SARS CoV-2 coronavirus / Covid-19 (No tin foil hat silliness please)

[Wibble]

It does look like strain isn't part of the official taxonomy of viruses. I think a strain is a genetic variant of a virus where that genetic variation causes changes to the phenotype e.g. protein shape of the antigen has changed and thus changes the behaviour of the virus whcih could occur by either antigen drift (gradual evolution) or antigen shirt (recombination with another virus). That might explain why the term seems to be used loosely as it isn't an official taxonomic term.

 

[Wibble]

Did you actually watch the video in the link?

Yes. He seemed quite certain that is was a deliberate political decision. But now it was due to email invites being late. Sure it was

 

[Wibble]

 

[Revan]

Aussies showing how this is done correctly. Together with Iceland and New Zealand, the only Western countries who have really done a great job. And for Australia is it even more impressive considering how big and populous it is (relatively speaking).

 

[christy87]

Aussies showing how this is done correctly. Together with Iceland and New Zealand, the only Western countries who have really done a great job. And for Australia is it even more impressive considering how big and populous it is (relatively speaking).

What have Australia done to achieve this

 

[Wibble]

What have Australia done to achieve this

We locked down hard enough just soon enough to avoid mass community infection (which was partly initial luck). Geography helped but we do (or did) have a large amount of air traffic with China, the US and Europe. We have tested more than most and contact traced a large proportion of infections. Although a fairly big population (22 million I think) we do tend to have fairly low density populations.

We did let a cruise ship offload lots of infected people but we have rounded that up reasonably well. NZ did an even better job and locked down far harder than us. We closed gyms, pubs, restaurants and the like but most other shops can open. That said we have compulsory 14 police supervised hotel quarantine for everyone who flies in or crosses a state border. And despite Aussies thinking of themselves as wild and free they actually embrace regulation more than most nations so in the main we have done what we are told.

I think we may even eliminate SARS-CoV-2 but then we would have to maintain virtually locked borders until .......... who knows how long.

Another thing that helped is that our government had repeatedly fecked up, most notably with the recent bushfires, and they couldn't afford another inadequate response to something. I can't stand our PM or this government but they haven't done too badly this time so far especially on the health front.

 

[TheGame]

This is getting embarrassing now, rushed apology but the Government has said differing views on this as well. Gove said himself it was communication confusion.

 

[Classical Mechanic]

That study looks at viral isolates from patients in China. Where did you read about New York having a particularly bad strain?

On a side note, the study above is done in vitro. In a non-human cell line. So certainly doesn’t tell us anything about death rates.

There is evidence albeit often incomplete and in some cases conflicting (which will be explained in due course). And while there is some talk of strains from researchers (often in very small isolated studies) the big picture data so far suggests that there isn't enough variation to prevent the development of a vaccine and if we do so (not a given of course) then the immunity will last a reasonable time. Most of the talk of different strains seems to be bad reporting from idiots like the Daily Mail.

The articles supposedly come from quotes the scientists from an article in the South China Post as far as I can see.

https://news.sky.com/story/coronavi...n-30-strains-say-scientists-in-china-11976380

 

[Wibble]

The articles supposedly come from quotes the scientists from an article in the South China Post as far as I can see.

https://news.sky.com/story/coronavi...n-30-strains-say-scientists-in-china-11976380

I think I read the source paper

https://www.medrxiv.org/content/10.1101/2020.04.14.20060160v1

and if it is it should be noted that the paper isn't peer reviewed and also says "However, no mutation has been directly linked with functional changes in viral pathogenicity."

 

[Classical Mechanic]

I think I read the source paper

https://www.medrxiv.org/content/10.1101/2020.04.14.20060160v1

and if it is it should be noted that the paper isn't peer reviewed and also says "However, no mutation has been directly linked with functional changes in viral pathogenicity."

I’m only reporting what they’re reporting, which is supposedly the opinions of some of China’s top epidemiologists. I have no clue what type of paper the South China Post is or if the quotes are real.

