Naked Science Forum

Life Sciences => Physiology & Medicine => Topic started by: Jolly2 on 31/10/2020 20:25:25

Title: How do you test a covid test?
Post by: Jolly2 on 31/10/2020 20:25:25
How do you test a test for covid 19?

I heard some speculation that maybe the covid tests themselves are contaminated with covid, if true those contaminating the tests could control the numbers of infected peoples.

There was a report for Africa where an African leader tested different things around his home and was given a positive test result from objects. 

How could we then tests the tests to ensure that wasnt happening?
Title: Re: How do you test a covid test?
Post by: evan_au on 31/10/2020 21:32:16
Quote from: OP
speculation that maybe the covid tests themselves are contaminated with covid
Professionally manufactured medical tests are produced in sterile facilities, with staff following infection-control procedures. So this should not occur, any more than you might catch COVID-19 from a vitamin pill.
- In reality, there is a delay of a week or more between manufacture and use of a test kit, so no infectious virus will remain.
- Unlike vitamin pills (where a delicate protein must be protected), the standard COVID-19 nasal swab can be sterilized at high temperatures, ensuring that no intact virus or virus components remain.

More risky is the sample processing at a central laboratory, where it is known that some incoming samples do contain SARS-COV2 virus. In this case, use of sterile reagents and sterile equipment is essential, again with staff following infection-control procedures.
- A "false-positive" result due to cross-contamination (ie saying the person is sick when they are not) will certainly be inconvenient for the patient, as they may have to self-isolate for 14 days, but it won't actually make them sick.

There is another sense in which antibody tests might be said to contain SARS-COV2 virus: these tests detect parts of the virus coat or spike protein. Like pregnancy tests, the device also contains a validation sample, to show what a "positive" result looks like. This will typically contain part of the virus coat which the antibody will detect. However:
- The test does not contain whole virus (only one protein), so it is not infectious
- The user's input to the test is typically a drop of saliva or a drop of blood, so it's not like the user is eating the test device

Quote
There was a report for Africa where an African leader tested different things around his home and was given a positive test result from objects.
If someone in the household had been infected, they will leave virus particles on many surfaces.
- Taking swabs from surfaces and doing a PCR test on them will show the presence of virus fragments.
- This is why people are told to self-isolate if they are infected.

Quote
How do you test a test for covid 19?
You compare it with a known "good" test. Since the publication of the virus RNA sequence in January 2020, the PCR test (Polymerase Chain Reaction) has become the "gold standard".
- It is extremely sensitive; it multiplies any virus RNA by a factor of a million or more before attempting to detect it.

The PCR test can still produce an incorrect result if:
- The person was infected 1 hour or 1 day ago, and they are not yet exhaling virus (a "false negative"). But by day 4 when the patient becomes infectious, it gives a solid positive result.
- The person was infected 3 weeks ago. The test is perhaps "too" sensitive, as it continues to detect virus fragments long after it is believed the patient is no longer infectious (a "false positive")
- The test was not conducted properly, and it didn't reach down far enough into their throat (expect to gag when they do the test!)
- The wind blows a virus particle from an infected person onto the swab taken from another person. Quickly sealing sample tubes is important
- The sample tubes get mislabelled, lost or swapped.
- Great sensitivity, proper procedures for collecting and handling samples, and awareness of the limitations of the test make it the "gold standard".

A new test (eg the proposed fast antibody tests) would be compared to the results from a PCR test taken on the same people.
- Statisticians would compare the "false positive" and "false negative" rates of a new test against the PCR test
- Antibody tests are generally less sensitive, since they don't multiply the virus with PCR. This can be a good thing, since it doesn't give a positive result when the person is not infectious.
- Then comes a value judgement - is the risk of the false negatives and the inconvenience of the false positives a good thing for community health and wealth?
- If you are trying to protect the White House from its own wilful ignorance, testing staff daily is cheap, and someone who shows as positive can be easily replaced by someone else (unless you are the President, and you don't want your nominated replacement to take your spot in TV prime time).
- Fast tests may also be useful for clearing people to travel on international airline flights. It doesn't say that they aren't infected, but it does say that they are unlikely to infect anyone else on the flight. 2 weeks of quarantine on arrival may still be needed if you are coming from a country with high rates of infection (eg UK, USA, France) to a country with low rates of infection (eg China, Vietnam, Australia, New Zealand).

