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

    https://www.theguardian.com/world/20...r-of-mutations

    Scientists have said a new Covid variant that carries an “extremely high number” of mutations may drive further waves of disease by evading the body’s defences.

    Only 10 cases in three countries have been confirmed by genomic sequencing, but the variant has sparked serious concern among some researchers because a number of the mutations may help the virus evade immunity.



    The B.1.1.529 variant has 32 mutations in the spike protein, the part of the virus that most vaccines use to prime the immune system against Covid. Mutations in the spike protein can affect the virus’s ability to infect cells and spread, but also make it harder for immune cells to attack the pathogen.
    ...
    Dr Tom Peacock, a virologist at Imperial College London, posted details of the new variant on a genome-sharing website, noting that the “incredibly high amount of spike mutations suggest this could be of real concern”.

    In a series of tweets, Peacock said it “very, very much should be monitored due to that horrific spike profile”, but added that it may turn out to be an “odd cluster” that is not very transmissible. “I hope that’s the case,” he wrote.
    Last edited by kiwibird; November 24, 2021, 05:28 PM. Reason: B.1.1.529 assigned
    ?The only security we have is our ability to adapt."

  • #2

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    Prof. Christina Pagel
    @chrischirp
    ·
    39m
    THREAD on the new variant B.1.1.529 summarising what is known from the excellent South African Ministry of Health meeting earlier today TLDR: So much uncertain but what *is* known is extremely worrying & (in my opinion) we should revise red list immediately. This is why: 1/16
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    Prof. Christina Pagel
    @chrischirp
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    39m
    The South African Ministry of Health had a live streamed briefing today on the new variant detected there. https://youtube.com/watch?time_continue=2999&v=Vh4XMueP1zQ&feature=emb _logo… The variant was identified this week and has been found in three countries so far: Botswana, South Africa and Hong Kong (returning traveller). 2/16

    youtube.com
    WATCH LIVE | Urgent briefing on latest developments around the...
    The Minister of Health Dr Joe Phaahla and Deputy Minister of Health Dr Sibongiseni Dhlomo, will convene an urgent virtual media briefing on the latest develo...
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    Prof. Christina Pagel
    @chrischirp
    ·
    39m
    In South Africa it has been detected in Guateng province - positivity rates in Tshwane (part of Guateng) have increased massively in the last 3 weeks from less than 1% to over 30%. 3/16

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    Prof. Christina Pagel
    @chrischirp
    ·
    39m
    Because of this increase, COVID sequencing has been concentrated on samples from Guateng. Almost all recent samples from there (77) have been this new variant (blue dots) - taking over from a background of Delta (red) and C.1.2 (also a concerning variant, yellow). 4/16

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    Prof. Christina Pagel
    @chrischirp
    ·
    39m
    SA had a big Delta surge over June and July but recent rates were very very low. Most recent days have seen early surge, mainly driven by Guateng. SA has high levels of prev infection from 3 very large waves but relatively low levels of vaccination (~24% fully vaxxed). 5/16






    Prof. Christina Pagel
    @chrischirp
    The SA science establishment & Ministry of Health transparency are doing *a global service* - we *cannot* underestimate how important their work and transparency are this week. They are urgently doing lab experiments to understand it more & continuing to track spread 11/16
    10:01 AM · Nov 25, 2021·Twitter Web App
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    Prof. Christina Pagel
    @chrischirp
    ·
    37m
    Replying to
    @chrischirp
    A new UKHSA technical briefing on variants is due tomorrow - I am sure they will at least mention this variant. WHO are meeting about it today as well. People working in this field in England at the highest levels are very concerned 12/16


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    Prof. Christina Pagel
    @chrischirp
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    37m
    Given the speed with which this variant has spread & mutations which *might* mean signifcant vaccine escape, in my opinion the UK should get ahead of this *right now*. As far as we know, it's not here yet. *Adding SA and close neighbours to the red list seems sensible* 13/16
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    Prof. Christina Pagel
    @chrischirp
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    37m
    Because of UK status as international travel hub, v few restrictions in UK and the worrying signs from SA, we must act now or risk it being too late. Regardless of travel restrictions, supporting S African response as Barrett suggests is the right thing to do. 14/16

