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

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  • Here we detail three possible origins of the new variant of concern: Omicron.

    Coronavirus | Dec 2, 2021,03:07pm EST
    Omicron Origin
    William A. Haseltine

    ...
    Molnupiravir-induced

    The final theory, and perhaps the most troubling one, is that Omicron is a result of our own doing, through the treatment of a Covid-19 patient with the highly mutagenic antiviral drug molnupiravir. Molnupiravir works by introducing errors into the virus’ genetic code. When enough errors are introduced, virus replication slows and the patient clears the virus.

    Under less than ideal conditions — when the full dose of molnupiravir is not taken over the full period of five days, for example — the drug could lead to the creation of highly mutated, but viable, strains of SARS-CoV-2. Even under ideal conditions, patients treated with molnupiravir produced viable virus a few days into their course of treatment. The extent of the mutations which appeared due to molnupiravir are significant. In the FDA analysis of Merck’s clinical trial results, the authors note that patients who received molnupiravir showed more viral variation than those who did not, including amino acid substitutions, deletions or insertions in the spike gene, and amino acid changes were scattered throughout the coding sequence. A total of 72 emergent spike substitutions or changes was detected among 38 molnupiravir-treated patients.

    In South Africa, where Omicron was first detected, molnupiravir has been taken in both ideal and non-ideal conditions. Four different South African locations were used in Merck’s clinical trial of molnupiravir, which began in October 2020. The drug was given to patients at what we now know to be the “optimal” dosage, but also at lower doses to test the drug’s efficacy in smaller amounts. There is by no means a foolproof connection between molnupiravir and Omicron, but molnupiravir is known to induce a preponderance of two types of mutations: cytosine to uridine (C→U) and guanosine to adenosine (G→A). If you look at the difference in the Omicron genome and the original Wuhan variant, these C→U and G→A mutations comprise the majority of differences, with C→U mutations more prevalent to G→A. The same has been observed for molnupiravir-induced mutations in other coronaviruses (see Figure below). Agostini et al. note that exposure to molnupiravir resulted in up to 162 mutations in MHV and 41 mutations in MERS-CoV.


    There is still much more study to be done before we will know with any degree of certainty which of these three scenarios led to Omicron’s evolution. But we know enough today to make a few assumptions and assertions.

    First, until we can say with certainty that molnupiravir did not and could not create a highly infectious and highly mutated variant like Omicron, it should be pulled from the market and any debate over approval of the drug should be paused.
    _____________________________________________

    Ask Congress to Investigate COVID Origins and Government Response to Pandemic.

    i love myself. the quietest. simplest. most powerful. revolution ever. ---- nayyirah waheed

    "...there’s an obvious contest that’s happening between different sectors of the colonial ruling class in this country. And they would, if they could, lump us into their beef, their struggle." ---- Omali Yeshitela, African People’s Socialist Party

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

    Comment


    • gsgs
      gsgs commented
      Editing a comment
      sounds unscientific. E.g. C-T is common in other strains as well, they should have mentioned that.

    • Emily
      Emily commented
      Editing a comment
      The author seems well-credentialed in the science field. https://en.wikipedia.org/wiki/William_A._Haseltine
      But he could be wrong about some things. What is C-T? I don't see that mentioned in the article.

  • SARS-CoV-2 variants of concern and
    variants under investigation in
    England


    Technical briefing 33
    23 December 2021

    This briefing provides an update on previous briefings up to 17 December 2021
    ...
    Comparative demographics

    Relative to Delta, Omicron is currently more concentrated in young adult age groups (20
    to 29) and is less prevalent in children
    . Whilst there were initially higher rates of Omicron
    cases in persons of Black ethnicity, the rates of all ethnic groups have now converged
    reflecting widespread community transmission. These demographic factors should be
    borne in mind when interpreting comparative analyses.
    Hospitalisation and death

    Using data up until 20 December, 132 individuals with laboratory confirmed Omicron
    have been admitted or transferred from emergency departments. Over 40% of
    admissions were in London. Of those patients admitted to hospital, 17 (12.9%) had
    received a booster dose, 74 (56.1%) a second dose and 27 (20.5%) were not vaccinated

    (less than 10 were unlinked or had one dose). At the data cut off, 14 people were
    reported to have died within 28 days of an Omicron diagnosis, age range 52 to 96 years.

