Announcement

Collapse
No announcement yet.

UK - B.1.1.7 Variant of COVID19 coronavirus thread. More contagious. May increase the death rate by a multiple of 1.3

Collapse
This is a sticky topic.
X
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #61
    Source: https://www.cnn.com/2020/12/23/healt...-19/index.html

    Genetics experts worry coronavirus vaccines might not work quite as well against UK variant
    By Elizabeth Cohen, CNN Senior Medical Correspondent
    Updated 6:14 PM ET, Wed December 23, 2020

    (CNN)Michael Worobey, a biologist at the University of Arizona, has seen more than 100,000 different strains of the virus that causes Covid-19. But when he saw the new variant from the UK, he noticed something different.

    "This is the first variant I've seen during the whole pandemic where I took a step back and said: 'Whoa,' " he remembers.
    Health officials have downplayed the possibility that the coronavirus vaccines won't work against the UK strain, but Worobey and other scientists thinks it's a possibility -- and it's just a possibility -- that this new variant might, to a small extent, outsmart the vaccines.

    "This is the first variant I've seen where I think there is this burning question," said Worobey, head of the department of ecology and evolutionary biology at the University of Arizona...

    Comment


    • #62

      The UK has recorded 744 more deaths, the highest daily toll since last Spring, along with more than 39,000 new coronavirus cases - the highest case number yet.

      The Government said a further 744 people had died within 28 days of testing positive for Covid-19 as of Wednesday, bringing the UK total to 69,051.

      It is the highest deaths figure reported on one day since April 29 during the first peak of the virus.

      more....

      https://www.standard.co.uk/news/uk/u...s-b460321.html

      Comment


      • #63

        UK coronavirus variant found in Malaysia and Singapore
        ---------------------------------------------------------
        Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England
        https://cmmid.github.io/topics/covid...l-variant.html
        56% more transmissible
        found no evidence for greater or lesser severity
        Our estimates suggest that control measures of a similar stringency to the national lockdown
        implemented in England in November 2020 are unlikely to reduce the effective reproduction
        number Rt to less than 1, unless primary schools, secondary schools, and universities are also closed.
        -----------------------------------------------
        there is another strain , B.1.1.70 with equally many mutations, again mostly nonsynonymous,
        but not so many in spike, which grew remarcably. But only in Wales it rarely went to England.
        http://magictour.free.fr/b117a.GIF
        ------------------------------------------
        England bans flights and visitors from South Africa due to coronavirus mutation
        in SA, cases are increasing at a slower rate since 1 week, still increasing a lot, though
        http://magictour.free.fr/e-1222.GIF
        --------------------------------------------------------
        China bans flights to and from the UK due to coronavirus mutation
        -----------------------------------------------------
        Detection of SARS-CoV-2 P681H Spike Protein Variant in Nigeria
        -------------------------------------------------
        Last edited by gsgs; December 24, 2020, 03:20 AM.
        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
          33 cases of B.1.1.7 SARS-CoV-2 in Denmark from 14 nov to 14 dec out
          of 7805 genomes. 12 of these from contact tracing.
          --------------------------------------------------

          one "South-African" virus is now at cogconsortium.uk , it has these 24 mutations ::
          >England/ALDP-C497BF/2020,UK,UK-ENG,2020-12-12,50,B.1.351,1.0,G,N,L,A,Y,Y,T,P,Q,ref,24
          G174T,C241T,C1059T,A2692T,C3037T,C4202T,G5230T,T61 06C,C9344T,A10323G,
          C14408T,A21801C,A22206G,G22813T,G23012A,A23063T,A2 3403G,C23664T,G25563T,C25904T,
          C26456T,T27193C,C28253T,C28887T
          -----------------------------------------------------------------
          @AineToole 1h
          We're now hosting a daily global report tracking new variant #SARSCoV2 lineage B.1.1.7 and B.1.351 on
          http://cov-lineages.org/global_report.html
          Data displayed in the report pulled from GISAID this morning 2020-12-24 and pangolin was
          run on the entire dataset.
          --------------------------------------------------------------------
          Introduction into the Marseille geographical area of a mild SARS-CoV-2 variant originating from
          sub-Saharan Africa https://medrxiv.org/cgi/content/shor....23.20248758v1 #medRxiv
          have been submitted to the GISAID database.
          The Marseille-1 variant emerged in week 27, when it accounted for 100% of
          sequenced genomes (Figure 1)
          We obtained SARS-CoV-2 full-
          length genome sequences from 916 patients (submitted to the GISAID database). These
          included 429 genomes from episode 2, which were added to 487 genomes from episode 1 11.
          we cannot rule out that the mutations observed in the Marseille-1 variant
          ... occurred in an animal population in sub-Saharan countries,
          # they really should hve told us earlier. The strains in SA and UK may have been deteted earlier.
          # This scientific process with publishing in papers and funding is unfortunate
          # Why is it so bad for researchers to report about interesting facts directly ?
          # Can't we protect their "copyright" if they do ?


