It was inevitable . . .

December 1, 2021 • 2:15 pm

CNN and other sites report that the first infection with the multiply-mutant “Omicron” strain of coronavirus has been found in the U.S.

The United States’ first confirmed case of the Omicron coronavirus variant has been identified in California.

In a White House news briefing, Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, said the case was in an individual who traveled from South Africa on November 22 and tested positive for Covid-19 on November 29.

That individual, Fauci said, is self-quarantining and close contacts have tested negative for the coronavirus so far.

The person was fully vaccinated and is experiencing “mild symptoms, which are improving at this point,” Fauci said.

Asked by CNN whether that person had a booster shot, Fauci said, “To my knowledge, no.”

The hope, of course, is that the mutant, though a fast spreader, will trade that off against a milder illness. It’s clear this mutation spreads rapidly and looks as if it can sneak past existing vaccination, so let’s hope it doesn’t go for the whole trifecta.

Here’s a NYT figure showing the large number of mutations in the Omicron strain vs. the other strains.  The right figure shows the spike protein, the virus’s armament. Look at all those mutations!


22 thoughts on “It was inevitable . . .

  1. I’m glad Fauci regained his confidence (I just watched him on CNN). The past days he has been attacked by idiots and he seemed somewhat rattled.

    1. There are far too many Covidiotic Maskholes in the Disunited States of America (DSA)!

      In short, such Covidiots are no longer concerned with objective reality and impartial truth, nor reachable with verifiable facts, argumentation and fair reasoning.

      Yours sincerely,

      1. Nicely put. Often when dealing with idiots spouting their idiocy, the most appropriate response, if any, is a quick eye roll and a sighed, “Anyway…” before going on with whatever one was already doing or saying.

  2. There’s probably more people carrying it in the United States, but this is the only instance confirmed.

    So it probably has a good head start.

    1. It is cunningly hidden in the words :

      the case was in an individual who [blah]
      The person was fully vaccinated

      1. Sure, but that’s just a break-through infection, as is somewhat common with previous variants. Is there any evidence that Omicron is more capable of evading existing vaccinations than, say, Delta?

        1. Its early days, and we will know more later. I think the main evidence for being at least concerned about it regarding bypassing current vaccines is the # of amino acid changes in the spike protein, which is the focus of many vaccines, and it really spread rapidly in South Africa which had a high rate of prior natural infections against the old variants.

  3. It’s not clear to me that it spreads rapidly. So far it has been kind of punk about that. Countries are reporting 1, or 4, or other small numbers of cases. How is that rapid?

    1. Here in South Africa infections have risen from around 3000 to over 8500 in less than a week, with 74% of new infections a result of the new variant (according to official stats), so yes, it does seem to spread rapidly indeed…

        1. It is entirely unclear what you ARE trying to say, much less from where your info comes.

          If claiming that an increase by a factor of 85/30 happens per day, then the number infected would increase by a factor of over a million in less than 20 days. And so the entire population of South Africa would have been infected in a few days more than 3 weeks.

          Please clarify.

          And don’t wait a month to do that if you are living there, because if so and that’s what you are trying to say, and if you are even close to correct, depending on the lethality now you are somewhat unlikely to survive the month.

          Sounds to me like an attempt at panic-inducing bullshit.

          Perhaps you meant to say the report from one particular day (not the actual infections PER DAY) made that increase. If so, perhaps the report on Monday versus the report on Sunday?? Anybody who doesn’t use averages over at least a week should turn off their TV and internet for a while and maybe drink a bottle of beer.

  4. When “they” say fully-vaccinated, that doesn’t mean much to me. First off, what vaccine? Were they boostered? If they didn’t have a booster, when did they get their last jab? I’d also want to know how diligent the person was at donning a mask or staying clear of large crowds, etc. I know this kind of thing will always get reported, but saying the individual was fully-vaccinated just opens the door to more questions and causes needless worry. I wish the media would get more pertinent information before reporting these incidents- goes against the business model I suppose, pity.

    1. For a moment I thought you were referring to the ‘big 0’ versus the ‘little o’ notation in mathematics, esp. number theory! To make a long story short, I’ll just shut up now!

