PCR Test, number of cycles

[odysseus2000]

I am confused about the PCR test which as I understand it is the worldwide standard used to determine if someone has Covid.

This test as I understand it is a multiplier, i.e. you take a small amount of a sample from some one and then you amplify that amount by a series of repeat steps so that the small and undetectable amount in the original sample can then be measured.

The natural question this is how many cycles should this be and in practice it seems to be taken as 40, whereas clinicians have argued that this is too many and will amplify noise and give a false positive and that the number of cycles should be 30 to 35 and defined worldwide to allow comparable reporting.

This 10 min 56 seconds video is the best account I have found that discusses this:

https://youtu.be/g2aR2UInnug

Is my understanding correct that covid is being diagnosed by this test around the world and that using a multiplier of 40 is likely to lead to false positives?

If not what is wrong with my understandings?

Regards,

[redsturgeon]

Yes, it is well known that the PCR test is not really a diagnostic tool but more of a research tool. It will find the smallest traces of viral DNA, whether they are active or not is another question. Someone who tests positive on a PCR test may or may not be capable of spreading the virus.

John

[XFool]

I am confused about the PCR test which as I understand it is the worldwide standard used to determine if someone has Covid.

This 10 min 56 seconds video is the best account I have found that discusses this:

https://youtu.be/g2aR2UInnug

Unfortunately I cannot answer your question.

I will just say that one needs to be careful when using the Internet for 'research' into such matters. There are any number of people prepared to tell you, and anybody who will listen, any number of things. Whether they are really qualified to do so is another matter.

With reference to Dr. Sam Bailey on YouTube (have you read the accompanying Comments?), here is a commentary on a previous example of her videos:

New Zealand doctor makes misleading claims about the country’s PCR testing regime in widely shared YouTube

https://factcheck.afp.com/new-zealand-doctor-makes-misleading-claims-about-countrys-pcr-testing-regime-widely-shared-youtube

If it were me, I'd be looking elsewhere for explanations.

[odysseus2000]

XFool
Unfortunately I cannot answer your question.

I will just say that one needs to be careful when using the Internet for 'research' into such matters. There are any number of people prepared to tell you, and anybody who will listen, any number of things. Whether they are really qualified to do so is another matter.

With reference to Dr. Sam Bailey on YouTube (have you read the accompanying Comments?), here is a commentary on a previous example of her videos:

New Zealand doctor makes misleading claims about the country’s PCR testing regime in widely shared YouTube

https://factcheck.afp.com/new-zealand-d ... ed-youtube

If it were me, I'd be looking elsewhere for explanations.

As a PhD research physicist with many years experience I am quite able to determine what is science and what isn't. In all science and engineering one needs standards to work with so that one can make things that will fit those made by someone else and so that one can do like for like comparisons.

If, as alleged, the PCR test is being done with arbitrary cycles it is not science. One needs an equal testing routine so that one can compare results with out any systematic bias.

Unless i a misunderstanding the PCR test it is not being done in this way making comparisons and policy determined from measurements unreliable.

From an investors perspective I can see why a PCR lab would be super happy with this arrangement. They will be getting unprecedented income and they can arbitarily set up what they do and what they measure. The scientists and technicians doing the work might not like it but they are employees and the directors will love the income and lack of constraints.

I have looked at the rebuttal and once i saw Gold-Standard I was put on my guard as to this being written by a non-scientists and so it is as they do not address the number of cycles which is the point I was asking about. Sure they say these comments are coming from senior scientists, but they are not what a scientist would write.

In terms of looking elsewhere, where do you suggest? I have given up watching the UK briefings. What ever data they do show is so smoothed as to be meaningless, the questions from the audience are from people who have no idea how to ask science questions. The science committee I saw interviewing Whitty and Valance last year failed totally to ask sensible questions and showed that the MP's on the committee had not prepared for their job, the chairman was pitiful in what he allowed as questions.

The more I look into the science of the Covid war, the less acceptable it is and from this are coming wild political decisions, such as send school children to school and then the next day send them home.

To win a war like this requires the methods of science to be applied correctly and for the politicians to have good data and good suggestion from which to construct policy.

At the moment as far as I can tell, the science is not being correctly done and that is leading to all manner of very bad decisions and policy and creating future debt and business problems that will be with us for generations.