          ------------------------------------------------------
          SAGE : The entire UK needs to go into Tier 4 *TODAY*
          Last edited by gsgs; December 24, 2020, 11:23 AM.

        • Sally Furniss
          Sally Furniss commented
          Editing a comment
          I assume a higher viral load means that fomites carry a higher viral load too?

        • gsgs
          gsgs commented
          Editing a comment
          I'd assume it grows better in human respiratory cells.

          several possibilities :
          More viruses per cell
          Replicates faster
          More successful to find new cells
          Escapes better the antibodies
          ...

          --------------------------------------------------------
          wrt. the more infections in younger people - I now read this could just have been
          because of lockdown with schools open.

      • #64
        Genetics experts worry coronavirus vaccines might not work quite as well against UK variant
        By Elizabeth Cohen, CNN Senior Medical Correspondent
        Updated 10:28 PM ET, Wed December 23, 2020

        (CNN)Michael Worobey, a biologist at the University of Arizona, has seen more than 100,000 different strains of the virus that causes Covid-19. But when he saw the new variant from the UK, he noticed something different.

        "This is the first variant I've seen during the whole pandemic where I took a step back and said: 'Whoa,' " he remembers.
        Health officials have downplayed the possibility that the coronavirus vaccines won't work against the UK strain, but Worobey and other scientists thinks it's a possibility -- and it's just a possibility -- that this new variant might, to a small extent, outsmart the vaccines.

        <snip>

        https://www.cnn.com/2020/12/23/healt...-19/index.html

        Comment


        • #65
          New COVID variant reaches Germany from UK

          Date 24.12.2020

          German authorities on Thursday confirmed the presence of the new coronavirus variant on German soil, adding to fears that the it could start spreading beyond the UK and South Africa.

          A woman who flew in from London Heathrow this Sunday tested positive at the Frankfurt airport. Further genetic analysis of the sample at a lab in Berlin identified a case of B.1.1.7, as the variant is known, said authorities in the German state of Baden-Württenberg in a statement.

          "It is the first known case in Germany," they said.

          https://www.dw.com/en/new-covid-vari...-uk/a-56054140

          Comment


          • #66
            Interesting thread on S gene dropouts in PCR tests that are increasing in the US. Indicative that the B.1.1.7 variant may be
            present as it has this effect on PCR tests. The UK used the same technique to track the variant there.
            - we observe S gene drop out since mid October in US. Up to 0.5% last week.
            t looks like the highly contagious UK COVID-19 variant (B.1.1.7) is probably undergoing community
            transmission in at least MA, OH, and FL, based on prevalence of S-dropout tests increasing over
            time. If the 0.25% increase is representative, that’d be ~500 cases/day vs. UK’s 15k.
            ----------------------------------------------------------------------------------------
            Two new sequences of B.1.1.7 lineage from Hongkong and one from Israel. One of the genome
            from Hongkong doesn't have HV69-70 and Y144 deletion (GISAID: EPI_ISL_733577).
            -----------------------------------------------------------------------------------------
            that looks as if it was imported through the tunnel
            https://twitter.com/DrEricDing/statu...596544/photo/1
            --------------------------------------------------------------------------------------------

            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
              CDC (USA) to Require Negative COVID-19 Test from Air Travelers from the UK since Dec.28

          • #67
            Look at the time. 11:09 PM



            From: "Media@cdc.gov (CDC)" <sohco@CDC.GOV>
            To: MMWR-MEDIA@LISTSERV.CDC.GOV
            Subject: CDC Media Statement: CDC to Require Negative COVID-19 Test from Air Travelers from United Kingdom
            Date: Dec 24, 2020 11:09 PM




            Media Statement

            For Immediate Release
            Thursday, December 24, 2020
            Contact: CDC Media Relations
            (404) 639-3286

            CDC to Require Negative COVID-19 Test from Air Travelers from the United Kingdom


            Today, President Trump is taking another step to protect the health of the American people by requiring air passengers arriving from the United Kingdom (U.K.) to test negative, via PCR or Antigen test, no more than 72 hours before departure from the U.K. to the United States.

            The public health authorities in the United Kingdom recently announced the discovery of a new variant of SARS-CoV-2. Viruses constantly change through mutation, and preliminary analysis in the U.K. suggests that this new variant may be up to 70% more transmissible than previously circulating variants.

            On March 14, President Trump issued a Presidential Proclamation to suspend the entry of foreign nationals who visited the United Kingdom in the past 14 days. This has reduced air travel to the U.S. from the U.K. by about 90%. This additional testing requirement will fortify our protection of the American public to improve their health and safety and ensure responsible international travel. The order is consistent with existing CDC testing guidance and U.S. Department of Transportation / Federal Aviation Administration guidance in the “Roadway to Recovery” document.

