NON_POLITICAL China Coronavirus THREAD

[Brainonska511]

I was under the impression that PCR (polymerase chain reaction) WAS the genetic test. As far as I know, the "quick" half-hour tests are looking for antigens - basically, the same types of proteins that the mRNA vaccines stimulate your muscle cells to make. Presumably not the same ones as the vaccines create or at least not ALL the same ones.

PCR is the technique. There are different types and different ways to sequence with that underlying technique. More rapid PCR-based tests might only look for a smaller, unique part of the coronavirus genome in order to provide faster results.

 

[dullard]

I was under the impression that PCR (polymerase chain reaction) WAS the genetic test. As far as I know, the "quick" half-hour tests are looking for antigens - basically, the same types of proteins that the mRNA vaccines stimulate your muscle cells to make. Presumably not the same ones as the vaccines create or at least not ALL the same ones.

<- Works on PCR instruments for a living

The best that I can describe it would be like this:
1) Genetic sequencing (which does utilize PCR as part of it) is like listening to a speech and transcribing the entire set of noises into a specific sequence of letters. The letters represent exactly what the speech said in it's entirety. You can read those letters and very clearly see if the speech contains "Covid-19" and "Omicron".

2) PCR is asking an instrument to listen to the speech and say "yes" or "no" if the word "Charmonium" was in the speech. That is it. You get a yes/no answer*. Quick, cheap, and damn accurate if the answer is "yes". If the answer is "no" then there still may have been a speech, it just didn't contain "Charmonium". Or, maybe there was no speech at all. Or maybe there was a speech but the instrument was too far away to hear it (i.e. you need to wait a couple more days for your viral load to increase to detectable levels). From a single PCR test, you just don't know when the answer is "no". But, you can quickly do many different PCR tests looking for various words such as, did the speech contain "Covid-19", or did it contain "Omicron", etc.

3) Antibody tests are like asking a 3-year old to listen to the speech and to raise her hands if she liked it. Maybe she is accurate, maybe not, maybe she just likes raising her hands and didn't hear anything.

The problem with the "stealth" version is that it spells it "Omcron" not "Omicron" so just asking PCR if "Omicron" is in the speech gives you the wrong answer. But, any good PCR test would still say that "Covid-19" was in the speech.




* If anyone wants to be very pedantic you can also get a reasonably accurate idea of how many times "Charmonium" was in the speech.

 

[Charmonium]

PCR is the technique. There are different types and different ways to sequence with that underlying technique. More rapid PCR-based tests might only look for a smaller, unique part of the coronavirus genome in order to provide faster results.

Cool, thank you. I know you're probably not a virologist, but you seem to have a much better understanding than many of us. So if you happen to know the answer, great.

When you have a virus like this that mutates this easily, can you count on there being any "conservered domains?" You can beat me with a cat-o-nine tails if I used the term incorrectly . . . or, you know, even if I didn't.

 

[pmv]

Two things to clarify:
1) This "stealth" variant is still being detected as Covid positive correctly by all tests.
2) The specific "stealth" variant could be identified with standard cheap PCR tests in the future, it just means the tests need to be modified to do so. Until they are modified, the strain of Covid needs to be determined by more expensive and slow genetic sequencing.

This is the equivalent of an email spammer changing the letter "O" to the number "0" to get around a simple email filter. You still spot the spam email, but it shows up in your inbox instead of in the spam folder until the spam filter is updated.

I get (1), i.e. that one can still detect the virus.
But for (2) I thought the point about the PCR tests was that it was only a happy-accident that meant the existing tests in common use could quickly identify the omicron variant. Good to know they can be modified to find even the new variant-of-the-variant, but it seems to mean that for the time being we won't necessarily get a full picture of the spread of omicron.

 

[Brainonska511]

Cool, thank you. I know you're probably not a virologist, but you seem to have a much better understanding than many of us. So if you happen to know the answer, great.

When you have a virus like this that mutates this easily, can you count on there being any "conservered domains?" You can beat me with a cat-o-nine tails if I used the term incorrectly . . . or, you know, even if I didn't.

