Good morning, omicron!


We’ve got the omicron variant in Minnesota.

Minnesota has the second confirmed case of omicron COVID-19 variant in the United States, after California announced the nation’s first confirmed case on Wednesday. The Minnesota resident tested positive for COVID-19 on Nov. 24, shortly after attending an anime convention at the Javits Center.

The Minnesota Department of Health says they confirmed the presence of the omicron variant Wednesday afternoon. They say the man, who lives in Hennepin County, is quarantining at home. He experienced mild symptoms and is recovering. The man “most likely” contracted the variant in New York, authorities said.

This is not grounds for panic. We don’t know enough about the omicron variant to get too worked up about it — it may be a bit nastier than the delta variant, but if you’ve been vaccinated, it’s probably not going to affect you directly. Of course, that’s only the case if you’re some kind of weird Libertarian hermit with no friends who has retreated from society. The rest of us should be concerned about our unvaccinated (for any reason) loved ones, or other contributing members of our communities.

What does worry me is that this is a symptom of our lackadaisical approach to dealing with a worldwide pandemic. It’s like our health care system is an old car that we maintain poorly — sure, there’s some rust on the body, and the muffler is held in place with a twist of wire, and the engine makes a funny noise when it first turns over in the morning, but it would cost money to patch it up, and it still runs, so we can ignore it for a few more months or years. So what if it just now started leaking oil? It’s fine.

New variants are what you get when you let the virus run rampant in large segments of the population, when you slack off on basic preventive measures, and when you figure I’ve got mine, so what if there isn’t enough vaccine in India or Bulgaria or whatever — that’s not our problem. Until it is.

Comments

  1. ajbjasus says

    Yup, we need to be alert, but early signs are that the symptoms are relatively mild, but that might be a sign that the vaccination program is helping. It might even be good news if that is true and it becomes the dominant strain.

    The places it is popping up suggest it might have been around for some time.

  2. strangerinastrangeland says

    Seven omicron cases so far here in Iceland, all linked, but also so far unknown how the variant came into the country as none of those people traveled abroad recently. Luckily, only mild symptoms for all of them. Wouldn’t it be nice if omicron would outpace delta but only show mild symptoms as a rule? :-)

    But in related news: A new statistics was published today from the National Hospital in Iceland, showing the incidence per 100.000 people for hospitalizations due to Covid. Fully vaccinated with booster: 0,5; fully vaccinated without booster: 5,9; unvaccinated: 34. Any question left about the usefulness of vaccinations against Covid? No? Get the shots!

  3. hemidactylus says

    I think it’s way too early to lean in any direction on this variant. What do all the mutations actually mean for tradeoffs of transmissibility, escape, and disease severity??? They are at the amino acid level, but is there some neutrality or more adaptive to some end?

    In this TWiV video toward the end one of them speculates on the eventuality (if I understand correctly) of SARS-CoV-2 getting normalized into a sort of seasonal HCoV thing where the virus becomes its own booster:
    https://youtu.be/9RX5gQltqBw

    Maybe an eventuality??? Too optimistic. Not quite the same as Campbell’s optimism here where after stating seeming inevitability that we all get exposed to this variant, the best case is it’s mild, ends the pandemic, and rides into the sunset “Shane! Shane! Come back!”
    https://youtu.be/Ls7zy6_0Z2s
    Wishful thinking? I think we are all hoping for good news, but is apparent mildness a result of age groups in South Africa so far and lack of time of analysis?

    This preliminary video seemed to be the best I’ve seen overall:
    https://youtu.be/LKT7fGL_Uh0

    Is his analysis of mutations across variants accurate numberwise? Will T-cell immunity be sufficient fall back in case of immune escape?

    Aside from early runaway speculation and understandable panic how did this thing take such an apparent evolutionary leap? Undetected mundane evolution due to incomplete sequencing data across the world? Rapid evolution in an immune compromised person? Spill back from animals (eg- deer we heard about in news)?

