There is old saying “Cats got your tongue”. It emerges when you are at a loss for words…. or potentially choking on a Nerd Sweater.
This is an excellent presentation on the evolutionary trajectory of SARs-CoVs-2 and just as fascinating as the genomics, is the content that is explicitly not spoken about. You see, NextStrain and GISAID all have alot of uncle Bills grant money and he loves vaccines so much, that he has over $100M in BioNtech stock and CureVac stock tucked away in the Bill and Melinda Gates Foundation. As a result, many people in the Epi space we affectionately refer to as the Nerd Sweater Mafia…. they know to never speak ill of vaccines. See if you can find the word vaccine anywhere in the first 24 minutes of this very well done analysis on the directed evolution of this virus.
The fascinating aspect of this presentation is that it highlights the mutational spectrum of C19 during 2021 and it is as clear as day that there is a massive enrichment for mutations in the spike protein compared to other parts of the genome.
There is also a lot of squid ink diverting the viewers attention as to the cause of this. Let’s look at the running hypothesis they float to explain such an enrichment of mutagenesis in spike.
1.Natural selection against Host immunity.
Note the language.. not vaccine immunity.. host immunity. Blame the victim some more and redirect attention from the obvious selective pressure going on with “Spike only vaccination” to those immunocompromised people (the ones you need to get vaccinated to save).
Note at 8:52 he mentions this is speculative as they didn’t see any of this happening in the Spring 2020 during the ‘first’ pandemic wave. Remember this point as the emergence date of C19 continues to back into October 2019 with WIV employees losing their sense of smell. The first wave (in Trevor’s eyes) is only the wave he could see with qPCR but he forgets that viruses with R0 this high are unlikely to be at their first rodeo when we wise up and point our sequencers at them.
They begin to see spike mutagenesis in the fall of 2020 but it really takes off in 2021. This is where they will play their magic tricks. They will claim this was witnessed before the vax roll out therefore the vax is innocent. Watch them like a hawk.
A fly in their ointment: You will also see them speak about convergent evolution being evident (min 20+) in the data which refutes their own chronological argument that attempts to blame this on pre-vax “partially immune” people. Convergent evolution is where the same mutations appear to evolve independently over and over again around the world as similar selective pressures are applied.
The polymerase doesn’t make random errors. It has propensity to make some of the same errors due to the sequence context of the virus. This means an ORF8 deletion can occur in Africa and Australia independently without anyone traveling between the two continents to spread it there.
There are also similar selective pressures being applied in geographically distant places. In some of these cases, we can see different RNA variants emerge across the globe which may differ at a RNA sequence level but code for the same amino acid change. Let’s take the UUC codon for Phenylalanine. You can mutate it to UUA or UUG and still code for the same alternative amino acid Leucine.
More than one way to skin a cat…. but dont skin cats!! We kill bats.
When you see evidence of convergent evolution, you need to take arguments that rely on “we saw this variant before the vax, therefore the vax didnt cause it” with a pound of salt.
To drive this speculative “partial immunity population” home, the author displays an outlier case of a patient who had COVID for 150 days and was surely a breeding ground for new variants that emerge under a clearly immunocompromised setting. They sequenced the virus throughout this fight to watch the evolution in a single patient over time. Fascinating stuff.
This is an important anecdote that actually better supports the narrative he’s not allowed to talk about as its one patient and to believe this is happening population wide would require something to weaken millions of peoples immune systems synchronously.
By Spring 2021 Delta scariant takes over. This contains multiple mutations in the Spike sequence coinciding with the largest vaccination campaign ever seen in history…
… with a leaky vaccine that only immunizes against spike but DOES NOT lower the viral loads of the patients. Some papers report higher viral loads with the vaccinated (Vietnam). A few papers report equal viral loads but fewer days at those high levels if you are vaccinated. But one thing is different with the recently vaccinated….
They are immunocompromised.
Fellow Feline El Gato Malo covers this nicely.
So what is the more likely the case?
A) A population of people who have natural immunity which has been shown to be 13X-26X more robust, contains more diverse epitopes (full 29Kb not 3.6Kb from the vax) that are harder to mutate around, have and more durable immunity than spike only vaccination..That these people are the “partially immune” plague rats….
B) You recklessly vaccinated millions of people, all at the same time with untested vaccines that drive Neutropenia and Lymphocytopenia for 7-14 days after the jab.
