Daily numbers, graphs, analysis thread 20

[BigChocFrenzy]

Welcome to thread 20 of the daily updates

Resource links:

Uk dashboard deaths, cases, hospitals, tests - 4 nations, English regions & LAs
Imperial UK weekly LAs, cases / 100k, table, map, hotspots
Modelling real number of infections February to date
MSAO Map of English cases
Cases Tracker England Local Government
ONS MSAO Map English deaths
CovidMessenger live update by council district in England
Scot gov Daily data
Scotland TravellingTabby LAs, care homes, hospitals, tests, t&t
PH Wales LAs, tests, ONS deaths
NI Dashboard
Zoe Uk data
UK govt pressers Slides & data
ICNRC Intensive Care National Audit & Research reports
NHS t&t England & UK testing Weekly stats
R estimates UK & English regions
PHE Surveillance reports & LA Local Watchlist Maps by LSOA
ONS England infection surveillance report each Friday
Datasets for ONS surveillance reports
ONS Roundup deaths, infections & economic reports
ECDC rolling 14-day incidence EEA & UK
Worldometer UK page
Our World in Data GB test positivity etc, DIY country graphs
FT DIY graphs compare deaths, cases, raw / million pop
Alama Personal COVID risk assessment
Local Mobility Reports for countries
UK Highstreet Tracker for cities & large towns Footfall, spend index, workers, visitors, economic recovery

⏭ Our STUDIES Corner ⏮

We welcome factual, data driven, and civil discussions from all contributors 📈 📉 📊 👍

Request to posters giving a link:
Please do so in full, so people can see in advance what they are clicking
Also at least a brief title so we know what the link is about

I think I read the dogs detected covid infections up to 3 days before symptoms

Is there any way of finding out how many of the daily deaths were in hospital and how many in care homes/community?

Richard @RP131** on twitter publishes daily breakdowns of total death numbers. I have attached the slide for today.

Public Health of England additional deaths (the second table on the right hand side) represent deaths in community and care homes. In practice, the vast majority of the cases relates to care homes so we are definitely seeing an increase there. The numbers are still small but they are slowly going up.

@BigChocFrenzy

Well, training tens of thousands of dogs would be much cheaper than a £100 billion moonshot

Probably more effective too!

Not if DIdo Harding was in charge of the system:

The dog would probably sniff your pockets, eat your chocolate & tissues, pee on your suitcase and hump yout leg as a grand finale
... having forgotten all Corona in the excitement

DS and his friends would love a covid dog at pre-school. How long do they take to train?

I'm imagining the reaction to parents being tolf to collect kids who failed the sniff test. And front pages of the tabloids bringing out every dog pun they can think of: "Grrr! Kids sent outside by dogs". Rabid parents. School pack.

But we could get the dogs to train Dido Harding!

France

16,096 new cases - big increase from previous record of 13,498
51 deaths

SPain

10,653 new cases making > 700,000 cases total
84 deaths

Madrid alone hospitalising 500 new cases per day over the last week

500 hospitalisations a day in a city is really scary - particularly as some of those will be there for quite a while. How close to capacity are they in Madrid?

Genetic / Immune defects may be imparing ability to fight Covid

https://www.theguardian.com/world/2020/sep/24/genetic-immune-defects-may-impair-ability-fight-covid-19
www.covidhge.com

In papers published in the journal Science, the Covid Human Genetic Effort international consortium describes two glitches in severely ill Covid-19 patients that prevent them from making a frontline immune molecule called type 1 interferon.

The patients would have carried these glitches for years before the pandemic, or in the case of the genetic errors, all their lives.
The discovery may help to explain a mystery surrounding the coronavirus:
why it leaves some sufferers sick or dying in intensive care, while others remain barely affected or asymptomatic.

Together, the two types of error account for about 15% of life-threatening Covid-19 cases
.....
Casanova suspects human genetics will end up explaining the majority of such cases, however,
because the consortium has only looked for mutations in 13 of the 300-odd type 1 interferon-related genes so far – already a huge undertaking.

Many other genes, including ones not related to interferon, could affect a person’s response to the virus.

Type 1 interferon is a molecule produced by the immune system as soon as it detects infection.
It works by stopping a virus from replicating.

If this first-line defence is effective, a person may not even feel unwell.

Even if it is not, it buys the body time to mount an immune response that is more targeted to the virus in question, involving antibodies and immune cells.

Without interferon, severely ill Covid-19 patients rely solely on this second defence mechanism,
which may take several days to reach full strength
– giving the Sars-CoV-2 virus a head start on damaging the body’s tissues.

Here is an article on the Madrid hospital/ICU situation:

english.elpais.com/society/2020-09-23/spain-adds-241-deaths-to-official-toll-the-highest-figure-so-far-of-the-second-coronavirus-wave.html

In summary:

• 36% of ICU beds in Madrid are occupied by COVID patients;
• While the health care system is not yet overwhelmed, Madrid may be coming close to the limit.

eurapa.biomedcentral.com/articles/10.1186/s11556-020-00249-3

Pretty negative on Physical Activity in pandemic among the older groups - The only 5% inactive over 55's in Sweden also shows how much healthier the older groups were almost certainly there compared to other European countries.

The link to the paper on 3 months detraining having very negative outcomes for 75 year olds is pretty worrying given how much "habitual physical activity" is almost certainly the norm in this group, and much of that will be gone, and how much worse outcomes are in all winter diseases with lack of fitness.

