they are. If they say they have symptoms they are turned away and told to get a PCR test. I work in a LFT centre.

To add to the bad news on the South African variant - sorry I know it’s a bad name but it’s what we’ve got - mobile.twitter.com/kakape/status/1356359522177179662

[quote ATieLikeRichardGere]To add to the bad news on the South African variant - sorry I know it’s a bad name but it’s what we’ve got - mobile.twitter.com/kakape/status/1356359522177179662[/quote]
Bit more here, (from the Virologist quoted in the tweet from Kai K)
mobile.twitter.com/_b_meyer/status/1356342110115475466

[quote ATieLikeRichardGere]To add to the bad news on the South African variant - sorry I know it’s a bad name but it’s what we’ve got - mobile.twitter.com/kakape/status/1356359522177179662[/quote]
Do you understand what that means? I'm confused - as someone in the comments below the Twitter post has said, viruses don't reproduce sexually so how can one type "pick up" another mutation? Or does it mean it's just mutated further?

Re the name - I wouldn't feel bad calling it the South African variant - the rest of the world is calling our Kent one the UK variant. B117 just isn't catchy!

The government's decision to do the mass testing tells us all we need to know about how worried to be doesn't it? They're not known for moving fast....

How long does genomic sequencing take? How up-to-date is the count of 105 cases including 11 without travel links?

Also, a twitter thread on this here:
mobile.twitter.com/theosanderson/status/1356310927239471107

@Firefliess the mutation has developed independently in the B117 lineage. We see the same mutations in different lineages - convergent evolution - because wherever that mutation arises it gives an advantage and the thing propagates.

The E484K mutation seen in SA and Brazil lineages and now independently again in some B117 is associated with immune escape. Partial immune escape but we think it leads to more reinfections and vaccines don’t work as well. Herd immunity then slips away from us again.

Two Patients in Brazil test positive for two different covid variants at the same time according to the Daily Fail:

www.dailymail.co.uk/news/article-9210695/Brazil-patients-test-positive-TWO-coronavirus-variants-time.html

It is concerning. On one hand vaccination is going well but mutations are worrying

[quote ATieLikeRichardGere]@Firefliess the mutation has developed independently in the B117 lineage. We see the same mutations in different lineages - convergent evolution - because wherever that mutation arises it gives an advantage and the thing propagates.[/quote]
Thanks. That makes more sense - so it's not that the two strains have "mixed" in any way, but rather that the new UK/Kent strain has independently evolved a further mutation that's similar to the SA strain? Presumably no-one knows anything definitive about how well this extra-mutated strain transmits, but there's strong reason to be concerned that it might be extra-tramsmissible?

@Firefliess Exactly. But I think the bigger concern to add to the transmissibility issue is that this mutation is associated with immune escape.

Dropping the spike has occurred independently a number of times: Kent, Wales, SA, Brazil and Nigeria. Also the earlier mink versions in Denmark and Netherlands.

There's also the California variant CAL.20C, which sounds a bit like the Brazil one in having the "immune escape" bit, which SA has but to a lesser extent. Brazil also has a more UK style variant that independently arose in addition, just to add to the puzzle.

For people interested in summaries, wiki has started summarising info about the variants, which is quite useful at least for looking up the codes to search GISAID and research papers if things like P.1 aren't obvious. Most of the research papers are linked, so is actually ever so handy. By the way, why can't a variant be called B.1.1.28.1, if that's what it is? Who decides there must be a fixed number of generations and then start over, and why?
"Variants of SARS-CoV-2 - Wikipedia" en.m.wikipedia.org/wiki/Variants_of_SARS-CoV-2

Reading wiki, I see that I missed Columbus Ohio from the reduced spike list.

Listening to shadow Home Secretary talk about border quarantine. Does anyone know the barrier for government introducing it?

From a non sneery POV (which I’d get elsewhere if asked)

• is it capacity
• how long would it last?
• aviation sector
• risk of vaccine escaping variant not that high

Or other of course.

January I think they're finally realising they have to adopt the approaches taken in China and other more prepared parts of the world.

@Marsha I suspect capacity is the biggest barrier to quarantining all international arrivals. New Zealand and Australia have both struggled with it, and have their hotels booked up for weeks, and places only available to returning nationals and compassionate cases (family there about to die I think). And the whole way in which international travel works in the UK is very, very different - we are only 21 miles from France (as well as having a land border with Ireland of course) A lot of new arrivals come by boat/tunnel. Even if you banned all legal travel, there are hundreds of asylum seekers coming across the channel in dingies, which we've never been able to stop. We require lorry drivers to bring our food across so can't ban them. So all in all, a quarantine system would cause big damage to a variety of industries (airlines, other transport, businesses trading oversees where staff need to travel), tension in Northern Ireland (unless we had a joint approach with Ireland) and then probably not work anyway. I suspect there is also an issue of bolting the stable door after the horse has bolted....

With the LF tests is it the case that if they've not been carried out effectively the result is an error reading ? I know there is an "error" reading but no idea what would cause it .

I worry that for a LF test to be done correctly it's actually quite uncomfortable for the recipient .That people self testing will result in lots of tests with a false negative .

@peridito - I located stats for sometime before. LFT accuracy ranged from something like 73/76% when done by a healthcare professional to 57% done by a random. So that suggests almost half could be missed from poor testing (though maybe fewer of the healthcare worker ones). Finding half is better than none, when the alternative is people not having a test.
As @lonelyplanet says, I wouldn't like to see them used to say it's fine to visit grandpa. I also really wouldn't want to see them replace PCR tests nor replace close contact isolation requirements like the schools proposal. But they do add something useful when used in place of nothing.

Thanks Mrex ,yes I posted the link referencing those stats ,completely agree with point about finding half ( some, even) better than finding none .
I just wondered if anyone knew about the "error" reading .I've read the instructions on my son's LF tests and they mention it ,but not what might give rise to it .Maybe contamination ?

The 'error' reading seems to be if there's no control line, is that right? If so then I think that - like a pregnancy test - what it means is 'this test isn't working' not 'you've done this test incorrectly' and so that if you've not taken the sample correctly you'll just get a negative, not an error - but that's just a guess!

Or, rather, it could mean you've done it 'wrong' but in a basic way - e.g. not putting enough liquid on the test spot - but it seems unlikely that it could detect that you'd done a poor sample and so give an error for that reason. But again, happy to be corrected by someone who knows!

The error result is called "Invalid result". I can't find any list of causes. I suppose it could be contamination, or insufficient liquid, or excessive liquid, or a borderline result... Not sure, sorry.