  5. Unsurprisingly woke media like CNN and the Guardian are blaming this on the Western world for failing to share vaccines with poorer nations.
    Which is garbage. Sure, wider circulation of virus means higher mutation rate-raw material for evolution to work with. But vaccine availability is only part of the picture; vaccine hesitancy, mask hesitancy etc are just as important. What does it say about viruses chances to mutate and spread in large clusters in vaccine hesitant America and even larger clusters in the even more vaccine hesitant Russia? Spread of new mutants is only to a small extent due to malevolence, if it all. Ignorance and stupidity play much larger parts.
    The Guardian is indeed the enemy of western civilization.

    1. “Vaccine hesitant” is a whitewash phrase describing many people who are statistically mass murderers of elderly and immune compromised people, simple as that. And the motivation in US of trying to make the Democratic party’s present stay in government look bad is almost certainly in the forefront of most such peoples’ minds. Mass murder, nothing less.

  6. I make no claims to expertise in these matters, but I have understood that the linking up of these molecules with antibodies is a question of shape — the lock and key idea. If that is so, then what are the shapes which count on the viruses (viri?) in the image? The three big lobes or the multiple small objects?

    1. Both are important.

      The binding site of an enzyme onto its substrate, which is another lock-and-key model, can be just a handful of amino acids which have to be in precise proximity to each other for the enzyme to work. These are represented as the multiple small objects in the image. Changing one amino acid at the binding site typically renders it inactive, like filing a nick into one tooth of a key — even if the key goes in it won’t turn the lock if the nick is big enough. An amino acid change a great distance away can also impair binding if it changes the 3-D structure of the enzyme so that the binding site is no longer the right shape even if the amino acids right there are intact. This is sort of like bending the key so it won’t slip into the lock.

      Between spike and antibodies against it, the interaction builds on this model. Recall that antibodies are large Y-shaped proteins. The ends of the 2 arms are the keys that recognize their antigenic target. They have identical amino-acid sequences and so both must recognize the same small-object keyways on two places on the spike. Here’s where it gets complicated. The antibody is rigid except for a hinge at the crotch. So the two places (epitopes) on the spike where the one antibody has to bind its two ends have to be the right distance apart and oriented that the antibody can span the gap. Once bound, the single free end of the antibody signals the next steps in the immune response.

      You can see from the image that the two spike proteins have different size and orientation of the lobes (which is a consequence of different amino acids in the primary sequence.). You can imagine two ways how an antibody made against the wild spike could fail to bind to the mutated spike. First, the amino acid sequences (small objects) that the arms of the Y were looking for are no longer a match or are covered up by new folds of protein. Second, the sequences might be present but the conformation of the large lobes no longer allows that antibody to bind to both sites within the limits of its hinge.

      Unlike a lock and key, antibody binding is statistical and kinetic, not all or nothing. If the fit is really good, the antibody binds tightly and stays bound, keeping up the pressure on the virus. If the fit is only so-so, it is more likely to fall off one of both of its binding sites in the molecular turmoil of the battlefield and the virus gets a reprieve. But a so-so fit might mean that the antibody can maintain at least intermittent binding with many more different so-so fits, and many more antibodies will be so-so matches than perfect matches. Good enough might be better than perfect.

      Remember also that when you get vaccinated or infected, your immune system doesn’t order up a suite of antibodies made to measure against the virus or vaccine. Instead, it stimulates clones of immune cells that just happened to already match (more or less) the epitopes on the virus proteins. These immune cells and the antibodies they will produce were each committed, through random mutation of “hyper-variable” DNA regions during fetal life, to forever recognize a single specificity of charge and shape without fetal you ever having encountered the material that those cells might one day save your life against. Not surprising then, that lots of near-enoughs can beat a few perfect matches. (I thought that was the coolest thing I learned in first year meds basic science. If someone tells me it’s all wrong I will be crushed.)

      Hope you’re not sorry you asked. 🙂

  7. First 40min here is a discussion of Omicron by competent virologists and immunologists. Early on and before getting down to business, some humorous bits about why many Greek letters were jumped over to get to Omicron.

Leave a Reply