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Medicine United States

US Confirms Nation's First Case of Omicron Covid Variant In California (cnbc.com) 116

An anonymous reader quotes a report from CNBC: U.S. health officials have confirmed the country's first case of the new, heavily mutated coronavirus variant called omicron in California, the Centers for Disease Control and Prevention said Wednesday. White House chief medical advisor Dr. Anthony Fauci said the individual, who was fully vaccinated, had just returned from traveling in South Africa to the San Francisco area on Nov. 22 and tested positive on Nov. 29.

"The individual is self quarantining and all close contacts have been contacted and all close contacts, thus far, have tested negative," he announced at a White House press briefing providing more details of the case. "We feel good that this patient not only had mild symptoms, but actually the symptoms appear to be improving." The CDC said genomic sequencing was initially conducted at the University of California, San Francisco and confirmed by the CDC as the omicron variant.
On Twitter, California Gov. Gavin Newsom said: "CA's large-scale testing and early detection systems have found the Omicron COVID-19 variant in California. We should assume that it's in other states as well. There's no reason to panic--but we should remain vigilant. That means get vaccinated. Get boosted. Wear a mask indoors."

Further reading: WHO Says Omicron Has Been Found in 23 Countries Across the World
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US Confirms Nation's First Case of Omicron Covid Variant In California

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  • ok (Score:3, Interesting)

    by phantomfive ( 622387 ) on Wednesday December 01, 2021 @03:44PM (#62037209) Journal

    Can we remove the travel ban from African countries now?

    • Re:Ok (Score:5, Interesting)

      by ranton ( 36917 ) on Wednesday December 01, 2021 @03:56PM (#62037255)

      We need to find something better than travel bans to combat situations like this. Limiting travel can be very useful in slowing the progression of new variants, but small targeted travel bans like this could arguably do more harm than good. Omicron most likely did not originate in the countries which first found it, they simply were the countries with the best variant identification systems in place. We certainly don't want to discourage such practices.

      Putting severe restrictions on all travel, such as no un-vaccinated passengers allowed (and even them being required to test), would be better than localized travel bans. I'm not sure what the best forms on restrictions would be, but I hope they find something better than these bans.

      • The best travel ban is a ban on all actual travel into the country, even the vaccinated. But I guess quarantines are too inconvenient, we'd rather people just die so you can go on vacation.
        • But I guess quarantines are too inconvenient,

          If people think what is taking place is a "quarantine", they should learn some history [imgur.com].*

          * Yes, I realize who we are talking about.

      • Putting severe restrictions on all travel, such as no un-vaccinated passengers allowed (and even them being required to test)...

        The first person identified with it is vaccinated, and you want to ban the unvaccinated from travel?

    • by crow ( 16139 )

      No. The purpose of the ban isn't to stop it from getting here, but to delay it becoming endemic so that we have more data on it when it does hit. We should also implement testing of travelers on arrival as well as departure. If we delay it a few weeks, that's a win.

  • by dmay34 ( 6770232 ) on Wednesday December 01, 2021 @03:53PM (#62037243)

    Does anyone know what percentage of tests in the US are sequenced? It can't be a lot.

    • by crow ( 16139 ) on Wednesday December 01, 2021 @04:23PM (#62037365) Homepage Journal

      My understanding is that we got lucky with Omicron, and it shows up differently in a standard PCR test. The report I saw said a PCR test shows three indicators, and with Omicron, only two show up, making it very obvious and easy to distinguish. Now this may have been for a particular PCR test; I don't know if this is true in general, or which PCR tests it applies to.

      But your question is important for tracking variants in general, and I don't have the answer.

      • by tlhIngan ( 30335 )

        My understanding is that we got lucky with Omicron, and it shows up differently in a standard PCR test. The report I saw said a PCR test shows three indicators, and with Omicron, only two show up, making it very obvious and easy to distinguish. Now this may have been for a particular PCR test; I don't know if this is true in general, or which PCR tests it applies to.

        But your question is important for tracking variants in general, and I don't have the answer.

        PCR tests are the gold standard because they basic

        • by Cyberax ( 705495 ) on Thursday December 02, 2021 @01:38AM (#62038451)

          PCR tests are the gold standard because they basically return the entire genetic sequence of the viral material.

          No, they do not. They return a "true/false" answer to the question: "does the material has a sequence that matches the supplied template (called "primer")". In this case we're lucky because one of the mutations happened to be in the location that was chosen for one of the primer sequences.

    • by timeOday ( 582209 ) on Wednesday December 01, 2021 @04:25PM (#62037379)
      "the U.S. is now sequencing more than 80,000 specimens of the virus each week, representing one out of every seven that test positive.

      One of the things about this variant is that there is a tell in laboratory tests, so you don't even have to do the full genetic sequencing," says Dr. David Kessler, chief science officer for the federal COVID-19 response. There's a kind of signature - called S gene target failure - that some tests can pick up. In those cases "there is an ability to do an early, quick analysis," Kessler adds, and then prioritize those tests for genetic sequencing. " https://www.npr.org/sections/h... [npr.org]

    • by houstonbofh ( 602064 ) on Wednesday December 01, 2021 @05:10PM (#62037573)
      We do a lot of sewage testing. That is cheaper and will cover larger regions with less testing, but does not identify individualizes.
  • The most successful variants are good at spreading. This one may act like it "should", ( Delta didn't seem to) and be more contagious but LESS dangrous.
    • I suppose if it kills you too quickly, it can't reproduce as easily.
    • by crow ( 16139 )

      That's only if being dangerous causes behavior that reduces spread. I'm under the impression that most of the spread with COVID is before one becomes terribly sick, so it doesn't matter how sick you get from a transmission standpoint.