    Severity

    The risk of hospital admission for a person detected as a case of Omicron appears
    reduced compared to a case of Delta.
    This analysis excludes known reinfections. The
    current hazard ratio is 0.62 (95%CI 0.55-0.69) for emergency department attendance or
    admission, and 0.38 (95% CI 0.3-0.5) for admission alone. This analysis is preliminary
    because of the small numbers of Omicron cases currently in hospital and the limited
    spread of Omicron into older age groups as yet. It has not been adjusted for
    undiagnosed reinfections. It will be iterated regularly. In addition, Imperial reported
    analysis using the same data set but imputing a potential previous infection variable and
    estimated the intrinsic risk difference between Delta and Omicron as between 0 to 30%
    and the reduced risk of hospitalisation in those previously infected estimated as 55 to
    70%.
    In the Scottish study, the range of estimates for their analysis was similar, though
    based on only 18 total admissions detected for Omicron in the study and only 7
    individuals admitted with 7 or more days of follow-up.

    Vaccine effectiveness

    Repeated VE analysis continues to show lower VE for symptomatic Omicron disease
    compared to Delta. There is evidence of waning of protection against symptomatic
    disease with increasing time after dose 2, and by 10 weeks after the booster dose, with
    a 15 to 25% reduction in vaccine effectiveness after 10 weeks. This waning is faster for
    Omicron than for Delta infections. There are insufficient severe cases of Omicron as yet
    to analyse vaccine effectiveness against hospitalisation,
    but this is expected to be better
    sustained, for both primary and booster doses. This analysis will be iterated next week,
    although numbers may still restrict a robust analysis of protection against more severe
    outcomes. The VE data will also appear in the weekly COVID-19 vaccine surveillance
    report published routinely on a Thursday.

    Reinfections

    The population reinfection rate has increased sharply and disproportionately to the
    number of first infections. 9.5% of Omicron infections have been identified to have
    previous confirmed infections, which is likely to be a substantial underestimate of the
    proportion of reinfections.
    The first infections of the individuals with Omicron reinfections
    occurred in both the Alpha and Delta waves and are likely to have been undetected if in
    the first wave. There were 69 identified cases with Omicron as a third episode of
    infection and 290 cases where the Omicron infection was between a 60 to 89 day
    interval after a confirmed first infection.

    Secondary attack rates

    Iterated secondary attack rates calculated using routine contact tracing continue to show
    higher secondary attack rates for Omicron than for Delta
    . The difference between
    Omicron and Delta is currently greater for non-household contacts than for household
    contacts

    ...
    2.3 Severity

    Descriptive epidemiology of severe outcomes of Omicron in England

    To monitor the severe outcomes of Omicron infections, Omicron cases are linked to NHS data
    on presentation to emergency care and to UKHSA data on deaths following confirmed COVID19 test results.
    Hospitalisation was defined as attendance to emergency care which resulted in
    admission or transfer, and the Omicron specimen date was between 14 days prior to
    attendance and 1 day after attendance.

    Using data up until 20 December 2021, a total of 132 individuals with laboratory-confirmed
    (sequencing, genotyping or SGTF) Omicron have been admitted or transferred from emergency
    departments.
    Of these, 54 (40.9%) admissions were in London.

    The age range of admitted individuals was 0 to 98, years (median: 45.5); 74 (56.1%) were aged
    40 years or more; 25.8% were aged 70 years or more.
    55% of Omicron hospitalisations
    occurred in people whose self-reported ethnicity was White (British) and 8% among Black
    (African) people.

    A total of 14 people have been reported to have died within 28 days of an Omicron COVID-19
    diagnosis. The median time from Omicron specimen date to death was 4 days (range 1 to 10).
    The age of those dying ranged from 52 to 96 years.

    ...
    2.4 Vaccine effectiveness
    ...

    Vaccine effectiveness was estimated by period after dose 2 and dose 3. The final analysis
    included 147,597 Delta and 68,489 Omicron cases. Vaccine effectiveness against symptomatic
    disease by period after dose 2 and dose 3 is shown in Figure 7 for those who received a
    primary course of the AstraZeneca vaccine (Figure 10A), Pfizer (Figure 10B) or Moderna
    (Figure 10C). Booster estimates are separated for Pfizer and Moderna boosters. In all periods,
    effectiveness was lower for Omicron compared to Delta. Among those who received an
    AstraZeneca primary course, vaccine effectiveness was around 60% 2 to 4 weeks after either a
    Pfizer or Moderna booster, then dropped to 35% with a Pfizer booster and 45% with a Moderna
    booster by 10 weeks after the booster. Among those who received a Pfizer primary course,
    vaccine effectiveness was around 70% after a Pfizer booster, dropping to 45% after 10-plus
    weeks and stayed around 70 to 75% after a Moderna booster up to 9 weeks after booster.

    ...
    https://assets.publishing.service.go...riefing-33.pdf
    "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


    • France -

      Translation Google

      Coronavirus: delay for booster dose reduced to 3 months tomorrow

      Present at a press conference, Jean Castex announces that the deadline for receiving a booster dose will be reduced from 4 to 3 months from tomorrow.