The worst defect in a COVID-19 test occurs in countries without a public health system (eg the USA).
- Patients showing symptoms were initially denied tests because they didn't meet over-strict criteria like having visited China in the past 2 weeks, or having been in contact with a person who had a positive test.
- Tests were initially only allowed to be provided by a single lab, and processed at a single lab. This led to enormous delays in returning results, by which time more people had become infected.
- Even after the criteria were made more realistic, some patients were slugged with a bill for $9,000 to have the test
- This led to significant community spread among people who didn't have health insurance and couldn't afford to visit hospital unless they were deathly ill.
- Not helped by a President who continually dismissed the virus as nothing to be worried about (even after he had been infected!)
- Canada, with a very similar demographics to the USA, had far lower infection rates, due to an effective public health system.
Title: Re: How do you test a covid test?
Post by: alancalverd on 01/11/2020 00:07:52
The simplest test for false positive rate is to take a test kit fresh from the factory and test it without it being unwrapped before it reaches the lab. You can do every kind of intermediate test  on a "blank" kit,  including infection by the tester or infection from handling the return packaging, to get some idea of third party contamination rates.

If you have a known source of your target analyte  in another laboratory, you can send a test pack to it to check for false negatives.

You can ask your target population to volunteer for multiple tests: you hope that anyone tested with, say, 3 packs within 30 minutes,  will return 3 positives or 3 negatives: this may identify inadequate or contaminated testers. 

The measured spread of less serious bugs is often surprising, one of the simplest being campylobacter distributed around the kitchen by someone washing a piece of raw chicken, and despite good practice, the tiniest spill of radioactive liquid can often be detected on everyone and everything in the laboratory, so the African story is not at all remarkable.
Title: Re: How do you test a covid test?
Post by: Jolly2 on 13/11/2020 22:55:33
The simplest test for false positive rate is to take a test kit fresh from the factory and test it without it being unwrapped before it reaches the lab. You can do every kind of intermediate test  on a "blank" kit,  including infection by the tester or infection from handling the return packaging, to get some idea of third party contamination rates.

If you have a known source of your target analyte  in another laboratory, you can send a test pack to it to check for false negatives.

You can ask your target population to volunteer for multiple tests: you hope that anyone tested with, say, 3 packs within 30 minutes,  will return 3 positives or 3 negatives: this may identify inadequate or contaminated testers. 

The measured spread of less serious bugs is often surprising, one of the simplest being campylobacter distributed around the kitchen by someone washing a piece of raw chicken, and despite good practice, the tiniest spill of radioactive liquid can often be detected on everyone and everything in the laboratory, so the African story is not at all remarkable.

Ok and what is your suggestion as to why Elon Musk has just taken 4 Corona virus  tests and received 2 positive and 2 negative test results?

Title: Re: How do you test a covid test?
Post by: alancalverd on 13/11/2020 23:15:54
In another thread I have explained how I intend to make a fortune, but I'll repeat it here.

Unlike the European regulations, to get a medical device approved in the USA you have to prove that it actually works and has some advantage over another device. So I'm going to register a 10 cent coin as a COVID tester. It is at least as accurate as whatever Musk used, is 99.999% reproducible, does not require any skill, and costs nothing because you can re-use it in a parking meter.
Title: Re: How do you test a covid test?
Post by: Jolly2 on 13/11/2020 23:37:47
In another thread I have explained how I intend to make a fortune, but I'll repeat it here.

Unlike the European regulations, to get a medical device approved in the USA you have to prove that it actually works and has some advantage over another device. So I'm going to register a 10 cent coin as a COVID tester. It is at least as accurate as whatever Musk used, is 99.999% reproducible, does not require any skill, and costs nothing because you can re-use it in a parking meter.

And here you make no sense as Musk was tested in America,  where apparently test have to be proven to work to be considered tests.

I'm sure Musk now has covid, I just ponder if it wasnt the test that infected him.

I have a funny feeling even if musk wasnt tested at all, and as was suggested before if you just ran the test blank they would show up with positive results.

If you had to activate a test so it gave a positive test result,  I mean if you had a test that had Corona virus inside it,  but needed to be activated to show up, hence if you ran the test without activating it you would gain a negative result, how could you do so?


