When will this shit end?

[Doug85]

I've still been at work, classed as a key worker and Mrs Doug is working on the front line in the NHS, it's been a tiring time. 1 thing is for certain that far more people have either had Covid 19 or have it now (with or without symptoms). We need the tests to show how many people have had it. Mrs Doug tells me it is brutal in the NHS at the moment and it really is pot luck if you get Covid with mild symptoms or with symptoms bad enough to put you on a ventilator.

The most frustrating thing is people who are using this as a holiday and are going out and about to meet friends and go for a sit at the beach etc, FFS even if they think it won't impact them stop being so bloody selfish and try not to pass it on to other people. 

Stay at home, Stay safe. We will get through it (eventually) and then we will have a great 2021 festival!

[Toilet Duck]

1 hour ago, eFestivals said:

found it.  

https://www.fagain.co.uk/node/60

It's about the 'Genomic epidemiology of novel coronavirus'.

(will have another read of it now).

It’s an interesting analysis Neil, the sequencing data is fine, the phylogenetic tree looks ok too (also shows us the virus is reasonably stable, like most Coronaviruses)...in terms of who patient zero is in Europe though, this is the key disclaimer...”Although the genetic relationships among sampled viruses are quite clear, there is considerable uncertainty surrounding estimates of transmission dates and in reconstruction of geographic spread. Please be aware that specific inferred transmission patterns are only a hypothesis”

[Deaf Nobby Burton]

6 minutes ago, Toilet Duck said:

It’s an interesting analysis Neil, the sequencing data is fine, the phylogenetic tree looks ok too (also shows us the virus is reasonably stable, like most Coronaviruses)...in terms of who patient zero is in Europe though, this is the key disclaimer...”Although the genetic relationships among sampled viruses are quite clear, there is considerable uncertainty surrounding estimates of transmission dates and in reconstruction of geographic spread. Please be aware that specific inferred transmission patterns are only a hypothesis”

TD what is the relationship between the info in this article (that the virus doesn’t mutate much) and the one Neil has posted about being able to trace it back?

https://techcrunch.com/2020/03/25/new-coronavirus-research-suggests-vaccines-developed-to-treat-it-could-be-long-lasting/

[eFestivals]

6 minutes ago, Toilet Duck said:

in terms of who patient zero is in Europe though, this is the key disclaimer

ahhh, OK. Thanks for the clarification.

I'd taken the bits that appeared to be factual (such as where zero was) as good. The rest of it (geezer's take on what it was saying) I'd put in the "layman's opinion" pile .

[Toilet Duck]

24 minutes ago, Deaf Nobby Burton said:

TD what is the relationship between the info in this article (that the virus doesn’t mutate much) and the one Neil has posted about being able to trace it back?

https://techcrunch.com/2020/03/25/new-coronavirus-research-suggests-vaccines-developed-to-treat-it-could-be-long-lasting/

Howdy,

Basically, the relationship is that the virus doesn't mutate rapidly, it's fairly stable. All virus mutate (all DNA mutates, our own DNA accumulates mistakes pretty much every time it replicates...most of the time it happens in parts of the genome that make no difference, so that's why we all have the same genetic code to make all the things that make us a human, but when we look closely, the fine details are different for everybody (that's how we can do DNA fingerprinting)). Anyway, things that replicate quickly (like viruses and cancer cells) accumulate more errors, and "drift" in terms of their genetic code. Coronaviruses are no different in this respect, they will accumulate small differences, but most of the time it won't make any difference to how it functions or how our body recognises it. From time to time it will gain an error (mutation) that gives it a new property (like jumping from bats to humans, possibly via some other animal). Viruses like flu are entirely different. They have what is known as a "segmented" genome. They are kind of like those puzzles you had when you were a kid with a picture on them, but you can shuffle the picture by sliding the squares around in the puzzle. Every year, flu slides the squares around a bit so that the picture gets a bit jumbled up and looks different to our immune systems (so we need to make a new vaccine every year). This is how "genetic drift" works in flu viruses. On the whole, most people's immune systems recognise it as flu as even though the picture is a bit jumbled up, it's still close enough to what our body's have seen before. Every now and again, flu changes the picture entirely by putting new squares in the puzzle (by getting bits of flu virus from other species...hence we call them "avian" or "swine" flu). This is called "genetic shift" and it stymies even immune systems that have seen flu before, so we get large outbreaks. The H1N1 1918 pandemic was as a result of a genetic shift, likewise the recent H5N1 and H1N1 outbreaks. Coronaviruses are not built like this, so are less prone to making large jumps in their genetic code, therefore when we do have a vaccine, its likely to work for a good while until an entirely new strain jumps out of some other bat! 

