COVID-19 (f/k/a "the Coronavirus")

[MU82]

https://www.vox.com/the-goods/22410017/dating-post-vaccine-kinsey-relationships-hookups

Dating podcasters, condom companies, bartenders, and college students weigh in on the horny months to come.

 

Eye gess Doc Dribble wuz rite abowt da fookin' starting May furst, nu?

[pacearrow02]

Anyone know why the CDC is lowering the cycle threshold for PCR tests when trying to identify these break through cases after vaccinated?

[forgetful]

Anyone know why the CDC is lowering the cycle threshold for PCR tests when trying to identify these break through cases after vaccinated?

Can you provide a link to the story indicating exactly what they are doing?

[pacearrow02]

Can you provide a link to the story indicating exactly what they are doing?

Attached is cdc guidelines saying for breakthrough cases it needs to be less then 28.  From what I understood this whole time it was up to 40?

[rocky_warrior]

Attached is cdc guidelines saying for breakthrough cases it needs to be less then 28.  From what I understood this whole time it was up to 40?

I souldn't pretend to understand any of this, but it looks like anything requiring > 38 Ct would be  indeterminate or negative result.  Detection at Ct <= 28 would be the "sweet" spot (according to these graphs) of positive results.

But maybe I've got that all wrong. 
https://www.publichealthontario.ca/-/media/documents/ncov/main/2020/09/cycle-threshold-values-sars-cov2-pcr.pdf?la=en

[jficke13]

Weird timing, but I just listened to a podcast that discussed at length what cycles in a PCR test meant. It was in the context of Andrew Wakefield's fraud, but the concept is relevant to this as well: https://peterattiamd.com/briandeer/ (I think the relevant discussion occurs at about the 1 hour mark)

Essentially the explanation is that PCR engages in an exponential replication of the thing its testing for, so the difference between a positive test at 28 cycles and 40 cycles is the difference between 2^40 - 2^28. The numbers get massive, and the sense is that the farther you push, either the less was there in the first place or the more chance for error.***

*** I am not a scientist, merely a parrot for the podcast I linked above

[pacearrow02]

Weird timing, but I just listened to a podcast that discussed at length what cycles in a PCR test meant. It was in the context of Andrew Wakefield's fraud, but the concept is relevant to this as well: https://peterattiamd.com/briandeer/ (I think the relevant discussion occurs at about the 1 hour mark)

Interesting!  If that’s the case, does it essentially mean they aren’t looking as “hard” for breakthrough cases as they do if you’re not vaccinated? 

If true wonder what the motivation or reason why would be

Essentially the explanation is that PCR engages in an exponential replication of the thing its testing for, so the difference between a positive test at 28 cycles and 40 cycles is the difference between 2^40 - 2^28. The numbers get massive, and the sense is that the farther you push, either the less was there in the first place or the more chance for error.***

*** I am not a scientist, merely a parrot for the podcast I linked above

[jesmu84]

Attached is cdc guidelines saying for breakthrough cases it needs to be less then 28.  From what I understood this whole time it was up to 40?

Where did you find/read/hear about this discrepancy?

Or do you read cdc guidelines frequently enough to notice a change like that?

[rocky_warrior]

Interesting!  If that’s the case, does it essentially mean they aren’t looking as “hard” for breakthrough cases as they do if you’re not vaccinated?

If true wonder what the motivation or reason why would be

Well, as mentioned, this appears to be a "amplification" factor, so the more you push it, the less reliable the "positive" test results are.  Like using zoom on a digital picture -  once you get down to seeing only a few pixels, you don't really know what you're looking at.

But 3 things.  1) Hopefully someone smart will chime in here.  2) You seem to be assuming this has "changed" for vaccinated people, but haven't provided references for " normal" PCR test cycles.  3) You seem to be assuming (or someone else has suggested to you) that there is "motivation" for the change.  Do you have a news source for that?

Without confirming the last 2, this seems like a non-issue to a simpleton like me.

[forgetful]

Attached is cdc guidelines saying for breakthrough cases it needs to be less then 28.  From what I understood this whole time it was up to 40?

Also curious to where you found that.

Here's what you are reading. That is not any change in cdc guidelines. That is a study the CDC is conducting to look for COVID breakthrough cases, and to do surveillance to identify possible new strains that emerge that may be more resistant to the vaccines.

The cycle threshold you are seeing isn't any change regarding positive tests etc., it is the threshold requirement for those specimens to be subjected to sequencing to determine if it represents a new variant, or which variant it represents.

You don't want to be sequencing any false positives, so the threshold for sequencing will be more stringent than a simple positive test to ensure it represents an active infection.

Also, Rocky and others are correct. The PCR cycles are an amplification factor, so for 40 cycles you have an amplification factor of roughly 2^40.

