Kings College Hospital - PCR Test Cycles

[Robbie]

Given that the recommendation for PCR Test Cycles to be at 25-30 cycles in order to maintain accuracy and a reliable result, I'm shocked to have discovered that as per this FOI request, the 3 trusts that do the tests for Kings College run theirs at 45 cycles.

From what I've read, the rate of which false positives occur and increase is from 35 cycles upwards.

Why would they run tests at such high cycles knowing all of this?

https://www.whatdotheyknow.com/request/710545/response/1701868/attach/html/3/FOI%207062%20Q%20and%20A%20Response.pdf.html

[zog]

Are you an expert in this field? If you're worried about King's using an inaccurate testing process then I think it's best to bring it up with them. King's is going through a really difficult time with the number of patients in ICU at the moment so I think questioning their testing processes on here is a bit unfair. I've had a quick look at the PCR tests they use and (although I'm no expert) it appears they are using the recommended number of cycles for the tests they are using.

[Robbie]

ant12 Wrote:

-------------------------------------------------------

> Are you an expert in this field? If you're worried

> about King's using an inaccurate testing process

> then I think it's best to bring it up with them.

> King's is going through a really difficult time

> with the number of patients in ICU at the moment

> so I think questioning their testing processes on

> here is a bit unfair. I've had a quick look at the

> PCR tests they use and (although I'm no expert) it

> appears they are using the recommended number of

> cycles for the tests they are using.

A public forum to spread awareness and encourage debate is the perfect platform for the local community. The issue has been raised with the trusts directly.

As for unfair, running PCR cycles as almost double the threshold (25.6), and in excess of the maximum (40 as per the Public Health England publication) )is the epitome of unfair. It creates a high number of false positives, leading to unnecessary self-isolation, loss of income etc.

https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/926410/Understanding_Cycle_Threshold__Ct__in_SARS-CoV-2_RT-PCR_.pdf

Do you have a link that claims 45 cycles is the recommended number?

[Northern Star]

But doesn?t the relative fluorescence just plateau before 40 cycles anyway, so it doesn?t matter if more cycles are done? And the test result is dependent on the value reached at that point?

[zog]

@Robbie

You're not 'spreading awareness', you're misrepresenting or misunderstanding information.

If you had any credentials to verify people should listen to you about something like this then fair enough but I don't think you should be posting misleading information about PCR tests when a) you're not qualified to do so b) you don't understand how they work.

I personally also find it pretty depressing that you're bringing up the test accuracy of PCR tests at King's while just down the road from you there are nurses, doctors etc working their arses off trying to save people's lives.

One of the reason's we're in such a dire position is because people have been spreading false information such as tests being inaccurate or even covid being a hoax. 1,800 registered deaths were recorded today- is that down to PCR testing cycles? Even after all the verifiable information about full hospitals and excess deaths do you really think that we're in this position due to false positives?

Regarding your original PCR test claims, you do realise there are loads of different PCR tests for covid? Why don't you bother to actually look at the specific tests that you originally linked? The downloadable info is on their website (Altona Real Star, Cepheid GenExpert). You've taken two figures from two different documents to make your point. PCR tests aren't perfect but your claims above are misleading.

Even the latest link you posted it says the following "Ct values cannot be directly compared between assays of different types due to variation in the sensitivity (limit of detection), chemistry of reagents, gene targets, cycle

parameters, analytical interpretive methods, sample preparation and extraction techniques."

Anyway, I wish your family well- hopefully lockdown will end very soon for all of us! :)

[zog]

This will explain PCR cycles much better than I can (from an actual expert):

But I guess you've got all your info from David Icke's son

And before you post that publication from WHO (as all the other covid deniers seem to be doing) regarding PCR tests- that does not say anything that verifies your claims about the PCR cycles used at King's.

That's me done on this topic.

[Robbie]

ant12 Wrote:

> But I guess you've got all your info from David

> Icke's son

> https://twitter.com/garethicke/status/135202175524

> 2668038?s=20

>

> And before you post that publication from WHO (as

> all the other covid deniers seem to be doing)

> regarding PCR tests- that does not say anything

> that verifies your claims about the PCR cycles

> used at King's.

I'm not sure why you felt the need to mention Icke or try and label me as a Covid denier. Both are grossly incorrect, and such embarrassing accusations to make.

Dr Fauci was the first that I can recall mentioning cycle thresholds.

'If you get a cycle threshold of 35 or more, the chances of it being replication competent are miniscule'

Skip to 03:50 for the relevant question and subsequent answer.

My initial point about the number of cycles that the 3 trusts which the hospital utilises (not the hospital itself - selective reading much?) providing unreliable results is valid.