 

[Rajma]

In Lithuania, we’ve started to ease some restrictions, another wave of loosening measures (barbers, cafes/restaurants with outside terraces, planned operations etc.) will come next week if all goes well. Looking at yesterday’s test results I think optimism is not totally baseless as from 6k+ tests only 20 came back positive.

 

[Feed Me]

I dare you to go down this rabbit hole thread

Every time I see a Katie Hopkins Tweet I wish she would die.

 

[Feed Me]

Those are suspiciously normal. All your equipment must be faulty.

 

[Rajma]

That said we have compulsory 14 police supervised hotel quarantine for everyone who flies in or crosses a state border. And despite Aussies thinking of themselves as wild and free they actually embrace regulation more than most nations so in the main we have done what we are told.

I think we may even eliminate SARS-CoV-2 but then we would have to maintain virtually locked borders until .......... who knows how long.

Yeah, very much like in Lithuania, we’re on the course to eradicating this nasty thing internally but the real hard word will begin on trying to not let it find its way back into the country.

The mandatory two weeks quarantine will definitely be a thing, however, I guess with improved contact tracing and testing volumes as they’re even if virus spreads again it will be managed in smaller clusters thus keeping it under control.

 

[Wednesday at Stoke]

Apparently even the patients who recover don't appear to have developed enough IgF antibodies and even the antibodies don't sustain longer than two months, causing reinfection to be a possibility.

This virus is biologically worse than any kind of catastrophe anyone even imagined.

 

[Rajma]

Apparently even the patients who recover don't appear to have developed enough IgF antibodies and even the antibodies don't sustain longer than two months, causing reinfection to be a possibility.

This virus is biologically worse than any kind of catastrophe anyone even imagined.

That was my main worry with countries who let the virus spread with little regard to it. It will be a monumental job trying to eliminate it for countries that let it spread uncontrollably if long term immunity is not a thing.

 

[CassiusClaymore]

Apparently even the patients who recover don't appear to have developed enough IgF antibodies and even the antibodies don't sustain longer than two months, causing reinfection to be a possibility.

This virus is biologically worse than any kind of catastrophe anyone even imagined.

Source for that?

 

[F-Red]

Apparently even the patients who recover don't appear to have developed enough IgF antibodies and even the antibodies don't sustain longer than two months, causing reinfection to be a possibility.

This virus is biologically worse than any kind of catastrophe anyone even imagined.

I think you need to caveat with that the above hasn’t been conclusive yet, even the WHO are saying they don’t have an answer on it as it’s unknown still.

 

[Wibble]

Apparently even the patients who recover don't appear to have developed enough IgF antibodies and even the antibodies don't sustain longer than two months, causing reinfection to be a possibility.

This virus is biologically worse than any kind of catastrophe anyone even imagined.

Source? Not sure I believe that.

 

[Wednesday at Stoke]

Source for that?

Here's a thread with an explainer and a preprint.

 

[TheGame]

 

[Sparky Rhiwabon]

It depends. There can be false pulse oximeter readings sure, in cases of hypoperfusion (e.g Raynaud's disease), nail varnish or incorrect use but finger tip sats probe are fairly easy to use, if somebody called me with COVID symptoms with repeated Sats readings in the 80s yeah I'd be confident they should be phoning 111 or an ambulance if symptoms suggestive of respiratory distress

There are some instances for example where we accept low Sats readings, e.g. COPD patients or a recovering infant with bronchiolitis. But its an important clinical vital sign, and in the case of COVID (after respiratory rate) probably the most important factor in deciding whether somebody needs an admission or not. There are plenty of clinical symptoms though however people need to be mindful of, severe shortness of breath and fatigue are red flags.



I'd recommend the paediatric ones still, there's one for kids aged around 2-12 years old, neonatal ones for younger than that. Accuracy for adult ones on kids is less, I think its to do with finger diameter and the sensors

Thanks

 

[Pogue Mahone]

Here's a thread with an explainer and a preprint.