Not a virologist, but I did my PhD in biophysical chemistry, and understand PCR, having used it in the lab setting; and my current job in medical communications requires me to understand some of these techniques particularly within the context of molecular testing in oncology.

There will almost certainly always be conserved domains within a virus. Many mutations are deleterious or lethal to a virus, and only benign or beneficial mutations will see success in being passed on. And certain regions of a virus are going to be more or less sensitive to any mutations. Conserved could generally be read as a region less tolerant to mutations.

 

[dullard]

When you have a virus like this that mutates this easily, can you count on there being any "conservered domains?" You can beat me with a cat-o-nine tails if I used the term incorrectly . . . or, you know, even if I didn't.

Most viruses are RNA-based. RNA is similar to DNA, but it is ~1000 times more likely to mutate than DNA. RNA is often used by life as short messages that vanish right away. Think of it as passing notes between people written on toilet paper with a marker in a rain storm. The messages are fragile, smear, and disappear all the time. You have to keep writing and rewriting the message for it to get through. Maybe a smeared message is what actually makes it to the other person. Maybe they understand it, maybe not. This is why viruses are so much harder than bacteria to work with. Viruses change and keep changing.

Covid-19 has found a specific sequence of RNA that codes for proteins that act as keys to enter our cells. Most changes to that RNA will change the protein, and then the changed protein doesn't fit the lock. So while Covid is mutating rapidly, almost all mutations are failures. To answer your question, the region of Covid-19 RNA that lets it into our cells is mostly conserved. But like no two keys are 100% identical, there is some chance for multiple different keys to unlock a door. Thus, there is no perfectly conserved region here. Nature will keep trying different keys until new ones work. I haven't looked into Omicron much yet, but it appears from initial reports to have borrowed a key from one of the strains of a common cold (I think this is still to be confirmed).

The hard task with PCR is to find a conserved region that is also unique to Covid-19. Many RNA codes are conserved but are in almost everything. That would be like looking for the word "the" in a speech. If you find it, what did you really learn? Did you find the right speech?

You need to look for (A) something that is conserved and unique to Covid-19. Then you need to find something that is unique and conserved for each variant of Covid-19 that you want to look for (B) wild type, (C) delta, (D) Omicron, etc. Then you test for all of them that concern you. Is it (A) Covid yes or no? Is it (B) wild type, yes or no? Is it (C) Delta? Is it (D) Omicron? A well designed test would then say something like yes to (A) and (D) then you know you have Covid and it is the Omicron variant.

 

[MrSquished]

everything is still pointing to that omicron is not bad.

All systems go for the holidays up here in mostly vaccinated people land!

 

[dullard]

I get (1), i.e. that one can still detect the virus.
But for (2) I thought the point about the PCR tests was that it was only a happy-accident that meant the existing tests in common use could quickly identify the omicron variant. Good to know they can be modified to find even the new variant-of-the-variant, but it seems to mean that for the time being we won't necessarily get a full picture of the spread of omicron.

You are correct. We will detect Omicron, but not necessarily know if it is Omicron or another variant until new tests are developed.

I'm sure the people who design the tests may dispute the phrase "happy accident", but I'm okay with it. They try their best to find something that is conserved and will always detect Covid-19. It just may mutate more in the future and they can't know for certain until that time comes.

 

[Kaido]

Dang

Michigan sets hospitalization record, leads nation in new coronavirus cases per capita | CNN

Michigan continues to struggle amid the pandemic, setting a record this week for Covid-19 hospitalizations and leading the nation in per capita case rates, new data reveal.

www.cnn.com

"Following Thanksgiving, we're seeing cases going up again now over 100,000 new cases every day, and we didn't want to be there, and hospitalizations also going up, and, sadly, deaths now in excess of 1,000 every day, the vast majority of those being unvaccinated people," Collins said.

 

[[DHT]Osiris]

<- Works on PCR instruments for a living

The best that I can describe it would be like this:
1) Genetic sequencing (which does utilize PCR as part of it) is like listening to a speech and transcribing the entire set of noises into a specific sequence of letters. The letters represent exactly what the speech said in it's entirety. You can read those letters and very clearly see if the speech contains "Covid-19" and "Omicron".

