Contagion 2020

[Cheeky Gnando’s]

An increase of 41 in hospital (1133 total) and up 4 in ICU (41 total).

[Aim High]

An increase of 41 in hospital (1133 total) and up 4 in ICU (41 total).

I think it's actually 69 in ICU in Scotland ATM. 

Just for context, at the peak on 12th April, we had 208 in ICU.

[Cheeky Gnando’s]

I think it's actually 69 in ICU in Scotland ATM. 

Just for context, at the peak on 12th April, we had 208 in ICU.

Yeah that was a typo - I put the 41 increase in as the total by mistake.

981 deaths in the UK today

[Shteve]

has anyone on here tested positive yet? surely to fuck at least one has had it.

[Shuto Makino]

I think it's actually 69

nice

[Half Time Guest]

has anyone on here tested positive yet? surely to fuck at least one has had it.

I got a call about an hour ago saying I'm to isolate. Get tested in a few days so we'll soon find out if I'm the first.

The anticipation 

[CritchSmile]

nice

Childish but

[Mr A]

has anyone on here tested positive yet? surely to fuck at least one has had it.

I've come close. Guy I met for coffee had been in contact with a guy that got a positive test result on Christmas morning.

We were meant to be popping over to my parents' for an outside visit so had to cancel that.

Guy that had tested positive was sure he didn't have it (his son had symptoms but the rest of his immediate family tested negative) so got another test on Christmas Day.

Came back negative as did all of his family's.

[Shteve]

How accurate are the tests? apparently you can order one and do it yourself so how can you trust people to do it right? Plus do they test for all the 'new varients'? seems like a bit of a minefield if you ask me.

[Mr A]

How accurate are the tests? apparently you can order one and do it yourself so how can you trust people to do it right? Plus do they test for all the 'new varients'? seems like a bit of a minefield if you ask me.

The UK checks for sequencing as well as a positive result. So they know the variant of covid that you've got.

We're imputing 50% into the world's sequencing data base. The Danish are doing loads too. So no surprise that we've found this new variant - as with them finding the stuff in Mink.

There'll be loads of variants world wide that just haven't been sequenced as the country doing the test doesn't have the capacity to do it or is too lazy to do it.

A few weeks ago there was more sequencing done in test results done in Wales in one week than the French have done since March

[Drederick Shanktum]

So our PCR testing does confirm only coronavirus and not as has been going around that the detect all viruses?

[Mr A]

So our PCR testing does confirm only coronavirus and not as has been going around that the detect all viruses?

If you get a test you get a positive or negative result.

Those tests are then sent off for sequencing (which I think is basically drilling down into the result) to see what variant.

https://www.sciencemag.org/news/2020/12/...ns-unclear

“Other countries may have the variant as well, says epidemiologist William Hanage of the Harvard T.H. Chan School of Public Health; the United Kingdom may have just picked it up first because it has the most sophisticated SARS-CoV-2 genomic monitoring in the world. Many countries have little or no sequencing.“

[Mr A]

And also when you see what other countries have done to the UK (banning flights etc) it's hard to see what incentive other countries will have to do much sequencing as finding a new variant (that's almost certainly already there) will lead to sanctions.

[CritchSmile]

Mags isn't answering the question of PCR test accuracy.

Shteve, Drederick to go someway to answering our question, here was one of the studies from the BMJ:

https://www.bmj.com/content/bmj/371/bmj.m4848.full.pdf

From the Abstract:
"The rapid test kits most widely used in UK universities, schools, and care homes detect just 48.89% of covid-19 infections in asymptomatic people when compared with a polymerase chain reaction (PCR) test, real world data from the Liverpool pilot have shown".

There was also some confusion earlier in the year as to whether the inventor of the PCR tests said that it is not suitable for detecting viruses.
Here's a link fact checking this from Reuters:  https://www.reuters.com/article/uk-factc...SKBN24420X

It includes clarification of the PCR inventor's position below:

“PCR is intended to identify substances qualitatively, but by its very nature is unsuited for estimating numbers. Although there is a common misimpression that the viral load tests actually count the number of viruses in the blood, these tests cannot detect free, infectious viruses at all; they can only detect proteins that are believed, in some cases wrongly, to be unique to HIV. The tests can detect genetic sequences of viruses, but not viruses themselves.”