      The good thing here is that Omicron doesn't descend from Delta, so it doesn't have all of those changes which made Delta worse. Of course, someone will get both, and they'll end up producing a new strain that's the worst of everything; this pandemic does not inspire optimism.

    • Re:Virus Behavior (Score:4, Insightful)

      by jeff4747 ( 256583 ) on Wednesday December 01, 2021 @04:39PM (#62037459)

      Eventually the most successful variants are more contagious and less dangerous. In the short run, there's nothing that requires the virus to mutate such that it's both less dangerous and more contagious. A very fatal and extremely contagious variant is just about as likely to arise as a 0% fatal and extremely contagious strain.

      We can't count on only less deadly mutations happening. Especially because the way those win the evolutionary race is the more deadly killing a lot of people.

      • Re:Virus Behavior (Score:5, Interesting)

        by mark-t ( 151149 ) <markt AT nerdflat DOT com> on Wednesday December 01, 2021 @08:24PM (#62038059) Journal
        All that is required for it to be highly contagious is to not give outward signs of infection for an extended period. The duration in which asymptomatic transmission is possible does not necessarily reflect how dangerous the virus can be once symptoms develop.
        • All that is required for it to be highly contagious is to not give outward signs of infection for an extended period.

          That's quite a big "all", given that under those circumstances it must be doing well enough that significant numbers of virions are present on the required surfaces of the host humans in order to spread. IOW all it has to do is utterly defeat our immune system.

          • by mark-t ( 151149 )
            Not really. As COVID itself has shown. It can as about as often as not give any of the typical social cues we ordinarily associate with a sick person while still being highly transmissable, and how little it might ultimately affect one person has no bearing on how little it will affect anyone else they transmit it to.
      • by Kaenneth ( 82978 )

        " and less dangerous. "

        I have my doubts on that; it could just be those most susceptible to death are removed from the host population, and those traits become rarer.

  • by dmay34 ( 6770232 ) on Wednesday December 01, 2021 @04:00PM (#62037275)

    The biggest mystery to me about Covid transmission is that the waves have a reliable 4-month peak-to-peak wavelength. This is true from the county level, the state level, the national level, all the way out to the global scale.

    I haven't seen any good explanation for why the global covid infection rate is showing itself to be so reliably circular.

    https://twitter.com/1DalM/stat... [twitter.com]

    • by Anonymous Coward
      It tends to peak in holidays (i.e. when there is lots of people movement) or during indoor weather seasons. generally those peaks will align pretty well with that.
      • by dmay34 ( 6770232 )

        Locally I can understand that, but I don't think the holidays argument works out well for the entire globe. Every nation and culture has it's own set of holidays. Just would expect daily infections to just look more like noise globally, not a nearly perfect sin wave.

      • by jabuzz ( 182671 )

        Actually in the UK school holidays seem to drive the case rate down. Schools go back and infection rates go up.

        Everyone in my family who has had it, caught it from a child bringing it home from school. Ignore the idiots in charge who say there is no evidence of schools driving the infection rates.

    • by Anonymous Coward

      This is true from the county level, the state level, the national level, all the way out to the global scale.

      Some places have had four peaks, my county has had three. The gaps were 6 months and 7 months. Humans love to see trends that don't really exist.

      • Exactly. Humans love to see trends that don't exist... And yet pushing these trends is the foundation of modern propaganda... confuse and divide. I am rather sure most informed readers can know which country pushes this and maybe even why... Ends up Dune isn't much different from life...

    • by zeeky boogy doog ( 8381659 ) on Wednesday December 01, 2021 @07:31PM (#62037967)
      10 infection numbers surge
      20 two weeks later hospitalizations surge
      30 oh shit it didn't go away
      40 mandatory changes to human behavior (i.e. universal indoor mask mandates)
      50 infection rate drops
      60 oh hey it went away, everybody party like it's 1999
      70 mask mandates cancelled
      80 complacency returns
      90 goto 10

      It is not difficult to see how this cycle takes roughly 4 months. This exact scenario that was predicted waaay back at the start by the Lancet as the "rolling lockdowns" model: rises and falls in social regulations that are somewhere between 90 and 0 degrees phase advanced vs the waves of infection.
      • by dmay34 ( 6770232 )

        Yeah, that seems like a good explanation, until you zoom out to the global level. You don't have waves everywhere at once, but when you add up all of the cases you get very predictable waves where I personally would expect it to look like noise.

    • I follow the following countries in more or less detail, due to having family and colleagues (from) there, alongside of traveling there from time to time: Austria, France, Germany, Italy, Netherlands, Portugal, Switzerland. These countries have had peaks at different points in time, but it was always explained with change in behaviour. Sometimes the rules got relaxed, sometimes it was triggered by holidays. Check out world in Data and you'll see that the peaks don't coincide for those countries, nor are the
    • Well next up is Pi, so it will perhaps stop repeating or become a circle.
  • One of the symptoms is being turned into low poly david bowie

  • by zeeky boogy doog ( 8381659 ) on Wednesday December 01, 2021 @06:06PM (#62037739)

    "The individual is self quarantining and all close contacts have been contacted and all close contacts, thus far, have tested negative"

    So much for the first round hysterical doom-shrieking that it has an R0 of 50.

    Earliest available data - what very little there is - leans toward "about as bad as delta." Certainly within the margin of error on that, given how wide said margin is at this point.

  • I've seen nothing but "mild symptoms" in every news story. So why are so many so afraid of it? Are you also afraid of life? Because a completely risk-free life is not only impossible, it would negate the purpose of it.

  • Seeing as how things are hitting new levels of surreal, why not some David Bowie to give it flavor?

    https://www.youtube.com/watch?... [youtube.com]

"The whole problem with the world is that fools and fanatics are always so certain of themselves, but wiser people so full of doubts." -- Bertrand Russell

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