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Omicron - COVID-19 Variant (B.1.1529) a "Variant of Concern"

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  • Alex Sigal
    @sigallab
    We have completed our first experiments on neutralization of Omicron by Pfizer BNT162b2 vaccination elicited immunity Manuscript available at https://sigallab.net and should be available on medRxiv in the coming days
    4:02 PM · Dec 7, 2021·Twitter Web App
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    Alex Sigal
    @sigallab
    ·
    13h
    Replying to
    @sigallab
    There are a few results: 1. Omicron still uses ACE2 2. There is a very large drop in neutralization of Omicron by BNT162b2 immunity relative to ancestral virus 3. Omicron escape from BNT162b2 neutralization is incomplete. Previous infection + vaccination still neutralizes
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    Alex Sigal
    @sigallab
    ·
    13h
    This is our first set of data and is not corrected for values going below the lowest dilution used - we present the raw fold change, which is likely to be adjusted as we do more experiments.
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    Alex Sigal
    @sigallab
    ·
    13h
    Thank you
    @Sandile_Cele22
    for leading,
    @KhadijaKhan24
    ,
    @farinakarim
    ,
    @Dr_L_Jackson
    for making it possible, and our terrific collaborators
    @PennyMo70026063
    ,
    @Tuliodna
    ,
    @rjlessells
    ,
    @houzhou
    . There are many more key people to thank, but I need to get some sleep first
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    Alex Sigal
    @sigallab
    ·
    12h
    Just be be clear on something as I'm still awake, this was better than I expected of Omicron. The fact that it still needs the ACE2 receptor and that escape is incomplete means its a tractable problem with the tools we got
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    • Comment




      • A Marm Kilpatrick
        @DiseaseEcology
        ·
        9h
        We found that measurements are moderately consistent in terms of relative differences w/in a study (lines in fig are parallel), but there are huge diffs b/w studies (methods, samples, etc.), so need to have all the variants you want to compare in 1 study.

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        A Marm Kilpatrick
        @DiseaseEcology
        ·
        9h
        Studies above suggest a 7 - 41 fold difference, with weight leaning towards the upper end (20-40-fold reduction). What does this mean in terms of vaccine effectiveness? It does NOT mean a 20-40-fold reduction in VE. But...
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        A Marm Kilpatrick
        @DiseaseEcology
        ·
        9h
        We can estimate the reduction using data on VE for a vaccine & neutralizing antibody titers. Two papers that did this are: https://medrxiv.org/content/10.1101/2021.10.25.21265500v3… https://nature.com/articles/s41591-021-01377-8… However - these studies compared VE across vaccines, NOT across virus variants. Can we do that directly?


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        A Marm Kilpatrick
        @DiseaseEcology
        ·
        9h
        We used VE data from
        @alison_l_hill
        https://medrxiv.org/content/10.1101/2021.09.17.21263549v1… for specific vaccines & variants & paired them w/ neutralizing antibody titers for vaccines & variants to estimate VEs for symptomatic disease, doc infection & hospitalization.

        medrxiv.org
        A systematic review of COVID-19 vaccine efficacy and effectiveness against SARS-CoV-2 infection and...
        Billions of doses of COVID-19 vaccines have been administered around the world, dramatically reducing SARS-CoV-2 incidence in some settings. Many studies suggest vaccines provide a high degree of...
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        A Marm Kilpatrick
        @DiseaseEcology
        ·
        9h
        Here are VE for SYMPTOMATIC DISEASE & antibody neutralization fold-reductions for 4 vaccines & 4 variants. We could fit models to these data but notice empty space on graphs for >7-fold reductions - there are NO DATA. Thus we can't reliably estimate Omicron VE from these data.

        Comment


        • WHO: Omicron could have ‘major impact’, but no definitive answers yet

          8 December 2021
          Health

          Features of the new COVID-19 variant Omicron, including the extent to which it will spread, and the sheer number of mutations, suggest that it could have a major impact on the course of the pandemic, but it’s still too early to say for sure.