  4. robro says

    As my wife said days ago, and as Dr. Fauci confirmed later that day, “It’s everywhere.” The first confirmed and reported US case was just a couple of days ago here in San Francisco. Now we just wait to see how lethal it is.

    My worry is what else is already out there and undetected so far, but soon to be everywhere if not already.

    And, when we get to the Omega variant will the religious fanatics who refuse to accept reality and vaccinations vanish from the face of the earth forever? Yeah!

    In other hopeful news, the Pfizer and Merck pills are coming with the promise to reduce serious illness, overtasking the health care system, and increasing deaths for all things.

  5. raven says

    Yup, we need to be alert, but early signs are that the symptoms are relatively mild,…

    No.
    We don’t know that.

    This was based on an off hand comment by a GP in South Africa dealing with a small subset of young and mostly partially or fully vaccinated people.
    It’s wishful thinking and we all know how well that has worked in this pandemic.

    The Omicron variant is potentially dangerous and we all want answers and as soon as possible. So far, everything has been speculation based on more or less no data.
    We will know a lot more in 2 or 3 weeks.
    If it can’t outcompete Delta, it may not be of any importance.
    Or in a few months, it may be the dominant variant and Delta will be history.

  6. raven says

    It’s unlikely that Delta will be the last variant of this pandemic.
    Why should it be anyway?
    When WHO adopted the Greek letter naming system, I wondered what they were going to do when we run out of Greek letters. Start on the Hebrew and Hindu alphabets I guess.

    So when will this pandemic be over with?
    I have no idea.
    Neither does anyone else right now.

    One epidemiologist made a guess that it will be when the Covid-19 virus has explored and exhausted its entire evolutionary potential.
    That sounds plausible but it is not very useful.
    We have no idea what the entire evolutionary potential of this virus is and we have no idea how to determine when that has happened. Assuming it ever happens.

  7. raven says

    One effect of this pandemic has been noted but not really emphasized. When the hospitals and ICUs are full of Covid-19 virus patients, they crowd out all other patients seeking care.
    The numbers are high, 80,000 extra patients dying every two weeks.

    The local hospital sent everyone an email months ago, saying their ICU was full of Covid-19 virus patients and not to get sick because you might not get treated. This was useful since everyone plans their serious medical events out in advance.
    FWIW, the ICU is still full and it is 100% unvaccinated patients.

    The reasons are somewhat known.
    “The study authors noted that emergency department crowding, high ICU occupancy, and ambulance diversion were reported to lead to poor patient outcomes (eg, medical errors, low quality of care, treatment delays, increased deaths) even before the pandemic.”
    It’s also a lack of rehab/physical therapy programs. Patients recovering from prolonged hospitalization, ventilators/ECMOs, cardiac events, injuries, etc.. need and can benefit greatly from these programs and services. When Covid-19 virus infections are high, these are curtailed or stopped as being elective and hazardous.

    Full ICUs amid COVID surges could lead to thousands of extra deaths
    Mary Van Beusekom | News Writer | CIDRAP News | Nov 19, 2021 Edited for length

    A modeling study today in Morbidity and Mortality Weekly Report estimates that 12,000 more people die 2 weeks after US hospitals reach 75% adult intensive care unit (ICU) occupancy amid COVID-19 pandemic surges, a figure that rises to 80,000 when ICUs are full—which is the case now in many hospitals in multiple US states.

    Researchers from the US Department of Homeland Security’s Cybersecurity & Infrastructure Security Agency COVID Task Force evaluated the relationship between overwhelmed hospitals and excess deaths from Jul 4, 2020, to Jul 10, 2021. The end of the study period included the emergence and eventual dominance of the more transmissible Delta (B1617.2) variant.

    The Centers for Disease Control and Prevention (CDC) provided data on excess all-cause deaths, and the Department of Health and Human Services (HHS) provided hospitalization data. Excess deaths were estimated as the difference between observed and expected deaths over specific periods.

