General Coronavirus (COVID-19) chat

[Cloo]

Our neighbour who has been in hospital with COVID since early Feb has messaged street WhatsApp group for first time since he went to hospital - really lovely to hear from him again, though he says his energy is still very low and walking is still a strain. He is still in ICU but definitely recovering.

 

[kropotkin]

I thought their main problem was with false negatives.

You are quite correct.

The false negative rate is high as they have a "sensitivity" of between around 50 and 75% depending on who does them. The sensitivity if you are ill and have high viral load is much higher (over 95%), which is what swing the decision making around them - very useful to pick up the most infectious people.
Sensitivity is the liklihood it tests positive if you do have the disease.

Specificity if the opposite: the probability it says you don't have it when you don't have the disease. This is very high with this test (99.7%) meaning a false positive rate of 0.3%.

The problem comes when you multiply it up hugely by a massive number of people doing the test, and you need to take the base rate into account (the actual prevalence of a disease on the population). When there is high prevalence (like when something like 1 in 4 people had coronavirus in London), then the chance of a random person having a positive test result would be 25%*75% = 18%
The chance of a random false positive would be 0.3%*75%=0.2%


Now, if the rate dropped hugely as we controlled the pandemic to more like 1% of people things become trickier.
The chance of a random true positive test is now not 1% but only 75%*1%=0.75%
The chance of a false positive is now 0.3%*99%=0.3%

So if the population prevalence drops to 1%, the chance of a positive lateral flow being correct is just over twice the chance it is wrong.
The further the base rate falls, the worse this balance becomes until it flips. The latest stat I can find for England is an estimated rate of 1 in 340 = 0.3%.

So
True + = 0.3%*75%= 0.2%
False += 0.3%*99.7%=0.29%

So by my shakey maths we've reached the point at which a positive lateral flow is more likely to be wrong than right. I'm tired and just finished my shift a couple of hours ago, so apols if I've misremembered and fucked all the above up

 

[Cloo]

Parents have second jab date, pretty much bang on 12 weeks after their first - I'm pleased and much happier to potentially have to wait another month for my first if they and other more vulnerable people are getting their 2nd sooner/on time.

 

[Cloo]

Other good news, neighbour is coming back home from hospital tomorrow. He still can't do stairs or walk very much, and will have visiting carers, plus his wife is at home but it won't be easy for her. Whole street willing to help out at least.

 

[Yossarian]

Unless this is an April Fool's joke, the Ontario government has decided that their policy of opening things up while cases are rising steeply has not been a success, for some mysterious reason.

Ford government applying emergency brake to place Ontario in month-long shutdown: sources

The Ontario government will use its emergency brake and place the province in a shutdown for at least a month to reverse the rapid rise in COVID-19 cases and hospitalizations, CTV News has learned.

www.cp24.com

 

[DaveCinzano]

Unless this is an April Fool's joke, the Ontario government has decided that their policy of opening things up while cases are rising steeply has not been a success, for some mysterious reason.

Ford government applying emergency brake to place Ontario in month-long shutdown: sources

The Ontario government will use its emergency brake and place the province in a shutdown for at least a month to reverse the rapid rise in COVID-19 cases and hospitalizations, CTV News has learned.

www.cp24.com

Maybe Doug has been visited by the ghost of Rob or something

 

[Yossarian]

Maybe Doug has been visited by the ghost of Rob or something

I can only imagine what the headlines would have been like if Rob Ford had been mayor of Toronto during the pandemic - "43 People, 3 Raccoons Test Positive After Illegal Party at Ford Residence."

 

[MBV]

Not at all scientific but it feels like the stay local guidance is being ignore by most people. I've flexed the rules myself by taking a relative to a medical appointment but I'd much prefer to travel a couple of hours to enjoy the countryside.

 

[Cloo]

Went to synagogue today, was a bit odd, very cold (but I guess that means well ventilated!) but still nice. Rabbi's new dog decided to join in with the sermon at one point

 

[zahir]

A thread on architecture and the pandemic, arguing that seasonal risk is about building design not the weather.

 

[hash tag]

The end is in sight UK - Grayson Perry is casting a bell to ring at the end of the Covid-19 pandemic

 

[Yossarian]

Back under a four-week stay-at-home order in Ontario as of today - the last couple of weeks in this chart are a good demonstration of what happens when you start reopening things while cases are rising.

