Coronavirus - Data Analysis Thread

Coronavirus - Data Analysis Thread

Author
Discussion

gazapc

955 posts

128 months

Wednesday 16th June
quotequote all
Am I reading this SAGE paper right, 80% of those in hospital with covid acquired it in hospital?


spikeyhead

12,864 posts

165 months

Wednesday 16th June
quotequote all
gazapc said:
Am I reading this SAGE paper right, 80% of those in hospital with covid acquired it in hospital?

What do you make of the words "fourth generation of transmission following discharge?"

and

"these estimates are preliminary and dependent on modelling assumptions made?"

It seems to me that someone's done some sums in an assortment of ways and one of those has come up with some odd numbers.

gazapc

955 posts

128 months

Wednesday 16th June
quotequote all
spikeyhead said:
gazapc said:
Am I reading this SAGE paper right, 80% of those in hospital with covid acquired it in hospital?

What do you make of the words "fourth generation of transmission following discharge?"

and

"these estimates are preliminary and dependent on modelling assumptions made?"

It seems to me that someone's done some sums in an assortment of ways and one of those has come up with some odd numbers.
So turns out this was from June 2020 not 21.
https://t.co/Mdog9J1ch3

But even so... It is funny how they are so keen to present the modelling of future cases but not this model (if that is what it is).

If the numbers are anywhere near correct then similar %s will apply this year. Shows how limited an effect restrictions in the community can have.

I wonder if there are equivalent 2021 numbers published.

simoid

19,474 posts

126 months

Wednesday 16th June
quotequote all
spikeyhead said:
gazapc said:
Am I reading this SAGE paper right, 80% of those in hospital with covid acquired it in hospital?

What do you make of the words "fourth generation of transmission following discharge?"

and

"these estimates are preliminary and dependent on modelling assumptions made?"

It seems to me that someone's done some sums in an assortment of ways and one of those has come up with some odd numbers.
4th generation of transmission… someone catches it in hospital and their husband’s auntie’s dentist’s dogwalker catches it?

Vanden Saab

8,872 posts

42 months

Wednesday 16th June
quotequote all
havoc said:
Elysium said:
I realise that this is a popular narrative and that it is the story that Labour tell us as they lend their support to the extension of restrictions. I’m much less convinced.

Variants spread everywhere and the idea that they have a particular geographic origin is more media concoction than reality. It’s no more than the location where they are first found. As an example the Alpha variant occurred pretty much simultaneously in Kent and the Netherlands, but the UK sequenced it first and as a result it became the UK Variant. The confusion this creates is one of the reasons why the WHO switched to Greek letters.

I don’t think we can keep variants out by closing borders. It’s more that we get the variant that suits our environment. The UK went a certain way with vaccinations giving most of us a single AZ shot with a 12 week gap. That seems to create a window for Delta that is less obvious elsewhere.

https://time.com/6073345/delta-variant-covid-19/

I would lay blame for many things at Johnson’s door, but this one is, in my opinion, rather more complex.
Possibly.

But you cannot deny a few very simple facts:-
- The Delta variant was originally diagnosed late last year in India
- India was, by April, being overwhelmed by a massive spread in the virus
- Flights from India were still permitted, unlike (nearly?) every other red-list country, between 2nd April and 23rd April. That HAD to have been a political decision.
- Coincidentally, Boris and the Foreign Office were talking to the Indian leadership. This may just be coincidence, but the timing is questionable...
- The initial concentrations of this new variant were in areas with a large ethnic-Indian population.

Please see this article - the Independent, as a rule, is the most centrist of all the broadsheets, so I take their commentary as usually more reliable.
https://www.independent.co.uk/news/health/covid-de...


Elysium said:
simoid said:
Ashfordian said:
100% agree.

A few million additional infections in the young and heathly last year would have lessoned the winter wave and paid forward benefits that we would have seen over the winter and today.

It's the arogant belief that science thinks it is better than this virus that is causing the most deaths and damage.

The only good thing is the day of reckoning gets closer every day.
Could that not have overwhelmed the NHS even worse than it did? Cancellation of even more cancer scans, operations etc and therefore more deaths and damage?
Very few young people require hospital treatment. This is the basis of the Great Barrington Declaration 'focused protection' argument.

The burdon of risk from COVID varies spectacularly with age.
But how do you ensure only the young get the virus - that's the thing about Coronaviruses, as you've said many times - they spread, they can't be easily controlled or directed.

