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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

#211

Post by simpleguitar »

timr wrote: post #34
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…

> 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…

A PCR test that is sensitive is a great tool. Remember the NBA bubble? A less sensitive test would have allowed outbreaks inside the bubble, making some player sick and unable to play, as well as eroding the public's confidence on PCR tests.

Factories and meat packing plants used negative PCR tests to create their own bubbles and keep them running.

There is large positive economic value to a highly sensitive test with a small false negative and a larger false positive. There is much less economic value in a test that allows escapes (rapid tests).

Re: Over half of Covid hospitalisations tested positive after admission

#212

Post by timr »

simpleguitar wrote: post #211
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…

A PCR test that is sensitive is a great tool. Remember the NBA bubble? A less sensitive test would have allowed outbreaks inside the bubble, making some player sick and unable to play, as well as eroding the public's confidence on PCR tests. Factories and meat packing plants used negative PCR tests to create their own bubbles and keep them running. There is large positive economic value to a highly sensitive test wit…

> A PCR test that is sensitive is a great tool. Remember the NBA bubble? A less sensitive test would have allowed outbreaks inside the bubble, making some player sick and unable to play, as well as eroding the public's confidence on PCR tests.

A hammer is a great tool. It is not a great tool for repairing broken pottery.

PCR is the ideal tool if you want to detect infinitesimal amounts of a specific nucleic acid sequence. It is not a great tool if you want to use it to define "illness" or "infectivity", for it cannot tell you anything about those questions.

Can you use PCR to cast the widest possible net, and isolate literally everyone who has any shred of viral RNA? Yes. That's essentially what we've been doing. It is a strategy, and this strategy is appropriate in some situations. This strategy becomes a problem when you forget that you're allowing a lot of false positives to be caught up in the process, and start behaving as if "a positive" is a meaningful clinical diagnosis. Now that we have highly effective vaccines and are out of the acute phase of the crisis, it's time to adjust our definition of "infection" to more accurately reflect the true clinical meaning of the word.

Re: Over half of Covid hospitalisations tested positive after admission

#213

Post by timr »

cameldrv wrote: post #124
aeternum wrote: post #122

Earlier quoted context omitted.

The problem is the false positive isn't truly independent of environmental factors. PCR determines how many exponential amplifications are necessary to get a detectable amount of the target RNA sequences. The amount of that target RNA floating around in the environment does slightly impact the base amount present in even covid-negative patients.

It's true that people who had COVID can still have viral RNA in their noses for a while and still test positive. The most sensitive tests have a limit of detection of a couple hundred copies/ml, and the collection kits usually use 1ml of VTM or equivalent. I find it hard to believe that a significant number of people will have enough viral RNA in their nose to put hundreds of copies onto a swab unless it's their own…

> I find it hard to believe that a significant number of people will have enough viral RNA in their nose to put hundreds of copies onto a swab unless it's their own body that's producing those copies.

This has been confirmed in studies. Researchers have taken samples that are PCR positive at various cycle counts, and tried to culture viruses from them. Here's one:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7427302/

"RT-PCR cycle threshold (Ct) values correlate strongly with cultivable virus. Probability of culturing virus declines to 8% in samples with Ct > 35 and to 6% 10 days after onset; it is similar in asymptomatic and symptomatic persons."

(Note: this is not the only one of these papers that has been published. This is just the first one I found with a quick search.)

Re: Over half of Covid hospitalisations tested positive after admission

#214

Post by [deleted] »

javagram wrote: post #177
washadjeffmad wrote: post #168

Earlier quoted context omitted.

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 teste…

> Denialism and skepticism are often used as slurs in the absence of strong evidence by those who favor popular consensus over evidence. OK? That doesn’t change the massive weight of evidence in favor of HIV causing AIDS.

[deleted]

Re: Over half of Covid hospitalisations tested positive after admission

#215

Post by nickthemagicman »

shadowgovt wrote: post #208
nickthemagicman wrote: post #206

Earlier quoted context omitted.

The average death is 80 years old with two comorbidies so....the natural cycle of life?

There's nothing natural about dying from COVID-19, except in the broadest of definitions of "natural" (i.e. the definition that we developed technology to minimize, control, and avoid).

I don't know how you define Natural.

Re: Over half of Covid hospitalisations tested positive after admission

#216

Post by timr »

javagram wrote: post #178
themark wrote: post #151

Earlier quoted context omitted.

The video they are referring to has a very specific part about pcr testing (relevant to the discussion here). I think it is reasonable to trust his opinion on the matter regardless of what he thinks about AIDS.

The video pretty clearly shows that his view is that testing for HIV is a conspiracy by the CDC to get funding to fight AIDS.[1] Unless you agree with him that AIDS isn’t caused by HIV, it doesn’t make much sense to trust him rather than all the scientific experts who have worked on PCR testing and virus detection in the last few decades. ( edit: Moreover, suppressing HIV using drugs has been successfully treating AI…

> Moreover, PCR testing during the covid epidemic, which he was not alive for, has clearly been working well. High cases later correspond to high hospitalizations and high covid-19 deaths and high excess deaths across many different countries.