Edited March 26, 2020 by Toilet Duck
correcting typos!

[Toilet Duck]

15 minutes ago, eFestivals said:

ahhh, OK. Thanks for the clarification.

I'd taken the bits that appeared to be factual (such as where zero was) as good. The rest of it (geezer's take on what it was saying) I'd put in the "layman's opinion" pile .

No worries, it's a useful analysis one way or another (I only had a quick look at the underlying bioinformatics, I'd have to get one of my computational biologists to really dig into to it to see if it's entirely correct....and scientists can always find something wrong with someone else's work!). 

[stuartbert two hats]

1 hour ago, Matt42 said:

This is why we need wider testing. We need to try and work out how far this has spread. I don’t understand the logic behind only testing those with critical symptoms, it means that the public have a warped sense of how intense the virus is and leads to more panic.

If in theory we test a million people and all of those tests came back positive, and say 900,000 report that they didn’t even notice they had it — it would greatly improve how we deal with this virus. I’m sure there is a strong argument on the other side, but the WHO all along have been advocating for greater testing as this tells us the most about the virus.

We don't have enough tests.  That's the logic.

[zahidf]

1 minute ago, stuartbert two hats said:

We don't have enough tests.  That's the logic.

Yup. Basically every country in the world wants tests and there is a limited supply 

[steviewevie]

1 hour ago, Madyaker said:

Oh an app is a good idea. Yeah healthcare staff should obviously get it first, but even so this should still be widely available in the next few months, much sooner than a vaccine. I suspect most of us will test positive.

Based on what, a hunch?

[jparx]

1 hour ago, Toilet Duck said:

Howdy,

Basically, the relationship is that the virus doesn't mutate rapidly, it's fairly stable. All virus mutate (all DNA mutates, our own DNA accumulates mistakes pretty much every time it replicates...most of the time it happens in parts of the genome that make no difference, so that's why we all have the same genetic code to make all the things that make us a human, but when we look closely, the fine details are different for everybody (that's how we can do DNA fingerprinting)). Anyway, things that replicate quickly (like viruses and cancer cells) accumulate more errors, and "drift" in terms of their genetic code. Coronaviruses are no different in this respect, they will accumulate small differences, but most of the time it won't make any difference to how it functions or how our body recognises it. From time to time it will gain an error (mutation) that gives it a new property (like jumping from bats to humans, possibly via some other animal). Viruses like flu are entirely different. They have what is known as a "segmented" genome. They are kind of like those puzzles you had when you were a kid with a picture on them, but you can shuffle the picture by sliding the squares around in the puzzle. Every year, flu slides the squares around a bit so that the picture gets a bit jumbled up and looks different to our immune systems (so we need to make a new vaccine every year). This is how "genetic drift" works in flu viruses. On the whole, most people's immune systems recognise it as flu as even though the picture is a bit jumbled up, it's still close enough to what our body's have seen before. Every now and again, flu changes the picture entirely by putting new squares in the puzzle (by getting bits of flu virus from other species...hence we call them "avian" or "swine" flu). This is called "genetic shift" and it stymies even immune systems that have seen flu before, so we get large outbreaks. The H1N1 1918 pandemic was as a result of a genetic shift, likewise the recent H5N1 and H1N1 outbreaks. Coronaviruses are not built like this, so are less prone to making large jumps in their genetic code, therefore when we do have a vaccine, its likely to work for a good while until an entirely new strain jumps out of some other bat! 

