Kannapedia.net is getting a good face-lift.
Samples now have variant tables with annotation on their impact to the gene.
There is also an IGV integration. You need IGV installed locally but the Start|Jump links will open up you BAM file in IGV.
You must have IGV open and then click the start link.
The sample's BAM will show up for viewing in IGV.
Once open, you can use the jump link to move swiftly around to each variant. This is a variant in THCAS.
You can jump to other variants in the same gene. In this case we have one non-synonymous variant in phase with a synonymous variant in THCAS.
While a lot has been written about false positives, the nasal swabs can vary 1,000-10,000 fold in their collection efficiency (Dahdouh et al) and many jurisdictions are using human gDNA internal controls to normalize for this large variance.
This variance implies many false negatives mixed in with many false positives.
More sensitive PCR tests won’t fix false negatives that are a result of poor swabs.
They aggravate the problem as track and trace becomes a completely futile boondoggle.
If you are in the UK, this is the serial dilution of the test being run on you for C19.
For each 10 fold drop in Copies/ml, you should see a 3.3 increment in Ct.
What do you see?
Why does a 5000 copies/ml sample have a lower Ct than a 10,000 cp/ml sample?
The paper does speak to a spike in MS-2 control but this isn't a true internal control like RNaseP.
Spike-in internal controls are important for measuring assay drop out. They prove the PCR was functional.
But RNaseP controls which amplify human DNA/RNA harvested on the Swab..
These ICs are more important as you really cant quantitate viral load and make claims about S gene knock outs being higher copy number if you don't normalize the Swab collection and sample prep issues. These can vary 10-16 Cts according to Dahdouh et al.
I've been known to make a stink about public Ct data.
This is helpful. Tabs 6a, and 6b.
A few concerns.
1)Weekly not daily releases
2)Starts in Sept so its difficult to compare to 1st wave
3)No Ct by amplicon. Some info on amplicon fails but Ct are means ons.gov.uk/peoplepopulati…
What do we see in Tab 6b?
Take the Mean and chart it across time by jurisdiction.
Keep in mind the Ct is LOG 2.
So Yorkshire went from a mean Ct of 21.5 in Sept to 30.8 in Nov 30th. This is 512 fold drop in viral load from Sept-> Dec. Did you hear that in the news?
How could this happen?
First thing I look for is internal control data? Do they have a human gene in their assay like RNaseP?
This can be used to normalize sampling bias in the nasal swab. This has been reported contribute 10-13Cq variance in Dahdouh et al.
When respected Scientists resign over the false narrative... Take notice... and thank them.
Google Translated Letter from
Prof. Dr. Thomas Aigner,
Department of Geosciences,
University of Tuebingen, Sigwartstrasse 10,
D-72076 Tuebingen Germany
It was with the greatest astonishment, deepest concern, and indeed bewilderment, that I took note of the "7th ad hoc statement" from the National Academy of Sciences Leopoldina on December 8th, 2020.
In my opinion, this paper is not worthy of an honest, critical-
weighing science oriented towards the service and well-being of man. I do not have any medical expertise. However, as a scientist committed to nothing but the pure truth, I take the liberty of speaking up. I feel very alarmed by several points:
Many folks voice concerns over the viral isolation being incomplete. It's not my field so I tend to ask these folks what methods would they use to perfectly isolate a virus that opens up human tissue without opening up the capsid? We have new tools now. Why not use them.
This paper comes to mind. Samples directly from sick patients (not vero cell cultured with antibiotics). Whole Transcriptome sequencing (not PCR targeted so hypothesis free) reveals C19 coverage maps that correlate with Ct scores. ncbi.nlm.nih.gov/pmc/articles/P…
This paper has them compared to Corman primers and they have lower Ct's which isn't surprising. I dont see the primer sequences anywhere to confirm they hit Pfizer mRNA of Spike. Anyone know if the Altona primers are public? sciencedirect.com/science/articl…
To help liberate these renegade drugs we have been sequencing the genomes of many of the plants and fungi that can enable people to grow their own medicine. There is certain empowerment and agency over addiction and disease that occurs when the patient is vested in the solution
While cannabinoids are exceptional for opiate replacement therapy, over 6M people in the country resort to Kratom. This is from Mitragyna speciosa.
Related to the Coffee plant, Mitragyna synthesizes mitragynine and 7-hydroxymitragynine.
Let's toss in some Vogel et al.
Note the Charite' primers are in bold due to the error that would have been picked up if a reviewer simply BLASTed these primers (5 mins).
Wait... 99.8% of RdRp_R primer has the wrong base in it for C19 amplification?
Let's add to the chorus.
Kuchinski et al. has a whole section of the paper dedicated to the errors in the Charite' primers.
Let's walk through the much more complicated problem of identifying pathogens on Cannabis flower. These are inhaled products in an industry that just experienced EVALI.
This will provide a few examples of which steps in the process are prone to producing illusions with qPCR.
The first problem is that Cannabis microbes can be both Endophytes and Epiphytes. These live inside the plant or on the surface of the plant. This changes how you survey them. If you don't lyse open plant cell walls, you cant see the Endophytes. You need proof of lysis.
We accomplish this by targeting a conserved cannabis sequence in qPCR. Every PCR assay must have a qPCR target that proves you lysed open the plant cells.
Many SARs-CoV-2 assays accomplish this by targeting a human gene known as RNaseP.