Omicrons (B.1.1.529) most recent common ancestor is AV.1. Relative to this MRCA, Omicron has 25 nonsynonymous and 1 synonymous mutation in Spike, and 13 nonsynonymous and 6 synonymous mutations in the entire rest of the genome. This is very strange & I don't understand.
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I have re-done the alignments and counting up of mutations, and it's even weirder than i first said.
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34 discontinuous changes (that are likely independent events). only one of them is silent. the rest change amino acid. see attached pictures. to quote this is inconsistent with expectations from standard evolutionary theory.
![Image](data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="680" height="375"><rect fill-opacity="0"/></svg>)
![Image](data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="336" height="360"><rect fill-opacity="0"/></svg>)
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this is just bonkers. there should be a butt-tonne of other silent passenger mutations hitching a ride with nonsynonymous changes under positive selective pressure. i am not invoking a sinister lab engineering event here, just something important that i do not know.
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Spike is 3819 coding nucleotides. It has 33 NS and 1 S changes. The neighboring ORF3A-E-M-ORF6-ORF7A-ORF8-N-ORF10 genes have 4000 coding nucleotides. They have eight NS and three S changes. Spike is smaller and has four times the NS changes.
![Image](data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="293" height="360"><rect fill-opacity="0"/></svg>)
![Image](data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="680" height="398"><rect fill-opacity="0"/></svg>)
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positive selection on spike should drag a bunch of synonymous changes in the neighborhood along for the ride. unless spike can evolve separately from the rest of the genome.
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then NS/S ratio in spike is evidence of very strong selective pressure. but it also has higher mutations per mb than the rest of the genome, so something does not make sense.
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Lab made with low pathogenesis and high transmissibility, created to replace Delta.
Like a firebreak.
Because, why not?
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You don't need a lab when you have immunodeficient humans, they are walking GoF reservoirs for viruses.
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Molnupiravir?
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I'm just a twitter novice here, but isn't this what it would look like if a lab had AV.1 and was selecting for transmisibility in their experiments and then it leaked?
![Image](data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="650" height="432"><rect fill-opacity="0"/></svg>)
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Seems likely it's a similar situation.
![](data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="625" height="350"><rect fill-opacity="0"/></svg>)
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Are you familiar with the work of ? Probably has something to do with this virus gatekeeping back through being a live-attenuated vaccine…
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yes, but i am not qualified to comment on that one.
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Could it be that Spike duplicated & then one copy was released from purifying selection & nonfunctionalized? (I don’t know anything about viral gene dupes)
i do not know. i am not in charge of naming. thats another department.
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I also don't understand and it's strange. After I realized that it's not strange because I'm just a fucking Commerce graduate and not a doctor or Microbiologist 
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has there been efforts to model these mutations as alleles of a quasi-species swarm? where the mutations themselves may make more sense when the entire genomic picture is taken into account? i wonder if the anomalies are a result of classical microbiology constricting the picture
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But SA vax rate is low!
Makes me wonder if pets should be vaccinated.
At least those that aren't strictly housebound.
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This Tweet is from a suspended account. Learn more
Supposedly two days after Botswana had declined to accept anymore Pfizer vaccine shipments after being little affected by covid, maybe it’s political..
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Watch my talk on how most of these new variants are arising. It may help:
youtube.com
How the Evolution of Novel COVID-19 Variants Validates the Mojiang...
There is one aspect of our Mojiang Miners Passage theory that some readers have found difficult to accept. It is the idea that one or more bat coronaviruses ...
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1. Don’t know if this is a coincidence, but the 7 samples which came to WIV for sequencing, one had HIV seq. Remember? Patient 7 I guess. He had highest numbers of HA of H7N9 too. What could be the link? Relation to lab leak?
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You expect a uniform distribution of synonymous mutations (SM) throughout the genome. So 1 in the Spike region and 6 outside is ~right.
Spike=3821 nt. Genome =30k/3821=~8 total SM.
So you expect 7 outside Spike instead of 6. Seems within margin of error.
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you are right about the ratio of synonymous mutations inside and outside of spike. there are just too many NS mutations in spike given that background rate. if each new NS variant is like a new clonal event, there should have been lots of silent passengers as well.
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