There are some of these tests that my lab runs where we restrict our cycles to around 20-24 instead of 35 or more, because simple background (DNA in that case) will give false positives. Controlling the number of PCR cycles is essential to ensuring that the resulting data is robust and accurate. That's why these different testing platforms are rigorously tested to identify the cycle threshold that one deems a positive, that one deems a negative, and ones that are inconclusive.

[pacearrow02]

Well, as mentioned, this appears to be a "amplification" factor, so the more you push it, the less reliable the "positive" test results are.  Like using zoom on a digital picture -  once you get down to seeing only a few pixels, you don't really know what you're looking at.

But 3 things.  1) Hopefully someone smart will chime in here.  2) You seem to be assuming this has "changed" for vaccinated people, but haven't provided references for " normal" PCR test cycles.  3) You seem to be assuming (or someone else has suggested to you) that there is "motivation" for the change.  Do you have a news source for that?

Without confirming the last 2, this seems like a non-issue to a simpleton like me.

It’s been reported on for awhile that labs had the testing set to 40 far more often then not, on rarer occasions labs used 37.  Attached is snipped from NY Times article back in August 2020.

[pacearrow02]

Also curious to where you found that.

Here's what you are reading. That is not any change in cdc guidelines. That is a study the CDC is conducting to look for COVID breakthrough cases, and to do surveillance to identify possible new strains that emerge that may be more resistant to the vaccines.

The cycle threshold you are seeing isn't any change regarding positive tests etc., it is the threshold requirement for those specimens to be subjected to sequencing to determine if it represents a new variant, or which variant it represents.

You don't want to be sequencing any false positives, so the threshold for sequencing will be more stringent than a simple positive test to ensure it represents an active infection.

Also, Rocky and others are correct. The PCR cycles are an amplification factor, so for 40 cycles you have an amplification factor of roughly 2^40.

There are some of these tests that my lab runs where we restrict our cycles to around 20-24 instead of 35 or more, because simple background (DNA in that case) will give false positives. Controlling the number of PCR cycles is essential to ensuring that the resulting data is robust and accurate. That's why these different testing platforms are rigorously tested to identify the cycle threshold that one deems a positive, that one deems a negative, and ones that are inconclusive.

Ok that makes sense enough for a layman like myself.  Do you know outside the parameters of this study will the higher CT values on breakthrough cases still be caught somewhere else and reported?

A lot to be learned from these breakthrough cases, so would hate to see some go unidentified/looked into further.

[pacearrow02]

https://www.nytimes.com/2020/08/29/health/coronavirus-testing.html

Really interesting to go back and read this article.  Helps me better understand the belief by some that a good chunk of the death total attached to this pandemic was folks that died with Covid not necessarily from Covid. 

Not sure I fully align with that but can at least understand why some might feel that way.

[forgetful]

Ok that makes sense enough for a layman like myself.  Do you know outside the parameters of this study will the higher CT values on breakthrough cases still be caught somewhere else and reported?

A lot to be learned from these breakthrough cases, so would hate to see some go unidentified/looked into further.

It's a good question. My assumption is that the data regarding breakthrough cases will be recorded. The description of the study essentially indicates that this is so. One of the metrics they will be recording is the number of cycles for positive cases.

What I'm not certain of is how widespread this study is. It would require that people disclose a prior vaccine when getting tested, and I'm honestly not certain how common that is, and who that is being reported to.

[jesmu84]

Where did you find/read/hear about this discrepancy?

Or do you read cdc guidelines frequently enough to notice a change like that?

Any response, pace?

[pacearrow02]

Any response, pace?

To what?

[TSmith34, Inc.]

https://www.nytimes.com/2020/08/29/health/coronavirus-testing.html

Really interesting to go back and read this article.  Helps me better understand the belief by some that a good chunk of the death total attached to this pandemic was folks that died with Covid not necessarily from Covid. 

Not sure I fully align with that but can at least understand why some might feel that way.

Sigh.

[pacearrow02]

Sigh.

Nothing from the article (assuming you read it) put the slightest skepticism in your mind? 

When they went back and did retrospective analysis to find that 60-70% of positive cases had such a high Ct value that they would not have even suggested doing contact tracing for those covid+ folks because the viral load was next to non-existent in their system, that’s enough for me to at least question some (not all) of the mortality numbers pinned to this.  Not sure how one could objectively/honestly take that information any other way. 

This is in no way suggesting Covid isn’t real just maybe not quite as high of mortality rate, that’s it.   It would be good news!