Interestingly, we don’t have to guess at this as the data delivers a glaring middle finger to us and the cats seem to have Trevor’s tongue.
By 18 minutes in, Trevor does a brilliant job explaining the dS/dN analysis. This is just another name for Ks/Ka analysis that I touched on the during Directed Evolution Part I. You look at the ratio of Nonsynonymous/Synonymous mutations in Spike (S1) and compare that to RdRp as a control. RdRp is the RNA Dependent RNA polymerase and is believed to be fairly conserved. Although, this conservation I suspect is a temporary mirage as we have applied no selective pressure against RdRp. It’s possible, with enough use of drugs that reduce RdRp activity, we will select for mutation that evade the RdRp inhibitors.
So here we have beautiful evidence of elevated Spike mutations in the lineages that become dominant post vaccination with Spike only vaccines and no such elevated mutagenesis outside of spike.
But it gets better.
Oddly, Spike is the only region of the genome that is showing this? Why would that happen with “partially immune people” that were naturally infected but their immunity fades? Does it only fade for non-Spike epitopes forcing the virus to mutate around what’s left of a spike specific residual partial immunity? Seems like a stretch. What else could provide spike selective pressure to this virus?
S1 (part of Spike) has the highest Clade growth of all genes in SARs-CoV-2 and this trend became dominant in Spring of 2021. I wonder what happened then?
This appears to have created 5X higher mutagenesis on the Spike protein in less than a year. They will try to claim this preceded the vax program but you must keep in mind that samples that had S gene target failure were prioritized for sequencing ever since the emergence of B.117 (Alpha variant). So we began oversampling this problem just before the vax was deployed and have watched it wipe out all other strains ever since.
His presentation also underscores certain bursts of mutagenesis or punctuated mutagenesis. It is not clear to me how this occurs in the “partially immune population” unless that partially immune population all signed up for neutropenia in a tight time scale (Get Vaxxed Now!).
The nail in the coffin is seeing convergent evolution in addition to high growth rates of those same variants, in addition to dS/dN analysis that points to strong selective pressure on spike. This is a text book case of a man made vaccine escape program. Great for Booster revenue. Poor for trust in public health officials that have politicized these obsolete and somewhat useless vaccines.
The vaccines may play a role in focused protection of the vulnerable if they really do limit hospitalizations and death, but they kick the can down the road by failing to limit viral load while creating more asymptomatic carriers.
This is now a disease of the vaccinated and we have just evolved a variant that creates asymptomatic spread when it never really existed before.
The solution to this problem lies in drugs that limit the polymerase and reduce viral load so we can stop this losing evolutionary race.
Or vaccines that are not so narrow (full 29kb immunity) and easy to mutate around. Sterilizing vaccines would be nice.
What I find most dystopian about this wonderful presentation, is that the glaringly obvious conclusion from the data is left unspoken and some other blame game is played: Those people with natural and impure pagan immunity must be at fault.
The Salem witch trials never really left us.
A helpful comment from El Gato Malo- How do you explain the chart that shows Spike protein NonSynon/Synon ratios going up in 2020.78 when the vax program wasn’t in full gear yet?
One must keep in mind that the Nonsynon/Synon chart is derived not from population prevalence but from DNA sequencing pipelines that were selecting for Variants of Concern to sequence. This is not random sampling. There are several filters applied to what gets sequenced but Ct scores lower than 32 is one filter. Likewise, if PCR pipelines found a S-gene target drop out where one PCR amplicon is positive but the S-gene target fails to PCR, these samples were prioritized for sequencing. This prioritization began after the B.1.1.7 variant began to evade qPCR pipelines in late 2020 and early 2021. So these variants can be created but remain at low levels in the population until a selective pressure is applied such as a vaccine program (or something else). You can see the delta variant population prevalence dramatically rises concurrent with the vaccine roll out, despite it existing at lower levels prior to this. It’s worth reiterating that this is a hypothesis (not fact but correlative with a strong thesis behind it) that is better understood reading over the references in the first Directed Evolution thread.
Trevor Bedford - the same guy that pushed 'zoonosis' theory from the very beginning while heavily discounting 'lab-origin' hypothesis.
Brilliant, thorough, humble and honest and way over my head but I have a rock solid bullshit meter that did not go off. Thank you so much for putting this work out.