These are the trying times where trust is gone completely.
Title: Re: How do you test a covid test?
Post by: alancalverd on 14/11/2020 13:53:41
where apparently test have to be proven to work to be considered tests.


The FDA requirement is "equivalent to or better than" something that is already approved.

Tossing a coin has proven equivalent performance (see "Musk") but wins on "better than" criteria because it can be self-administered, is instantaneous, unequivocal and requires no skill - all significant parameters in FDA assessment.

It will also appeal to a significant section of the US electorate because it can be administered remotely by a psychic diagnostician or faith healer, with no loss of performance.

And since I'm only going to charge 15c plus postage and state tax for each (reusable) device, what's to lose? 
Title: Re: How do you test a covid test?
Post by: Jolly2 on 19/11/2020 10:09:59
where apparently test have to be proven to work to be considered tests.


The FDA requirement is "equivalent to or better than" something that is already approved.

Tossing a coin has proven equivalent performance (see "Musk") but wins on "better than" criteria because it can be self-administered, is instantaneous, unequivocal and requires no skill - all significant parameters in FDA assessment.

It will also appeal to a significant section of the US electorate because it can be administered remotely by a psychic diagnostician or faith healer, with no loss of performance.

And since I'm only going to charge 15c plus postage and state tax for each (reusable) device, what's to lose?

Sorry a coin flip is hardly equivalent.

Supposedly the only way a positive test result is found is if RNA/DNA from covid19 is present on the swab. If Musk as an example, doesn't have covid, where has that material come from to generate a positive  test result?
Title: Re: How do you test a covid test?
Post by: Bored chemist on 19/11/2020 10:43:27
Supposedly the only way a positive
Title: Re: How do you test a covid test?
Post by: alancalverd on 19/11/2020 11:47:15
Sorry a coin flip is hardly equivalent.
It has exactly equivalent accuracy to any other test with a demonstrated 50% consistency, such as whatever Musk underwent.

On a serious note, my colleagues are now reporting 100% consistency between our breath sample test and the gold standard laboratory PCR test for COVID-19, down to usefully low concentrations of analyte. That is the best available test of a test, and in the case of our exhalate detector, is independent of operator skill and therefore translatable to real life. Other exhalate tests are, allegedly, available.
Title: Re: How do you test a covid test?
Post by: Jolly2 on 19/11/2020 12:52:44
Sorry a coin flip is hardly equivalent.
It has exactly equivalent accuracy to any other test with a demonstrated 50% consistency, such as whatever Musk underwent.


Which simply gives an equal 50/50 result, but in no way relates to the actual point or answers the question does the person have covid?

On a serious note,

Would be nice...

Considering the current tests are supposedly finding evidence of infected people on remote isolated islands,  is it not a possible explaination that the tests are infected with covid? I mean the people testing could also be bringing the virus there but seems a bit quick for a positive test result when the tested person just met the tester.
Title: Re: How do you test a covid test?
Post by: Bored chemist on 19/11/2020 13:05:24
Which simply gives an equal 50/50 result, but in no way relates to the actual point or answers the question does the person have covid?
Elon Musk has just taken 4 Corona virus  tests and received 2 positive and 2 negative test results?
Did you not see the similarity?
Title: Re: How do you test a covid test?
Post by: alancalverd on 19/11/2020 14:11:56
Considering the current tests are supposedly finding evidence of infected people on remote isolated islands,  is it not a possible explaination that the tests are infected with covid? I mean the people testing could also be bringing the virus there but seems a bit quick for a positive test result when the tested person just met the tester.

Absolutely, which is why I designed a disposable test capsule (the serious one) that is only handled by the testee, not the tester.

Not sure that having anyone else handle the coin would significantly bias the result, so my joke test is inherently more reliable than whatever Elon Musk paid for.  That should impress the FDA, who get very concerned about operator contamination.
Title: Re: How do you test a covid test?
Post by: alancalverd on 19/11/2020 14:22:31
infected people on remote isolated islands
You can't get much further from Wuhan than, say, Great Britain, nor more isolated by at least 20 miles of sea. But if anyone has travelled from A to B, even with  the best of intentions (like, say, looking for COVID) they have probably carried an endemic virus with them. 

