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Omicron - COVID-19 Variant (B.1.1529) a "Variant of Concern" & BA.2 sub-variant, XE

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  • As we are beginning to get some useful data on the current VOC this may be a good time to review what we know.
    Case counts are rocketing (nearly 3 times any previous wave), and showing no signs of slowing, as the graph below shows.

    cov jan 2022.JPG

    There is some, very tentative, evidence that it may be less clinically severe but it is doubtful that this will be enough to stop a flood of hospitalisation and probably deaths. Even if the hoped for drop in virulence significantly reduces the severity, on a case by case basis, the far higher case loads will negate that advantage. Looking at the graph there has not been enough time between the start of the current exponential case growth (the last 3 weeks) to see how that plays out in terms of the deaths due to the lag time of about two weeks for hospitalisations and a month for fatalities.

    Omicron definitely has a significant fitness advantage over the other variants but it is very hard to compare with Alpha and Delta, which also rapidly established themselves, as the population's immune profiles have changed so much.
    The graph below shows how quickly Alpha (red), Delta (greens) and Omicron (purple) established themselves and then got supplanted. I have used the UK data as they do the most case sequencing and are well globally connected.

    covar UK.JPG

    What data there is comes from early case data in South Africa which shows lower, or at least slower, hospitalisations than delta and very different demographic profiles. The age, sex, comorbidities and O2 need are all very different. (compare column 4 to the earlier VOCs. N.B. also that this is a smaller data set so the confidence limits will be larger).

    SA data.JPG

    The next bit of useful data comes from https://www.medrxiv.org/content/10.1....27.21268278v1 which basically shows that at least part of Omicron's fitness advantage comes from immune evasion but a booster vaccine dose helps reduce this. It, along with other data, shows Omicron has a shorter incubation period.

    There is also good evidence that Omicron cause less sever symptoms in mice and hamster models with less replication in the lung but high replication in the nose. As usually with animal models it is difficult to say if this has any relevance in humans.


    My guess would be that it is a bit milder but very fit. This is good if it reduces morbidity but probably also bad if it leaves more mild and asymptomatic cases shedding and accounting for its explosive growth. I would be very cautious for a while in your contacts with others - distance, wear a mask and, if you can, get vaccinated and boosted. I think our health care services are going to have a hard time coping over the next few months and will need all of us to reduce our risk as much as we can.


    The top graph is from the current WHO sitrep
    https://www.who.int/docs/default-sou...&download=true

    The variants tables can be found here
    https://covariants.org/per-country

    The SA data
    https://jamanetwork.com/journals/jam...rticle/2787776

    The mouse/hamster data
    https://pubmed.ncbi.nlm.nih.gov/34981044/
    Attached Files

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      • UK -

        Endemic Covid: Is the pandemic entering its endgame?


        James Gallagher
        Health and science correspondent
        @JamesTGallagheron Twitter

        Published 2 days ago

        ...
        "We're almost there, it is now the beginning of the end, at least in the UK," Prof Julian Hiscox, chairman in infection and global health at the University of Liverpool, tells me. "I think life in 2022 will be almost back to before the pandemic."
        ...
        There will be people - mostly the old and vulnerable - who will die from endemic Covid. So there is still a decision to be made about how we live alongside it.

        "If you're willing to tolerate zero deaths from Covid, then we're facing a whole raft of restrictions and it's not game over," Prof Hiscox explains.

        But, he says, "In a bad flu season, 200-300 die a day over winter and nobody wears a mask or socially distances, that's perhaps a right line to draw in the sand."

        Lockdowns and restrictions on mass gatherings will not come back and mass testing for Covid will end this year, he expects.

        The near certainty is there will be booster vaccines for the vulnerable come the autumn in order to top up their protection through winter.

        "We need to accept the fact that our flu season is also going to be a coronavirus season, and that is going to be a challenge for us," says Dr Groppelli.

