The Omicron Variant: COVID or Common Cold?

 
Genetic relationship between SARS-Cov-2 variants.

Omicron variant and other major or previous variants of concern of SARS-CoV-2 depicted in a tree scaled radially by genetic distance, derived from Nextstrain on 1 December 2021 (Wikipedia)

Now that the full sequence of Omicron has become known it’s remarkable to see how different Omicron is from all the other SARS-CoV-2 variants. It did not arise as a simple mutation of the others, it’s different in several ways. It has 60 RNA mutations causing 36 amino acid changes, several in the all-important spike protein. In a radial graph of genetic distance Omicron forms its own group way off to the side of the other variants (see diagram).

This is reflected in the fact that Omicron is very different in the way it affects humans.  It grows 70 times faster than Delta and is more infectious than Delta but it is less likely to cause death.  Officials have been reluctant to acknowledge that Omicron is milder, but huge increases in infection rates have resulted in very small increases in the death rate in the latest wave.  It’s more like the common cold than other SARS-CoV-2 causing a runny nose, sore throat, and a fever.  It acts like the common cold, blitzing through an office or classroom just like a cold strain does —  causing typical cold-like symptoms.

So it strikes me that Omicron might not be a true SARS-CoV-2 variant at all.  Perhaps it arose from one of the many other coronaviruses out there.  We know that several coronavirus are recognized as causes of the common cold, of which there are hundreds, most of which are rhinovirus variants.  Not to get too deep into the weeds, but some of these cold-producing coronavirus variants bind to ACE receptors like SARS-CoV-2, and some bind to other things.  All of these viruses cause the cold syndrome and are only very rarely deadly toward immunocompromised people.

But Omicron still shares some features of the original SARS-CoV-2 strains, so it shows up in the PCR and antigen detection systems — it’s recognized as a cause of COVID and officials are treating it that way even though it’s not causing typical COVID.

The difference is important.  We can’t be shutting down and killing the economy every time another coronavirus comes along if it just causes a common cold.  Some common sense needs to be employed in implementing public policy.

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  1. WiesbadenJake Coolidge
    WiesbadenJake
    @WiesbadenJake

    Interesting; I tested positive for Covid last week. I became quite ill for the first several days–it did not feel like any of the colds I have had in 65 years visiting this planet. Medical providers told me it is assumed that I have the omicron variant as approx. 90% of cases in our area are omicron (tested by sending large batches of samples to the CDC–they cannot test for the specific variant locally). If what I had was omicron, it was much worse than what I would have anticipated based on news reports regarding its effect compared to delta or other variants. I was vaccinated with 2 boosters prior to getting sick; I am hopeful there will be some natural immunity benefit as a result of this experience.

    • #1
  2. Locke On Member
    Locke On
    @LockeOn

    What’s missing in that diagram is the variant strains leading up to Omicron.  It didn’t just wake up one day with 60 mutations all at once.  It appeared in Africa, where there is little or no effective public health structure or genetic monitoring in many places.  A number of intermediate strains were likely missed before Omicron got to South Africa, which does have some degree of effective monitoring.

    Short form:  Missing data.

    • #2
  3. DonG (CAGW is a hoax) Coolidge
    DonG (CAGW is a hoax)
    @DonG

    Roderic: In a radial graph of genetic distance Omicron forms it’s own group way off to the side of the other variants (see diagram).  

    I don’t understand what the radial axis represents.  I suspect it is meaningless.   The NextStrain folks have better images on their site:  https://nextstrain.org/ncov/gisaid/global

    This is more clear to me.  Omicron is tightly cluster (so far) and has a similar number of variants as Delta.

    • #3
  4. MarciN Member
    MarciN
    @MarciN

    I read somewhere a week ago that there is also some sort of bad cold circulating in the Boston area as well. It is January, after all. :-) One doctor was quoted as saying something to the effect of, “It’s just a normal cold. Just stay home, drink lots of fluids, get lots of rest. You’ll get better.” :-)

    Made me think of the doctor in Africa who told the press one day years ago, “We do have health issues other than AIDS.” :-)

    The most recent Boston sewage study gives cause for some optimism:

    The levels of COVID-19 in the Boston area appear to be dropping from historic highs, according to the latest update from its sewer system.