 

[zahir]

More on the lab escape theory.





e2a: a short video from 2019 on the Chinese bat research

Is a Wuhan lab leak the origins of the Covid-19 pandemic? - Thai Enquirer Covid-19

Latest Thailand English Online News Is a Wuhan lab leak the origins of the Covid-19 pandemic? Covid-19 - Thai Enquirer %

www.thaienquirer.com

Hi, joining me today on the podcast is Alina Chan, a Post Doctorate researcher at the Broad Institute of MIT and Harvard.

Alina has made headlines over the past year for being one of the advocates of investigating all plausible explanations of Covid-19. Specifically, she has drawn the ire and fury of some scientists and the Chinese government for suggesting that the pandemic could be the result of a lab leak from a virology lab in Wuhan.

She talks today about the evidence that she and other scientists have found that suggests that the hypothesis might be true and why natural causes might not be as apparent an explanation as one may think.

The World Health Organization recently sent a team to China to investigate the origin of the coronavirus that sparked our pandemic. But they returned with little new information beyond a vague assertion that the virus probably had a “natural” origin in an animal. There was no explanation for how, where or when it jumped to humans.

Matt Ridley, a journalist with a background in biology, says the possibility of a lab accident is far from ruled out. He talks about potential clues being withheld, including a database cataloguing the genetic sequences of viruses studied at the Wuhan Institute of Virology. He calls out, “an appalling lack of transparency,” and applauds a group of volunteer internet sleuths.

 

[Orang Utan]

There are children running around my library screaming again and it’s music to my ears. Feeling quite emotional!

 

[rubbershoes]

More on the lab escape theory.





e2a: a short video from 2019 on the Chinese bat research

Is a Wuhan lab leak the origins of the Covid-19 pandemic? - Thai Enquirer Covid-19

Latest Thailand English Online News Is a Wuhan lab leak the origins of the Covid-19 pandemic? Covid-19 - Thai Enquirer %

www.thaienquirer.com

Sounds like a lot of bollocks to me
A lot of talk about the lab escape theory but dismissing the jump from animals out of hand

 

[elbows]

Sounds like a lot of bollocks to me
A lot of talk about the lab escape theory but dismissing the jump from animals out of hand

Which one dismisses the jump from animals out of hand? I've only read the written articles, because I have little time for videos and podcasts. The written one does not dismiss the jump from animals out of hand, it talks about what evidence has and has not been found so far.

My own opinion on these matters has not changed at all, in contrast to some mainstream media etc sources that have felt the need to shift a little bit over time. My opinion remains that both sorts of possibilities are worthy of further investigation, nothing has come up so far which would lead me to rule the lab stuff in or out. And that it would be especially stupid of me to rule it out because of the nature of the lab work done at Wuhan, and because of certain lessons from history. And so I have to keep an open mind unless something more concrete emerges. I dont have high hopes of the pertinent facts emerging, unless we get lucky on the animal front, or, if it was a lab thing, someone blabs or obtains sensitive info.

 

[elbows]

Hmm maybe sloppy language from me there, if ruling something in just keeps the option open rather than indicating certainty, then I do rule the lab stuff in.

 

[rubbershoes]

Which one dismisses the jump from animals out of hand? I've only read the written articles, because I have little time for videos and podcasts. The written one does not dismiss the jump from animals out of hand, it talks about what evidence has and has not been found so far.

My own opinion on these matters has not changed at all, in contrast to some mainstream media etc sources that have felt the need to shift a little bit over time. My opinion remains that both sorts of possibilities are worthy of further investigation, nothing has come up so far which would lead me to rule the lab stuff in or out. And that it would be especially stupid of me to rule it out because of the nature of the lab work done at Wuhan, and because of certain lessons from history. And so I have to keep an open mind unless something more concrete emerges. I dont have high hopes of the pertinent facts emerging, unless we get lucky on the animal front, or, if it was a lab thing, someone blabs or obtains sensitive info.

The bottom box of zahir's post

The World Health Organization recently sent a team to China to investigate the origin of the coronavirus that sparked our pandemic. But they returned with little new information beyond a vague assertion that the virus probably had a “natural” origin in an animal. There was no explanation for how, where or when it jumped to humans.