I’ve been making a similar point for a while. Permanent (or even long term) immunity by no means guaranteed after being vaccinated. Crucially, same caveat applies after being infected.

Although, annual booster jab might fix that issue. Or at least take the edge off.

 

[Regulus Arcturus Black]

11 of 100 blood donors in Stockholm have had it.
Prof Jan Albert in clinical microbiology at Karolinska reckons it’s over 20% as the antibody test doesn’t catch all cases by any stretch.
Karolinska did this test last week.

https://www.svt.se/nyheter/inrikes/11-procent-av-stockholmarna-har-antikroppar-mot-covid-19

Thoughts @Pogue Mahone & especially @massi83 who doubted my 7.5% optimism last week as “pregnant women are at higher risk”.

They utterly fecked up this small test study by the way, some research gimp is defo getting the sack.
The person who collected the samples didn’t realise that some now healthy Covid-19 survivors were also in there as they have donated plasma.
Shouldn’t be possible, but happened. Now they have to do the test all over again after going out to the World with the results. One of the top medical research universities in the World.
You’d almost laugh if it wasn’t so serious.

 

[Wibble]

Here's a thread with an explainer and a preprint.

His is warning that we haven't developed a vaccine for other human Coronavirus (we haven't but we have done for animals I believe) and that immunity from a vaccine may only last a couple of years. So he is correct that this may be an ongoing fight even if we get a vaccine.

 

[Pogue Mahone]

They utterly fecked up this small test study by the way, some research gimp is defo getting the sack.
The person who collected the samples didn’t realise that some now healthy Covid-19 survivors were also in there as they have donated plasma.
Shouldn’t be possible, but happened. Now they have to do the test all over again after going out to the World with the results.
You’d almost laugh if it wasn’t so serious.

Jaysus. That’s not good. I do have some sympathy for the researchers as everyone is doing their research in a crazy hurry, with good reason. Firing out press released based on tiny studied, with dubious design is bad form though. That’s on the health ministry.

 

[Regulus Arcturus Black]

Jaysus. That’s not good. I do have some sympathy for the researchers as everyone is doing their research in a crazy hurry, with good reason. Firing out press released based on tiny studied, with dubious design is bad form though. That’s on the health ministry.

The health ministry didn’t release it. Karolinska Institute did.

 

[Wednesday at Stoke]

His is warning that we haven't developed a vaccine for other human Coronavirus (we haven't but we have done for animals I believe) and that immunity from a vaccine may only last a couple of years. So he is correct that this may be an ongoing fight even if we get a vaccine.

Yeah, his argument is that even flu vaccines which we have been developing for ages are not effective enough against the seasonal flu and it has a way smaller spread/severity compared to the coronavirus. So even if you have a first vaccine that reaches human trials and subsequent approval, it will only be semi-effective and considering the R0, the virus would still be a slightly lesser nightmare to contain.

The best case scenario is one where we do have a vaccine and make a quarterly trip to the hospital or a pop-up tent close-by to get a shot.

 

[Pogue Mahone]

His is warning that we haven't developed a vaccine for other human Coronavirus (we haven't but we have done for animals I believe) and that immunity from a vaccine may only last a couple of years. So he is correct that this may be an ongoing fight even if we get a vaccine.

He includes a review paper on animal CoV vaccines. It’s not encouraging. They’ve been trying to make them for decades with very limited success.

The only licensed animal CoV vaccines targeted to prevent respiratory CoV infections are IBV vaccines for chickens. These vaccines, administered parenterally, may not protect against the infection but they can reduce the severity of the respiratory signs and prevent involvement of the kidney and reproductive tract

 

[cyberman]

His is warning that we haven't developed a vaccine for other human Coronavirus (we haven't but we have done for animals I believe) and that immunity from a vaccine may only last a couple of years. So he is correct that this may be an ongoing fight even if we get a vaccine.

Maybe this is a stupid qurstion but could we not get just get vaccinated every few years?