2) PCR is asking an instrument to listen to the speech and say "yes" or "no" if the word "Charmonium" was in the speech. That is it. You get a yes/no answer*. Quick, cheap, and damn accurate if the answer is "yes". If the answer is "no" then there still may have been a speech, it just didn't contain "Charmonium". Or, maybe there was no speech at all. Or maybe there was a speech but the instrument was too far away to hear it (i.e. you need to wait a couple more days for your viral load to increase to detectable levels). From a single PCR test, you just don't know when the answer is "no". But, you can quickly do many different PCR tests looking for various words such as, did the speech contain "Covid-19", or did it contain "Omicron", etc.

3) Antibody tests are like asking a 3-year old to listen to the speech and to raise her hands if she liked it. Maybe she is accurate, maybe not, maybe she just likes raising her hands and didn't hear anything.

The problem with the "stealth" version is that it spells it "Omcron" not "Omicron" so just asking PCR if "Omicron" is in the speech gives you the wrong answer. But, any good PCR test would still say that "Covid-19" was in the speech.




* If anyone wants to be very pedantic you can also get a reasonably accurate idea of how many times "Charmonium" was in the speech.

You know, a few lines of regex could work this out.

 

[Charmonium]

First of all, I love you . . . persons. This stuff is so fascinating.

Not a virologist, but I did my PhD in biophysical chemistry, and understand PCR, having used it in the lab setting; and my current job in medical communications requires me to understand some of these techniques particularly within the context of molecular testing in oncology.

There will almost certainly always be conserved domains within a virus. Many mutations are deleterious or lethal to a virus, and only benign or beneficial mutations will see success in being passed on. And certain regions of a virus are going to be more or less sensitive to any mutations. Conserved could generally be read as a region less tolerant to mutations.

Hence the term "conserved" rather than say "immutable." Hahaha

Most viruses are RNA-based. RNA is similar to DNA, but it is ~1000 times more likely to mutate than DNA. RNA is often used by life as short messages that vanish right away. Think of it as passing notes between people written on toilet paper with a marker in a rain storm. The messages are fragile, smear, and disappear all the time. You have to keep writing and rewriting the message for it to get through. Maybe a smeared message is what actually makes it to the other person. Maybe they understand it, maybe not. This is why viruses are so much harder than bacteria to work with. Viruses change and keep changing.

Covid-19 has found a specific sequence of RNA that codes for proteins that act as keys to enter our cells. Most changes to that RNA will change the protein, and then the changed protein doesn't fit the lock. So while Covid is mutating rapidly, almost all mutations are failures. To answer your question, the region of Covid-19 RNA that lets it into our cells is mostly conserved. But like no two keys are 100% identical, there is some chance for multiple different keys to unlock a door. Thus, there is no perfectly conserved region here. Nature will keep trying different keys until new ones work. I haven't looked into Omicron much yet, but it appears from initial reports to have borrowed a key from one of the strains of a common cold (I think this is still to be confirmed).

The hard task with PCR is to find a conserved region that is also unique to Covid-19. Many RNA codes are conserved but are in almost everything. That would be like looking for the word "the" in a speech. If you find it, what did you really learn? Did you find the right speech?

You need to look for (A) something that is conserved and unique to Covid-19. Then you need to find something that is unique and conserved for each variant of Covid-19 that you want to look for (B) wild type, (C) delta, (D) Omicron, etc. Then you test for all of them that concern you. Is it (A) Covid yes or no? Is it (B) wild type, yes or no? Is it (C) Delta? Is it (D) Omicron? A well designed test would then say something like yes to (A) and (D) then you know you have Covid and it is the Omicron variant.

You know, I never really understood the idea of life evolving from RNA but now that makes sense. It seems like this is something I might have known at some point, but, oh well. That mutation rate for RNA is crazy.

OK, I'm probably pushing my luck here, but another question I had (let me know when I start to get on your nerves) is can viruses dock to allosteric sites like some drugs? And if so, can those sorts of dockings still get them into the cell?

