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Hi Ghia.
"The PCR test looks for 3 distinct signals in each sample (i) a positive or negative COVID19 signal based off E and N genes, (ii) an internal control signal to tell you that the PCR reaction has worked and (iii) an human “RNaseP” signal that tells you there is human DNA in the sample. Ideally, you get all 3 amplifying in a positive case. If you get no COVID signal and also get no RNaseP signal, good chance it’s not the best sample, or no sample at all."
If you don't have one of the following:
i) a positive or negative COVID19 signal based off E and N genes,
ii) an internal control signal to tell you that the PCR reaction has worked
iii) an human “RNaseP” signal that tells you there is human DNA in the sample.
...then I would assume the sample cannot be further tested, because the lack of any one of these signals is a show stopper.
I notice that i) includes the use of more than one gene, - we know the Primerdesign test uses just one gene, and we don't know if using one more gene is an easy task.
The Primerdesign assay is one if the fastest PCR tests available, so to detect and use more signals may increase processing time.
The company must be aware of the incorrect swabbing issue, as it will have had numerous discussions on the issue.
I trust the company to assure that if it is possible to modify a test to indicate when human error has occured during swabbing, then they would take steps to rectify is possible.
B2HS2L - This is the approach another manufacturer has taken to detect swabbing issues. Would have thought something similar from Primer would be sensible, if looking to deploy the test widely not using experienced clinicians.
"The PCR test looks for 3 distinct signals in each sample (i) a positive or negative COVID19 signal based off E and N genes, (ii) an internal control signal to tell you that the PCR reaction has worked and (iii) an human “RNaseP” signal that tells you there is human DNA in the sample. Ideally, you get all 3 amplifying in a positive case. If you get no COVID signal and also get no RNaseP signal, good chance it’s not the best sample, or no sample at all."
i neglected to include a smiley face to show my warm, cuddly side... : )
like that!
++++
i have included my backside to show my revulsion at the thought of being considered in league with Macron...(][)
com ca
Here's another reason why the French Govnt is wrong to require a 2 gene approach to SARS-Cov-2 detection:
"Once a virus is well established in a population, variation within a virus is less likely to occur. As is now the case with COVID-19 being so widespread, one, specific sequence, in one gene target, is preferential."
"But I guess my question still stands will Primer add additional checks in their test to identify where Human Error May have given a false negative."
Ghia, I don't think I have read anything which states the company is working on such additional checks, - or even if it is possible to detect human error in gathering the samples.
https://blog.primerdesign.co.uk/1-vs-2-gene-covid-19-assay-find-out-from-our-experts-which-is-best-for-testing-during-the-covid-19-pandemic/
It explains why the French Govnt is wrong to require a 2 gene approach to SARS-Cov-2 detection:
"To ensure the COVID-19 primers and probe remain specific to detect SARS-CoV-2 genomes, Primerdesign’s Bioinformaticians review daily the SARS-CoV-2 sequence submissions on the GISAID EpiCoV database.
!!Each new sequence presents a risk to kit detection and false negatives for competitors without surveillance programs.!! The potential risk of false negatives increases with 2/3 target assays meaning a patient with a false negative will potentially be back in the community affecting the general population by spreading COVID19.
“Unlike the SARS outbreak of the early 2000s, the amount of sequencing conducted by diagnostic laboratories around the world is unprecedented. The GISAID database EpiCoV currently contains over 6,000 sequences, of which are good quality full length genome sequences. It enables us to check our assay design against the database daily, to ensure that mutations are not accumulating in the target region of the primers and probes. We are therefore confident that our assay will still detect 100% of the sequences available, giving our customers confidence that the easy to use one assay approach will not miss any positive cases due to mutations. It also won’t give conflicting results which may arise if mutations accumulate in one of two assays, leading to a decrease in sensitivity of that assay.” Gemma Stokes, Bioinformatician Scientist Primerdesign.
“If clinical diagnosis is being performed, complete confidence is needed in your test. At Primerdesign our bioinformatics team check our COVID-19 CE design daily against all globally published sequence information for assurance in a comprehensive SARS-CoV-2 detection profile. Ultimately, we have complete confidence in our unique design and product. We therefore do not need to target multiple genes. ” Adam Herridge, Product Manager Primerdesign."
VanV has stated the our bioinformaticians can confirm the COVID-19 assay primers and probe still show 100% homology with the latest SARS-CoV-2 sequences in his 12:56 post, and latest homology report can be found here:
https://twitter.com/PrimerdesignLtd/status/1267389572788469761/photo/1
The marketing team have a report available, proving assay efficacy updated weekly, that no other assay supplier bothers to provide.
B2H2SL - Thanks for posting that. I think I personally have misunderstood the multiple gene target science and have joined the dots between the French decision and human error during swabbing.