      Credit: GEOFFROY VAN DER HASSELT / AFP
      Thibault Nadal & AFP
      published on 12/27/2021 at 7:28 PM - updated on 12/27/2021 at 19:37

      Another change for the French. After reducing the time to receive from 5 to 4 months in mid-December, Jean Castex has just announced that the time to receive the booster dose will be reduced, this time, from 4 to 3 months. This measure will enter into force tomorrow morning, if the High Authority of Health gives a favourable opinion.

      As of Tuesday, "it will only take three months after your second injection or your first if you have had Covid to benefit from your booster," Prime Minister Castex announced at a press conference following a health defense advice.

      https://www.rtl.fr/actu/politique/co...ain-7900109231
      "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


      • MONDAY 27 DECEMBER 2021 11:59 AM

        South Africa jubilant as Omicron wave subsides rapidly with minimal Covid hospital admissions and Delta killed off: ‘Expect the same in other countries’

        BY:MICHIEL WILLEMS

        Optimism is growing rapidly in South Africa as the wave of Covid infections caused by the Omicron variant seems to subside as quickly as it came.
        ...
        The Covid expert who has been leading the country’s pandemic response, Salim Abdool Karim – South Afrcia’s most important infectious-diseases scientist – said the peak of the Omicron wave has passed and he is convinced “every other country, or almost every other, will follow the same trajectory.”

        “If previous variants caused waves shaped like Kilimanjaro, omicron’s is more like we were scaling the North Face of Everest,” Abdool Karim told The Washington Post, referring to the near-vertical increase in infections that South Africa recorded in the first weeks of December.
        ...
        https://www.cityam.com/south-africa-...ta-killed-off/

        -------------------------------------------------------------------------------

        THE 7-DAY MOVING AVERAGE NUMBER OF NEW CASES BY PROVINCE

        The proportion of positive new cases/total new tested today is 22.0% which is lower than yesterday (27.2%). The 7-day average is 27.4% today, which is lower than yesterday (28.5%). The 7-day moving average daily number of cases has decreased.




        For more detailed information, visit the GIS Dashboard.

        ...
        https://www.nicd.ac.za/latest-confir...december-2021/
        "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


        • bump this

          Comment




          • A new Delta variant has emerged with 10+ more mutations, similar to Omicron. Are the two variants merging?
            https://nextstrain.org/ncov/gisaid/global
            "The only security we have is our ability to adapt."

            Comment


          • bump this

            Comment


            • Hat tip Sharon Sanders

              https://flutrackers.com/forum/forum/...nt-fourth-wave


              The Lancet
              Clinical severity of COVID-19 patients admitted to hospitals in Gauteng, South Africa
              during the Omicron-dominant fourth wave

              --Manuscript Draft--


              ...
              The reasons for the lower admission rates and less severe infections in admitted patients during the
              Omicron-dominated fourth wave are not known but are likely to be due to a less virulent virus, and high
              immunity from prior infection(s) or vaccination, especially the large numbers of vaccinated individuals
              who had prior infection and so have “hybrid immunity” (14). A tissue-based study showed that Omicron
              infects the cells of the bronchus faster but cells of the lung slower than Delta (15); which may at least
              partially account for the less severe infections observed in the Omicron-dominated wave.

              Immunity stemming from prior infection has provided protection against symptomatic infection with
              previous variants (16) however preliminary data from South Africa (17) suggest that reinfections with
              Omicron are high. While prior infection may not prevent symptomatic breakthrough infection, it may
              generate T-cell responses that provide protection from severe disease (18), thereby contributing, at
              least partially to the observed high infection rate but low severity due to Omicron. The province of
              Gauteng experienced a particularly severe wave of Delta infection leading to a large increase in
              seroprevalence following the Delta-driven third wave. If prior infection with the Delta variant specifically
              provides some T-cell immunity that protects against severe disease from Omicron infection, this could
              be a contributor to the less severe Omicron infections observed in the Omicron-driven fourth wave.

              While SARS-CoV-2 vaccine effectiveness in preventing symptomatic infection has been impacted by
              the emergence of variants (19), vaccination has reduced the risk of severe disease from past variants
              (20). Since vaccination coverage in Gauteng is higher in individuals aged above 60 years, it may have
              made an important contribution to the lower severity of Omicron infections, especially in the elderly. But
              vaccination cannot fully account for the markedly lower numbers of severe infections in 20-39 year-old
              individuals, as less than a third of this age group was vaccinated. One of the two vaccines being rolled
              out in South Africa is the Ad26.CoV2.S vaccine which generates lower antibody but better T-cell
              responses (21). The role of this specific vaccine in reducing disease severity but not clinical infections
              needs to be assessed.
              ...
              "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