 

[Captante]

Connecticut daily positivity-rate @ 8.33%

Not good.

 

[pmv]

I'm not sure what this really means, but it's being reported all over the place that pfizer seems to be "40 times less effective against omicron".

Omicron significantly reduces Covid antibody protection in small study of Pfizer vaccine recipients

The Covid omicron variant significantly reduces antibodies generated by Pfizer and BioNTech's vaccine, according to a small preliminary study released Tuesday.

www.cnbc.com

 

[Brainonska511]

I'm not sure what this really means, but it's being reported all over the place that pfizer seems to be "40 times less effective against omicron".

Omicron significantly reduces Covid antibody protection in small study of Pfizer vaccine recipients

The Covid omicron variant significantly reduces antibodies generated by Pfizer and BioNTech's vaccine, according to a small preliminary study released Tuesday.

www.cnbc.com

It's sample size is 12 patients and it's only really examining antibodies: doesn't seem very useful - maybe just a tiny puzzle piece. Especially when you also consider that it is in vitro data with dubious implications for its applicability to real-world immunity.

 

[K1052]

Its the first neutralization data we've seen so far and it is very limited but the gist is looking like people should get boosted, which with Delta hitting another wave is a real good idea anyway. . Pfizer/BNT will have something more substantial soon.

https://twitter.com/x/status/1468339655762276353

 

[Brainonska511]

Its the first neutralization data we've seen so far and it is very limited but the gist is looking like people should get boosted, which with Delta hitting another wave is a real good idea anyway. . Pfizer/BNT will have something more substantial soon.

https://twitter.com/x/status/1468339655762276353

While that is true and it is useful, it isn't the complete immune picture by far. I guess my main issue is that it's just a crappy surrogate.

The message should just be: get vaccinated, get booster (if previously vaccinated), have good widely available rapid testing, and shun the unvaccinated from public life.

 

[K1052]

While that is true and it is useful, it isn't the complete immune picture by far. I guess my main issue is that it's just a crappy surrogate.

I know but we've got what we've got and people want answers of some sort. The headlines around this preprint are not particularly informative, sort of the opposite so far. Though if it spooks people who just haven't gotten boosted yet I guess I can live with it.

The message should just be: get vaccinated, get booster (if previously vaccinated), have good widely available rapid testing, and shun the unvaccinated from public life.

Agreed. We've got one hell of a Delta problem right now still which booster definitely help with.

 

[Brainonska511]

I know but we've got what we've got and people want answers of some sort. The headlines around this preprint are not particularly informative, sort of the opposite so far. Though if it spooks people who just haven't gotten boosted yet I guess I can live with it.

Yes, it's what we've got. As someone that's constantly reading about clinical trials and whatnot, and being well-versed in science by training, it's probably just my long running gripe with news and how much of the science has been reported in the media.

 

[njdevilsfan87]

Agreed. We've got one hell of a Delta problem right now still which booster definitely help with.

Something I wonder: if Omicron evades immunity, then does that mean Delta would also evade any immunity from Omicron? If that turns out to be the case, a booster would be wise. At least you'd be well protected against what may be the worse of the two in that case.

 

[Muse]

Saw interesting story on news tonight. Labs are testing waste water in my region and seeing evidence of Omicron being here beyond the clinically determined individual cases. They're saying that testing waste water may be the best way to find new variants and existing variants.

 

[BarkingGhostar]

Maybe this NYC mandate means my trip in a couple of weeks will have less crowds. Hopefully, though, it doesn't mean places start to shut down.

 

[K1052]

https://twitter.com/x/status/1468548443194941445

 

[zinfamous]

It's a French republic where the 1% do their business and spend time on vacation. Also has a population of under 100K.

I thought it was actually France, and not a republic or colony or anything like that?

 

[Roger Wilco]

How many Americans still don't have any immunity (via infection and/or vaccine)? I've seen estimates that ~60% of Americans have natural immunity, but I can't find anything showing how that overlays with vaccinations.

 

[K1052]

https://twitter.com/x/status/1468584771597045765