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    Prof. Christina Pagel
    @chrischirp
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    37m
    If it's a false alarm, then we can step down response in a few weeks. But this is our window to act. As with Delta (and B.1.1.529 seems to spreading as or more quickly), waiting for certainty risks waiting too long. 15/16
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    Prof. Christina Pagel
    @chrischirp
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    37m
    Finally, this is just my opinion. It's hopefully not here yet. We don't have definitive evidence on transmission advantage or immune escape but we have plenty of cause to suspect both. Let's be super protective of our vaccine programme and take precautionary action. 16/16

    Comment


    • #3
      Source: https://www.msn.com/en-us/money/othe...ica/ar-AAR7yUH


      New Coronavirus Variant a ‘Serious Concern’ in South Africa
      Prinesha Naidoo and S'thembile Cele - 2h ago

      (Bloomberg) -- Scientists in South Africa are studying a recently identified new coronavirus variant that is a cause for serious concern, stoking fears the country may face a potentially severe fourth wave that could spread internationally.

      The new discovery, called B.1.1529 until a Greek letter is assigned, carries an unusually large number of mutations and is “clearly very different” from previous incarnations, Tulio de Oliveira, a bio-informatics professor who runs gene-sequencing institutions at two South African universities, said at a briefing on Thursday.

      “Here is a mutation variant of serious concern,” Health Minister Joe Phaahla said at the same media event. “We were hopeful that we might have a longer break in between waves -- possibly that it would hold off to late December or even next year January.”

      Virologists have detected almost 100 cases linked to the variant in the country to date, said Anne von Gottberg, clinical microbiologist & head of respiratory diseases at the National Institute for Communicable Diseases. World Health Organization officials have met to discuss the virus, which has also been detected in Botswana, according to a separate statement.

      The new variant is likely to have evolved during a chronic infection of an immuno-compromised person, possibly in an untreated HIV/AIDS patient, Francois Balloux, director of the UCL Genetics Institute, said in a statement published by the Science Media Centre. The world’s biggest number of HIV cases has complicated South Africa’s efforts to fight the coronavirus pandemic, as immuno-compromised people can harbor the virus for longer, scientists say....

      Comment


      • #4
        https://www.ndtv.com/india-news/covi...strain-2624909

        New Delhi:
        India on Thursday called for rigorous screening and testing of fliers coming from South Africa, Hong Kong and Botswana where a new variant of COVID-19 has been found with multiple mutations that have led to a surge in infections.

        In a letter to states and union territories, Union Health Secretary Rajesh Bhushan asked them to ensure that samples of travellers turning positive are sent to designated genome sequencing laboratories promptly. The contacts of these international travellers must also be closely tracked and tested as per Health Ministry guidelines, he said.
        ?The only security we have is our ability to adapt."

        Comment


        • #5
          HK detects new mutant variant, adds six imported cases

          Local | 25 Nov 2021 8:52 pm

          snip

          A total of 12 persons, who lived in the three rooms to the left and to the right of the two patients in the hotel during November 11 to 14, have been sent to Penny's Bay Quarantine Center to undergo compulsory quarantine for 14 days.

          So far no related case was detected.

          The center also reported six imported cases, including a one-year-old baby girl, two men and three women aged 17 to 45.

          Apart from the baby girl, the other five patients had received two doses of Covid-19 vaccine before.

          Among them, four arrived in Hong Kong on Tuesday, including a 28-year-old man from France on flight CX260, a 35-year-old woman from the Philippines on flight 5J272, a 45-year-old man from Russia on flight FV4501 and a 32-year-old woman from Nepal on flight RA409.

          The baby girl and a 17-year-old girl traveled to Hong Kong on Sunday on flight EK384. The baby traveled from Bangladesh via the United Arab Emirates while the teenager traveled from Thailand.

          snip

          https://www.thestandard.com.hk/break...imported-cases

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

          Okieman Comment: It appears that this variant is very transmissible. And based upon the information in this article one should consider that it has already spread all over the world. The next question for me is how well it gets around the vaccine or immunity and how capable it is at causing severe health effects? This article and data about it's spread in in Gauteng Province seem to indicate some ability to get past the vaccine.