    New data unveiled Tuesday showed the level of COVID dropping back down to where it was on Dec. 30. While that’s only two weeks ago, and still higher than any point before this winter, it’s still down nearly half from peak levels and could indicate that the current surge is subsiding.

    The Massachusetts Water Resources Authority’s tracking system, run by Cambridge-based Biobot, works by analyzing bits of genetic material in the Boston area’s sewers to indicate how much of the virus is circulating in the community.

    As of Tuesday, when data was available through Jan. 11, COVID levels were averaging about 6,000 RNA copies of COVID per milliliter and trending down from a peak near 10,000.

    Other than tracking sewage, I think a good tracker would be a 24-hour picture of Amazon orders. People make online purchases they they are bored and stuck at home. :-)

    • #4
  5. Susan Quinn Contributor
    Susan Quinn
    @SusanQuinn

    WiesbadenJake (View Comment):

    Interesting; I tested positive for Covid last week. I became quite ill for the first several days–it did not feel like any of the colds I have had in 65 years visiting this planet. Medical providers told me it is assumed that I have the omicron variant as approx. 90% of cases in our area are omicron (tested by sending large batches of samples to the CDC–they cannot test for the specific variant locally). If what I had was omicron, it was much worse than what I would have anticipated based on news reports regarding its effect compared to delta or other variants. I was vaccinated with 2 boosters prior to getting sick; I am hopeful there will be some natural immunity benefit as a result of this experience.

    Jake, forgive me for “playing doctor,” but isn’t your immune system being challenged at this time? Also, any co-morbidities?

    • #5
  6. Hammer, The (Ryan M) Member
    Hammer, The (Ryan M)
    @RyanM

    Roderic: The difference is important.  We can’t be shutting down and killing the economy every time another coronavirus comes along if it just causes a common cold.  Some common sense needs to be employed in implementing public policy.  

    This is true whether it is derived from sars-cov2 or not.  Regardless of where it came from, it has supplanted covid.  Democrats and your public health officials want to maintain the covid-hysteria status quo regardless of the illness.  They will next argue (some already have) that we should keep doing all of this for flu and the actual common cold.  We will not get our freedoms back until we refuse to go along with these would-be tyrants.  They should all be pushed from office and held to account – state and federal legislatures should be taking steps to ensure that these power grabs cannot happen again.  Unfortunately, I live in WA state, where that sort of action is off the table.  But fortunately, I live in a part of the state that has less regard for Jay Inslee than for a mosquito, and we treat him accordingly.

    • #6
  7. OldPhil Coolidge
    OldPhil
    @OldPhil

    WiesbadenJake (View Comment):
    I tested positive for Covid last week.

    Same here. A sore throat & lots of mucus for two days, then a headache and stuffed sinuses for two, then gone. Pretty much a 4-day cold.

    • #7
  8. WiesbadenJake Coolidge
    WiesbadenJake
    @WiesbadenJake

    Susan Quinn (View Comment):

    WiesbadenJake (View Comment):

    Interesting; I tested positive for Covid last week. I became quite ill for the first several days–it did not feel like any of the colds I have had in 65 years visiting this planet. Medical providers told me it is assumed that I have the omicron variant as approx. 90% of cases in our area are omicron (tested by sending large batches of samples to the CDC–they cannot test for the specific variant locally). If what I had was omicron, it was much worse than what I would have anticipated based on news reports regarding its effect compared to delta or other variants. I was vaccinated with 2 boosters prior to getting sick; I am hopeful there will be some natural immunity benefit as a result of this experience.

    Jake, forgive me for “playing doctor,” but isn’t your immune system being challenged at this time? Also, any co-morbidities?

