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Over half of Covid hospitalisations tested positive after admission

telegraph.co.uk

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Re: Over half of Covid hospitalisations tested positive after admission

#161

Post by blywi »

mizzack wrote: post #39
timr wrote: post #34

Earlier quoted context omitted.

> I have looked and I cannot even find how increasing CT values affect the false positive rate for the PCR testing. If my understanding is correct a single increment of CT essentially doubles the sensitivity of the test, so difference between CT value of 35 and 40 is 32 fold. I have never used this particular set of primers, but have done a lot of PCR. In general, at 30+ cycles, PCR is prone to spurious amplification…

> I strongly suspect that the goal was to cast a wide net (i.e. bias toward false positives) at the expense of accuracy, but then "cases" became some kind of top-line media metric... Then in January the WHO updated the diagnostic protocol [1] because of that false positive/low confidence problem. Unsurprisingly, case counts plummeted in the following weeks. [1] https://www.who.int/news/item/20-01-2021-who-information…

This WHO statement has been widely misinterpreted, is is not the case that PCR tests were resulting in inflated numbers of false positives, see Reuters fact check [1] from February 4, 2021, and [2] from April 8, 2021.

[1] https://www.reuters.com/article/uk-factcheck-who-instruction... [2] https://www.reuters.com/article/factcheck-who-pcr-idUSL1N2M1...

Re: Over half of Covid hospitalisations tested positive after admission

#162

Post by rsfern »

briefcomment wrote: post #155
xyzzy21 wrote: post #134

Earlier quoted context omitted.

Well if you want to "control public fear" for political and economic gain, you just adjust the CT value as required to bump up the positive rate or to lower it. Note that the US CDC is using two different CT values: a higher one for unvaccinated and a lower one for vaccinated. That doesn't make any sense until you start thinking Hobbsian/Hegalian/Machiavellian. If I was wanting to exploit the situation, this is exact…

Is there any proposed logic behind the difference in thresholds between the two groups? It seems designed to do just one thing - overestimate cases in the unvaccinated, and underestimate cases in the vaccinated. What is the actual rationale the CDC provides?

Vaccinated people have a strong immune response to the virus, and presumably it would take a much higher viral load to make them clinically ill.

To me this seems like a much more plausible explanation for dual thresholds than some kind of conspiracy to inflate numbers for political reasons. Immunology is not my field though.

Re: Over half of Covid hospitalisations tested positive after admission

#163

Post by blywi »

jonahbenton wrote: post #156
forcry wrote: post #20

The most baffling thing is not standardising CT values for RT-PCR tests. I have looked and I cannot even find how increasing CT values affect the false positive rate for the PCR testing. If my understanding is correct a single increment of CT essentially doubles the sensitivity of the test, so difference between CT value of 35 and 40 is 32 fold. CDC is suggesting CT value of 28 for detecting breakthrough infections a…

No. Nearly all EUA PCR COVID tests are qualitative. On saliva/sputum samples, that's really the best that can be done. They can report one or more Ct values, but those reflect specific characteristics of the platform and can not be normalized across platforms and cannot be used even to infer things like viral load.

Well apparently it is possible, and it has been done, probably more than once.

In his German language podcast Dr. Drosten, a Coronavirus specialist from Charite Berlin, is addressing this exact issue. In case you have never heard of him, his lab was the first to publish a working PCR test protocol for SARS-CoV-2 back in January 2020 [1]

Here is an DeepL translated excerpt from the transcript for his latest podcast [2]

"The whole thing has a certain complication. The Ct values that we have here are not easily comparable between the individual test manufacturers. Basically, you can say that a high Ct value always indicates a low viral load. And if the Ct value then becomes lower, then that also becomes a higher viral load. But we can only compare them numerically as long as we are in the same test system. The differences there are sometimes considerable. There are test manufacturers where a value of, let's say, 25 is nothing at all worrying, while the same value of 25 in another manufacturer's test shows that this is already a seriously infectious concentration. This is simply because these test manufacturers do not standardize on the Ct value. That would not make sense either. Instead, it makes sense to simply determine what lies behind the Ct values, namely the actual viral load. You can do that, you have to calibrate that."