[Robbie]

ant12 Wrote:

-------------------------------------------------------

> And before you post that publication from WHO

Are you referring to this one that was released yesterday?

https://www.who.int/news/item/20-01-2021-who-information-notice-for-ivd-users-2020-05

'WHO reminds IVD users that disease prevalence alters the predictive value of test results; as disease prevalence decreases, the risk of false positive increases (2). This means that the probability that a person who has a positive result (SARS-CoV-2 detected) is truly infected with SARS-CoV-2 decreases as prevalence decreases, irrespective of the claimed specificity.

Most PCR assays are indicated as an aid for diagnosis, therefore, health care providers must consider any result in combination with timing of sampling, specimen type, assay specifics, clinical observations, patient history, confirmed status of any contacts, and epidemiological information'

[Robbie]

Mrs D Wrote:

-------------------------------------------------------

> But doesn?t the relative fluorescence just plateau

> before 40 cycles anyway, so it doesn?t matter if

> more cycles are done? And the test result is

> dependent on the value reached at that point?

According to the PHE publication that I linked, it plateaus at 28 cycles.

[Northern Star]

Agreed, so if you haven?t hit your target viral load by then for positive , it doesn?t matter if you do more cycles as you have already hit the plateau?!

[ianr]

Robbie wrote:

> According to the PHE publication that

> I linked, it plateaus at 28 cycles.

What does "it" mean here? Where do you think a sample with a Ct of, say, 30, plateaus?

And, in the OP:

> Given that the recommendation for PCR Test

> Cycles to be at 25-30 cycles in order to

What do you mean by "PCR Test Cycles" being "at 25-30 cycles".

And later:

> A public forum to spread awareness and

> encourage debate is the perfect platform

> for the local community.

> maintain accuracy and a reliable result,

So can you please point us to the websites where you got (a) your information about the King's FOI requests; (b) the recommendation I've just quoted; and © the information that "In Oxfordshire, the number of cycles on average used in the 21-30 age group was just over 58."

[Blah Blah]

Robbie, here are some points for you to consider.....

First of all, people who are so ill they die are not returning 'false positive' test results. There are several ways to test patients for the virus, and trust me when I say that a person who is in an ICU is not returning a 'false positive'. Why? Because by that point, the viral load is so high that it is undeniable as covid, or any other virus or bacteria in play. One of the most offensive ideas out there has been doubt cast on the numbers of hospital deaths. So let's not repeat that here.

Now, have another think about what you are arguing. 'False positives' do not increase spread of the virus or the numbers of people ending up in hospital. If you believe in the existence of prevalent 'false positives', then that should also tell you that this virus is in fact, more deadly than you think, making the argument for more testing and isolating, not less.

On PCR tests, the number of cycles isn't the reason for false positives. To be clear, there is no such thing as a false positive (and I will come back to that). Once the machine finds a trace of SARS cov 2, it stops and beeps. That means most positive results are identified before they get anywhere near 40 cycles. So this comes down to a question of viral load. If your positive test results from a trace detection, then how contagious are you in reality? In other words, every positive result finds a trace of SARS cov 2 RNA (ie no such thing as a false positive), but that trace can be detected in the first cycle as easily as it can be in the 40th. So at present, the policy is to er on the side of caution, when it comes to any person showing traces of the virus. And the number of cycles just makes sure that every person carrying any trace of the virus can be found.

New surges have come after releasing lockdown restrictions. The virus has already mutated in a more infectious form. That could only happen while the virus is still spreading. What if it mutates into a form that starts making younger people seriously ill (as seems to be the case with the new variant in Brazil)? I would worry less about false positives but the surge that is now testing the NHS to its limits. Any idea that life can return to normal, if only we don't count low RNA counts, is naive. That ship sailed some time ago. Look to Taiwan if you want to see what needed to happen to avoid a lockdown. We never did any of it.

[Robbie]

ianr Wrote:

-------------------------------------------------------

> Robbie wrote:

>

> > According to the PHE publication that

> > I linked, it plateaus at 28 cycles.

>

> What does "it" mean here? Where do you think a

> sample with a Ct of, say, 30, plateaus?

>

> And, in the OP:

>

> > Given that the recommendation for PCR Test

> > Cycles to be at 25-30 cycles in order to

>

> What do you mean by "PCR Test Cycles" being "at

> 25-30 cycles".

>

> And later:

>

> > A public forum to spread awareness and

> > encourage debate is the perfect platform

> > for the local community.