    Susan, the daily chemo pill I am on is known to somewhat diminish immune response, though not to the degree of traditional infusion chemo drugs. The only comorbidity I have is the Stage 4 lung cancer (I say that somewhat sheepishly). I always prided myself on being able to tell medical providers that I was on no medications; the nurses would always tell me I was one of the few people in my age group living drug-free. Cancer has brought low that sense of pride. I have had colds and flu while on this med; did not feel the same to me as my recent Covid experience. I had several days of that sense of impending doom I had not felt since infusion chemo. Susan, I respect your judgment–life experience is the greatest teacher.

    • #8
  9. Susan Quinn Contributor
    Susan Quinn
    @SusanQuinn

    WiesbadenJake (View Comment):

    Susan Quinn (View Comment):

    WiesbadenJake (View Comment):

    Interesting; I tested positive for Covid last week. I became quite ill for the first several days–it did not feel like any of the colds I have had in 65 years visiting this planet. Medical providers told me it is assumed that I have the omicron variant as approx. 90% of cases in our area are omicron (tested by sending large batches of samples to the CDC–they cannot test for the specific variant locally). If what I had was omicron, it was much worse than what I would have anticipated based on news reports regarding its effect compared to delta or other variants. I was vaccinated with 2 boosters prior to getting sick; I am hopeful there will be some natural immunity benefit as a result of this experience.

    Jake, forgive me for “playing doctor,” but isn’t your immune system being challenged at this time? Also, any co-morbidities?

    Susan, the daily chemo pill I am on is known to somewhat diminish immune response, though not to the degree of traditional infusion chemo drugs. The only comorbidity I have is the Stage 4 lung cancer (I say that somewhat sheepishly). I always prided myself on being able to tell medical providers that I was on no medications; the nurses would always tell me I was one of the few people in my age group living drug-free. Cancer has brought low that sense of pride. I have had colds and flu while on this med; did not feel the same to me as my recent Covid experience. I had several days of that sense of impending doom I had not felt since infusion chemo. Susan, I respect your judgment–life experience is the greatest teacher.

    Stay strong!

    • #9
  10. DrewInWisconsin, Oaf Member
    DrewInWisconsin, Oaf
    @DrewInWisconsin

    Locke On (View Comment):
    What’s missing in that diagram is the variant strains leading up to Omicron.  It didn’t just wake up one day with 60 mutations all at once.

    From what I’ve read, it did just that. Which boggles scientists. It appears to be a variant of the long-gone original version of the virus, rather than an evolution from the intermediate strains.

    Some to believe this indicates that it is, in fact, an engineered variant. That it is a variant of the original that sat in a lab in South Africa for awhile, while scientists tinkered with it to create a variant that could bypass vaccines (which it does), and it either escaped much like the original variant, or was deliberately released again, and perhaps we’re just lucky that it’s not severe.

    • #10
  11. Hammer, The (Ryan M) Member
    Hammer, The (Ryan M)
    @RyanM

    DrewInWisconsin, Oaf (View Comment):

    Locke On (View Comment):
    What’s missing in that diagram is the variant strains leading up to Omicron. It didn’t just wake up one day with 60 mutations all at once.

    From what I’ve read, it did just that. Which boggles scientists. It appears to be a variant of the long-gone original version of the virus, rather than an evolution from the intermediate strains.

    Some to believe this indicates that it is, in fact, an engineered variant. That it is a variant of the original that sat in a lab in South Africa for awhile, while scientists tinkered with it to create a variant that could bypass vaccines (which it does), and it either escaped much like the original variant, or was deliberately released again, and perhaps we’re just lucky that it’s not severe.

    Or maybe some genius released the common cold variant to end this idiotic pandemic.  😉

    • #11
  12. Hans Gruber Pfizer President Inactive
    Hans Gruber Pfizer President
    @Pseudodionysius

    Hammer, The (Ryan M) (View Comment):

    DrewInWisconsin, Oaf (View Comment):

    Locke On (View Comment):
    What’s missing in that diagram is the variant strains leading up to Omicron. It didn’t just wake up one day with 60 mutations all at once.