That article seems to suggest the French government decision is questionable.
But I guess my question still stands will Primer add additional checks in their test to identify where Human Error May have given a false negative.
This appears to be Possible looking at other PCR tests.
Ghia 12:17 - Has there been any comment from the company on whether they will adapt their test design
in light of the rejection from the French Government?
https://blog.primerdesign.co.uk/1-vs-2-gene-covid-19-assay-find-out-from-our-experts-which-is-best-for-testing-during-the-covid-19-pandemic/
Ghia, - It seems the French Govnt. needs to get with the program, (modernise its views).
Here Primerdesign discusses view on 1, 2 and 3 gene testing.
Because symptoms of cough, headache and tiredness etc or flu like symptoms covers a huge variety of illness. Such as asthma, COPD, early signs of lung cancer, inflammation of the throat, gastric reflux etc the list goes on. There will also be lots of people who are hypochondriacs who will want a test when they don't have any COVID symptoms
Seadoc - what is this near test you speak of? The 104 copies per ml that a large minority of patients have is going to be difficult without concentration or amplification, which take time.
Hello, I never post in this bb but I'm invested in ncyt and I always read your posts with interest.
I suspect that a large part of false negatives are due to the sampling, not the test itself, which in ncyts's case has been certified many times to be 100% specific and highly sensitive (I don't remember the figure sorry).
With a PCR swab we look for the virus RNA, which implies taking a good sample with adequate cellular yield on it, and possibly mucous/degenerated tissue where the virus may be lurking. I wonder how many of these swabs don't even touch the affected area in any significant way, ie collecting enough viable material, for many reasons, especially the home kits.
Also, on a different note, I have been puzzled for days at the numbers: they test 100k (roughly, just as an example as end of April aim figure) people a day but only have 6k positives, sooo.. the 94k negatives, why were they tested in the first place if only people with symptoms are tested? These are not random tests of random people to see the prevalence in the population, they specifically look for the virus in affected people.
can anybody explain, please?
Interesting article on South Korean diagnostics company Seegene
Chun launched Seegene in 2000 with a 300 million Korean won investment from his uncle (about $240,000 in today’s dollars). For the first three years, Seegene had zero revenue. “Even though it was a difficult time, I was determined to do this,” says Chun. “If I produce something extraordinary, then all of the world will be watching.”
Seegene developed kits for diagnosing respiratory, digestive, sexually transmitted diseases and cancers, but found few takers at local hospitals, Chun recalls. It was abroad where Seegene finally found its market: 82% of Seegene’s revenue now comes from exports. The U.S. and Europe are Seegene’s major markets. Chun says he has traveled all over the world to personally demonstrate Seegene’s tests, and credits that for the company’s global success. Even before the coronavirus outbreak, the company's net income last year more than doubled to $23 million on a 19% increase in sales, to $105.3 million. Seegene’s stock has more than doubled since January to a recent 88,100 Korean won, and the company sports a market cap close to $2 billion.
Seegene’s test resides in a single test tube, where it identifies three target genes present in Covid-19. Because it streamlines the testing process, it takes a tenth the time of manual tests and reduces the risk of human error in diagnosis.
While other tests look for the presence of antibodies, Seegene’s uses what’s called a polymerase chain reaction to spot the virus present in body fluids before antibodies form. Such molecular diagnostics—in contrast to older immunodiagnostics—are faster and more accurate, Chun says. It also means people infected with Covid-19 can be spotted before they show any symptoms.
In addition to stemming the spread of the coronavirus, Chun sees his testing approach as a victory for molecular diagnostics. “In ten years,” he says, “I aim to make molecular diagnosis easier, affordable and widespread.”
Ghia, always fantastic posts on S very well researched, afraid second guessing Primer involved in unproven stats quoted in press is not up to your usual level of much appreciated research in the share you are invested in.
Seegene are developing a saliva based PCR kit. Hopefully NCYT can follow
“Future diagnostic kit will also focus on convenience in sampling to enable precise diagnosis with a saliva sample alone,” Chun added. The current sampling method is nasal swabbing which often causes discomfort.
this strong buying in france today has surprised
had not expected to see the buying coming from france
Has there been any comment from the company on whether they will adapt their test design in light of the rejection from the French Government?
It's clear that the weakness in the PCR process is the accuracy of the sample collection, if we envisage this being used in a mobile setting or home delivery swabs etc. we will have to build in controls to detect where false negatives are because of poor sample quality.
The 30% failed test number being thrown around in the media could very well apply to primer design tests, not because the test itself is bad but the swab collection is inadequate.
There are other PCR tests entering the market that have in built controls to trap sample collection errors I think we would be wise to follow suit or risk falling behind.