            This new order is consistent with the measures that have been taken so far to increase our ability to detect and contain COVID-19 proactively and aggressively.

            Passengers are required to get a viral test (i.e., a test for current infection) within the 3 days before their flight from the U.K. to the U.S. departs, and provide written documentation of their laboratory test result (in hard copy or electronic) to the airline. Airlines must confirm the negative test result for all passengers before they board. If a passenger chooses not to take a test, the airline must deny boarding to the passenger.


            This order will be signed tomorrow, December 25, and become effective on December 28, 2020.

            Comment


            • #68
              Originally posted by sharon sanders View Post
              Look at the time. 11:09 PM



              From: "Media@cdc.gov (CDC)" <sohco@CDC.GOV>
              To: MMWR-MEDIA@LISTSERV.CDC.GOV
              Subject: CDC Media Statement: CDC to Require Negative COVID-19 Test from Air Travelers from United Kingdom
              Date: Dec 24, 2020 11:09 PM




              Media Statement

              For Immediate Release
              Thursday, December 24, 2020
              Contact: CDC Media Relations
              (404) 639-3286

              CDC to Require Negative COVID-19 Test from Air Travelers from the United Kingdom


              Today, President Trump is taking another step to protect the health of the American people by requiring air passengers arriving from the United Kingdom (U.K.) to test negative, via PCR or Antigen test, no more than 72 hours before departure from the U.K. to the United States.

              The public health authorities in the United Kingdom recently announced the discovery of a new variant of SARS-CoV-2. Viruses constantly change through mutation, and preliminary analysis in the U.K. suggests that this new variant may be up to 70% more transmissible than previously circulating variants.

              On March 14, President Trump issued a Presidential Proclamation to suspend the entry of foreign nationals who visited the United Kingdom in the past 14 days. This has reduced air travel to the U.S. from the U.K. by about 90%. This additional testing requirement will fortify our protection of the American public to improve their health and safety and ensure responsible international travel. The order is consistent with existing CDC testing guidance and U.S. Department of Transportation / Federal Aviation Administration guidance in the “Roadway to Recovery” document.

              This new order is consistent with the measures that have been taken so far to increase our ability to detect and contain COVID-19 proactively and aggressively.

              Passengers are required to get a viral test (i.e., a test for current infection) within the 3 days before their flight from the U.K. to the U.S. departs, and provide written documentation of their laboratory test result (in hard copy or electronic) to the airline. Airlines must confirm the negative test result for all passengers before they board. If a passenger chooses not to take a test, the airline must deny boarding to the passenger.


              This order will be signed tomorrow, December 25, and become effective on December 28, 2020.

              Too late.

              Comment


              • #69
                many S-gene dropouts in USA (mainly MA) since October :
                https://twitter.com/alexbolze/status...55134943879170
                these could be B.1.1.7 (or B.1.5 = DK,minks)
                -------------------------------------
                La Comunidad de Madrid confirma cuatro casos de la cepa británica B.1.1.7 del COVID-19
                ----------------------------------
                Last edited by gsgs; December 26, 2020, 07:22 AM.
                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
                  > My husband and I oversee a few labs with high volume Covid testing.
                  > We have been watching for S gene drop-outs in the tests that we know
                  > don’t cover the S gene in B.1.1.7 but would detect ORF1ab and N gene.
                  > None detected by far in our US-based labs. It’ll be here soon.
                  ------------------------------------------------------------
                  I wonder what that dropout means, is it like this 218-"deletion" that we see in
                  >England/ALDP-C497BF/2020,UK,UK-ENG,2020-12-12,50,B.1.351,1.0,G,N,L,A,Y,Y,T,P,Q,ref
                  {South Africa -variant}
                  at position 22323-22540 ? the other 2 deletions are at 11288-11296 and 22281-22289
                  ---------------------------------------------------------
                  when the dropout is easy to detect, that may be a method to find and eliminate the
                  new English variant, {but not the others in South Africa, Nigeria? and all the future ones ?!}
                  -------------------------------------------------
                  Last edited by gsgs; December 26, 2020, 11:39 PM.

                • gsgs
                  gsgs commented
                  Editing a comment
                  @Cedders68
                  Should a PCR test be developed to look specifically for the 501Y spike RNA?
                  That would allow batch testing for the new variant among multiple samples where
                  occurrence of the variant is low? S drop-out doesn't
                  ----------------------------------------------------------

              • #70

                New variant report 2020-12-27

                Data source and processing


                All whole genome SARS-CoV-2 sequences were pulled from GISAID at 2020-12-27 12:19 GMT. The genomes were de-duplicated based on GISAID sequence name – note that the publically available metadata may not fully allow us to de-duplicate by patient. Full data processing pipeline found here.