          That was one key takeaway from Wednesday’s latest weekly briefing on the virus from WHO Director General, Tedros Ghebreyesus, speaking to journalists in Geneva.

          So far, Omicron has been reported in 57 countries, and WHO expects the number to continue growing.

          Tedros highlighted “a consistent picture of rapid increase in transmission” but said that the exact rate of increase relative to other variants remains difficult to quantify.

          Despite some data from South Africa suggesting increased risk of re-infection with Omicron, more data is needed. The variant might also cause milder disease than Delta, but there is no definitive answer yet.


          “New data are emerging every day, but scientists need time to complete studies and interpret the results. We must be careful about drawing firm conclusions until we have a more complete picture”, Tedros explained.

          In this context, the WHO chief called on all countries to increase surveillance, testing and sequencing.

          “Any complacency now will cost lives”, he warned.

          ‘Act now’
          Even though the world still needs answers to some crucial questions, Tedros said people everywhere are not defenceless against Omicron, or Delta.

          “The steps countries take today, and in the coming days and weeks will determine how Omicron unfolds. If countries wait until their hospitals start to fill up, it’s too late. Don’t wait. Act now”, he said.

          Tedros also asked countries to avoid “ineffective and discriminatory” travel bans.

          This week, France and Switzerland have lifted their travel bans on southern African countries, and Tedros urge other countries to follow their lead.

          WHO’s work
          Every day, the UN Agency is convening thousands of experts around the world to share and analyse data and drive research forward.

          For example, the Technical Advisory Group for Virus Evolution is assessing Omicron’s effect on transmission, disease severity, vaccines, therapeutics and diagnostics.

          The Joint Advisory Group on COVID-19 Therapeutics Prioritization is analysing the possible effects of Omicron on treatment of hospitalized patients.

          The R&D Blueprint for Epidemics is working with researchers to identify knowledge gaps, and the Technical Advisory Group for COVID-19 Vaccine Composition, is assessing impacts on current vaccines and determining whether changes are needed.

          No ‘forced’ vaccines: UN rights chief
          Also on Wednesday, the UN High Commissioner for Human Rights, Michelle Bachelet, said that “in no circumstances should people be forcibly administered a vaccine”.

          In a video address to the Human Rights Council, Ms. Bachelet maintained that it was “profoundly fortunate” that medical research had enabled vaccine development to move so swiftly to prevent the most severe forms of the coronavirus.

          But the UN Human Rights chief warned that it seemed very unlikely that the target of protecting 40 per cent of the world's population by the end of 2021 will be met. And the target of 70 per cent by mid-2022 also appears unrealistic at this stage, Ms. Bachelet said.

          https://news.un.org/en/story/2021/12/1107452
          "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


          • ECDC -

            Epidemiological update: Omicron variant of concern (VOC) – data as of 8 December 2021 (12.00)

            Epidemiological update
            8 Dec 2021

            ...
            All cases for which there is available information on severity were either asymptomatic or mild. No deaths have been reported among these cases so far. These figures should be assessed with caution as the number of confirmed cases is too low to understand if the disease clinical spectrum of Omicron differs from that of previously detected variants.
            ...
            Overall, globally there have been 1 458 confirmed cases reported by 55 countries, based on epidemic intelligence data from public sources (Table 1).
            ...
            https://www.ecdc.europa.eu/en/news-e...ata-8-december
            "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


            • https://www.capetalk.co.za/articles/...-as-with-delta
              > Three-quarters of Covid patients were in the hospital for other conditions, and only found out they had Covid-19 upon arrival.
              > Hospital stays seem considerably shorter (2.8 days, on average) than during the pre-Omicron pandemic (8.5 days, on average).

              {my estimate ; 5% of cases get hospitalised instead of 15% and 5% of hospitalised die instead of 15%)
              I'm interested in expert panflu damage estimates
              my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

              Comment


              • cases in Tshwane were very low on Dec07 (Dec08 not yet available) is it going down in Tshwane already ?
                Dec06:1698
                Dec07: 461
                looks like some reporting artefact
                https://gis.nicd.ac.za/portal/apps/o...7606c1248578ff
                some Tshwane newspaper should have it ?!
                I'm interested in expert panflu damage estimates
                my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                Comment



                • https://www.citizen.co.za/news/vacci...-unvaccinated/



                  24/38 adults in the Covid wards on 2 December, 24 were unvaccinated,

                  eight had unknown vaccination status and only six had had the jabs.