> > maintain accuracy and a reliable result,

>

> So can you please point us to the websites where

> you got (a) your information about the King's FOI

> requests; (b) the recommendation I've just quoted;

> and © the information that "In Oxfordshire, the

> number of cycles on average used in the 21-30 age

> group was just over 58."

A) Linked in the original post but here is the full FOI request

https://www.whatdotheyknow.com/request/covid_19_deaths_7#incoming-1701868

B) I've seen quite a few publications that quote around this range over the past year or so. You're more than welcome to provide a link to something that suggests otherwise.

C) Apologies this was for Wales, specifically in October, and I misread the data as being the CT when in fact the data shows a % breakdown of all positive cases by age group. I have deleted this error from the original post.

https://www.whatdotheyknow.com/request/cycle_threshold_values_of_positi_2#incoming-1690451

[Robbie]

Blah Blah Wrote:

-------------------------------------------------------

> Robbie, here are some points for you to

> consider.....

>

> First of all, people who are so ill they die are

> not returning 'false positive' test results. There

> are several ways to test patients for the virus,

> and trust me when I say that a person who is in an

> ICU is not returning a 'false positive'. Why?

> Because by that point, the viral load is so high

> that it is undeniable as covid, or any other virus

> or bacteria in play. One of the most offensive

> ideas out there has been doubt cast on the numbers

> of hospital deaths. So let's not repeat that here.

>

>

> Now, have another think about what you are

> arguing. 'False positives' do not increase spread

> of the virus or the numbers of people ending up in

> hospital. If you believe in the existence of

> prevalent 'false positives', then that should also

> tell you that this virus is in fact, more deadly

> than you think, making the argument for more

> testing and isolating, not less.

>

> On PCR tests, the number of cycles isn't the

> reason for false positives. To be clear, there is

> no such thing as a false positive (and I will come

> back to that). Once the machine finds a trace of

> SARS cov 2, it stops and beeps. That means most

> positive results are identified before they get

> anywhere near 40 cycles. So this comes down to a

> question of viral load. If your positive test

> results from a trace detection, then how

> contagious are you in reality? In other words,

> every positive result finds a trace of SARS cov 2

> RNA (ie no such thing as a false positive), but

> that trace can be detected in the first cycle as

> easily as it can be in the 40th. So at present,

> the policy is to er on the side of caution, when

> it comes to any person showing traces of the

> virus. And the number of cycles just makes sure

> that every person carrying any trace of the virus

> can be found.

>

> New surges have come after releasing lockdown

> restrictions. The virus has already mutated in a

> more infectious form. That could only happen while

> the virus is still spreading. What if it mutates

> into a form that starts making younger people

> seriously ill (as seems to be the case with the

> new variant in Brazil)? I would worry less about

> false positives but the surge that is now testing

> the NHS to its limits. Any idea that life can

> return to normal, if only we don't count low RNA

> counts, is naive. That ship sailed some time ago.

> Look to Taiwan if you want to see what needed to

> happen to avoid a lockdown. We never did any of

> it.

Informative, thank you. It's good to hear a logical explanation regarding false positives, especially when that terminology has been freely banded about my so many Health Organisations and professionals (the WHO as I quoted above in particular). I agree with pretty much everything you've said there.

I can sympathise with those that cast doubt on the reported number of Covid deaths, when using the argument that the data includes deaths for any reason within 28 days of a positive result. Now that data has been recently increased increasing this to 60 days, it will only inflame those opinions unfortunately. I believe that more transparency on deaths as a result of Covid would have appeased them somewhat.

https://www.gov.uk/government/publications/covid-19-reported-sars-cov-2-deaths-in-england/sars-cov-2-confirmed-england-deaths-report-to-31-december-2020?fbclid=IwAR2ND7_1DADcfBEs0iwoE-GwJP2FGrgrmsyR4pCiAugRBJmsvHwlxVu09WA#covid-19-deaths

[Blah Blah]

Yes, I agree on how misleading terminology has caused confusion. Medical practitioners spend every day explaining what is often complex science, in simpler terms to help patients understand what is happening to them. Government however, has no such skill. Plus, their considerations go beyond solely what is happening epidemiologically, and they often assume the public are too stupid to understand complex science. That is a whole other thread though :D

But to answer your question specifically. You can see from the FOI replies that you link to, that there is a big drop off in positives at the 40-45 cycle point. So the logic there is, that is the number of cycles needed to catch everyone with any trace of SARS cov 2. It is a matter of being thorough, and taking no risks, over any notion of flawed science.

And that is not to undermine the other valid point you make about people's livelihoods and wellbeing. Those things are serious issues too. That unfortunately has no answer in a pandemic. There is more government could do to take care of people through that, but again, subject for a different thread.