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(NPR)   Scientists think the Omicron variant of COVID-19 evolved all its mutations in one very diseased person with a weak immune system. Mom?   (npr.org) divider line
    More: Interesting, Immune system, HIV, Africa, discovery of the omicron variant of the coronavirus, Trevor Bedford, Richard Lessells, virus's genome, Evolution  
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510 clicks; posted to STEM » on 06 Dec 2021 at 9:37 PM (7 weeks ago)   |   Favorite    |   share:  Share on Twitter share via Email Share on Facebook



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2021-12-06 10:48:15 PM  
Omicron split off from its nearest genetic relative August/September of 2020. That split off from the rest in February of 2020. Wherever it came from it's been percolating a long time.
 
2021-12-06 10:49:02 PM  
 
2021-12-06 10:53:15 PM  
Mr. Burns is Indestructible
Youtube aI0euMFAWF8
 
2021-12-06 11:21:17 PM  
Too many cases of untreated HIV in South Africa. Article says this is the most likely place omicron mutated in an immunodeficient person.
 
2021-12-06 11:34:56 PM  

Mr. Eugenides: Omicron split off from its nearest genetic relative August/September of 2020. That split off from the rest in February of 2020. Wherever it came from it's been percolating a long time.


This definitely lends credence to the idea that some patients may obtain permanent infections from OG Wuhan. We were definitely discussing this at the time, scraping through SARS-1 research papers showing the same. I've hypothesized for a while about how the mechanics of this would work, but I've always come back to the point that as far as we know it is only transmissible at a distance while it is in your respiratory tract. When it burns down to the lungs and cannot sustain infection of respiratory tract lining it is no longer transmissible through the air, although I suspect that blood-borne infection is a vector.

The animal hypothesis makes sense here to act as a reservoir that never allows the clade to fade into the background, but TFA insists that is not the case. Is there a primate vector component? Can you differentiate the sequence from homo sapiens?

Likewise, the cryptic spread hypothesis would be highly unlikely for the reasons given; it's just too transmissible to not notice, and the population that would have incubated this strain should, theoretically, have acquired resistance/immunity. Could this be detected in a region with abnormally low omicron spread? Is natural resistance to omicron even possible in humans?

Immunosuppressed patient zero: We saw this in alpha, but we caught it fairly quickly because it was highly adapted for spread over the original strain, as well as it occurred in a first world country with good genomic surveillance. It could be possible for the same to occur again, why not? But the history suggests that both alpha patient zero and omicron patient zero caught the same strain likely around the same time. It is well known that immunocompromised patients are infectious for extended periods of time, is it really possible for someone to be so infectious for so long without anyone noticing? Homeless transient, perhaps? Probably rural?

TFA leaves off with that same question: how did this go under the radar for so long without spilling over before now? If we knew more about patient zero and how their underlying medical diagnosis has progressed or collapsed within the last few months it would be enlightening. I would suspect that perhaps HIV going into AIDS would be the right catalyst. Makes sense, right? Train it up with a bum immune system and then it stops working entirely which goes into full-blown infectious covid disease.

But that brings up the question I had earlier; assume that covid disease progresses normally, the patient loses infectiousness at some point, even if it's still raging in the bloodstream and throughout the rest of the body. But you aren't infectious by typical means, because it's not in your respiratory tract. This line of reasoning makes me wonder if it is possible for a blood-borne infection to retransmit through the blood in the lungs? Is it? Because if it is, then we were right all along about this possibility, and it's quite a fearsome prospect to consider about the pandemic going forward.

We shall see in the next few months how this plays out, but seeing how the symptoms progress it seems as though it is diffusing directly through mucosal membranes and into the bloodstream. (Pretty sure OG Wuhan did this.) If this is true that it is pre-alpha, then it shouldn't have much in the way of lateral transmission functions like filopodia we see in delta, and would suggest the transmissibility of omicron is an original strain upgrade for better cellular binding and not too much replication, and other alpha/delta-specific spread mechanics remain undiscovered or unviable.

Assuming that, because of the lack of lateral transmission mechanics and absurd replication of delta it would make sense that this strain does not pose a particularly bad prognosis for lung damage, no worse than the original strain anyway. This may also be facilitated further if the innate immune response is to flood infected sites with mucous, coating the viral particles and inhibiting aerosol spread. Without filopodia, infectious spread is diminished greatly and it more resembles a cold-like illness. Unlikely for naive infection, but a likely response to prior infection.

This is probably the most trivial and overlooked symptom, but I've consistently maintained it's been by far the most important factor for aerosol and dry particulant spread.
 
2021-12-06 11:57:38 PM  
Come on, omicron! You couldn't kill that one weak-ass person after all this time? You're weak! You're a weak-ass variant. And that's all you'll ever be.
 
2021-12-07 8:29:37 AM  

Stibium: This definitely lends credence to the idea that some patients may obtain permanent infections from OG Wuhan.


This thought has been in my head for a while. What if we end up with some Typhoid Marys walking around, permanently incubating and spreading new strains of COVID? How do we effectively deal with that?
 
2021-12-07 10:06:34 AM  

mrmopar5287: Stibium: This definitely lends credence to the idea that some patients may obtain permanent infections from OG Wuhan.

This thought has been in my head for a while. What if we end up with some Typhoid Marys walking around, permanently incubating and spreading new strains of COVID? How do we effectively deal with that?


Have them all wear red hats so we can easily identify them?
 
2021-12-07 11:05:29 AM  

Stibium: ...

TFA leaves off with that same question: how did this go under the radar for so long without spilling over before now? If we knew more about patient zero and how their underlying medical diagnosis has progressed or collapsed within the last few months it would be enlightening. I would suspect that perhaps HIV going into AIDS would be the right catalyst. Makes sense, right? Train it up with a bum immune system and then it stops working entirely which goes into full-blown infectious covid disease.

But that brings up the question I had earlier; assume that covid disease progresses normally, the patient loses infectiousness at some point, even if it's still raging in the bloodstream and throughout the rest of the body. But you aren't infectious by typical means, because it's not in your respiratory tract. This line of reasoning makes me wonder if it is possible for a blood-borne infection to retransmit through the blood in the lungs? Is it? Because if it is, then we were right all along about this possibility, and it's quite a fearsome prospect to consider about the pandemic going forward.

...


I think your HIV/AIDS scenario is possible, but a few more just spitballing ideas (I'm only trained in first aid, not virology):

There were some early cases where a patient left the hospital (tested negative), and then seemed to have a flare up, as they couldn't trace them to a re-infection event.  If you get a case where it hides in the lungs deep enough that a nasal swab can't detect it, could a new respiratory infection leading to coughing cause it to become infectious again?  (If so, could this be checked via stool samples to identify the 'hidden' Covid reservoirs?)

South Africa is in the Southern Hemisphere, so they're in spring, not autumn.  Could an individual (or small group) have hunkered down for the winter, remained asymptomatic (or a mild case that they survived), and only spread the disease once things warmed back up and they resumed contact with other groups?

In a similar vein, what if patient zero wasn't a human?  Are there any critters that can catch Covid that hibernate?
 
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