    From what I’ve read, it did just that. Which boggles scientists. It appears to be a variant of the long-gone original version of the virus, rather than an evolution from the intermediate strains.

    Some to believe this indicates that it is, in fact, an engineered variant. That it is a variant of the original that sat in a lab in South Africa for awhile, while scientists tinkered with it to create a variant that could bypass vaccines (which it does), and it either escaped much like the original variant, or was deliberately released again, and perhaps we’re just lucky that it’s not severe.

    Or maybe some genius released the common cold variant to end this idiotic pandemic. 😉

    Wile E. Coyote, Genius. 

    • #12
  13. Old Bathos Moderator
    Old Bathos
    @OldBathos

    No policy interventions did any good.
    We seemed to do testing just to generate numbers of “cases”.
    We were not allowed to tailor policies to the stark difference in vulnerabilities by age and specific health conditions.
    We were put on a policy path to eliminate COVID which was always infeasible.
    Instead of celebrating the benefits the vaccines do provide we got caught up in absurd claims of full immunity and unlawful, divisive mandates.

    So how do we not back down from a bad cold without admitting that the sum of last two years was an health “expert” iatrogenic disaster on a global scale? Aren’t we required to mask up, close down, get that fourth booster and test as many as often as possible forever? What is the exit ramp?

    • #13
  14. James Salerno Inactive
    James Salerno
    @JamesSalerno

    Common cold. Time to get on with life.

    • #14
  15. Hammer, The (Ryan M) Member
    Hammer, The (Ryan M)
    @RyanM

    James Salerno (View Comment):

    Common cold. Time to get on with life.

    One step ahead of you. Many of us got on with life 2 years ago. Just waiting for the rest of the country to wake up.

     

    • #15
  16. Doctor Robert Member
    Doctor Robert
    @DoctorRobert

    Locke On (View Comment):
    What’s missing in that diagram is the variant strains leading up to Omicron.  It didn’t just wake up one day with 60 mutations all at once.

    Perhaps it didn’t just wake up.  Perhaps it was invented.  The Wuhan Institute of Virology is still open, you know.

    • #16
  17. Headedwest Coolidge
    Headedwest
    @Headedwest

    DonG (CAGW is a hoax) (View Comment):

    Roderic: In a radial graph of genetic distance Omicron forms it’s own group way off to the side of the other variants (see diagram).

    I don’t understand what the radial axis represents. I suspect it is meaningless. The NextStrain folks have better images on their site: https://nextstrain.org/ncov/gisaid/global

    This is more clear to me. Omicron is tightly cluster (so far) and has a similar number of variants as Delta.

    How are those images better? They have zero value in terms of understanding the differences.

    • #17
  18. Henry Racette Member
    Henry Racette
    @HenryRacette

    Old Bathos (View Comment):
    What is the exit ramp?

    The exit ramp looks very much like a steady decline in Democratic polling numbers and the reluctant realization that the voting public’s willingness to suspend courage and common sense has been exhausted. It looks like that followed by a spike in mainstream news stories suggesting that it’s time we learned to live with the virus, that we’ve achieved herd immunity, that there’s a difference between dying of and dying with, etc.

    I think that’s the exit ramp, and I think we see it up ahead.

    • #18
  19. The Reticulator Member
    The Reticulator
    @TheReticulator

    DonG (CAGW is a hoax) (View Comment):

    Roderic: In a radial graph of genetic distance Omicron forms it’s own group way off to the side of the other variants (see diagram).

    I don’t understand what the radial axis represents. I suspect it is meaningless. The NextStrain folks have better images on their site: https://nextstrain.org/ncov/gisaid/global

    This is more clear to me. Omicron is tightly cluster (so far) and has a similar number of variants as Delta.

