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Omicron

Happy Thanksgiving weekend! I hope you are all well and recovering from an excess of butterfat and tryptophan.

Speaking of tryptophan, some of you may have heard of the discovery of a new Covid variant that originated in Botswana or Covid B.1.1529. The various news media sources are reporting a “horrific number of mutations”.

Yes, first they scare you into a self-imposed lockdown and then they tell you they’re going to keep a close eye on it because it might not have more than a few cases.

Omg. What should we believe??

Well, if my MacBook Pro wasn’t a decade old, I’d fire it up to take a look at the sequences and structure because it depends on where those mutations are located, how different they are from the original Covid structure sequence and how different they are from the vaccine sequences.

Let’s take that one at a time.

The mutations are located on the spike protein. 32 mutations are a lot but the spike protein is hundreds of amino acids in length.

Those mutations could make it easier for the spike protein to latch onto cells, though it’s hard to imagine that it would be more efficient than the delta variant.

The mutations could be “conservative”. That means a mutation is similar to the original amino acid and doesn’t change the structural integrity or function of the protein in any significant way. Sometimes the mutations do make a difference as in the case of delta. But sometimes, just a single non-conserved mutation in the right place can screw up the protein making it more floppy or closing off an area that makes it harder to interact with the target. If you have 32, that could make it a really screwed up protein and not in a more infectious way.

But what about the vaccine? Could these mutations make the vaccines less effective? Yeah, this is a possibility. If the mutations are different enough, then the protein segments that Pfizer and Moderna have included in their vaccines might not trigger the production of the right antibodies. The genius of the mRNA vaccine technology is that they can be changed relatively easily. There could be a new vaccine on the horizon sooner than you think. And there is usually a pattern to which amino acids are more apt to mutate than others. So you can probably make some predictions.

So, does omicron freak me out? A little. It just demonstrates how important it is for us to get the rest of the world vaccinated asap so variants do not arise. On the other hand, it’s not like we don’t know how to slow down the rate of transmission by wearing masks and observing social distancing guidelines.

I’ve always wondered why we greet each other with a variation of “how are you?” in so many languages. It never really made much sense to me since it seemed like a formality. No one really expects us to go into detail about how we are. But it makes sense to me now. There were times in the past when knowing the state of the health of people you met was vitally important. I’m watching all the curtsying and bowing in Jane Austen adaptations with new eyes.

You can never be too careful.

2 Responses

  1. RD, thank you for the cogent and intelligent insights! Gosh, we could certainly use some positive news, which you have provided, though of course with the necessary caution.

  2. Weekly off-topic reminder:

    Friday nights 7 PM – 8 PM North American Central Time:

    The Magical Mystery Tour. Host Tom Wood takes a look at the Beatles from a different angle each week.

    Friday nights 8 PM – 12 AM North American Central Time:

    Beaker Street, the legendary rock radio program, has returned. Iconic host Clyde Clifford has returned from his medical absence.

    Both shows can be found at http://arkansasrocks.com/

    If you can’t catch Beaker Street live, MP3 files are available soon afterward at https://beakerstreetsetlists.com/

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