        However, it is still uncertain how bad winters will be as the people who die from flu and Covid tend to be the same. As one scientist put it, "You can't die twice."
        ...
        https://www.bbc.co.uk/news/health-59970281
        "Safety and security don't just happen, they are the result of collective consensus and public investment. We owe our children, the most vulnerable citizens in our society, a life free of violence and fear."
        -Nelson Mandela

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          • This public health messaging from a county in Colorado is excellent.

            https://www.youtube.com/watch?v=kewTSSmSk10
            Douglas County COVID-19 Message
            21,779 views
            Jan 13, 2022


            _____________________________________________

            Ask Congress to Investigate COVID Origins and Government Response to Pandemic H.R. 834

            i love myself. the quietest. simplest. most powerful. revolution ever. ---- nayyirah waheed
            Governments don't have or own souls.

            (My posts are not intended as advice or professional assessments of any kind.)
            Never forget Excalibur.

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              • Please see:

                Denmark SSI: Omicron Subvariant BA.2 Now Accounts For Nearly Half Of All Danish Cases + Rising in Norway, Sweden & UK

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                • delta(D) and omicron(O) waves in US-regions :
                  http://magictour.free.fr/us-0207v.GIF
                  omicron overlaps with the 2nd delta-wave and "kills it"

                  hosp. delta1 + (delta2+omicron)
                  NE:20+40
                  MW:33+47
                  S:52+35
                  W:34+38

                  short overview , 4 census-divisions :
                  http://magictour.free.fr/us0207a.GIF
                  I'm interested in expert panflu damage estimates
                  my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

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                  • Emily
                    Emily commented
                    Editing a comment
                    gsgs, do you conclude that Omicron is genetically equally dangerous, or do you think the increased transmissibility is the cause of the case counts?

                  • gsgs
                    gsgs commented
                    Editing a comment
                    omicron is more transmissable, it induces (shortterm) immunity in many people who are then
                    also less likely to get delta.
                    We may get some analysis, some papers which examine the sequences and separate the
                    delta and omicron cases/hossp/ICU/deaths.
                    In total omicron may have prevented more delta deaths than it caused omicron deaths
                    in some regions.
                    This wave and future waves .... i.e. in low-vaxed countries we'll see.

                    --------------------------------------------------
                    comparing with 1918 :
                    after the bad years 1918-1920 in USA there was almost no flu in the 1920/1 season.
                    After that it was milder, another decline in deaths since 1942 (1940 was flu-B)
                    http://magictour.free.fr/ALL4A.GIF

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                  • Updated 9:28 PM EST, Thu February 17, 2022

                    By Brenda Goodman

                    The BA.2 virus – a subvariant of the Omicron coronavirus variant – isn’t just spreading faster than its distant cousin, it may also cause more severe disease and appears capable of thwarting some of the key weapons we have against Covid-19, new research suggests.

                    New lab experiments from Japan show that BA.2 may have features that make it as capable of causing serious illness as older variants of Covid-19, including Delta.

                    And like Omicron, it appears to largely escape the immunity created by vaccines. A booster shot restores protection, making illness after infection about 74% less likely.

                    BA.2 is also resistant to some treatments, including sotrovimab, the monoclonal antibody that’s currently being used against Omicron.

                    ... BA.2 is highly mutated compared with the original Covid-causing virus that emerged in Wuhan, China. It also has dozens of gene changes that are different from the original Omicron strain, making it as distinct from the most recent pandemic virus as the Alpha, Beta, Gamma and Delta variants were from each other.

                    Kei Sato, a researcher at the University of Tokyo who conducted the study, argues that these findings prove that BA.2 should not be considered a type of Omicron and that it needs to be more closely monitored.

                    ... because it doesn’t show up on PCR tests as an S-gene target failure, the way Omicron does. Labs therefore have to take an extra step and sequence the virus to find this variant.

                    “Establishing a method to detect BA.2 specifically would be the first thing” many countries need to do, he says.

                    ... The US Centers for Disease Control and Prevention estimates that about 4% of Americans with Covid-19 now have infections caused by BA.2, but many other parts of the world have more experience with this variant. It has become dominant in at least 10 other countries: Bangladesh, Brunei, China, Denmark, Guam, India, Montenegro, Nepal, Pakistan and the Philippines, according to World Health Organization’s weekly epidemiological report. ...

                    https://www.cnn.com/2022/02/17/healt...ity/index.html

                    Comment


                    • Mary Wilson
                      Mary Wilson commented
                      Editing a comment
                      Preprint: Virological characteristics of SARS-CoV-2 BA.2 variant

                      https://flutrackers.com/forum/forum/...2-ba-2-variant

                    • Mary Wilson
                      Mary Wilson commented
                      Editing a comment
                      Preprint: Virological characteristics of SARS-CoV-2 BA.2 variant

                      https://flutrackers.com/forum/forum/...2-ba-2-variant

                    • Mary Wilson
                      Mary Wilson commented
                      Editing a comment
                      Why does the Omicron sub-variant spread faster than the original?