          Comment


          • Okieman
            Okieman commented
            Editing a comment
            One more sentence from the article above:

            Health experts earlier suggested airborne transmission after inspecting the Chek Lap Kok hotel, saying a patient spread the virus to another person living across the corridor through the air.

          • blacknail
            blacknail commented
            Editing a comment
            It appears that the index case at the Regal Airport Hotel didn't follow quarantine procedures...

            They were a 36-year-old man arriving in Hong Kong from South Africa confirmed with the infection on November 15 and a 62-year-old man from Canada diagnosed on Saturday. They lived in opposite rooms on the fifth floor.

            Yuen said the 36-year-old man did not wear proper surgical masks in his hotel room and sometimes even opened the door without wearing any masks, allowing the coronavirus to get into the corridor and eventually infect the elder man living opposite him.

            https://www.thestandard.com.hk/break...-on-same-floor

          • blacknail
            blacknail commented
            Editing a comment
            Update, patient zero at the Regal Airport Hotel wore an exhale valved mask...

            The traveller from South Africa used a mask with a valve that doesn’t filter exhaled air and may have transmitted the virus to his neighbour when the hotel room door was open, a health department spokesperson said Friday.

            https://nationalpost.com/news/world/...ed-from-canada

        • #6
          https://www.bbc.co.uk/news/uk-59424269

          Some African countries to be added to the UK Red List from Friday.

          Africa travel restrictions over Covid variant fear
          Travellers arriving from several southern African countries will have to quarantine amid warnings over a new Covid variant.

          Health Secretary Sajid Javid said from 12:00 GMT on Friday six countries would be added to the red list, with flights being temporarily banned.
          The news report listed 6 different southern African nations.
          ?The only security we have is our ability to adapt."

          Comment


          • #7
            https://www.haaretz.com/israel-news/...ain-1.10416908

            Israel Bars Travel to and From South Africa Over New COVID Strain


            Prime Minister Naftali Bennett announced South Africa and some neighboring countries were added to the list of 'red' countries after scientists announced the detection of the B.1.1.529 COVID-19 variant
            ?The only security we have is our ability to adapt."

            Comment


            • #8
              Okieman Comment: This article is about the new variant and how it is effecting a university in Gauteng Province, South Africa. The university is Tshwane University of Technology. The Tshwane region/area has seen the greatest increase in cases. I wanted to post this because it has some important information concerning the increase of cases in one week in the Tshwane region. I will put the sentence containing that information in red.

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

              Cluster Covid-19 outbreak at TUT a concern

              snip

              The coronavirus infection cluster outbreak at the Tshwane University of Technology has become a concern as the Tshwane region recorded a sharp increase in cases this week.

              The institution recorded 55 positive cases of students including one staff member between November 16-18.

              snip

              Tshwane has seen a sharp increase in active Covid-19 cases in the past week. The National Institute for Communicable Diseases (NICD), said it has observed this increase in the Gauteng province, particularly in Tshwane, especially among the 10-29-year-olds over the past week.

              Tshwane has recorded 1 689 active cases as of Sunday, November 21.

              Last week Sunday, the number of active cases stood at 362. Contributing to these cases was a recently identified cluster in the 20-44 age group at the Tshwane University of Technology’s arts campus.

              snip

              https://rekord.co.za/399404/covid-19...ak-concerning/


              Comment


              • #9
                Four cases of the new COVID-19 variant recorded in Botswana
                Thursday, November 25, 2021

                The Presidential COVID-19 Task Force has revealed that four cases of a new COVID-19 variant now known as B.1.1.529 were reported and recorded on Monday November 22, 2021. This comes after the British media revealed that experts had discovered a new COVID-19 variant believed to have emerged in Botswana.

                snip

                According to a statement from the Presidential COVID-19 Task Force coordinator, Dr Kereng Masupu, the cases are said to have been detected among travellers who tested SARS-COV-2 positive on routine pre travel testing.