Raab needs correcting - in case you find another MN poster who has taken his statement the wrong way

Raab was confusing 🤦🏻‍♀️ in a Sky News interview
and I've already seen one MN poster claiming he said only 7% of positives were "real"

SkyNews@SkyNews

Foreign Secretary Dominic Raab says the "challenge" with testing for ‪#COVID19‬ in airports is 'the very high false positive rate'
and adds 'only 7% of tests will be successful in identifying those who have the virus'.
(video)
https://twitter.com/SkyNews/status/1308655561081225217

What Raab meant - if he understood the governments own publications -
is that there is a very high false negative rate especially on day of arrival

This government study on double testing for airport arrivals showed that
on day of arrival, only 7% of infected people showed as positive

However, after isolation, a 2nd test picked up 86% of those infected on day 6, or 98% if tested on day 10

Investigation into the effectiveness of “double testing” travellers incoming to the UK for signs of COVID-19 infection

https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/909382/s0544-phe-double-testing-travellers-170620-sage-42.pdf

NHS has started publishing daily breakdowns of hospital admissions. The information can be interesting because it allows to separate (i) admissions from care homes, (ii) cases of hospital spread and (iii) admissions from community:

www.england.nhs.uk/statistics/statistical-work-areas/covid-19-hospital-activity/

(bottom of the page)

The latter (admissions from community) is the most relevant data point for estimating virus prevalence.

The government dashboard shows the total numbers which are also useful but can fluctuate significantly when we see outbreaks in hospitals.

I've already got that NHS link marked for the next OP, as iirc Mrex also showed useful data from there

The NHS warns in its spreadsheet:

"Note that the last 5 days of this time series will always be an underestimate as they do not include diagnosed patients where the test was taken within 3-7 days of admission as that data element is not yet available.
These figures will be revised as the data becomes available"

I’m intrigued by the numbers in Italy staying so low, only 1,786 cases today - does anyone know what they are doing differently to France, Spain and us? Surely we should be following suit?

Lessons learnt from easing COVID-19 restrictions: an analysis of countries and regions in Asia Pacific and Europe

https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)32007-9/fulltext

Asia Pacific: Hong Kong, Japan, New Zealand, Singapore, South Korea
Europe: Germany, Norway, Spain, UK

Comparative framework for COVID-19 lockdown exit strategies

Knowledge of infection status
. Indicators to monitor the epidemiological situation

Community engagement
.Safe policies for physical distancing and mask wearing
. Precautionary measures in schools and workplaces
. Communication to secure public trust and cooperation
. Protecting vulnerable populations
. Providing socioeconomic support

Public-health capacity
. Testing, tracing, and isolating
. Role of experts

Health-system capacity
. Treatment facilities
. Medical equipment
. Health-care workforce

Measures for border control
. Inbound travel restrictions

@sleepwhenidie

I’m intrigued by the numbers in Italy staying so low, only 1,786 cases today - does anyone know what they are doing differently to France, Spain and us? Surely we should be following suit?

anecdotal from multiple friends living there They are scared enough to actually wear a mask properly everywhere, all the time and they are not being typical italians - no hugging, touching,.... All4 of my friends are in small towns or villages between Roma/Milano/Venezia

Based on the positivity rate though it might be that they are not testing too much? Although 100k/day seems a lot. Than again UK says a very high number and somehow I have my doubts....

@sleepwhenidie

I’m intrigued by the numbers in Italy staying so low, only 1,786 cases today - does anyone know what they are doing differently to France, Spain and us? Surely we should be following suit?

.... FT: Italy’s harsh lessons help keep second wave at bay

www.ft.com/content/6831be3e-2711-4ea3-8f62-daa82cf9ca11

• First-mover advantage - by definition, not something any other European country has ! Gave authorities more time to plan & develop SD measures e.g.

Early adoption of masks

More gradual lifting of restrictions
....
"In August, Rome ordered a closure of discos
and introduced a rule that face masks must be worn in all crowded places between 6pm and 6am.
....
Companies have been encouraged to extend remote working arrangements into the autumn with the government guaranteeing staff workplace insurance in their homes.
Those that have reopened have strict protocols — including the wearing of face mask all day, daily body temperature scans, social distancing and free Covid-19 swabs."

• High public compliance and stricter enforcement

• Effective testing and monitoring

FT article says 2% test positivity,
which is well within the 3% WHO limit of testing enough to keep infections well under control

It's about who you test, more than how many, at this stage of an epidemic
and of course efficiency of testing - turnround, not losing tests or letting them expire 🤦🏻‍♀️
providing a country has a good test / lab capacity

From that article, seems that Italy targets its tests well, like Germany,
which requires an efficient track & trace system, as well as being able to effectively apply criteria for testing

No country has limitless tests

I'm not sure how well the UK is targeting tests
Availability and turnround seem very poor atm

Countries that have done well for both deaths & reduced economy damage are in top left of chart:

The quality of response then, and of the care homes and healthcare systems and quality of test and trace seems crucial. The sophistication, targeting. Seeing that Italy has thought about masks and crowds for example, rather than the blunt rule of 6 that is harder to understand.

@sleepwhenidie

I’m intrigued by the numbers in Italy staying so low, only 1,786 cases today - does anyone know what they are doing differently to France, Spain and us? Surely we should be following suit?

Better / quicker track and trace. Italian labs have had capacity for uk tests, so numbers of cases have been sustained at a lower level. Their positivity rate is low.

It all points to higher compliance / awareness / management.

Place marking also Thankyou