We are not winning this war, the virus is and we need proper science to reverse that.

Regards,

[dealtn]

XFool
Unfortunately I cannot answer your question.

I will just say that one needs to be careful when using the Internet for 'research' into such matters. There are any number of people prepared to tell you, and anybody who will listen, any number of things. Whether they are really qualified to do so is another matter.

With reference to Dr. Sam Bailey on YouTube (have you read the accompanying Comments?), here is a commentary on a previous example of her videos:

New Zealand doctor makes misleading claims about the country’s PCR testing regime in widely shared YouTube

https://factcheck.afp.com/new-zealand-d ... ed-youtube

If it were me, I'd be looking elsewhere for explanations.

If, as alleged, the PCR test is being done with arbitrary cycles it is not science. One needs an equal testing routine so that one can compare results with out any systematic bias.

Unless i a misunderstanding the PCR test it is not being done in this way making comparisons and policy determined from measurements unreliable.
...

In terms of looking elsewhere, where do you suggest? I have given up watching the UK briefings. What ever data they do show is so smoothed as to be meaningless, the questions from the audience are from people who have no idea how to ask science questions. The science committee I saw interviewing Whitty and Valance last year failed totally to ask sensible questions and showed that the MP's on the committee had not prepared for their job, the chairman was pitiful in what he allowed as questions.

The more I look into the science of the Covid war, the less acceptable it is and from this are coming wild political decisions, such as send school children to school and then the next day send them home.

To win a war like this requires the methods of science to be applied correctly and for the politicians to have good data and good suggestion from which to construct policy.

At the moment as far as I can tell, the science is not being correctly done and that is leading to all manner of very bad decisions and policy and creating future debt and business problems that will be with us for generations.

We are not winning this war, the virus is and we need proper science to reverse that.

Regards,

Yes, some very good points, and they are just as applicable to other measures too, such as "what is a covid death?" and its comparability across multiple nations.

Yet it seems to me, in real life and on the Coronavirus Discussions Board here, some will see any reasonable questioning of data, or methodology, or conclusion as belonging to the subset of deniers. Others will see it as a reasonable search for (scientific) knowledge or understanding.

[Arborbridge]

XFool
Unfortunately I cannot answer your question.

I will just say that one needs to be careful when using the Internet for 'research' into such matters. There are any number of people prepared to tell you, and anybody who will listen, any number of things. Whether they are really qualified to do so is another matter.

With reference to Dr. Sam Bailey on YouTube (have you read the accompanying Comments?), here is a commentary on a previous example of her videos:

New Zealand doctor makes misleading claims about the country’s PCR testing regime in widely shared YouTube

https://factcheck.afp.com/new-zealand-d ... ed-youtube

If it were me, I'd be looking elsewhere for explanations.

As a PhD research physicist with many years experience I am quite able to determine what is science and what isn't. In all science and engineering one needs standards to work with so that one can make things that will fit those made by someone else and so that one can do like for like comparisons.

If, as alleged, the PCR test is being done with arbitrary cycles it is not science. One needs an equal testing routine so that one can compare results with out any systematic bias.

Unless i a misunderstanding the PCR test it is not being done in this way making comparisons and policy determined from measurements unreliable.

From an investors perspective I can see why a PCR lab would be super happy with this arrangement. They will be getting unprecedented income and they can arbitarily set up what they do and what they measure. The scientists and technicians doing the work might not like it but they are employees and the directors will love the income and lack of constraints.

I have looked at the rebuttal and once i saw Gold-Standard I was put on my guard as to this being written by a non-scientists and so it is as they do not address the number of cycles which is the point I was asking about. Sure they say these comments are coming from senior scientists, but they are not what a scientist would write.

In terms of looking elsewhere, where do you suggest? I have given up watching the UK briefings. What ever data they do show is so smoothed as to be meaningless, the questions from the audience are from people who have no idea how to ask science questions. The science committee I saw interviewing Whitty and Valance last year failed totally to ask sensible questions and showed that the MP's on the committee had not prepared for their job, the chairman was pitiful in what he allowed as questions.

The more I look into the science of the Covid war, the less acceptable it is and from this are coming wild political decisions, such as send school children to school and then the next day send them home.

