Daily stats, numbers, data thread 02 Jan

[PatriciaHolm]

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 [[imperialcollegelondon.github.io/covid19local/#table
School 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

I’m wondering about the death rate being so high today. I thought we were getting better at treating this? Early intervention with oxygen. Not going straight to ventilate etc. The steroid treatment. Testing people for vascular issues on arrival to hospital. Not waiting until people are blue and can’t talk! Etc.

At a guess cases are as high as in March/April. Though then wasn’t it estimated at 100,00 per day? And we had no measures for most of March...

I’m just confused!

4 of the 5 fallers in littleowl1’s table are at relatively less high levels to start with, two in Devon not that surprising and 2 in Lincolnshire. Then Hastings which needs to come down an awful lot so hopefully moving in the right direction continues. Especially as for months and months Hastings had some of the lowest rates in England it’s rate back at 1st November, so at the start of the previous lock down, was 41 per 100,000

I don’t actually think it’s as alarming as it looks. If you look at it by date of death, there is actually a small decline in the 7 day rolling average

I’m wondering about the death rate being so high today. I thought we were getting better at treating this? Early intervention with oxygen. Not going straight to ventilate etc. The steroid treatment. Testing people for vascular issues on arrival to hospital. Not waiting until people are blue and can’t talk!

At the last Indie Sage meeting there was a frontline doctor (london IIRC) who said they didn't have enough CPAP machines for all the patients who needed them - so they were having to put on a patient for a bit, then move to another patient etc. Other hospitals have reported problems with oxygen, and backlogs with getting patients admitted. So I think with hospitals at or over capacity the improvements in care might no longer be seen.

twitter.com/rp131/status/1346854074554134528?s=21

About 1/4 of today’s reported deaths are from over 7 days ago

Thanks @IloveJKRowling that makes sense but sad all the same that people aren’t getting the treatment they need.

A fairly damning stat. The rate for the original tier 2 councils (following the end of the November lockdown) is now over 700 per 100,000; whereas the original tier 3s overall are around 450. Strip out Kent from the original tier 3 group and that rate will be a bit lower again.

@Perihelion

According to this BBC article the answer is "not much".

The article is from 22nd December and states that "public health Wales sequenced about 4000 genomes in the past week, more than the whole of France since the beginning of the pandemic".

www.google.co.uk/amp/s/www.bbc.com/news/amp/health-55413666

if we have 150k cases a day (which I think is the ball park from the ONS figures) we can expect genuinely high numbers I think.

looks, depressingly, like that little bit of hope that it was starting to fall in the worst-affected bits of Kent and Essex was misguided? Universal rises in both counties today, and some terrifying rates in the worst of them, especially Essex.

Kent’s trajectory actually doesn’t look bad if you adjust for the holiday period (based on the most recent data - I think Covidmessenger goes until Jan 1 which gives us the most accurate but slightly lagging numbers).

coronavirus.data.gov.uk/details/cases?areaType=utla&areaName=Kent

Swale in particular is certainly on the downward trend.

coronavirus.data.gov.uk/details/cases?areaType=ltla&areaName=Swale

@Firefliess

Case rates high again today, and we should be starting to see a fall in numbers now we're away from the post-Christmas mixing. If we can bring rates down with schools closed and full lockdown, we are going to see most people catch it rather than get vaccinated

Deaths have a 3-4 week lag though?

@ceeveebee

I don’t actually think it’s as alarming as it looks. If you look at it by date of death, there is actually a small decline in the 7 day rolling average

I wouldn't get too excited about that - the last week in December is always terrible for reporting of deaths.

As a complete aside for those who get into the real nitty gritty of the daily cases file out of the blue 12 cases added to 1st Feb 2020 spec date yesterday and yet to disappear. An irrelevance in the great scheme of things but a minor distraction at least. All in London.

I think it’s going to take much longer for the effects of this lockdown to be seen. Firstly because of the strain difference and secondly because in terms of behaviour it seems nothing like the March lockdown. I work in manufacturing, last time round everyone in our industry shut for a few weeks until they could make their premises “safe” and there was a slow reopening of the industry. This time round, everyone is carrying on. There are support bubbles, you can go for walks with another person, the schools are much busier than they were etc etc.

