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Larry,
do carry on with your copy and paste skills
"highly innacurate"??
What did I say?
are you confusing the word gene with the word base pair, I was referring to a mutation which occurs in the omicron mutant,
do you have a degree in biochemistry?
From said WHO document:
Testing and sequencing
Genomic surveillance is of crucial importance for early detection of the presence and monitoring of epidemiological
trends of specific VOCs, VOIs and variants under monitoring, and will provide important information to guide
response for this new variant [16]. This includes regular testing of representative samples but also strengthening
targeted sampling from persons coming from high-risk areas.
The presence of the deletion ?69-70 means that S-gene target failure (SGTF) for the Thermo Fischer TaqPath
assay can be used as a screening method for Omicron. In a setting with the Delta variant dominating, this can be
used as a proxy for Omicron after confirmation of a subset of samples by sequencing. Currently there is no further
information available on any effect on sensitivity for other RT-PCR assays or for rapid antigen tests. Countries
could consider retrospective SGTF screening of SARS-CoV-2 positive samples from recently returned travellers from
Southern African countries to rapidly assess whether cases may have been recently introduced.
Rapid antigen tests should be unaffected based on the analysis of the mutations in the nucleocapsid (N gene) of
Omicron viruses, however, verification of this is underway [13].
Starbright - you would hope that genesig 2g or 3G could be used in the same way?
It looks like the "Thermo Fischer TaqPath assay" is the one that can be used as a proxy test. From the WHO document linked above:
" - Most diagnostic tests continue to work and can detect the variant Omicron.
- S gene dropout or S gene target failure (SGTF) due to deletion at Spike position 69-70, similar to the detection of the Alpha variant, has been reported. Thermo Fischer TaqPath assay can therefore be used as proxy test for this variant, pending sequencing confirmation. Use of the SGTF approach may lead to faster detection rates."
Drb83...Totally agree and this is not the time for ncyt to go all shy with their rns...we need more information and so do the market, also hoping the press pick up on it as well...
It could also be a reasonable assumption that given the number of mutations in the Omicron variant, at least one of those mutations would cause a s gene drop out.
As I said before, an RNS on Monday clarifying this would be great.
If it isn't coincidence that the Genesig test got approved Friday then that would indicate that the test does identify the s gene drop out. I'm clutching here so really need ncyt to update us.
Larry thank you for that link. That has really helped my understanding.
Sorry for spam but one other thing to add.
As we had no issue with the S gene with the alpha variant, its imo unprobable that we now have a dropout ourselves with our test.
PROmate is a no as only detects ORF1 gene.
PROmate™ COVID-19(Primerdesign Ltd) is direct qRT-PCR workflow solution that
detects a single ORF1ab region
However, we know Genesig both 2g and 3g do detect the s gene so I am assuming like the Thermofisher test it will also not be able to detect the s gene mutations of the Omicron variant thereby inadvertently detecting the Omicron variant. It would be really great if ncyt could clarify this.
Also, when a s gene drop out is recorded then the sample is sent to the lab for sequencing. This can take several days. If like in the past with Delta Ncyt come out and RNS a SNPsig that can confirm the Omicron variant then again Kaboom.
Got a feeling we are going to be inundated with news in December.
Bullraider, what youre telling is highly innacurate in a scientifc view. Omicron isnt a gene to start with...
Drb, here a proof for thermo :
https://www.google.com/url?q=https://cdn.who.int/media/docs/default-source/searo/whe/searo-technical-brief-enhacing-readiness-on-omicron.pdf%3Fsfvrsn%3D6457b0d7_15&sa=U&ved=2ahUKEwi6lbOvhLv0AhVh4uAKHfI6CwsQFnoECAQQAg&usg=AOvVaw1wzIz9B5S-MHuqApVDtyVc
S gene dropout or S gene target failure (SGTF) due to deletion at Spike position 69-70, similar to the
detection of the Alpha variant, has been reported. Thermo Fischer TaqPath assay can therefore be
used as proxy test for this variant, pending sequencing confirmation. Use of the SGTF approach may
lead to faster detection rate
I know thermofisher has a s dropout with the New variant.
For ours i dont know.
drb,
you are correct,it is the failure to dectect the omicron gene,ie it can be detected because it's not there! Absence makes the heart stronger.
Larry, I am not sure you're entirely correct. Please check the Xmas target thread. I believe our 3g PCR test may be able to inadvertently indicate if the positive is Omicron or not by a unique characteristic of Omicron making the s gene indicator drop out. The result would need validating by something like a SNPsig but as we don't have one yet the 3g test would offer enough indication to justify asking that person and all their contacts to isolate regardless of vaccine status. Correct me if I'm wrong of course
Thanks Larry.
It detects all strain.
So it's not a specific test for this strain.
Would need a snp test to target just this specific strain.
Please could anyone confirm whether ncyt are saying that their test can specifically identify omicron, as opposed to detect that it is covid?