                The preliminary report revealed that all the four had been fully vaccinated for COVID-19. As part of the continuing investigations into the virus to establish and contain its local transmissions, contact tracing has revealed close contacts who are currently awaiting their results and the public will be informed regarding the outcome of the exercise,” further read a statement from Masupu.

                snip

                https://www.mmegi.bw/news/four-cases...-botswana/news

                Comment


                • #10
                  B.1.1.529 (=Ny?) in South Africa is out-competing others *far* faster than Beta and even Delta
                  https://twitter.com/jburnmurdoch/sta...56686075580421

                  https://www.dailymail.co.uk/news/art...nt-strain.html

                  spreads much faster and
                  vaccines >40% less effective
                  I'm interested in expert panflu damage estimates
                  my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                  Comment


                  • Mary Wilson
                    Mary Wilson commented
                    Editing a comment
                    Today, 10:58 PM
                    Eric Tool

                    Nu (Ν,ν) will be the @WHO name/Greek letter for the new variant. Better than B.1.1.529. That's about the only good thing you can say about it right now.

                    https://twitter.com/EricTopol/status...75943257481216

                  • gsgs
                    gsgs commented
                    Editing a comment
                    35 amino-acid mutations in the spike protein alone !?!
                    incredible 9alpha had 7, delta 6)
                    68 nonsynonymous changes
                    plus the synonymous ones, which I don't have
                    (I don't know, what PL below means , from a tweet od @Tuliodna )

                    spike:
                    A67V
                    del 69-70
                    T95I
                    G142D
                    del 143-145
                    N211I
                    L212V_RE
                    V213P
                    R214E
                    G339D
                    S371L
                    S373P
                    S375F
                    K417N
                    N440K
                    G446S
                    S477N
                    T478K
                    E484A
                    Q493R
                    G496S
                    Q498R
                    N501Y
                    Y505H
                    T547K
                    D614G
                    H655Y
                    N679K
                    P681H
                    N764K
                    D796Y
                    N856K
                    Q954H
                    N969K
                    L981F


                    E:T9I
                    M3G
                    M:Q19E
                    M:A63T
                    N:P13L
                    N:del 31-33
                    N:R203K
                    N:G204R

                    orf1ab :
                    PL:K38R
                    PL:L862LF
                    PL:V1069I
                    PL:del 1265
                    PL:L1266I
                    PL:A1892T
                    nsp4:T492I
                    3CL:P132H
                    nsp6:F34FL
                    nsp6:F35FILV
                    nsp6:del 105-107
                    nsp6:I189V
                    RdRP:P323L
                    nsp14:I42V
                    nsp15:F122FILV

                • #11
                  Eric Tool

                  Nu (Ν,ν) will be the @WHO name/Greek letter for the new variant. Better than B.1.1.529. That's about the only good thing you can say about it right now.

                  https://twitter.com/EricTopol/status...75943257481216

                  Comment


                  • #12
                    WHO calls special meeting to discuss new Covid variant found in South Africa with ‘a large number of mutations’

                    PUBLISHED THU, NOV 25 202112:45 PM EST
                    UPDATED THU, NOV 25 20214:49 PM EST

                    Hannah Miao

                    KEY POINTS
                    • WHO is monitoring a new Covid variant, scheduling a special meeting Friday to discuss what it may mean for vaccines and treatments, officials said.
                    • The variant, called B.1.1.529, has been detected in South Africa in small numbers.
                    • South African scientists have detected 30 mutations to the spike protein, the part of the virus that binds to cells in the body, which could have implications for vaccine efficacy and transmissibility.
                    https://www.cnbc.com/2021/11/25/who-....PostToTwitter

                    Comment


                    • #13
                      New COVID Variant, B.1.1.529, could be the most dangerous yet as it spreads to Israel
                      NOVEMBER 26, 2021

                      snip

                      The strain was first seen in Africa and raised concern with its 32 spike protein mutations, but it has now been reported in Israel.

                      The person infected had returned from a trip in Malawi.


                      Two others returning from trips are suspected to be infected with the strain as well.

                      All three people are currently quarantined. They are all vaccinated individuals as well.

                      snip

                      https://www.fingerlakes1.com/2021/11...ads-to-israel/

                      Comment


                      • #14
                        bump this

                        Comment


                        • #15
                          The video does not copy/paste - Dr. Vankerkhove says it will take a few weeks to fully understand this variant.

                          https://twitter.com/WHO


                          Dr @mvankerkhove gives an update on #COVID19 virus variant B.1.1.529, during the #AskWHO session on 25 November 2021

                          Comment

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