[MU82]

Reaching ‘Herd Immunity’ Is Unlikely in the U.S., Experts Now Believe

https://www.nytimes.com/2021/05/03/health/covid-herd-immunity-vaccine.html?campaign_id=4&emc=edit_dk_20210504&instance_id=30184&nl=dealbook&regi_id=108420427&segment_id=57166&te=1&user_id=d36dcf821462fdd16ec3636710a855fa

Early in the pandemic, when vaccines for the coronavirus were still just a glimmer on the horizon, the term “herd immunity” came to signify the endgame: the point when enough Americans would be protected from the virus so we could be rid of the pathogen and reclaim our lives.

Now, more than half of adults in the United States have been inoculated with at least one dose of a vaccine. But daily vaccination rates are slipping, and there is widespread consensus among scientists and public health experts that the herd immunity threshold is not attainable — at least not in the foreseeable future, and perhaps not ever.

Instead, they are coming to the conclusion that rather than making a long-promised exit, the virus will most likely become a manageable threat that will continue to circulate in the United States for years to come, still causing hospitalizations and deaths but in much smaller numbers.

How much smaller is uncertain and depends in part on how much of the nation, and the world, becomes vaccinated and how the coronavirus evolves. It is already clear, however, that the virus is changing too quickly, new variants are spreading too easily and vaccination is proceeding too slowly for herd immunity to be within reach anytime soon.

[pacearrow02]

Reaching ‘Herd Immunity’ Is Unlikely in the U.S., Experts Now Believe

https://www.nytimes.com/2021/05/03/health/covid-herd-immunity-vaccine.html?campaign_id=4&emc=edit_dk_20210504&instance_id=30184&nl=dealbook&regi_id=108420427&segment_id=57166&te=1&user_id=d36dcf821462fdd16ec3636710a855fa

Early in the pandemic, when vaccines for the coronavirus were still just a glimmer on the horizon, the term “herd immunity” came to signify the endgame: the point when enough Americans would be protected from the virus so we could be rid of the pathogen and reclaim our lives.

Now, more than half of adults in the United States have been inoculated with at least one dose of a vaccine. But daily vaccination rates are slipping, and there is widespread consensus among scientists and public health experts that the herd immunity threshold is not attainable — at least not in the foreseeable future, and perhaps not ever.

Instead, they are coming to the conclusion that rather than making a long-promised exit, the virus will most likely become a manageable threat that will continue to circulate in the United States for years to come, still causing hospitalizations and deaths but in much smaller numbers.

How much smaller is uncertain and depends in part on how much of the nation, and the world, becomes vaccinated and how the coronavirus evolves. It is already clear, however, that the virus is changing too quickly, new variants are spreading too easily and vaccination is proceeding too slowly for herd immunity to be within reach anytime soon.

Will be interesting to see how things play out.  Was reading an article about how Israel has all but wiped out hospitalizations and Covid deaths with some thinking they’re on the brink of herd immunity with around 60% of their population vaccinated. 

[jesmu84]

To what?

Where did you find/read/hear about this discrepancy?

Or do you read cdc guidelines frequently enough to notice a change like that?

[pacearrow02]

Where did you find/read/hear about this discrepancy?

Or do you read cdc guidelines frequently enough to notice a change like that?

The initial PCR Ct acceptance of laboratories running 37-40 has been reported outside of mainstream media for quite awhile.  I was wrong in that it was not a CDC requirement or guideline but in hindsight seems irresponsible for them to not require laboratories to run a little tighter ship.

As far as the new CDC study of requiring Ct of 28 or less was something I came across as I was reading about these breakthrough cases.  I was wrong in thinking these were official guidelines though.  Would be interesting once the dust settles to see what the Ct scores were for all the positive cases over the last 13 months and what % of deaths happened in folks with Ct greater then 30 or 35. 

What does it matter?

[jesmu84]

The initial PCR Ct acceptance of laboratories running 37-40 has been reported outside of mainstream media for quite awhile.  I was wrong in that it was not a CDC requirement or guideline but in hindsight seems irresponsible for them to not require laboratories to run a little tighter ship.

As far as the new CDC study of requiring Ct of 28 or less was something I came across as I was reading about these breakthrough cases.  I was wrong in thinking these were official guidelines though.  Would be interesting once the dust settles to see what the Ct scores were for all the positive cases over the last 13 months and what % of deaths happened in folks with Ct greater then 30 or 35. 

What does it matter?

It matters because it demonstrates your motive for this discussion.

So, as others have also asked, where did you originally come across this topic/difference?

[pacearrow02]

It matters because it demonstrates your motive for this discussion.

So, as others have also asked, where did you originally come across this topic/difference?

Nunya

[pacearrow02]

Forgetful or Goooo?

Any idea about furin cleavage?  Just read an article (linked below) suggesting the Covid furin cleavage site is unique and can only happen after circulating within humans for years or through laboratory intervention?

A lot of this might as well be written in Latin and way over my head so figured yo two might know a little more.

https://nicholaswade.medium.com/origin-of-covid-following-the-clues-6f03564c038