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

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  • #31
    South Africa accuses UK and others of ‘knee-jerk’ reaction to new variant

    Travel restrictions on southern African states imposed by countries after discovery of B.1.1.529 already harming economy

    Nick Dall in Cape Town and Lizzy Davies
    Fri 26 Nov 2021 13.09 EST
    ...
    Should the new variant prove to be highly transmissible, there are fears that a fourth wave could materialise – and in a more dangerous form than had been anticipated.

    However, Dr Angelique Coetzee, chair of the South African Medical Association and a practising GP based in Pretoria, said it was “premature” to make predictions of a health crisis.

    “It’s all speculation at this stage. It may be it’s highly transmissible, but so far the cases we are seeing are extremely mild,” she said. “Maybe two weeks from now I will have a different opinion, but this is what we are seeing. So are we seriously worried? No. We are concerned and we watch what’s happening. But for now we’re saying, ‘OK: there’s a whole hype out there. [We’re] not sure why.’”

    Coetzee said she would like to see the government embark on a push to get more people vaccinated, but added: “Unfortunately, it’s not only the responsibility of the government; it’s the responsibility of the public as well … You can only ask people so many times to go and get vaccinated, and if you don’t listen, then there’s consequences, and then you have to take the consequences.”
    ...

    https://www.theguardian.com/world/20...nt-vaccination
    "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

    Comment


    • #32

      https://twitter.com/RWMaloneMD/statu...03315265761280



      Robert W Malone, MD @RWMaloneMD

      "All four had been fully vaccinated" Any assertions that the emergence of the B.1.1.529 (Nu) variant emerged in unvaccinated or HIV-infected individuals in Africa is pure propaganda. This is yet more DISINFORMATION being pushed by legacy media such as "The Guardian".



      12:41 PM · Nov 26, 2021·Twitter Web App
      _____________________________________________

      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

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

      Comment


      • #33
        https://twitter.com/BWGovernment/sta...74240130785280

        Botswana Government @BWGovernment
        MEDIA RELEASE #LetsDefeatCOVID19Together #AReFenyengCOVID19Mmogo

        8:16 AM · Nov 25, 2021·Twitter for Android
        _____________________________________________

        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

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

        Comment


        • #34
          https://twitter.com/BWGovernment/sta...84386912501764

          Botswana Government
          @BWGovernment

          STATEMENT ON THE NEW COVID-19 VARIANT


          4:48 AM · Nov 26, 2021·Twitter for Android
          _____________________________________________

          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

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

          Comment


          • #35



            Florian Krammer

            @florian_krammer
            1) My gut feeling from hearing of Omicron cases in Botswana, ex-Malawi, ex-Egypt (2 now it seems) and in South Africa is, that the variant was flying under the radar in undersequenced countries for some time until Botswana and South Africa detected it and sounded the alarm.
            6:04 AM · Nov 27, 2021·Twitter Web App
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            Florian Krammer

            @florian_krammer
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            Replying to
            @florian_krammer
            2) However, the fact that European countries only detected it in travelers after South Africa and others warned about it, probably means that many cases so far went undetected. It also tells us a lot about genomic surveillance in some high income countries.
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            Florian Krammer

            @florian_krammer
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            3) The mutations in Omicron which seem to wipe out the majority of neutralizing antibody epitopes are very worrisome. Combined with the apparent fitness of the virus, this could be a problem. There is now a lot to do to get a better idea of the risk this virus variant poses.
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            Florian Krammer

            @florian_krammer
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            4) We need to first figure out how widespread it is, how well it escapes neutralizing antibodies (assumption: very well), what its R0 is, how well it does against Delta and if it can cause severe disease in vaccinated or recovered individuals.
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            Florian Krammer

            @florian_krammer
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            17m
            5) Adapted vaccines need to be tested (this has started already) etc. Also, we should not forget that non-neutralizing antibody epitopes and T-cell epitopes are likely largely intact. And even if a variant vaccine becomes necessary, we would not start from scratch....
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            Florian Krammer