In the case of Covid, "hospitalizations" are largely defined as "in the hospital with a positive PCR test", so this is a truism. Deaths are predominantly downstream of "hospitalizations", so again, this is a truism.

Any pathology in PCR testing would equally affect "hospitalizations" and "confirmed deaths".

Re: Over half of Covid hospitalisations tested positive after admission

#217

Post by timr »

doesnotexist wrote: post #51
timr wrote: post #37

Earlier quoted context omitted.

They say this in the article, so I'm not sure how it's "misleading". The point (which the article discusses) is that it's fairly unlikely that someone being admitted for severe Covid has not already had at least one positive test prior to admission.

It's entirely misleading. They don't write 87% of patients tested positive before or early on in their admission. Even, the headline is written to convey the opposite. What they are doing is breaking it into two numbers that are each less than 50% to obscure the magnitude of the sum and then lumping the second number (patients who tested early in their admission) with those who tested positive later. It's easy to ove…

> It's entirely misleading. They don't write 87% of patients tested positive before or early on in their admission.

Well, no, they didn't. They wrote the entirely true statement that over half tested positive after admission.

The fact that you disagree with one possible interpretation of this fact does not make it misleading. It's just a fact.

(I will grant you that the subhead is sensationalized, but the title on this one seems fine to me, and the article is fairly balanced.)

> It's more amazing that 44% tested positive prior to arriving at hospital!

It isn't "amazing"...we've been mass-testing for the better part of a year. I'd be shocked if most people who show up to the ER with respiratory illness didn't have a prior test result.

> But all of that is besides the point because the reported statistic wasn't even labelled or reported by the original source (the NHS) as "covid as cause of admission." The stat is labelled "covid positive admissions" which is not logically equivalent to "covid, as primary cause of admission"

Well, yes. That's exactly the point. Maybe you are not surprised by this, but a great many people are. And when you see that half of those "covid positive admissions" were only confirmed after admission, then it starts to raise alarms.

Re: Over half of Covid hospitalisations tested positive after admission

#218

Post by pwinnski »

nickthemagicman wrote: post #209
javagram wrote: post #205

Earlier quoted context omitted.

You can see that covid-19 related deaths aren’t “inflated” by comparing the numbers to excess deaths and seeing they correlate (not just nationally, but by region and time). When 100,000 people are reported to die of covid in the USA or another western country with a high quality reporting system, in the same region and time around 100,000 more deaths from any cause are recorded than would normally be expected. There…

Ah that's interesting. Thanks for sharing. Here's a good visualization as well. That looks pretty indisputable. https://ourworldindata.org/excess-mortality-covid "The raw death count helps give us a sense of scale: for example, the US suffered roughly 360,000 more deaths than the five-year average between 26 January and 3 October 2020, compared to 209,000 confirmed COVID-19 deaths during that period." The Covid death…

So you quote an eight-month figure, ignoring the nearly-nine months since then, and still cling to your narrative even when presented with facts that directly contradict your earlier assertions. Okay.

Try some math: 360,000 deaths higher than average over 251 days is 1434 excess deaths per day. From Oct 4 through yesterday is another 296 days, and 1434x296=424,464, so we're talking about a scale of around 780,000, which very much supports the total US COVID death count of 627,370.

If you think that's all 80-year-olds with multiple pre-existing conditions, and that you therefore have nothing to worry about, then I hope for your sake and the sake of those around you that you aren't proven wrong by an ICU stay.

Re: Over half of Covid hospitalisations tested positive after admission

#219

Post by shadowgovt »

nickthemagicman wrote: post #215
shadowgovt wrote: post #208

Earlier quoted context omitted.

There's nothing natural about dying from COVID-19, except in the broadest of definitions of "natural" (i.e. the definition that we developed technology to minimize, control, and avoid).

I don't know how you define Natural.

It's a good question and definitions vary. My working, broadest definition is "That which exists / that which occurs if humans do not use their intellect and ability to cause something else to exist / happen."

Starvation is natural. Death by predator is natural. Death due to exposure is natural. Death due to disease is natural. Tornadoes are natural. A biosphere-disrupting asteroid impact is natural. There are other things that are natural that are positives too, but it's good, I think, to keep in mind that "natural" doesn't always imply "good."

Re: Over half of Covid hospitalisations tested positive after admission

#220

Post by pwinnski »

nickthemagicman wrote: post #113
ssully wrote: post #86

Earlier quoted context omitted.

I understand that. But I would hardly call it sensationalizing. It's a mixture of the best of what we had at the time (others have posted talking about how the tests have changed/improved), and the fact that reporting on things in a simple and straight forward manner is hard because people simply don't have the time, or don't give a shit about nuance.

It's looking like the reported numbers may be over-estimated by one or more orders of magnitude....that's the definition of sensational.

This is completely contrary to what "excess death" statistics suggest, which is that we might be under-counting COVID deaths by quite a bit. We've had many more unexpected excess deaths in 2020 and 2021 than can be explained by the official COVID death counts, so it's highly possible that some COVID-caused deaths aren't being recorded as such.

It could be that a bit more than 625,000 people have died in the US due to COVID. Or it could be higher than that, and it may be a couple of years before we know for sure. It's not lower, though. Not at all.

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