To win a war like this requires the methods of science to be applied correctly and for the politicians to have good data and good suggestion from which to construct policy.

At the moment as far as I can tell, the science is not being correctly done and that is leading to all manner of very bad decisions and policy and creating future debt and business problems that will be with us for generations.

We are not winning this war, the virus is and we need proper science to reverse that.

Regards,

Some very good points with which none of us would disgree. Though we can already see the seeds of how pontetially fake news can spread when you say:-
If, as alleged, the PCR test is being done with arbitrary cycles it is not science. One needs an equal testing routine so that one can compare results with out any systematic bias.

Unless i a misunderstanding the PCR test it is not being done in this way making comparisons and policy determined from measurements unreliable.

From an investors perspective I can see why a PCR lab would be super happy with this arrangement. They will be getting unprecedented income and they can arbitarily set up what they do and what they measure. The scientists and technicians doing the work might not like it but they are employees and the directors will love the income and lack of constraints.


Anyone quoting you selectively, or not reading it properly and excising your "if" might take this all the wrong way and conclude the testing regime is to be ignored as it is nonsense.
I know that's not your intention, but I just thought it's interesting how quoting someone else who might not know their backside from their elbow, one can give oxygen to these rumours.

Sorry to pick on you as an example, - no offence, but it just struck me that this is how it happens.

Arb.

[XFool]

Yes, some very good points, and they are just as applicable to other measures too, such as "what is a covid death?" and its comparability across multiple nations.

Yet it seems to me, in real life and on the Coronavirus Discussions Board here, some will see any reasonable questioning of data, or methodology, or conclusion as belonging to the subset of deniers. Others will see it as a reasonable search for (scientific) knowledge or understanding.

Ah! I see somebody has decided to adopt the same game-plan on this board as they previously used on another one.

[dealtn]

Yes, some very good points, and they are just as applicable to other measures too, such as "what is a covid death?" and its comparability across multiple nations.

Yet it seems to me, in real life and on the Coronavirus Discussions Board here, some will see any reasonable questioning of data, or methodology, or conclusion as belonging to the subset of deniers. Others will see it as a reasonable search for (scientific) knowledge or understanding.

Ah! I see somebody has decided to adopt the same game-plan on this board as they previously used on another one.

You are denying some people act in such a way?

[XFool]

Yes, some very good points, and they are just as applicable to other measures too, such as "what is a covid death?" and its comparability across multiple nations.

Yet it seems to me, in real life and on the Coronavirus Discussions Board here, some will see any reasonable questioning of data, or methodology, or conclusion as belonging to the subset of deniers. Others will see it as a reasonable search for (scientific) knowledge or understanding.

Ah! I see somebody has decided to adopt the same game-plan on this board as they previously used on another one.

You are denying some people act in such a way?

Can't say I noticed it on TLF. But I noticed it was asserted, as if a fact - without evidence - on another board here.

[dealtn]

Ah! I see somebody has decided to adopt the same game-plan on this board as they previously used on another one.

You are denying some people act in such a way?

Can't say I noticed it on TLF. But I noticed it was asserted, as if a fact - without evidence - on another board here.

Happy for you to provide a link if that's the case, and equally happy for that to be done via private message if you are referring to me, if you would rather it wasn't done publically.

[XFool]

Yes, it is well known that the PCR test is not really a diagnostic tool but more of a research tool. It will find the smallest traces of viral DNA, whether they are active or not is another question. Someone who tests positive on a PCR test may or may not be capable of spreading the virus.

John

I'm sorry but I have some difficulty understanding this (all too common!) statement.

PCR is a tool. If it is used as a tool in research, it is a research tool. If it is used as a tool in diagnosis, it is a diagnostic tool. It is a matter of intentionality. Interestingly, this very point was mentioned in that AFP link I gave in my first post above.

Consider Nuclear Magnetic Resonance imaging:

1. It is used in research into the functioning of the brain, Functional Magnetic Resonance imaging (fNMR), so it is a "research tool". Therefore it CAN'T be suitable for "diagnosis purposes".

2. It is used in medicine for diagnostic purposed (its most common use), so it is a "diagnostic tool". Therefore it CAN'T be suitable for use as a "research tool".