            @florian_krammer
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            6).....since it is likely that one 'variant-booster' would do the job. Our B-cells can be retrained to recognize both, the old version and the variant, and it doesn't take much to do that.
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            Florian Krammer

            @florian_krammer
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            12m
            7) But there are a lot of unknowns, and many 'scariants' have come and gone. I assume we will have a much better idea about the actual risk in 2-3 weeks. We need to stay calm and do our work.
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            Florian Krammer

            @florian_krammer
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            10m
            8) A shoutout and big thank you to
            @Tuliodna
            and many other researchers from South Africa and Botswana for sharing sequences and information in real time!

            Florian Krammer

            @florian_krammer
            ·
            59s
            Replying to
            @florian_krammer
            9) There was an update on the second case from Egypt. It seems now it was not from Egypt:

            Comment


            • #37
              Re. Omicron
              There is not enough data to say anything very definitive about this variant yet - not that that will stop the media from writing exciting headlines and worst case scenarios.
              Speculation is all we have so lets look at what we know and what it is reasonable to infer.

              It was first found less than a month ago - Given that very few positive test are fully sequenced it is very likely to have been circulating below the radar for some time and is likely to have spread to several other areas/countries by now so travel restrictions will probably not delay international spread by much.

              It has a bucket load of AA changes many in the Spike - This is unusual, while the virus will be continuously making small changes in any infection most will be weeded out in that host with only one or two making it to the next host. Viruses with this many changes as a single jump are almost always dead ends except where the host is immunocompromised allowing 'damaged' viruses to keep on adding mutations until a new viable progeny is achieved. The high HIV prevalence is a suspect here but we will never be able to pinpoint the index case.
              These Spike changes are almost definitely going to reduce vaccine efficacy to some degree which will increase relative viral fitness in areas with high vaccine coverage. If the virus is relying on this to out perform the Delta variant it will spread well in high vaccine/prior infection areas but not in countries that are naive.
              As we have never seen all these changes in one variant before there is no way of guessing what impact they will have on transmission, virulence or other properties of the phenotype we are just going to have to wait and watch.
              As with the Alpha variant it is easier to pick up by rt PCR as the Spike probe (normally 1 of 3 probes) gives a reduced signal which in turn tends to lead to more full sequencing of that hosts viral genome which will skew the data compared to random sequencing so be wary of the relative numbers of sequences deposited at GISAID.

              As far as the impact on health services is concerned the key here is if, in people whose immune system is primed, there is adequate protection to limit the replication in the host sufficiently for somatic hyper-mutation to adjust the B cells' antibodies to the new virus (I wrote an explanation of B cell maturation here https://flutrackers.com/forum/forum/...701#post907701). In countries with high vaccination/prior infection rates (like mine, the UK) people have dropped their guard and are tolerating very high infection rates as it is only producing low hospitalisations. If this strain has retained its virulence and drifted away from vaccine strains enough to allow significantly more hospitalisation and we do not change our behaviour, physical distancing and masking, then our health systems hospitals are going to get swamped and will cause more lockdowns.

              A first look personal opinion only based on very little information - caveat emptor.

              Comment


              • Emily
                Emily commented
                Editing a comment
                Thanks for sharing your analysis, JJackson. Hopefully these unusual changes will turn out to be benign.

            • #38
              Tracking COVID-19 variant Omicron

              https://bnonews.com/index.php/2021/11/omicron-tracker/

              BREAKING: England reports first 2 cases of new coronavirus variant

              NEW: Czech Republic reports first suspected case of new coronavirus variant in returnee from Egypt

              NEW: Germany reports probable case of new coronavirus variant in returnee from South Africa

              Comment


              • #39
                What we know about Omicron variant that has sparked global alarm