I love this thread and the regular data updates, but I've got to disagree with you there - human nature (esp. in this country) would have meant the 'young' spreading it to the middle-aged and elderly, PRE VACCINE, and caused more unnecessary hospitalisations and deaths.
The Delta variant is in 74 countries now according to the WHO. if everybody else apart from us closed their borders how did it get to them? This whole close the borders thing is a huge red herring unless you are living at the end of the world which will be shown in time, meanwhile those who are going on about it are doing the Gov. a favour by keeping the focus on something that will be seen in the long run to have been of no consequence. If a variant can develop in one country it can develop in another there is no guarantee the variants are even connected.

spikeyhead

12,864 posts

165 months

Wednesday 16th June
quotequote all
simoid said:
spikeyhead said:
gazapc said:
Am I reading this SAGE paper right, 80% of those in hospital with covid acquired it in hospital?

What do you make of the words "fourth generation of transmission following discharge?"

and

"these estimates are preliminary and dependent on modelling assumptions made?"

It seems to me that someone's done some sums in an assortment of ways and one of those has come up with some odd numbers.
4th generation of transmission… someone catches it in hospital and their husband’s auntie’s dentist’s dogwalker catches it?
That's how I read it, and it's just a mathematician playing with mathematical models. It's something I do for a living, but related to complex electronics which does obey laws of physics, and even I often end up with a result that defies all logic, and that's of something I understand really really well. That paper, from June of last year was someone exploring possibilities and coming up with answers that even my favourite accountant would describe as "not proceedable."

ruggedscotty

3,741 posts

177 months

Wednesday 16th June
quotequote all
Vanden Saab said:
havoc said:
Elysium said:
I realise that this is a popular narrative and that it is the story that Labour tell us as they lend their support to the extension of restrictions. I’m much less convinced.

Variants spread everywhere and the idea that they have a particular geographic origin is more media concoction than reality. It’s no more than the location where they are first found. As an example the Alpha variant occurred pretty much simultaneously in Kent and the Netherlands, but the UK sequenced it first and as a result it became the UK Variant. The confusion this creates is one of the reasons why the WHO switched to Greek letters.

I don’t think we can keep variants out by closing borders. It’s more that we get the variant that suits our environment. The UK went a certain way with vaccinations giving most of us a single AZ shot with a 12 week gap. That seems to create a window for Delta that is less obvious elsewhere.

https://time.com/6073345/delta-variant-covid-19/

I would lay blame for many things at Johnson’s door, but this one is, in my opinion, rather more complex.
Possibly.

But you cannot deny a few very simple facts:-
- The Delta variant was originally diagnosed late last year in India
- India was, by April, being overwhelmed by a massive spread in the virus
- Flights from India were still permitted, unlike (nearly?) every other red-list country, between 2nd April and 23rd April. That HAD to have been a political decision.
- Coincidentally, Boris and the Foreign Office were talking to the Indian leadership. This may just be coincidence, but the timing is questionable...
- The initial concentrations of this new variant were in areas with a large ethnic-Indian population.

Please see this article - the Independent, as a rule, is the most centrist of all the broadsheets, so I take their commentary as usually more reliable.
https://www.independent.co.uk/news/health/covid-de...


Elysium said:
simoid said:
Ashfordian said:
100% agree.

A few million additional infections in the young and heathly last year would have lessoned the winter wave and paid forward benefits that we would have seen over the winter and today.

It's the arogant belief that science thinks it is better than this virus that is causing the most deaths and damage.

The only good thing is the day of reckoning gets closer every day.
Could that not have overwhelmed the NHS even worse than it did? Cancellation of even more cancer scans, operations etc and therefore more deaths and damage?
Very few young people require hospital treatment. This is the basis of the Great Barrington Declaration 'focused protection' argument.

The burdon of risk from COVID varies spectacularly with age.
But how do you ensure only the young get the virus - that's the thing about Coronaviruses, as you've said many times - they spread, they can't be easily controlled or directed.