Do these two statement, taken together, make sense?

[redsturgeon]

Yes, it is well known that the PCR test is not really a diagnostic tool but more of a research tool. It will find the smallest traces of viral DNA, whether they are active or not is another question. Someone who tests positive on a PCR test may or may not be capable of spreading the virus.

John

I'm sorry but I have some difficulty understanding this (all too common!) statement.

PCR is a tool. If it is used as a tool in research, it is a research tool. If it is used as a tool in diagnosis, it is a diagnostic tool. It is a matter of intentionality. Interestingly, this very point was mentioned in that AFP link I gave in my first post above.

Consider Nuclear Magnetic Resonance imaging:

1. It is used in research into the functioning of the brain, Functional Magnetic Resonance imaging (fNMR), so it is a "research tool". Therefore it CAN'T be suitable for "diagnosis purposes".

2. It is used in medicine for diagnostic purposed (its most common use), so it is a "diagnostic tool". Therefore it CAN'T be suitable for use as a "research tool".

Do these two statement, taken together, make sense?

Fair enough.

It is indeed down to intention. To be absolutely correct there needs to be work done to understand what level of virus DNA is appropriate to call a test "positive" and then the PCR test will of course give you the data. There is of course no right or wrong answer to this and different places seem to use different CTs but about 40 seems to be the one most have decided on.

John

[odysseus2000]

Fair enough.

It is indeed down to intention. To be absolutely correct there needs to be work done to understand what level of virus DNA is appropriate to call a test "positive" and then the PCR test will of course give you the data. There is of course no right or wrong answer to this and different places seem to use different CTs but about 40 seems to be the one most have decided on.

John

Yes and having done that in your best labs, then blind tests should go out to all labs doing this work to see what value they report from samples of known virus levels and with fragments that would be unlikely to lead to illness and this should be ongoing, both to be be sure the lab is continuing to do the test correctly and also that there are no systematic errors such as contamination occurring.

If the procedure has scientific merit one should be able to quantify things and set a standard test routine with known repeat tests to confirm all is continuing at the specified accuracy and have world standards that allow country by country comparisons and thence to find out which countries are doing the best jobs and have those that are doing worse able to consider if they can improve their techniques by adopting different practices.

If things are as I understand them, then country by country and state v state within a country measurements are subject to significant uncertainties and potential systematic errors that make the whole measurement procedure unsatisfactory. It should not e.g. be possible for a politician in one country to say that the results from another are wrong because they are different. For good science there should be the same standards of measurement.

Regards,

[redsturgeon]

Speaking as someone whose business at the moment is the day to day testing of individuals for Covid using a variety of tests including lateral flow and PCR testing I'd say that the introduction of standards within the laboratories is the easy part.

The taking of samples from the subject is the part of the process most subject to variation by a country mile. If you look at the swabs taken by some people on TV it seems like the most cursory wipe around the nostril is sufficient. I am sure when tests are done using self obtained samples the results are not much better than completely random.

John

[odysseus2000]

Speaking as someone whose business at the moment is the day to day testing of individuals for Covid using a variety of tests including lateral flow and PCR testing I'd say that the introduction of standards within the laboratories is the easy part.

The taking of samples from the subject is the part of the process most subject to variation by a country mile. If you look at the swabs taken by some people on TV it seems like the most cursory wipe around the nostril is sufficient. I am sure when tests are done using self obtained samples the results are not much better than completely random.

John

Thank you for that super valuable insight.

I was hoping there would be some consistency in the procedure, but as there isn't, the whole thing as a basis for making decisions upon is scinentifically unsatisfactory.

Garbage in, garbage out!

Is there no procedure that can be done in some consistent manner which would give a reliable measurement of the infection rate?

Or is it all about rubber stamping: Someone presents with symptoms, the test confirms and the authorities increment the covid count or the test doesn't confirm so the individual is re-tested till a positive test is obtained and then the covid count in incremented?

Regards,

[johnhemming]

Is there no procedure that can be done in some consistent manner which would give a reliable measurement of the infection rate?

The problem is measuring when someone has been infected.

If someone has symptoms and goes to the doctor or is admitted to hospital that has a time element to it. However, just testing positive has only quite an imprecise time link.