              • Omicron has Cracked Open the Overton Window

                Welcome to the new paradigm shift
                _____________________________________________

                Ask Congress to Investigate COVID Origins and Government Response to Pandemic.

                i love myself. the quietest. simplest. most powerful. revolution ever. ---- nayyirah waheed

                "...there’s an obvious contest that’s happening between different sectors of the colonial ruling class in this country. And they would, if they could, lump us into their beef, their struggle." ---- Omali Yeshitela, African People’s Socialist Party

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

                Comment


                • bump this

                  Comment


                  • Experts believe Omicron will soon displace Delta as the dominant global strain

                    Shabana Begum
                    UPDATED DEC 30, 2021, 7:30 PM SGT

                    SINGAPORE -
                    ...
                    Prof Fisher noted: “We are seeing a global transition from Delta to Omicron because with a greater transmissibility, the virus is fitter and has a reproductive advantage.”

                    The rise and fall of new variants over time follows the laws of nature and the survival of the fittest, he said.

                    All living things, including viruses, evolve and those changes that improve a species’ survival or its ability to reproduce will see it grow stronger over generations.

                    The Sars-CoV-2 virus needs to enter human cells to reproduce, Prof Fisher explained.

                    “The variant that is best at entering the cell will be better at reproducing, and then spreading to other people,” he said.

                    “Because of Omicron’s mutations in the spike protein, it is obviously better at entering the host because we see the numbers in many countries increasing steeply.”
                    ...
                    On what will happen to the Delta variant over time, Prof Fisher said: “Time will tell whether omicron replaces all variants or there is a coexistence. Certainly in flu, different types can circulate at the same time.”
                    ...

                    "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


                    • Sublineage BA.2 not spotted by S-gene drop tests. That variant does not have the spike del 69-70 mutation.

                      India News: The elusive sibling (sub-lineage) of the Omicron variant, BA.2, cannot be picked up by the imported RT-PCR kit having an S-gene drop, researchers invo


                      ‘Foreign test kits can’t spot Omicron's elusive sibling

                      Read more at:
                      http://timesofindia.indiatimes.com/a...campaign=cppst




                      _____________________________________________

                      Ask Congress to Investigate COVID Origins and Government Response to Pandemic.

                      i love myself. the quietest. simplest. most powerful. revolution ever. ---- nayyirah waheed

                      "...there’s an obvious contest that’s happening between different sectors of the colonial ruling class in this country. And they would, if they could, lump us into their beef, their struggle." ---- Omali Yeshitela, African People’s Socialist Party

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

                      Comment


                      • vaccines do not work well in Iceland
                        current vaccine effectivity in Iceland
                        see https://www.covid.is/data
                        VE(2shots,case) = -88% (Jan02)
                        VE(3shots,case) = 38% (Jan02)
                        VE(2shots,hosp) = 71% (Dec28)
                        VE(3shots,hosp) = 84% (Dec28)
                        -----------------------------------------------
                        and it's decreasing.. And Israel gives 4th doses
                        no vaccine report from the UK this week (why ?)
                        no vaccine update from Ontario Jan01-Jan03 (why ?)

                        cases are increasing now in the older groups in UK
                        hospitalisations are still going up everywhere, AFAIK
                        (admissions in London down the last 2 days)
                        cases in London seem to be going down
                        I'm interested in expert panflu damage estimates
                        my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                        Comment


                        • bump this

                          Comment


                          • Thread on twitter about the high levels of D-Dimer with Omicron.


                            Erin, from a lab perspective, our Omicron cases have had D-Dimer levels off the charts....I'm talking so high that the instrument cannot report a result. Previously, with Delta, we saw D-Dimers that required running in extended mode, but we were able to get results. Not now...
                            Have not been able to corroborate.
                            "The only security we have is our ability to adapt."

                            Comment


                            • kiwibird
                              kiwibird commented
                              Editing a comment


                              "Quote Tweet
                              WindUpBird
                              @MickieMo
                              · 4h
                              Replying to @4fucksssake @catnash37311 and @ErinSandersNP
                              My MIL is triple vaxxed and went to the ER for something other than covid but tested + for omicron. They gave her heparin as a precaution and her d-dimer results ended up being very high. The doc said the test is very sensitive and being in the ER probably saved her life."


                              Seems this might be a problem even with vaccination breakthrough cases.

                            • kiwibird
                              kiwibird commented
                              Editing a comment


                              "Funny that In South Africa the D-dimer levels were extraordinarily low with the new variant. My wife was tested when she got hers and no blood thinners were required. Unlike Delta where that was almost the standard.

                              The doc remarked that the new variant was changing treatment"

                              Conflicting statements about this.
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