                      Early studies suggest that the BA.2 lineage might prolong the Omicron wave, but won’t necessarily cause a fresh surge of COVID infections.

                      16 February 2022

                      Ewen Callaway

                      COVID-19 researchers are rushing to understand why a relative of the main Omicron variant is displacing its sibling in countries around the world.

                      The variant, known as BA.2, has spread rapidly in countries including Denmark, the Philippines and South Africa in the past few weeks. It follows the initial spread of the BA.1 Omicron variant of the virus SARS-CoV-2, which was first identified in southern Africa in late November and quickly spread worldwide.

                      A laboratory study1 of BA.2 suggests that its rapid ascent is probably the result of it being more transmissible than BA.1. And other preliminary studies suggest that BA.2 can readily overcome immunity from vaccination and previous infection with earlier variants, although it is not much better than BA.1 at doing so.

                      If real-world epidemiological studies support these conclusions, scientists think that BA.2 will be unlikely to spark a second major wave of infections, hospitalizations and deaths after Omicron’s initial onslaught.
                      ...

                      https://www.nature.com/articles/d41586-022-00471-2

                  • I copied a few posts to this thread. The original posts are still in the same forums as posted by Mary Wilson.

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                    • Omicron is causing plenty of trouble in Hong Kong. I've always felt this was a 'pay now or pay later' virus. Hopefully it really is an overall less severe virus for the sake of zero-Covid countries. It's in the world's best interests for these countries to regain full functionality as soon as possible, IMO.

                      https://flutrackers.com/forum/forum/...ng-kong-exodus
                      _____________________________________________

                      Ask Congress to Investigate COVID Origins and Government Response to Pandemic H.R. 834

                      i love myself. the quietest. simplest. most powerful. revolution ever. ---- nayyirah waheed
                      Governments don't have or own souls.

                      (My posts are not intended as advice or professional assessments of any kind.)
                      Never forget Excalibur.

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                        • During the recent human rights protests in Canada, I was viewing some videos posted by a Canadian woman who had COVID about the time Omicron was circulating. A lot of other Canadians were sharing their experiences with the infection in the comments. All the symptoms and severity levels were similar to my experience in early 2020 with either the Wuhan strain or Alpha. They kept talking about what a strange experience it was - and that was the hallmark of the illness for me. The first exposure is a bizzare, "invasion of the body snatchers" experience.

                          Most of Canada is vaccinated, so I assumed many of the Canadian commenters were vaccinated. If Omicron was a lot less severe than Alpha, it should have been much milder for these people. I wondered if the vaccine was causing ADE. The other possibility was that Omicron is as serious as Alpha. The fact that the death rates are lower could just be due to the grim fact that many vulnerables were killed during Delta.

                          I saw this new study that supports Omicron being just as severe as the first two major iterations of SARS2 as far as hospitalization. It jives with my little collection of comparative anecdotes.

                          https://www.nejm.org/doi/full/10.1056/NEJMp2119682
                          February 17, 2022
                          N Engl J Med 2022; 386:e14
                          DOI: 10.1056/NEJMp2119682
                          Challenges in Inferring Intrinsic Severity of the SARS-CoV-2 Omicron Variant

                          Although these studies were conducted in locations with very different case-ascertainment rates, after correcting for underascertainment, each study estimated that omicron was about 75% as likely as delta to cause hospitalization in an unvaccinated person with no history of SARS-CoV-2 infection.2,3 This meaningful but fairly small difference implies that omicron, alpha, and wild-type SARS-CoV-2 have similar intrinsic severity.
                          _____________________________________________

                          Ask Congress to Investigate COVID Origins and Government Response to Pandemic H.R. 834

                          i love myself. the quietest. simplest. most powerful. revolution ever. ---- nayyirah waheed
                          Governments don't have or own souls.

                          (My posts are not intended as advice or professional assessments of any kind.)
                          Never forget Excalibur.

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