What they say doesn't give any detail on the WHO assertion , but derides it as "vague"

Yet they're prepareed to go to any length to show that covid could have escaped from a lab despite there being no evidence that it did. As with many conspiracy theories, much time is spent looking at the holes in the net rather than the net itself

 

[elbows]

I guess you arent familiar with the criticisms of the WHO investigation then, or the fact that the head of the WHO had to admit to shortcomings. Honestly, dismissing the lab stuff as a conspiracy theory is really not the correct approach to this complex issue at all.

The US and the UK have sharply criticised a World Health Organizationreport into the beginnings of the coronavirus pandemic in Wuhan, implicitly accusing China of “withholding access to complete, original data and samples”.

The statement, also signed by 12 other countries including Australia and Canada, came hard on the heels of an admission on Tuesday by the head of the WHO, Tedros Adhanom Ghebreyesus, that the investigation was “not extensive enough” and experts had struggled to access raw information during their four-week visit to Wuhan in January.

Despite studying data of samples from large numbers of farmed wild animals the researchers were unable to find evidence of Covid-19.

UK and US criticise WHO's Covid report and accuse China of withholding data

Statement signed by 12 other countries says investigation into origins of virus was not extensive enough

www.theguardian.com

 

[elbows]

And to be quite clear, reasons I call it a complex issue very much include international politics. But also that some of the possibilities involving natural, animal->human origins can be difficult to get a proper handle on. If thats what actually happened then I wouldnt necessarily expect this to be discovered via the studies done to date, even if access to information had been much better.

I do understand some of the reasons why people would struggle to keep an open mind on this, but thats still not a stance I have much respect for at all.

 

[zahir]

The bottom box of zahir's post

What they say doesn't give any detail on the WHO assertion , but derides it as "vague"

Yet they're prepareed to go to any length to show that covid could have escaped from a lab despite there being no evide4nce that it did. As with many conspiracy theories, , much time is spent looking at the holes in the net rather than the net itself

I only copied that box of text as an indication of what the podcast with Matt Ridley is about. For me the podcast is worth listening to. It’s perfectly reasonable not to bother with listening to it but I don’t see you can then judge the arguments he’s making.

 

[rubbershoes]

If it's all the same to you I'm not going to listen. But I can still comment on the tone of what I see

 

[Supine]

The bottom box of zahir's post



What they say doesn't give any detail on the WHO assertion , but derides it as "vague"

Yet they're prepareed to go to any length to show that covid could have escaped from a lab despite there being no evide4nce that it did. As with many conspiracy theories, , much time is spent looking at the holes in the net rather than the net itself

There is plenty of evidence that it didn’t escape from a lab. It’s also impossible to say with certainty where it was first introduced into humans. There is no audit trail to follow. Expecting the who report to be able to say with certainty is naive.

 

[zahir]

There is plenty of evidence that it didn’t escape from a lab.

What would you say is the evidence against a lab escape?

 

[rubbershoes]

What would you say the evidence against a lab escape is?

That's not how evidence works

 

[zahir]

Another podcast with Alina Chan, this time with an edited transcript.

A Different Theory of COVID-19’s Origin

A previously fringe suggestion is getting more mainstream consideration.

slate.com

 

[Yossarian]

I think with Donald Trump out of office, people like former CDC director Robert Redfield coming out in support, and the Chinese government Streisand Effecting the hell out of it, the lab leak theory should probably at least be classed as a plausible alternative theory of COVID's origins instead of dismissed as a conspiracy theory.

 

[Teaboy]

A lab accident whilst devastating would seem to me to be slightly more comforting than the alternative.

Thing is it just seems like a dead end because the nature of the Chinese state means that there would be no chance of a proper open investigation. I'm not saying that other governments wouldn't cover up just that the Chinese government definitely would

 

[elbows]

A lab accident whilst devastating would seem to me to be slightly more comforting than the alternative.

Even if this one was lab-related it doesnt really change the fundamental risks of animal-human vectors for diseases. Viruses getting a chance to jump species barriers is a pretty well established part of orthodox understanding of where things like new influenza pandemics etc come from. Hence continued concerns over various avian influenza strains and the occasions where some limited animal->human infection occurs, there is always concern that such events could go beyond small outbreaks if the virus is able to spread effectively between humans, becomes better adapted to human hosts etc.

 

[elbows]

I should also have said that thats a big reason why labs like the Wuhan one do the sort of work they do in the first place. And that although flu has captured the lions share of attention in this area historically, the original SARS gave some focus to the possibilities of a similar picture with coronaviruses.