                Clive Cookson and Oliver Barnes in London
                YESTERDAY

                ... Slawomir Kubik, a genomics research expert at Geneva-based biotech Sophia Genetics, said many of Omicron’s mutations came “completely out of the blue” and had not been observed before in other strains. Therefore, scientists “have very little visibility on what these new mutations are doing to how the virus works”, he explained, adding that once it begins to spread more widely its “true fitness” will become clear. Some of the mutations indicate increased transmissibility, while changes in the genetic code make it harder for the immune system, trained by existing vaccinations or prior infection with another variant, to tackle a new strain. But it will take researchers several weeks or months to work out the interactions between them and their cumulative impact.



                https://www.ft.com/content/42c5ff3d-...f-7243a00cba5e

                Comment


                • #40
                  https://www.voiceforscienceandsolida...rican-variants

                  November 27, 2021
                  My opinion on the new African variants
                  Geert Vanden Bossche

                  The world may be taken by surprise but that doesn't include us. It remains to be seen whether Omicron can outcompete Delta (to be confirmed). If that’s the case, we're definitely not in good shape.
                  In case of CoV, innate immunity protects the individual and the 'herd' ( sterilizing immunity, no natural selection pressure, herd immunity) whereas adaptive immunity induced with leaky vaccines has exactly the opposite effect.
                  THE big Q is whether such an immune escape variant could even resist naturally acquired Abs in people who recovered from C19 disease. I am, indeed, cautious and worried about ADE, even in the unvaccinated who recovered from C-19 disease as they may no longer be able to control viral infection. ADE would equal ‘enhanced virulence’. Difficult to predict.
                  Mass vaccination has compressed the evolutionary trajectory of the virus from a few hundred years (?) down to one year. Hope that naturally primed individuals can deal with that speed.

                  _____________________________________________

                  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

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

                  Comment


                  • #41
                    https://www.telegraph.co.uk/global-h...says-symptoms/

                    The first South African doctor to alert the authorities about patients with the omicron variant has told The Telegraph that the symptoms of the new variant are unusual but mild.

                    Dr Angelique Coetzee said she was first alerted to the possibility of a new variant when patients in her busy private practice in the capital Pretoria started to come in earlier this month with Covid-19 symptoms that did not make immediate sense.

                    They included young people of different backgrounds and ethnicities with intense fatigue and a six-year-old child with a very high pulse rate, she said. None suffered from a loss of taste or smell.

                    “Their symptoms were so different and so mild from those I had treated before,” said Dr Coetzee, a GP for 33 years who chairs the South African Medical Association alongside running her practice.

                    On November 18, when four family members all tested positive for Covid-19 with complete exhaustion, she informed the country’s vaccine advisory committee.
                    Emphasis mine. The article further states that Dr. Coetzee was concerned for the six year old child but within two days the little girl was much better. This was nearly ten days ago and the variant must have been circulating in the community for longer than that. The people quarantined in Schiphol who were interviewed were not symptomatic.

                    https://www.telegraph.co.uk/news/202...iftigniter-rhr

                    New Covid variant is less worrying than delta, says Prof Chris Whitty

                    Chief Medical Officer urges calm in face of warnings around omicron mutation, saying concern should focus on ‘immediate threats’
                    T

                    A graph of South African deaths has not shown a dramatic spike. IMO the bottom line is you do not want to get Covid - whichever variant it is.



                    ?The only security we have is our ability to adapt."

                    Comment


                    • #42
                      https://www.cnbc.com/2021/11/27/the-...d-variant.html
                      An Italian who had traveled to Mozambique on business landed in Rome on Nov. 11 and returned to his home near Naples. He and five family members, including two school-age children, have since tested positive, the Italian news agency LaPresse said. All are isolating in the Naples suburb of Caserta in good condition with light symptoms.
                      This is 7 days before Dr Coetzee notified the South African Medical Association.
                      ?The only security we have is our ability to adapt."