                  8/9 of hospitalised for Covid pneumonia, were unvaccinated

                  80% of admissions were below the age of 50.
                  I'm interested in expert panflu damage estimates
                  my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                  Comment


                  • https://twitter.com/EthicalSkeptic/s...26432947593221


                    Ethical Skeptic
                    @EthicalSkeptic

                    Chart of concern. This red line from Omicron is false. Topol is a known source of propaganda - so this, as much as anything else, confirms that Omicron in no way originated from Alpha.

                    Quote Tweet


                    Eric Topol @EricTopol
                    · Dec 3

                    It took a year for #Omicron, the 5th variant of concern, to be detected after Gamma and Delta, picked up in late 2020

                    11:00 AM · Dec 8, 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


                    • Emily
                      Emily commented
                      Editing a comment
                      He (Topol) is proud of being a "full activist" - propaganda is used by activists. We are left to discern between science and activism.

                      https://www.auckland.ac.nz/en/news/2...-activist.html

                    • Okieman
                      Okieman commented
                      Editing a comment
                      There is some major irony here saying this guy "is a known source of propaganda". Read all of the article at the ink that Emily posted. Especially the last couple of sentences.

                    • Emily
                      Emily commented
                      Editing a comment
                      He does have a financial interest in all this, and Anderson has been involved in nasty tactics to suppress consideration of the lab-leak possibility for sars-cov-2. Read about the wearable sensor technology.

                      xhttps://www.scripps.edu/news-and-events/press-room/2021/20210614_radin_rockefeller-aws.html
                      "Eric Topol, MD, founder and director of the Scripps Research Translational Institute, contributed to The Rockefeller Foundation’s National COVID-19 Testing Action Plan, as well as an updated version of the report. Topol and Kristian Andersen, PhD, director of Infectious Disease Genomics at SRTI, also provided their expertise for the Foundation’s national disease surveillance plan, which calls for using genomic technologies and other sophisticated tools to detect and track viral threats. "


                  • https://twitter.com/pbleic/status/1468631269634461704


                    Paul Bleicher
                    @pbleic


                    3/ T cell epitopes are mostly unchanged in Omicron. This is really important news - this is for HLA-A, B, C, that is CD8+ T cell ag recognition molecules. For immunologist who understand the role of these cells in viral infections, this is great news.


                    11:19 AM · Dec 8, 2021·Twitter for iPhone

                    _____________________________________________

                    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


                    • JJackson
                      JJackson commented
                      Editing a comment
                      As a bit of background. The MHC type 1 cell surface receptor is made up of proteins which are coded for in an allele which is part of the HLA. For different HLAs these proteins will vary giving a slightly different binding affinity between the MHC, which presents the viral antigen and has a CD8 receptor, to the T cell antibody and its CD8 cell surface protein. The same applies to the MHC2 receptor which binds CD4 T cells & antibodies, but with a slightly longer antigenic peptide, giving a little more specificity. CD8 T cells are involved in killing infected cells while CD4 T cells help with B cell differentiation/class switching and antibody refinement.
                      Last edited by JJackson; December 9, 2021, 07:49 AM.

                  • bump this

                    Comment


                    • 20% of HCW in SA infected
                      https://mg.co.za/coronavirus-essenti...ontract-covid/
                      I'm interested in expert panflu damage estimates
                      my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                      Comment


                      • update week 48 , comparing hospital surveillance in Tshwane waves 2,3,4
                        https://www.nicd.ac.za/wp-content/up...8-2021_rev.pdf
                        http://magictour.free.fr/tshh48.GIF
                        I'm interested in expert panflu damage estimates
                        my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                        Comment


                        • bump this

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