                The sequences were then assigned lineages with pangolin v2.1.3, pangoLEARN version 2020-12-17.

                Pangolin assigns B.1.1.7 to sequences with more than 4 of the 17 defining B.1.1.7 SNPs – defined here – and B.1.351 to any sequences with more than 3 of the 5 defining B.1.351 SNPs.

                https://cov-lineages.org/global_report.html



                Comment


                • #71
                  COVID variant first identified in UK found in South Korea

                  Monday 28 December 2020 01:52, UK

                  South Korea has become the latest country to confirm the presence of the new coronavirus variant.

                  ... The Korea Disease Control and Prevention Agency said the variant had been seen in three people who arrived in South Korea from London on 22 December.

                  https://news.sky.com/story/covid-var...korea-12173983

                  Comment


                  • #72
                    @alanmcn1
                    Our % positive has jumped from 2 to 8 % over Xmas weekend.
                    S drop out sitting at 80% of those positives
                    (Birmingham)
                    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
                      @theosanderson
                      https://assets.publishing.service.go...ng_2_FINAL.pdf
                      S dropout now appears a very good indication of B.1.1.7 in all regions.
                      Roughly a third of swab tests are carried out with the TaqPath assay that serendipitously
                      allows this S dropout detection of B.1.1.7.
                      No differences seen in reinfections (small N in each case)
                      Big increase seen in secondary attack rate, consistent with increased transmission
                      (And an impressively powered analysis)
                      ---------------------------------------------
                      @youyanggu
                      I estimate that by the end of January, just 2% of the US population will have gained
                      full immunity by vaccination alone
                      ---------------------------------------------------------
                      @TWenseleers
                      More infectious SARS-CoV2 VOC 202012/01 strain is spreading at a similar rate across
                      the whole UK. Clearly not a founder effect. >90% of all infections will be by this strain
                      across the UK by February 1st.
                      ------
                      The study also calculated that either much stricter measures (such as prolonged remote
                      education) or vaccinating 0.4% of the whole population per day would be required to contain it.
                      The severity & infection fatality rate is most likely similar to that of the original type.
                      -----------

                    • gsgs
                      gsgs commented
                      Editing a comment
                      @HewittPete
                      This is worth watching. So far Denmark - which has a superb virus sequencing programme -
                      isn't seeing B117 growing faster than other lineages. T
                      -----------------------------------

                  • #73
                    Update: New UK, South African variant Covid strains detected in Finland

                    Three people have been diagnosed with two different strains of the virus.

                    Three people who recently returned to Finland from abroad have been diagnosed with new strains of the coronavirus, according to a joint press release from the Ministry of Social Affairs and Health (STM), the Finnish Institute for Health and Welfare (THL) and the Helsinki University Hospital District (HUS).

                    Two of the infections are a variant of the coronavirus that was recently identified in the UK and one has been confirmed to have been infected by the variant found in South Africa.

                    The strains were identified in a collaboration between the HUS and the virology laboratories of the University of Helsinki.

                    According to the joint statement, the infected patients are presently in good condition and are being treated in isolation. People who may have been exposed to the new virus variants have been quarantined and have been asked to undergo a coronavirus test.

                    <snip>

                    https://yle.fi/uutiset/osasto/news/u...nland/11716211

                    Comment


                    • gsgs
                      gsgs commented
                      Editing a comment
                      > Three people have been diagnosed with two different strains of the virus.

                      no double-infections, but just 3 people with a new lineage
                      -----------------------------------------------------------------
                      UK's new COVID-19 variant found in Nigeria, scientists say
                      -------------------------------------------------------------
                      Last edited by gsgs; December 30, 2020, 11:20 PM.

                  • #74
                    imperial college report 42 about b117 : https://www.imperial.ac.uk/media/imp...eprint-VOC.pdf

                    I'm interested in expert panflu damage estimates
                    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                    Comment


                    • #75
                      TWiV700,
                      02:40 , PHE technical briefing #2 ,
                      0900 wild-type def.
                      11:00 transmissible
                      16:07-16:59 silent = censored ? ,
                      1800 "allegedly" ,
                      {so proud he(VR) found a new word to obfuscate probability estimates ...
                      also "may" - but not "proof" , he is OK with possible (likely?) -but not proven-
                      increased transmissibility of b117}
                      25:00 never seen in an outbreak a virus becomes more and more transmissible
                      doesn't make sense to me
                      {but that's what usually happens, IMO, see seasonal flu}
                      41:00 immunocompromised
                      47:20 Daniel Griffin ... different topic
                      I'm interested in expert panflu damage estimates
                      my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                      Comment

                      Working...
                      X