and further

"We did that in the fall. All the laboratory work that is necessary for this was done in September and October. I had already explained that to the public in the summer, how that works. We worked in the lab to make this possible. We have also come so far that viral load standards... You really have to imagine it as a small plastic vial with a test solution in it. It contains killed virus of a known, defined concentration. You can order it in two or three defined concentrations from a company that sells such a thing. The purpose of this company is to provide quality assurance for laboratories and to offer the necessary calibration standards. And these calibration standards are produced here in our laboratory, this killed and exactly quantified virus. So we have produced this calibration standard. We have also developed instructions, which are then recommended by the Robert Koch Institute, on how the laboratories can use this calibration standard to convert their Ct values into viral load ranges, which either actually lead to an exact viral load or which - and this is our recommendation - lead to assessment ranges. And that is to an assessment of highly infectious, low infectious, and borderline. So roughly speaking, that is expressed a little bit more genteel and precise. There's even a recommendation on how to express that on the medical findings then. Medical laboratories can do all that. This is also done in practice in the hospital sector. routinely used for discharge decisions. For example, a patient is in the intensive care unit. He is getting better. He should be transferred to a normal ward. Now the question is: Can we do that? Is he still highly infectious? Then a quantitative PCR test is carried out with these findings."

[1] https://www.eurosurveillance.org/content/10.2807/1560-7917.E... [2] https://www.ndr.de/nachrichten/info/coronaskript306.pdf

Re: Over half of Covid hospitalisations tested positive after admission

#164

Post by blywi »

forcry wrote: post #20

The most baffling thing is not standardising CT values for RT-PCR tests. I have looked and I cannot even find how increasing CT values affect the false positive rate for the PCR testing. If my understanding is correct a single increment of CT essentially doubles the sensitivity of the test, so difference between CT value of 35 and 40 is 32 fold. CDC is suggesting CT value of 28 for detecting breakthrough infections a…

Do you have source for that claim? I tried to find that recommendation, but all I came up with, was this fact check [1]. According to the fact check the CDC did NOT change cycle threshold, and the thresholds used to decide if test result is positive, are not different for vaccinated and unvaccinated. The quoted 28 cycle threshold is apparently only used for deciding if a sample can be submitted for sequencing.

[1] https://www.politifact.com/factchecks/2021/jun/03/tweets/cdc...

Re: Over half of Covid hospitalisations tested positive after admission

#165

Post by areyousure »

javagram wrote: post #143
beerandt wrote: post #117

Earlier quoted context omitted.

It's harder to dismiss when you also consider the first vaccine approvals kept getting delayed until they were released immediately after the election.

Note that it was hardly “delayed” since all initial predictions for the vaccine to be approved were around 12 months, in the end it only took about 10 months. Reports last year indicated Trump’s own FDA was responsible for setting out the needed time for data gathering and review that pushed it into mid-November. https://abcnews.go.com/Politics/white-house-okays-fda-months... Meanwhile other countries including China…

Both Russia and China started using their vaccines in August 2020:

https://www.nbcnews.com/news/world/putin-claims-first-corona...

https://www.reuters.com/article/us-health-coronavirus-china-...

Re: Over half of Covid hospitalisations tested positive after admission

#166

Post by ericlavigne »

forcry wrote: post #20

The most baffling thing is not standardising CT values for RT-PCR tests. I have looked and I cannot even find how increasing CT values affect the false positive rate for the PCR testing. If my understanding is correct a single increment of CT essentially doubles the sensitivity of the test, so difference between CT value of 35 and 40 is 32 fold. CDC is suggesting CT value of 28 for detecting breakthrough infections a…

Imagine the CDC yelling: "Don't throw that away! I need more details! Please! If you won't finish the job, please let me do that work!"

That's my translation of the document I found when looking into this issue. More details below...

===

"CDC is suggesting CT value of 28 for detecting breakthrough infections after vaccinations... So that means, a breakthrough infection needs to have 128 times viral load in someone who has been vaccinated to be considered as positive, than it is required to have considered as positive in a non-vaccinated person."

This sounded strange to me, so I searched for more information about it. It looks like you just misunderstood the CDC's policy.

This document regarding breakthrough case investigations was the second result in a Google search for "cdc ct value 28". The relevant text can be found on page 5 of that document.

https://stacks.cdc.gov/view/cdc/105217/cdc_105217_DS1.pdf

"If SARS-CoV-2 sequencing will not be performed locally and a specimen is available, the state public health laboratory should request the residual clinical respiratory specimen for subsequent shipping to CDC. For cases with a known RT-PCR cycle threshold (Ct) value, submit only specimens with Ct value In other words... Imagine some lab just found a breakthrough case. And this breakthrough case had an especially high viral load (Ct 28). And the lab was just going to report a positive and throw away the sample...

Imagine the CDC yelling: "Don't throw that away! I need more details! Please! If you won't finish the job, please let me do that work!"