    Thanks. Going to the site is definitely more helpful. One thing I haven’t figured out, though, is how to pan right to left after zooming in on a clade in this rectangular tree format. Maybe it isn’t possible.

    • #19
  20. The Reticulator Member
    The Reticulator
    @TheReticulator

    Locke On (View Comment):

    What’s missing in that diagram is the variant strains leading up to Omicron. It didn’t just wake up one day with 60 mutations all at once. It appeared in Africa, where there is little or no effective public health structure or genetic monitoring in many places. A number of intermediate strains were likely missed before Omicron got to South Africa, which does have some degree of effective monitoring.

    Short form: Missing data.

    If you go to the website that DonG linked, you see that the tree doesn’t show it getting all 60 mutations at once.  But so far I haven’t figured out how to get it to show me when/where the biggest jump in mutations occurred.  Working on it. Maybe somebody else will figure it out before I do.

    I’ve also considered downloading the software so I don’t have to do it in a web browser, but I’m not sure I’m quite that interested.

    • #20
  21. The Reticulator Member
    The Reticulator
    @TheReticulator

    The Reticulator (View Comment):

    Locke On (View Comment):

    What’s missing in that diagram is the variant strains leading up to Omicron. It didn’t just wake up one day with 60 mutations all at once. It appeared in Africa, where there is little or no effective public health structure or genetic monitoring in many places. A number of intermediate strains were likely missed before Omicron got to South Africa, which does have some degree of effective monitoring.

    Short form: Missing data.

    If you go to the website that DonG linked, you see that the tree doesn’t show it getting all 60 mutations at once. But so far I haven’t figured out how to get it to show me when/where the biggest jump in mutations occurred. Working on it. Maybe somebody else will figure it out before I do.

    I’ve also considered downloading the software so I don’t have to do it in a web browser, but I’m not sure I’m quite that interested.

    It looks like the biggest jump is inferred to be back in May, when it went from 8 divergences to 33.  (I’m not sure if a divergence means a mutation. I haven’t found a glossary. Some people would object to the term mutation, anyway.)  But if I understand it correctly, that’s where the biggest jump of “missing data” occurred. Or started to occur.

    • #21
  22. The Reticulator Member
    The Reticulator
    @TheReticulator

    Roderic: So it strikes me that Omicron might not be a true SARS-CoV-2 variant at all. 

    It seems to be pretty clear that it diverged from the Gamma variant back in May or thereabouts. If somebody thinks I’ve interpreted the dendogram wrongly, I hope they speak up. (From what I’ve read on the site,  we’re supposed to take those particular date estimates with a grain of salt.)

    • #22
  23. Roderic Reagan
    Roderic
    @rhfabian

    Hammer, The (Ryan M) (View Comment):
    Democrats and your public health officials want to maintain the covid-hysteria status quo regardless of the illness.  They will next argue (some already have) that we should keep doing all of this for flu and the actual common cold.  We will not get our freedoms back until we refuse to go along with these would-be tyrants. 

    I don’t think that’s true.  As AOC went to Florida to be free of masks, so do other progressives dislike the restrictions they have imposed.  They advocate these policies because they think it’s the right thing to do and because it makes them feel superior to people who disagree.    No need to think too much about it when one’s feelings of superiority are at stake.

    • #23
  24. Roderic Reagan
    Roderic
    @rhfabian

    Old Bathos (View Comment):
    So how do we not back down from a bad cold without admitting that the sum of last two years was an health “expert” iatrogenic disaster on a global scale?

    A bureaucracy never considers anything it does to be a failure, but there may be some policy revisions as have already been taking place. 

    • #24
  25. Roderic Reagan
    Roderic
    @rhfabian

    DonG (CAGW is a hoax) (View Comment):

    Roderic: In a radial graph of genetic distance Omicron forms it’s own group way off to the side of the other variants (see diagram).