I love this thread and the regular data updates, but I've got to disagree with you there - human nature (esp. in this country) would have meant the 'young' spreading it to the middle-aged and elderly, PRE VACCINE, and caused more unnecessary hospitalisations and deaths.
The Delta variant is in 74 countries now according to the WHO. if everybody else apart from us closed their borders how did it get to them? This whole close the borders thing is a huge red herring unless you are living at the end of the world which will be shown in time, meanwhile those who are going on about it are doing the Gov. a favour by keeping the focus on something that will be seen in the long run to have been of no consequence. If a variant can develop in one country it can develop in another there is no guarantee the variants are even connected.
Was in the Isle of Man last week - normality no masks no restrictions bit of basic hand cleaning etc but no great shakes. You quickly forget about masks and return to normality.

How ? Well they have what one person in isolation just now.

They vaccinated as many as possible. And they have strict testing and isolation until your proved clear.

It may have worked if it had been done early enough. and strictly controlled.

the-photographer

1,985 posts

144 months

Thursday 17th June
quotequote all
REACT 17 June

108,911 people tested, 135 were positive - a rise from 0.1% to 0.15%

Most cases were among five- to 12-year-olds and 18- to 24-year-olds

The (R) number, of people the average infected person would infect, was an estimated 1.44

Loads of analysis

https://spiral.imperial.ac.uk/bitstream/10044/1/89...

the-photographer

1,985 posts

144 months

Thursday 17th June
quotequote all
Border policy?
Vaccine window?
Less Delta for sure

All those other countries have less total vaccine coverage (sure some age groups might have higher double dose coverage)


havoc

26,116 posts

203 months

Thursday 17th June
quotequote all
Vanden Saab said:
The Delta variant is in 74 countries now according to the WHO. if everybody else apart from us closed their borders how did it get to them?
But in most of them it is a handful of cases, not the thousands we're seeing.

If you read the article I posted, you'll see they referred to Denmark as an example - Delta has cropped up in isolated instances a few times, but the concentration has been too low for it to turn into a proper outbreak.

So I stand by my point - the open borders FUBAR led to high numbers (4 figures) of cases being imported, which gave that critical mass.

the-photographer

1,985 posts

144 months

Thursday 17th June
quotequote all
havoc said:
Vanden Saab said:
The Delta variant is in 74 countries now according to the WHO. if everybody else apart from us closed their borders how did it get to them?
But in most of them it is a handful of cases, not the thousands we're seeing.

If you read the article I posted, you'll see they referred to Denmark as an example - Delta has cropped up in isolated instances a few times, but the concentration has been too low for it to turn into a proper outbreak.

So I stand by my point - the open borders FUBAR led to high numbers (4 figures) of cases being imported, which gave that critical mass.
https://www.connexionfrance.com/French-news/114-ca...

France is currently seeing between 50 and 150 new cases of the Delta variant confirmed everyday, which equates to 2-4% of cases, Health Minister Olivier Véran said on June 15, admitting that it was “still only a few”.


In the UK, cases are doubling each week, with more than 7,000 cases now confirmed per day. In contrast, France’s cases are dropping by 40% each week, and have just dipped below the 5,000 mark.

Yet, Mr Véran has called for “caution” in the face of growing cases in France, saying that France could be on the same trajectory as seen in the UK “a few weeks ago”.

In the UK, it took just eight weeks for the Delta variant to go from accounting for 2% of all new confirmed cases, to accounting for 90%.

JeffreyD

3,669 posts

8 months

Thursday 17th June
quotequote all
havoc said:
Vanden Saab said:
The Delta variant is in 74 countries now according to the WHO. if everybody else apart from us closed their borders how did it get to them?
Are you being deliberately obtuse or do you really not understand the importance of delay and minimising spread whilst continue the vaccine programme.

Introducing 1000 cases in April has a totally different effect than introducing them now.

the-photographer

1,985 posts

144 months

Thursday 17th June
quotequote all
Coronavirus (COVID-19) Infection Survey technical article: analysis of positivity after vaccination, June 2021

https://www.ons.gov.uk/peoplepopulationandcommunit...


duckson

893 posts

150 months

Thursday 17th June
quotequote all
the-photographer said:
Border policy?
Vaccine window?
Less Delta for sure

All those other countries have less total vaccine coverage (sure some age groups might have higher double dose coverage)

We are doing 3 to 7 times the amount of tests per 1000 people than France, Germany, Portugal etc.
Surely need to change the comparison?

the-photographer

1,985 posts

144 months

Thursday 17th June
quotequote all
duckson said:
the-photographer said:
Border policy?
Vaccine window?
Less Delta for sure

All those other countries have less total vaccine coverage (sure some age groups might have higher double dose coverage)

We are doing 3 to 7 times the amount of tests per 1000 people than France, Germany, Portugal etc.
Surely need to change the comparison?
OK, some overlay of testing per 100,000 people then?