    Effects felt up to 6 weeks later
    Over the study period, excess deaths rose as ICU bed occupancy increased 2, 4, and 6 weeks after surges. A model based on data on all-cause excess deaths predicted that 75% ICU bed occupancy was tied to another 12,000 deaths (95% confidence interval [CI], 8,623 to 17,294) 2 weeks later, with more deaths at 4 and 6 weeks.

    When all ICU beds nationwide are full, 80,000 excess deaths can be expected (95% CI, 53,576 to 132,765).

    The study authors noted that emergency department crowding, high ICU occupancy, and ambulance diversion were reported to lead to poor patient outcomes (eg, medical errors, low quality of care, treatment delays, increased deaths) even before the pandemic.

    “Racial and ethnic subgroups experienced disproportionately higher percentage increases in deaths, with the most pronounced effect among the Hispanic/Latino communities who represent an estimated 21% of the essential critical infrastructure workforce.”

    While COVID-19–driven ICU bed occupancy is not a direct cause of excess deaths, the researchers said it indicates “broader issues that can contribute to excess deaths, such as curtailed services, stressed operations, and public reluctance to seek services.” They call for research assessing the cascading effects of pandemic-related healthcare system dysfunction.

  8. festersixohsixonethree says

    Discussion with friends during lunch yesterday yielded a hypothetical consensus: Let the unvaccinated be put into internment camps, or a situation like a WWII Ghettos. Let the pestilence burn itself out among them and then raze the ghetto and put up a plaque commemorating the horror. Of course that won’t happen in a civilized world, but it would solve the “problem”.

  9. says

    I know several people who caught Delta.
    They were all vaccinated. As am I.
    They had mild to acute symptoms for a week and recovered quickly.
    Omicron doesn’t scare me, but I’m still getting my booster ASAP.

  10. raven says

    I know several people who caught Delta.

    I know one who caught Delta and recently.
    He is now dead from it.
    He was unvaccinated and had decided the pandemic was over with so he didn’t need to bother with masks or avoiding crowds.
    His wife was vaccinated and never got sick.

  11. anthrosciguy says

    In my life I’ve hung around with a lot of good mechanics. Mechanics like that famously have one of two types of cars: super well rebuilt/maintained to better than new condition, or barely held together with duct tape and tinkering. In the USA we could have the former for our country but choose to have the latter.

  12. wzrd1 says

    So far, all cases reported have been mild symptoms to no symptoms in vaccinated persons, no reports on how the unvaccinated fare. Alas, those observation suffer from selection biases and small sample size enough to be nearly worthless.
    Still, a properly successful pathogen would generate significant symptoms, but happily spread amongst its targets with minimal impact and allowing much wider spread.

  13. davidc1 says

    Don’t know much about science ,but as this poem says ,

    “Great fleas have little fleas upon their backs to bite ’em,
    And little fleas have lesser fleas, and so ad infinitum.
    And the great fleas themselves, in turn, have greater fleas to go on;
    While these again have greater still, and greater still, and so on.[2]” .

    Is there anyway the boffins could come up with a virus that would kill off the
    Covid- 19 variants before they get a chance to infect us hoomans ?

    Sorry if that sounds like something The Snatch Snatcher would come out with.

  14. hemidactylus says

    @15- davidc1

    There are virophages that parasitize other viruses in a weird way, but SARS-CoV-2 isn’t on their menu:
    https://en.m.wikipedia.org/wiki/Virophage

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5127031/

    “Virophages replicate with giant viruses in the same eukaryotic cells. They are a major component of the specific mobilome of mimiviruses. Since their discovery in 2008, five other representatives have been isolated, 18 new genomes have been described, two of which being nearly completely sequenced, and they have been classified in a new viral family, Lavidaviridae. Virophages are small viruses with approximately 35–74 nm large icosahedral capsids and 17–29 kbp large double-stranded DNA genomes with 16–34 genes, among which a very small set is shared with giant viruses. Virophages have been isolated or detected in various locations and in a broad range of habitats worldwide, including the deep ocean and inland. Humans, therefore, could be commonly exposed to virophages, although currently limited evidence exists of their presence in humans based on serology and metagenomics. The distribution of virophages, the consequences of their infection and the interactions with their giant viral hosts within eukaryotic cells deserve further research.”