    I don’t understand what the radial axis represents. I suspect it is meaningless. The NextStrain folks have better images on their site: https://nextstrain.org/ncov/gisaid/global

    This is more clear to me. Omicron is tightly cluster (so far) and has a similar number of variants as Delta.

    If I read the diagram correctly, it means that Omicron did not descend from any of the other named SARS-CoV-2 variants but came from a strain that came before them.  This would explain why Omicron is so different from the others.

    • #25
  26. DrewInWisconsin, Oaf Member
    DrewInWisconsin, Oaf
    @DrewInWisconsin

    Roderic (View Comment):

    If I read the diagram correctly, it means that Omicron did not descend from any of the other named SARS-CoV-2 variants but came from a strain that came before them. This would explain why Omicron is so different from the others.

    But also quite different from the original.

    So . . . where did it come from?

    Some discussion of its origins from Substack land:

    https://igorchudov.substack.com/p/urgent-omicron-variant-likely-to

    https://eugyppius.substack.com/p/omicron-is-not-normal

    And the rabbit hole will open wide for you . . .

    • #26
  27. Doctor Robert Member
    Doctor Robert
    @DoctorRobert

    DrewInWisconsin, Oaf (View Comment):

    Roderic (View Comment):

    If I read the diagram correctly, it means that Omicron did not descend from any of the other named SARS-CoV-2 variants but came from a strain that came before them. This would explain why Omicron is so different from the others.

    But also quite different from the original.

    So . . . where did it come from?

    Some discussion of its origins from Substack land:

    https://igorchudov.substack.com/p/urgent-omicron-variant-likely-to

    https://eugyppius.substack.com/p/omicron-is-not-normal

    And the rabbit hole will open wide for you . . .

    Even rabbit holes can contain a hare of truth.  I have no doubt omicron was engineered.  Too many variations all at once.

    • #27
  28. The Reticulator Member
    The Reticulator
    @TheReticulator

    Doctor Robert (View Comment):

    DrewInWisconsin, Oaf (View Comment):

    Roderic (View Comment):

    If I read the diagram correctly, it means that Omicron did not descend from any of the other named SARS-CoV-2 variants but came from a strain that came before them. This would explain why Omicron is so different from the others.

    But also quite different from the original.

    So . . . where did it come from?

    Some discussion of its origins from Substack land:

    https://igorchudov.substack.com/p/urgent-omicron-variant-likely-to

    https://eugyppius.substack.com/p/omicron-is-not-normal

    And the rabbit hole will open wide for you . . .

    Even rabbit holes can contain a hare of truth. I have no doubt omicron was engineered. Too many variations all at once.

    Nice pun. But can you get quantitative and tell us your cutoff point for how many variations can occur within what period of time?  

    • #28
  29. Flicker Coolidge
    Flicker
    @Flicker

    The Reticulator (View Comment):

    Doctor Robert (View Comment):

    DrewInWisconsin, Oaf (View Comment):

    Roderic (View Comment):

    If I read the diagram correctly, it means that Omicron did not descend from any of the other named SARS-CoV-2 variants but came from a strain that came before them. This would explain why Omicron is so different from the others.

    But also quite different from the original.

    So . . . where did it come from?

    Some discussion of its origins from Substack land:

    https://igorchudov.substack.com/p/urgent-omicron-variant-likely-to

    https://eugyppius.substack.com/p/omicron-is-not-normal

    And the rabbit hole will open wide for you . . .

    Even rabbit holes can contain a hare of truth. I have no doubt omicron was engineered. Too many variations all at once.

    Nice pun. But can you get quantitative and tell us your cutoff point for how many variations can occur within what period of time?

    Did you read the articles?

    • #29
  30. Old Bathos Moderator
    Old Bathos
    @OldBathos

    Has Fauci funded any Chinese programs to infect Uighur subjects with whatever the boys in the lab in Wuhan have devised so the plasma can be harvested and reprocessed by Pfizer into a patented antiviral treatment? I have absolutely no evidence of this but nobody on that side is telling truth either so…

    • #30
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