@herecomesthesun. There is a 3-4 week lag in deaths, but only a 1 week or so lag in cases. People who caught it on Christmas Day would mostly have tested positive by around New year. So all these new cases coming in this week have caught it at a time when tier 4 rules were in place for most of the country and schools were closed (properly closed that is, for Christmas, not 50% open as they appear to be currently as increasing numbers of parents decide that they are critical workers).

And yes, the initial drop that we saw in Swale and Medway does not appear to have been sustained - their 7 day case rates are rising again, or at least bobbing around, not falling.

My friend who's a nurse tells me our local hospital now has twice as many Covid patients as we had in April, and they are expecting this to increase three fold (ie to 6 times as many, and also 6 times capacity) by next week. I think it looks pretty bad right now.

For those interested in the new variant, check out the preprint from COG today: www.medrxiv.org/content/10.1101/2020.12.30.20249034v2

Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data

The SARS-CoV-2 lineage B.1.1.7, now designated Variant of Concern 202012/01 (VOC) by Public Health England, originated in the UK in late Summer to early Autumn 2020. We examine epidemiological evidence for this VOC having a transmission advantage from several perspectives. First, whole genome sequence data collected from community-based diagnostic testing provides an indication of changing prevalence of different genetic variants through time. Phylodynamic modelling additionally indicates that genetic diversity of this lineage has changed in a manner consistent with exponential growth. Second, we find that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S-gene target failures (SGTF) in community-based diagnostic PCR testing. Third, we examine growth trends in SGTF and non-SGTF case numbers at local area level across England, and show that the VOC has higher transmissibility than non-VOC lineages, even if the VOC has a different latent period or generation time. Available SGTF data indicate a shift in the age composition of reported cases, with a larger share of under 20 year olds among reported VOC than non-VOC cases. Fourth, we assess the association of VOC frequency with independent estimates of the overall SARS-CoV-2 reproduction number through time. Finally, we fit a semi-mechanistic model directly to local VOC and non-VOC case incidence to estimate the reproduction numbers over time for each. There is a consensus among all analyses that the VOC has a substantial transmission advantage, with the estimated difference in reproduction numbers between VOC and non-VOC ranging between 0.4 and 0.7, and the ratio of reproduction numbers varying between 1.4 and 1.8. We note that these estimates of transmission advantage apply to a period where high levels of social distancing were in place in England; extrapolation to other transmission contexts therefore requires caution.

Very interesting @boys3 thanks for pointing it out - that’s about 10 days before we fell ill with what I’m almost certain was COVID-19. Presumably that’s from back checking suspected pneumonia’s etc. rather than confirmed cases at the time, and would support what most of us suspect that it was much more widely circulating around that time

Johnson and Johnson vaccine on course for phase 3 trial results and US EUA application by the end of this month. This has the advantage of being a single dose vaccine. The UK govt has ordered a potential 30 million doses with supply of these being fulfilled by end of Q2 2021.
mobile.twitter.com/SarahKarlin/status/1346866769764487174

I hope no one minds my digression but I’ve found myself thinking about the parameters they should be using to reopen lockdown this time.

We reopened in December at about 16/17k cases a day which quickly escalated (presumably due to this new variant). It seems sensible to presume that we need to be aiming much lower this time and I wondered if anyone knows what T&T’s capacity is? Clearly with the numbers at the moment they’re like a damp tea towel on a bonfire but there must be a level this service could be highly effective as a measure.

Full disclosure - I never agreed with the ridiculousness of having a concrete end date for the second lockdown - made the whole thing pointless.

J&J single dose vaccine also under rolling regulatory review by the EMA, the EU has ordered 400 million doses, so enough for almost the entire population of the EU.
ec.europa.eu/commission/presscorner/detail/en/qanda_20_2467

Who advise is 50 cases per 100,000 I think ?

@midgebabe

Who advise is 50 cases per 100,000 I think ?

I wonder if that’s within our capabilities to control though? I’m a big fan of ‘wiggle’ room myself.

@Cornetto Boris had already been clear that there won't be a sharp end to lockdown this time. Rather there will be gradual opening up - allegedly starting with schools, though the government found it harder to open up schools than other sectors last time round. It's hard to see at the moment how they'll manage anything at all while keeping case rates down with the new strain. At the moment it's set to burn through 50% of the population in a matter of weeks, so I guess after that we could open up a bit as there'd be some herd immunity. Not sure how much of the NHS will be left by then though :(

I'm not sure we could control a brick in a straighjacket