If anyone has a lot of spare time and Excel

https://www.ecdc.europa.eu/en/publications-data/co...

Or the graphs here

https://ourworldindata.org/coronavirus-testing

Edited by the-photographer on Thursday 17th June 11:51

duckson

893 posts

150 months

Thursday 17th June
quotequote all
the-photographer said:
duckson said:
the-photographer said:
Border policy?
Vaccine window?
Less Delta for sure

All those other countries have less total vaccine coverage (sure some age groups might have higher double dose coverage)

We are doing 3 to 7 times the amount of tests per 1000 people than France, Germany, Portugal etc.
Surely need to change the comparison?
OK, some overlay of testing per 100,000 people then?

If anyone has a lot of spare time and Excel

https://www.ecdc.europa.eu/en/publications-data/co...

Or the graphs here

https://ourworldindata.org/coronavirus-testing

Edited by the-photographer on Thursday 17th June 11:51
https://ourworldindata.org/grapher/covid-19-daily-...

Hopefully his works?
For some reason Germany isn’t showing up but anyway!
7 day rolling average, tests/cases;
UK 930k/7k
France 278k/4.7k
Italy 182k/1.7k

Edit
Spain up to 10th June; 92k/5.2k


Edited by duckson on Thursday 17th June 13:44

duckson

893 posts

150 months

Thursday 17th June
quotequote all
Ahonen said:
This page from the same website is even better:

https://ourworldindata.org/coronavirus-testing

The first data section is perfect, as it shows the percentage of positive tests.
It does, thanks.

Elysium

Original Poster:

10,720 posts

155 months

Thursday 17th June
quotequote all
Ahonen said:
duckson said:
the-photographer said:
duckson said:
the-photographer said:
Border policy?
Vaccine window?
Less Delta for sure

All those other countries have less total vaccine coverage (sure some age groups might have higher double dose coverage)

We are doing 3 to 7 times the amount of tests per 1000 people than France, Germany, Portugal etc.
Surely need to change the comparison?
OK, some overlay of testing per 100,000 people then?

If anyone has a lot of spare time and Excel

https://www.ecdc.europa.eu/en/publications-data/co...

Or the graphs here

https://ourworldindata.org/coronavirus-testing

Edited by the-photographer on Thursday 17th June 11:51
https://ourworldindata.org/grapher/covid-19-daily-...

Hopefully his works?
For some reason Germany isn’t showing up but anyway!
7 day rolling average, tests/cases;
UK 930k/7k
France 278k/4.7k
Italy 182k/1.7k

Edit
Spain up to 10th June; 92k/5.2k


Edited by duckson on Thursday 17th June 13:44
This page from the same website is even better:

https://ourworldindata.org/coronavirus-testing

The first data section is perfect, as it shows the percentage of positive tests.
Our World in Data have a Coronavirus 'data explorer' that includes test positiivity:

https://ourworldindata.org/explorers/coronavirus-d...



I think this is the best way to understand changes in prevalence. I use cases per 100k tests, which is essentially the same and it has, until recently, closely tracked with admissions and deaths.

Biker 1

5,724 posts

87 months

Thursday 17th June
quotequote all
Elysium said:
Our World in Data have a Coronavirus 'data explorer' that includes test positiivity:

https://ourworldindata.org/explorers/coronavirus-d...



I think this is the best way to understand changes in prevalence. I use cases per 100k tests, which is essentially the same and it has, until recently, closely tracked with admissions and deaths.
Interesting, although there appears to be an alarming uptick in Spain - thoughts as to why??

Elysium

Original Poster:

10,720 posts

155 months

Thursday 17th June
quotequote all
Biker 1 said:
Elysium said:
Our World in Data have a Coronavirus 'data explorer' that includes test positiivity:

https://ourworldindata.org/explorers/coronavirus-d...



I think this is the best way to understand changes in prevalence. I use cases per 100k tests, which is essentially the same and it has, until recently, closely tracked with admissions and deaths.
Interesting, although there appears to be an alarming uptick in Spain - thoughts as to why??
Probably a reporting 'artifact' rather than anything meaningful.