The article goes on to say:

Even if Mullis had voiced a similar statement before his death in 2019, this quote does not mean the PCR test is unable to detect the presence of SARS-CoV-2 - the virus that causes COVID-19 - rather that it cannot determine whether the individual tested is infectious.
The PCR test is the preferred COVID-19 testing method in England (tinyurl.com/u9xxxup). It detects the presence of the virus by amplifying the virus'genetic material to a point where it can be detected by scientists (tinyurl.com/y7rno7pf).

[CritchSmile]

The Lancet within their respiratory medicine journal posted False negative rates of up to 33%. This is from a systematic review, therefore a collection of testing, not just from one study like the Liverpool one above.

Published in Sept.
https://www.thelancet.com/journals/lanre...7/fulltext

[Drederick Shanktum]

So it's the genetic sequence that's confirming that the virus which has been detected is covid?

[CritchSmile]

Yeah. It doesn't find the virus itself, it finds the genetic sequence which I think can be quite similar to to other viruses.

The way I read it is that the PCR tests are not so suitable for testing, but it's the best we can do for mass-testing. The rapid test kits are even more inaccurate.

I really don't think we have a clue how many cases we have. It's likely the number is wrong but the PCR testing is still the best way we have of estimating cases.

Anyway, I won't say any more as I don't want to promote mis-information when I'm not clued up on stuff like this. I'm just interpreting the conclusions of the BMJ and Lancet through a laymans lens.

[Hammy]

Mags isn't answering the question of PCR test accuracy.

Shteve, Drederick to go someway to answering our question, here was one of the studies from the BMJ:

https://www.bmj.com/content/bmj/371/bmj.m4848.full.pdf

From the Abstract:
"The rapid test kits most widely used in UK universities, schools, and care homes detect just 48.89% of covid-19 infections in asymptomatic people when compared with a polymerase chain reaction (PCR) test, real world data from the Liverpool pilot have shown".

This was a study on the lateral flow tests which is different from the PCR tests. The 48.89% applies to that test compared against PCR. 

This was the published specificity for the PCR test.

"A false positive result occurred in two of 2981 PCR negative people—a specificity of 99.93% (99.76% to 99.99%)."

It's unlikely to be that high when running around 500,000 tests a day obviously but it's certainly not as low as 48.89%.

There was also some confusion earlier in the year as to whether the inventor of the PCR tests said that it is not suitable for detecting viruses.
Here's a link fact checking this from Reuters:  https://www.reuters.com/article/uk-factc...SKBN24420X

It includes clarification of the PCR inventor's position below:

“PCR is intended to identify substances qualitatively, but by its very nature is unsuited for estimating numbers. Although there is a common misimpression that the viral load tests actually count the number of viruses in the blood, these tests cannot detect free, infectious viruses at all; they can only detect proteins that are believed, in some cases wrongly, to be unique to HIV. The tests can detect genetic sequences of viruses, but not viruses themselves.”

The article goes on to say:

Even if Mullis had voiced a similar statement before his death in 2019, this quote does not mean the PCR test is unable to detect the presence of SARS-CoV-2 - the virus that causes COVID-19 - rather that it cannot determine whether the individual tested is infectious.
The PCR test is the preferred COVID-19 testing method in England (tinyurl.com/u9xxxup). It detects the presence of the virus by amplifying the virus'genetic material to a point where it can be detected by scientists (tinyurl.com/y7rno7pf).

Mullis was a firm believer that HIV didn't cause Aids and his comments from this subject have been taken wildly out of context to support the narrative that the PCR tests cannot detect viruses or shouldn't be used for covid testing generally by people who believe this is all a hoax.

[CritchSmile]

Cheers for the explanation of the bit at the end, I'd seen this stuff about PCR hoax passed around social media and had a dig myself to find my own some primary sources. So much misinformation being knocked about I don't want to be contributing to that.

[Zizou]

That's Oirland away back into lockdown for at least a month.

I think that's the only way to go for us tbh. We know the vaccine is going to have a huge impact in a matter of months, shut down and properly support businesses and get things back under control while vaccinating people. This tier shit is useless.