                      Comment


                      • #43
                        Screen Shot 2021-11-27 at 8.02.56 PM.png
                        Trevor Bedford

                        @trvrb
                        ·
                        Nov 26
                        You can see the striking accumulation of mutations in the S1 domain of the spike protein just by plotting S1 mutations against time and coloring by clade (https://nextstrain.org/ncov/gisaid/africa?l=scatter&scatterY=S1_mutations…). Omicron viruses bear many more S1 mutations than previously circulating variants. 7/16

                        The way I read this ‘family tree’ it’s like someone reached all the way back to April 2020, plucked out an existing variant (having only the D614G mutation in common with every other clade & variant) and then somehow, magically, all by itself, came up with not one, not two, not ‘a few,’ but twenty new mutations never before seen in any other variant of concern.

                        https://twitter.com/trvrb/status/146...243457/photo/1

                        Comment


                        • blacknail
                          blacknail commented
                          Editing a comment
                          This seems to support the theory that someone with AIDS (HIV, tragically, is commonly under-treated in that part of the World) acquired COVID last Spring and it spent more than a year evolving in their body until it produced Omicron.

                      • #44
                        PH Dependency Question: Is there any evidence that the PH Dependency related to endocytosis has changed in this new variant? Is there any suggestion that any of the specific Spike mutations would affect Ph Dependency? Any links / resources specific to this subject in Covid? Wondering if there is any specific ph range that is more optimum for endocytosis, what the trigger ph levels at which cell penetration is mitigated? Working on some research. Any guidance / feedback appreciated.

                        Comment


                        • JJackson
                          JJackson commented
                          Editing a comment
                          David I am not sure the pH is of much relevance in SARS-CoV-2 as the bulk of the fusion is occurring at the surface membrane due to the S1/S2 polybasic cleavage site (AKA furin cleavage site) allowing TMPRSS2 access to the S2' cleavage site at the cell surface. The increasing pH will become relevant for cathepsin-L cleavage for any uncleaved S1/S2 that does end up in an endosomic vesicle.
                          See https://journals.plos.org/plospathog...l.ppat.1009212

                          I note Omicron has a couple of deletions near the N terminal domain fusion peptide which may effect fusion there are some changes near S1/S2 but I doubt they will change balance between the two entry routes as this site is on an exposed loop giving easy access to a range of proteases.

                      • #45
                        some links to SA online-newspapers, sorted by my quick first impression of omicron-coverage

                        https://www.timeslive.co.za/
                        https://www.citizen.co.za/
                        https://www.businesslive.co.za/bd/
                        https://www.sowetanlive.co.za/
                        https://www.iol.co.za/the-star

                        https://en.wikipedia.org/wiki/List_o...n_South_Africa

                        daily numbers:

                        https://www.nicd.ac.za/latest-confir...november-2021/
                        [edit the date in the URL]
                        I'm interested in expert panflu damage estimates
                        my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                        Comment


                        • gsgs
                          gsgs commented
                          Editing a comment
                          NICD-reports
                          daily hospitalisations, powerpoint
                          several weekly reports .pdf
                          https://www.nicd.ac.za/diseases-a-z-...ecial-reports/

                          NATIONAL COVID-19 DAILY REPORT
                          DAILY HOSPITAL SURVEILLANCE (DATCOV) REPORT
                          WEEKLY EPIDEMIOLOGICAL BRIEF
                          WEEKLY RESPIRATORY PATHOGENS SURVEILLANCE REPORT
                          WEEKLY TESTING SUMMARY
                          WEEKLY PRIVATE CONSULTATIONS EPIDEMIC THRESHOLD
                          WEEKLY HOSPITAL SURVEILLANCE (DATCOV) UPDATE
                          WASTEWATER-BASED EPIDEMIOLOGY FOR SARS-COV-2 IN SOUTH AFRICA
                          THE INITIAL AND DAILY COVID-19 EFFECTIVE REPRODUCTIVE NUMBER IN SOUTH AFRICA
                          PRIVATE CONSULTATIONS EXCESS RESPIRATORY ENCOUNTERS
                          SPECIAL PUBLIC HEALTH SURVEILLANCE BULLETIN
                          MODELLING CONSORTIUM (PROJECTIONS)
                          COVID-19 SPECIAL REPORTS
                          MONTHLY COVID-19 IN CHILDREN
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