That's what the document is saying. There's a rare event that needs extra analysis. CDC is just letting the labs know in advance that if they ever see this event, and didn't have the resources to fully analyze it, please send that sample to the CDC so it gets the attention it deserves.

Nothing to do with whether the test is considered positive or a breakthrough - just about whether to put extra effort into gathering more details on that particular case. CDC is volunteering to do this extra effort only for higher Ct values. Whether or not they do this extra work, it's still a positive result either way.

Re: Over half of Covid hospitalisations tested positive after admission

#167

Post by fabbari »

Great journalism at work here! So - the expectation is that people with symptoms of Covid19 would be tested before being hospitalized? I am actually impressed that 44% were.

It would be standard operating procedure for an hospital receiving a patient showing symptoms to give a test. In fact 88% received the test results within two days of hospitalization.

I am still waiting for an explanation of ICU occupancy [0] if it wasn't for Covid 19.

[0] https://www.statista.com/chart/23746/icu-bed-occupancy-rates...

Re: Over half of Covid hospitalisations tested positive after admission

#168

Post by washadjeffmad »

javagram wrote: post #142
kook_throwaway wrote: post #116

Earlier quoted context omitted.

Abusing high cycle thresholds for false positives isn't a new strategy. PCR inventor Kary Mullis is on video calling Fauci out for doing exactly that. Unfortunately I can't even link the two videos because they keep getting memory holed. If you search around you might get lucky, otherwise I'll upload my saved copy when I get off work.

Note that the background for this is that Kary Mullis believed AIDS wasn’t caused by HIV and was therefore angry at Fauci and the entire medical/scientific establishment for linking HIV and AIDS. He died in 2019 so his criticisms of Fauci were related to HIV, not SARS-CoV-2. https://en.wikipedia.org/wiki/Kary_Mullis#Views_on_HIV/AIDS_...

Denialism and skepticism are often used as slurs in the absence of strong evidence by those who favor popular consensus over evidence.

A PI once confided in me that he didn't believe in the big bang. I was startled because creationism was on the rise, and I knew that he was Catholic. However, I also knew he was a natural empiricist, and after taking a quiet moment to think things through, I realized I was being tested to see if I could think critically and ask the right questions as a scientist.

He didn't deny the big bang, and he wasn't replacing it with a worse theory. After a few questions, he demonstrated that his understanding of the evidence and his tools to evaluate it were far better than mine, and that while it was the most probable and best supported explanation, because it was not observed and was not currently reproducible, it wasn't anything that warranted "belief".

Reality doesn't require our consent to exist.

Re: Over half of Covid hospitalisations tested positive after admission

#169

Post by simpleguitar »

jaywalk wrote: post #50
raziel2p wrote: post #14

Earlier quoted context omitted.

I mean, they may be catching covid in hospitals, there's no way to know for sure, but it seems unlikely to account for all these cases. But yeah this is going to be picked up by covid-deniers as more "proof" that covid is exaggarated.

I don't think "Covid deniers" make up any significant percentage of the population, but that doesn't change the fact that this is proof that Covid is exaggerated.

Not significant percentage?

https://www.politico.com/states/florida/story/2021/07/26/sel...

Re: Over half of Covid hospitalisations tested positive after admission

#170

Post by onecommentman »

I decided from the beginning to only focus on COVID deaths, and maybe intubation rates. Everything other measure seemed too fuzzy and ripe for manipulation. Death is a pretty definitive finding.

But even this death metric is fraught with issues of “death from COVID” v. “death with COVID”. Deaths among the elderly are often ascribed to just “old age”…nobody cared about exact root causes until COVID came along. Most of the fatalities came from the “under-forensic-ed” elderly population and (I read somewhere…source needed) hospitals got increased financial compensation if a patient was coded as a COVID patient. Who is doing the forensics and what is their motivation? So even assigning a cause of death by COVID is a mess, but less than the mess of defining “COVID cases”.

Modulo the “cause of death” issue, fortunately, for COVID deaths, the CDC has a nice website that presents the relevant National and State data

https://www.cdc.gov/nchs/nvss/vsrr/covid19/excess_deaths.htm

Ignore the silly “red +” over the data — just compare the deaths by week (in blue bars) to the expected deaths (as presented by the orange line).

(Any “statistically significant” overage gets a “red +” no matter how trivial the excess, so it distorts the essential trends. And the height of the “red +” over the data is the same no matter if it is one death over or 1000 deaths over the threshold for that week. Really questionable chart design veering into “lying with statistics” territory.)

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