Title: Re: How do you test a covid test?
Post by: Jolly2 on 23/11/2020 01:10:17
infected people on remote isolated islands
You can't get much further from Wuhan than, say, Great Britain, nor more isolated by at least 20 miles of sea. But if anyone has travelled from A to B, even with  the best of intentions (like, say, looking for COVID) they have probably carried an endemic virus with them.

https://principia-scientific.com/robert-f-kennedy-jr-covid19-vaccine-should-be-avoided-at-all-cost/

What do you think about Robert F Kennedy jr and his claims? He is a long term critic of the vaccine industry
Title: Re: How do you test a covid test?
Post by: evan_au on 23/11/2020 08:18:47
Quote from: Kennedy Jr
the so-called last generation mRNA vaccines intervene directly in the genetic material of the patient and therefore alter the individual genetic material, which represents the genetic manipulation, something that was already forbidden and until then considered criminal.
This shows that he does not understand: mRNA doesn't insert itself into the DNA of the cells where it has been injected, let alone affect every cell in the body, or affect germline DNA.
- It is only human germline DNA therapy that is banned, and mRNA vaccines do not do that.

Someone obviously understands the facts, because there is a little clarifying statement down the bottom of the page that correctly represents the situation - and contradicts what the main article says.

Quote from: Editorial Note
Note: messenger RNA or mRNA is the ribonucleic acid that transfers the genetic code of the DNA of the cell nucleus to a ribosome in the cytoplasm, that is, the one that determines the order in which the amino acids of a protein bind and act as a mold or pattern for the synthesis of that protein.

Kennedy obviously does not understand genetic diseases, since he tries to cure highly diverse polygenetic diseases like Downe's syndrome by simply:
Quote from: Kennedy
removing toxins from the human body, just as a person with a genetic defect like Down syndrome, Klinefelter syndrome, Turner syndrome, genetic cardiac arrest, hemophilia, cystic fibrosis, Rett syndrome, etc.), because the genetic defect is forever!

He obviously doesn't realize that the conditions he lists are genetic diseases which affect every cell in the body, and are forever (with today's technology).

He doesn't realize that the few cells which take in the mRNA will cause the immune system to recognize the viral protein, and then destroy the cells expressing the viral protein. So there is no possibility of permanent genetic changes to the human cells (apart from the desired immune response).
Title: Re: How do you test a covid test?
Post by: alancalverd on 23/11/2020 10:44:34
What do you think about Robert F Kennedy jr and his claims?
How about "ignorant parasite?"  That puts him one evolutionary level below malaria, and just as dangerous.
Title: Re: How do you test a covid test?
Post by: Colin2B on 23/11/2020 14:03:33
What do you think about Robert F Kennedy jr and his claims?
How about "ignorant parasite?"  That puts him one evolutionary level below malaria, and just as dangerous.
Just as dangerous are those who donít understand the problem with claims like this and pass them on without any health warnings.
Title: Re: How do you test a covid test?
Post by: Bored chemist on 23/11/2020 15:18:59
What do you think about Robert F Kennedy jr and his claims?
How about "ignorant parasite?"  That puts him one evolutionary level below malaria, and just as dangerous.
Just as dangerous are those who donít understand the problem with claims like this and pass them on without any health warnings.
Be careful,
Alan has the power to delete posts from people who point out that he says things that don't make sense.
He used it to delete something I posted (because or personal vanity- as far as I can tell).
He might abuse his authority again.
Title: Re: How do you test a covid test?
Post by: alancalverd on 23/11/2020 16:00:01
I mistakenly duplicated part of a posting. BC pointed out that I had repeated myself, so I deleted the repetition and his note, which now made no sense.

Part of the folklore at the Civil Service College was the chap who was sent a file in error. He read it, initialed it, and passed it on. A few days later it returned to his desk with the note "This was not intended for you. Please delete your initials and initial the deletion."

Being perfect in every way, I have no need for vanity.
Title: Re: How do you test a covid test?
Post by: Bored chemist on 23/11/2020 17:29:29

which now made no sense.
It made perfect sense; it showed that Alan messed up.

Alan told the same bit of story twice.
I skitted him for it- I quoted both versions and the word "Snap" as a comment.
There wasn't any need for Alan to delete his post; he chose to. That's his right.
But, unlike a normal rank and file member, Alan was able to delete my post too.- in order to make it look like he hadn't made the mistake in the first place.