    https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1007592

  15. unclefrogy says

    @9

    Of course that won’t happen in a civilized world, but it would solve the “problem”.

    as “nice” as that would be or just letting those deniers get sick and die where ever they are I am afraid it probably would not work out like that.
    since we really do not know that much about this virus yet either in humans or how it functions in its bat host. It is my understanding is that it does not have much of an effect on the bats due to how their immune systems functions. Could it be that this virus has the tendency to mutate to a form that does not harm the host very much?
    also just what does this “its entire evolutionary potential.” mean? since all life has evolved from “lesser” previous forms into all other forms both more complicated and less complicated and shows no sign of stopping example this very virus.

  16. raven says

    …also just what does this “its entire evolutionary potential.” mean? since all life has evolved from “lesser” previous forms into all other forms both more complicated and less complicated and shows no sign of stopping example this very virus.

    Good question.
    Who knows?

    There is such a thing as stabilizing selection.
    When an organism is well adapted to its ecological niche, there isn’t much pressure to change much.

    Stabilizing selection is a type of natural selection in which the population mean stabilizes on a particular non-extreme trait value. This is thought to be the most common mechanism of action for natural selection because most traits do not appear to change drastically over time. Wikipedia

    At some point, SARS-Cov-2 may enter the period of neutral drift. Some biologists think most lineages spend a lot of time in this phase.
    The usual picture is a cloud of genomes sitting on an adaptive peak on the fitness landscape. It can be a long way to the next fitness peak and not easy to get there.

    Some of the pathogens that infect humans, plants, and animals haven’t changed all that much that we know about.
    TB, malaria, Diptheria, Rabies, RSV, Hepatitis A, B, C etc.. all seem about the same as long as we’ve known them.
    Others such as wheat and corn pathogens seem to change all the time to evade our breeding of resistance and use of fungicides.

  17. brightmoon says

    Saw the title and the first thing that pops into my head is “ Good Morning,Heartache” sung by IIRC Diana Ross

  18. davidc1 says

    @16 I had forgotten about them .I saw a BBC programme years ago ,about scientists in Russia collecting samples of
    sewage to harvest them ,or something .

  19. brightmoon says

    Dealing with an antivaxxer neighbor now who I’ve been “screeching” at for the past year . Elderly with chronic health problems and she’s lucky that she’s mainly a housebound homebody. I’m dreading it if she gets Covid as I really like my neighbor. Oddly enough she hated tRump but she believes all the antivaxxer bs.

  20. chrislawson says

    The US is much more shortsighted than not caring what happens in Bulgaria. It doesn’t even care what happens inside its own borders if it’s the marginalised getting hit first. Case in point: one of the driving forces behind the spread of MDR-TB (multi-drug-resistant tuberculosis) and XDR-TB (extensively drug-resistant TB), now a major global health disaster, has been the US locking up undocumented immigrants in insanely crowded prisons with poor facilities and little access to healthcare. From there it spread to prison staff and non-immigrant prisoners who were eventually released once their sentences were complete, and to the immigrants who were eventually deemed legal, and to the immigrants who were deported but got back in later…and from there into the wider community. This has been documented and raised by public health specialists for more than a decade, but you know how much Americans like to listen to them when they could be whipping up a xenophobic frenzy instead.

  21. cvoinescu says

    Bulgaria and Romania, and to a lesser extent the other Eastern European countries, suffer from a surfeit of antivaxxers, not a lack of vaccine.

  22. epawtows says

    Re: #9: If anyone in government even remotely had the authority to round up unvaxxed people and put them in camps (which nobody does) it would make much, MUCH more sense to use a lesser version of that same authority to round them up and force-vaccinate them. Which is also something nobody has the authority to do.

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