Great information. Really appreciating your posts 🙂

[stuartbert two hats]

The thing I'm struggling to understand with this "half of us are already infected" theory is that surely we would be seeing some signs of the curve flattening out that couldn't just be attributed to lock-downs?  If half of us have been infected, then wouldn't we begin to see some clearer indications of herd immunity by now?  Or would it be too early to see that kind of effect?  It can't be more than a few weeks off surely? 

Or is the thinking that since lockdowns are also associated with high confirmed infection rates, we are seeing the effect of mass immunity in countries that are seeing a flattening of the daily death curve - but because they've also all locked down a few weeks ago, it's impossible to differentiate between flattening because of lockdowns and flattening because of immunity,

Personally, I don't buy it.  Sadly, I think we're nowhere near those levels of infection/immunity yet. But I'm far from an expert on these kinds of things.  I'm really relying on my gut quite a bit to reach that conclusion.

[steviewevie]

Govt fiddling death rates

[Toilet Duck]

13 minutes ago, stuartbert two hats said:

The thing I'm struggling to understand with this "half of us are already infected" theory is that surely we would be seeing some signs of the curve flattening out that couldn't just be attributed to lock-downs?  If half of us have been infected, then wouldn't we begin to see some clearer indications of herd immunity by now?  Or would it be too early to see that kind of effect?  It can't be more than a few weeks off surely? 

Or is the thinking that since lockdowns are also associated with high confirmed infection rates, we are seeing the effect of mass immunity in countries that are seeing a flattening of the daily death curve - but because they've also all locked down a few weeks ago, it's impossible to differentiate between flattening because of lockdowns and flattening because of immunity,

Personally, I don't buy it.  Sadly, I think we're nowhere near those levels of infection/immunity yet. But I'm far from an expert on these kinds of things.  I'm really relying on my gut quite a bit to reach that conclusion.

I think you are probably correct. Based on the only firm data out there, undocumented cases account for about 86% of infections. So, at a rough guess, the prevalence is about 10 times what we have found. That's nowhere near half the population. When documented cases hit 3m, then maybe (and the way things are currently playing out, that would entirely swamp the NHS and lead to a massive toll in terms of fatalities). Of course, it's still early days and there are any number of things that could be going on. The data suggesting only 1 in 10 cases are documented could be flawed (it's entirely based on one part of the outbreak in Wuhan and discounts asymptomatic cases that are not infectious since the model was based on transmission and if no transmission occurs, then it's hard to measure). If and when serology tests become available (looks like sooner rather than later), we'll get a clearer idea via systematic testing of more and more people. There were early suggestions that cross-reactivity with antibodies from other coronavirus infections were providing a degree of immunity to kids (they are basically little coronavirus factories...they pick up 10-20 viral infections a year in pre-school age..often rhinoviruses and coronaviruses). Haven't seen firm data to support that idea, but it's not entirely fanciful (the strongest argument against this is that adults were also exposed to a lot of coronaviruses when they were kids, so why aren't they protected? The answer to that may be related to underlying conditions and other things that impact on immune function, or that immunity might wane with time, but until there are in depth studies done, nobody really knows). Whether having the antibodies to other coronaviruses interferes with the accuracy of the new tests that are going to be rolled out is one of the key questions those validating the tests will need to answer before they can be used to determine the extent of infections on a wider scale. Anyway, keep safe, lie low, we'll get out the other side of this and rebuild a new normality!

[Toilet Duck]

35 minutes ago, jparx said:

Great information. Really appreciating your posts 🙂

No worries! If I can explain anything, I will. I don't have all the answers though!