Imagine that he had chosen to do that with some of his other absurd claims- like the one where he says that the conservation of angular momentum doesn't work.
Would that look to other members (who can't delete other people's posts to cover their own embarrassment) like abuse of power?
Would it look honest?


Title: Re: How do you test a covid test?
Post by: Jolly2 on 23/11/2020 17:38:48
What do you think about Robert F Kennedy jr and his claims?
How about "ignorant parasite?"  That puts him one evolutionary level below malaria, and just as dangerous.
Just as dangerous are those who donít understand the problem with claims like this and pass them on without any health warnings.

Can I ask how exactly can person not knowing the "dangers" possibly post a warning about them?

I find the thrust of your statements rather elitist. Are you suggesting only people qualified as yourself should be allowed to share information? Seems like a dangerous road to go down, the whole.point of a forum is to discuss these things.
Title: Re: How do you test a covid test?
Post by: alancalverd on 23/11/2020 17:48:56
Imagine that he had chosen to do that with some of his other absurd claims- like the one where he says that the conservation of angular momentum doesn't work.
which is why I haven't.
Title: Re: How do you test a covid test?
Post by: Bored chemist on 23/11/2020 17:59:27
Imagine that he had chosen to do that with some of his other absurd claims- like the one where he says that the conservation of angular momentum doesn't work.
which is why I haven't.
Yet.
Title: Re: How do you test a covid test?
Post by: Colin2B on 23/11/2020 22:55:42
I find the thrust of your statements rather elitist. Are you suggesting only people qualified as yourself should be allowed to share information? Seems like a dangerous road to go down, the whole.point of a forum is to discuss these things.
Iím not sure why you consider that my comment might be aimed at you or your post.
You quite rightly raised this as a discussion topic giving the full information, which as @evan au points out contains editorial warnings.

There are, however, those who would seek to present the information in a falsely positive light by excluding any warnings and extracting only parts of the information favourable to their point of view. These are to a great extent more dangerous than the originator.

Can I ask how exactly can person not knowing the "dangers" possibly post a warning about them?
By taking the trouble to examine sources, bias, and alternative views. Interestingly this critical examination of evidence is now being taught in French schools following some of the terror incidents there, the objective is to reduce the incidence of false news.
Title: Re: How do you test a covid test?
Post by: Jolly2 on 24/11/2020 18:36:37
I find the thrust of your statements rather elitist. Are you suggesting only people qualified as yourself should be allowed to share information? Seems like a dangerous road to go down, the whole.point of a forum is to discuss these things.
Iím not sure why you consider that my comment might be aimed at you or your post.
You quite rightly raised this as a discussion topic giving the full information, which as @evan au points out contains editorial warnings.

There are, however, those who would seek to present the information in a falsely positive light by excluding any warnings and extracting only parts of the information favourable to their point of view. These are to a great extent more dangerous than the originator.

Can I ask how exactly can person not knowing the "dangers" possibly post a warning about them?
By taking the trouble to examine sources, bias, and alternative views. Interestingly this critical examination of evidence is now being taught in French schools following some of the terror incidents there, the objective is to reduce the incidence of false news.

The trouble is that Fact checkers are often partisan to those seeking to impose a narrative.

"Fake news" is becoming a tool for establishment misinformation or a way to try an discredit legitimate points of concern, or truth about corporate or government mis-behaviour or dishonestly.

There is an endless example of the media, businesses and governments gas lighting their populations as a means to a political end.

The best predictor of future behaviour is past behaviour,  as such vigilance is needed especially when it comes to government and business claims.

Title: Re: How do you test a covid test?
Post by: evan_au on 24/11/2020 19:36:13
Quote from: John F Kennedy Jr
because they can no longer be cured simply by removing toxins from the human body, just as a person with a genetic defect like Down syndrome, ..hemophilia., etc.), because the genetic defect is forever!
I may have been a bit harsh on him.
At first reading, I thought that he (or his friends) were trying to peddle a treatment for severe genetic diseases.
- On rereading, I think he was saying that germline therapy affects the whole body, and is effectively untreatable. And that is a reasonable comparison.

The point he missed is that mRNA vaccine is not germline therapy, and does not contain reverse transcriptase, so it can't take any form of RNA, and insert it into DNA.
- And the editorial correction is written in such technical terms that it sounds like it is supporting his argument