 

[Pogue Mahone]

The health ministry didn’t release it. Karolinska Institute did.

Ok. My bad. They’re a top class institute too. That’s unlike them.

 

[Revan]

I’ve been making a similar point for a while. Permanent (or even long term) immunity by no means guaranteed after being vaccinated. Crucially, same caveat applies after being infected.

Although, annual booster jab might fix that issue. Or at least take the edge off.

I don't think anyone who knows something about it was expecting permanent immunity. The question is if we'll get immunity for 3 months or 3 years. If it is the former, then it is really bad.

Also, would be interesting to see what happens in the second infection. Would it be as bad as the first one (no immunity at all), worse (dengue fever), or not as bad as the first one? If it is the third case, then that is good news. Hard to know at the moment.

 

[Regulus Arcturus Black]

Ok. My bad. They’re a top class institute too. That’s unlike them.

The guy from Karolinska who lead the study was on this morning apologising for it, felt so sorry for him. You could genuinely see the utter horror of what a feck up this was from them.

 

[Pogue Mahone]

Yeah, his argument is that even flu vaccines which we have been developing for ages are not effective enough against the seasonal flu and it has a way smaller spread/severity compared to the coronavirus. So even if you have a first vaccine that reaches human trials and subsequent approval, it will only be semi-effective and considering the R0, the virus would still be a slightly lesser nightmare to contain.

The best case scenario is one where we do have a vaccine and make a quarterly trip to the hospital or a pop-up tent close-by to get a shot.

The flu vaccine comparison is a bit misleading as flu mutates much more quickly so is a much faster moving target. As per the first reply to his tweet, the low r0 for flu he mentions is probably down to existing herd immunity.

 

[Wednesday at Stoke]

Another thing worth noting from Scott Gottlieb:



The high false positive rate for serology based antibody tests mean that using them to determine letting people back to normalcy is basically like tossing a coin at this point.

 

[Revan]

They utterly fecked up this small test study by the way, some research gimp is defo getting the sack.
The person who collected the samples didn’t realise that some now healthy Covid-19 survivors were also in there as they have donated plasma.
Shouldn’t be possible, but happened. Now they have to do the test all over again after going out to the World with the results. One of the top medical research universities in the World.
You’d almost laugh if it wasn’t so serious.

Shit happens in every field. I have seen papers with totally amateurish mistakes (that wouldn't pass an assignment) in top venues of my field. The pressure is to high to do quick results, which also increases the chances of errors.

 

[Wednesday at Stoke]

The flu vaccine comparison is a bit misleading as flu mutates much more quickly so is a much faster moving target. As per the first reply to his tweet, the low r0 for flu he mentions is probably down to existing herd immunity.

That's a good point regarding R0 for the flu.

We also don't have adequate time to determine the mutation rate of the coronavirus, or more specifically this particular strain.

 

[Revan]

His is warning that we haven't developed a vaccine for other human Coronavirus (we haven't but we have done for animals I believe) and that immunity from a vaccine may only last a couple of years. So he is correct that this may be an ongoing fight even if we get a vaccine.

One year of immunity from the vaccine wouldn't even be that bad. Just make mandatory vaccination every year (and combine it with the flu vaccine, providing no side effects).

 

[Pogue Mahone]

That's a good point regarding R0 for the flu.

We also don't have adequate time to determine the mutation rate of the coronavirus, or more specifically this particular strain.

We don’t but if we’re making negative assumptions based on previous CoV (which he does in that thread) we can make positive ones too. CoV just don’t have the same “drift” that flu viruses do. They never have done. Would be extremely unlikely for this one to buck the trend.

 

[Pogue Mahone]

Another thing worth noting from Scott Gottlieb:



The high false positive rate for serology based antibody tests mean that using them to determine letting people back to normalcy is basically like tossing a coin at this point.

Another drum I’ve been banging! Immunity passports are a pipe dream. Serology will probably only be useful at a population, not individual, level.