[stuartbert two hats]

9 minutes ago, Toilet Duck said:

I think you are probably correct. Based on the only firm data out there, undocumented cases account for about 86% of infections. So, at a rough guess, the prevalence is about 10 times what we have found. That's nowhere near half the population. When documented cases hit 3m, then maybe (and the way things are currently playing out, that would entirely swamp the NHS and lead to a massive toll in terms of fatalities). Of course, it's still early days and there are any number of things that could be going on. The data suggesting only 1 in 10 cases are documented could be flawed (it's entirely based on one part of the outbreak in Wuhan and discounts asymptomatic cases that are not infectious since the model was based on transmission and if no transmission occurs, then it's hard to measure). If and when serology tests become available (looks like sooner rather than later), we'll get a clearer idea via systematic testing of more and more people. There were early suggestions that cross-reactivity with antibodies from other coronavirus infections were providing a degree of immunity to kids (they are basically little coronavirus factories...they pick up 10-20 viral infections a year in pre-school age..often rhinoviruses and coronaviruses). Haven't seen firm data to support that idea, but it's not entirely fanciful (the strongest argument against this is that adults were also exposed to a lot of coronaviruses when they were kids, so why aren't they protected? The answer to that may be related to underlying conditions and other things that impact on immune function, or that immunity might wane with time, but until there are in depth studies done, nobody really knows). Whether having the antibodies to other coronaviruses interferes with the accuracy of the new tests that are going to be rolled out is one of the key questions those validating the tests will need to answer before they can be used to determine the extent of infections on a wider scale. Anyway, keep safe, lie low, we'll get out the other side of this and rebuild a new normality!

I'm out of upvotes at the moment, but these detailed replies are really great.  What do you think or Dr John Campbell's videos?

https://www.youtube.com/channel/UCF9IOB2TExg3QIBupFtBDxg

I'm watching them daily, but I'm not sure on his credentials.  He's an ex-nurse, not a medical doctor, although has a Ph.D in nurse education.  

[Toilet Duck]

7 minutes ago, stuartbert two hats said:

I'm out of upvotes at the moment, but these detailed replies are really great.  What do you think or Dr John Campbell's videos?

https://www.youtube.com/channel/UCF9IOB2TExg3QIBupFtBDxg

I'm watching them daily, but I'm not sure on his credentials.  He's an ex-nurse, not a medical doctor, although has a Ph.D in nurse education.  

Watched his hand-washing video just now. Sensible enough! I've been whistling the chorus to Mr Brightside when I wash mine (its about 20 secs and I was was getting sick of singing happy birthday!). Our own advice in work always says to remove all jewellery, but wedding bands are fine...as a former microbiologist, I never really understood this! There's lots of informative videos and blogs out there, they can certainly help people to understand things. I would say though that the best source of factual information is always official sources. If you see or read something that seems in conflict with official advice, go with the official advice! 

[steviewevie]

UK changing how we count Covid-19 deaths, deviating from all European countries

- asking for family consent (shouldn't be necessary for basic data like numbers)

- not counting deaths which occur outside of hospitals

- not doing Covid 19 tests in post-mortems

[zahidf]

Good news couched as bad?

 

 

 

[steviewevie]

have to remember that won't see any affect from restrictions put in place now for at least a couple of weeks.

Edited March 26, 2020 by steviewevie

[efcfanwirral]

50 minutes ago, steviewevie said:

UK changing how we count Covid-19 deaths, deviating from all European countries

- asking for family consent (shouldn't be necessary for basic data like numbers)

- not counting deaths which occur outside of hospitals

- not doing Covid 19 tests in post-mortems

bloody hell what are they playing at? Back to work soon and loads of deaths caused by it unattributed? 

[kalifire]

56 minutes ago, Toilet Duck said:

I've been whistling the chorus to Mr Brightside when I wash mine

Immediately lost all respect for you.

Just kidding, your posts are brilliant, TD. Great to have detailed, informed opinion here.

[zahidf]

Just now, efcfanwirral said:

bloody hell what are they playing at? Back to work soon and loads of deaths caused by it unattributed? 

Yup

[efcfanwirral]

 

3 minutes ago, zahidf said:

Yup

I'm not going anywhere near normal life without the antibody test at the very least. I think a lot of people will be the same

[zahidf]

🤞

 

[DareToDibble]

So is the general thinking that the current measures may be loosened in a month or 2, but then tightened again coming into winter around October time?