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South Africa variant - 501.V2 thread

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  • South Africa variant - 501.V2 thread

    Dec 18th, 2020 | Minister Mkhize Speaks

    Health Minister Dr Zweli Mkhize on Friday announced that a variant of the SARS-COV-2 Virus (COVID-19) – currently termed the ‘501.V2 Variant’ – has been identified by genomics scientists in South Africa.

    Mkhize said a genomics team, led by the Kwazulu-Natal Research Innovation and Sequencing Platform, or KRISP, has sequenced hundreds of samples from across the country since the beginning of the pandemic in March. They noticed that a particular variant has increasingly dominated the findings of the samples collected in the past two months.

    In addition, clinicians have been providing anecdotal evidence of a shift in the clinical epidemiological picture- in particular noting that they are seeing a larger proportion of younger patients with no co-morbidities presenting with critical illness. The evidence that has been collated, therefore, strongly suggests that that the current second wave we are experiencing is being driven by this new variant.

    ... This particular virus has three mutations on the receptor-binding domain, which is the actual part of the virus that attaches to the human cell. One of the interpretations of these changes is that it increases the affinity for the ACE2 receptor. The other two mutations possible add some potential antibody escape but the full implications of the combination of the three mutations still need to be understood in more detail.”

  • #2
    South Africa identifies new coronavirus strain causing surge in cases

    JOHANNESBURG (Reuters) - South Africa has identified a new variant of the coronavirus that is driving a second wave of infections, the health minister said on Friday, days after Britain said it had also found a new variant of the virus boosting cases.

    “We have convened this public briefing today to announce that a variant of the SARS-COV-2 Virus - currently termed 501.V2 Variant - has been identified by our genomics scientists here in South Africa,” Minister of Health Zweli Mkhize tweeted.

    “The evidence that has been collated, therefore, strongly suggests that the current second wave we are experiencing is being driven by this new variant,” Mkhize added.


    South African health authorities said the new variant seemed to spread faster than the previous iteration, but that it was too early to tell its severity and whether current vaccines would work against it.

    “In the UK they have also identified a new variant ... there are quite a few similarities between the two lineages ... there are also a similar number of mutations” said Prof Tulio de Oliviera, a member of government’s genomics consortium in a televised briefing.


    • #3
      > quite a few similarities between the two lineages ... there are also a similar number of mutations”

      I haven't seen sequences or mutations yet, but this is hard to believe that the UK and SA strains have common mutations..
      Besides N501Y

      KRISP :

      data at GISAID, while claiming it were "public"
      I'm interested in expert panflu damage estimates
      my current links: ILI-charts:


      • #4
        bump this


        • #5
          December 19, 2020
          Dr Emma Hodcroft's current thread:

          Dr Emma Hodcroft@firefoxx66

          Is the new UK variant the same as the new South African variant (501Y.V2)?


          They both share the same mutation in spike: N501Y (N->Y at position 501). However, the 2 variants have arisen separately.

          12:14 PM · Dec 19, 2020·Twitter Web App

          Dr Emma Hodcroft

          In the tree below, the UK variant is in green at the top.

          The SA variant is the one with large yellow circles nearer the bottom.

          Though it's a bit hard to see in this tree, they are quite distant genetically: they have many mutations they do not share!

          UK variant & SA variant both have many other mutations that are being investigated.


          • #6
            Experts checking how COVID-19 variant emerged: Prof Karim

            19 December 2020, 9:30 PM

            Prof Karim says experts are also checking whether the vaccines that will be available next year will work with the variant of the virus.

            ...“How much of the virus has to change before we regard it as a change in the strain is something that has to be determined by the WHO. The level of reliability we are seeing now would not constitute a strain change. We are not dealing with strains at this time. We are just dealing with a variant so, if you wanna call it as it’s within the family,” says Karim.



            • #7
              South Africa appears to also have a rapidly transmissible strain that has arisen independently of the UK variant.


              It is feared the strain may now be immune to certain antibodies triggered at the start of the pandemic.

              Commenting on the strain, Dr Eric Feigl-Ding said: "New more worrisome South Africa strain: the new 501.V2 variant has troubling details as it seems to spread faster, has a higher viral load and possibly more severe among young adults."

              The health minister, Dr Zweli Mkhize has also stated it is unclear whether any current vaccine may have an effect on 501.V2.


            • #8
              Britain, Denmark, the Netherlands, and flights from South Africa to Turkey was halted

              Health Minister Fahrettin Koca said, "It has been decided to temporarily stop the flights from England, Denmark, the Netherlands and South Africa to our country." found in the description.
              Zafer Fatih Beyaz |20.12.2020
              Sağlık Bakanı Fahrettin Koca, "İngiltere, Danimarka, Hollanda ve Güney Afrika'dan ülkemize olan uçuşlarda geçici durdurma kararı alınmıştır." açıklamasında bulundu. - Anadolu Ajansı
              “Addressing chronic disease is an issue of human rights – that must be our call to arms"
              Richard Horton, Editor-in-Chief The Lancet

              ~~~~ Twitter:@GertvanderHoek ~~~ ~~~


              • #9
                New ‘more transmissible’ coronavirus variant discovered in UK

                New variant was brought in by travelers from South Africa.
                BY WILLIAM ADKINS
                December 23, 2020 5:44 pm

                British Health Secretary Matt Hancock announced that a new “highly concerning” variant of the coronavirus has been discovered in two individuals returning from South Africa.

                “It is yet more transmissible and it appeared to have mutated further than the new variant that has been discovered here,” Hancock said in Wednesday’s Downing Street news conference.

                The government is also asking anybody that has been to South Africa in the past two weeks and their close contacts to quarantine immediately. “These measures are temporary, while we investigate this further new strain, which is currently being analyzed,” he added.


                Last edited by sharon sanders; December 23, 2020, 01:47 PM. Reason: added bolding and red


                • #10


                  The number of deaths continues to rise at an alarming rate as well with 411 fatalities recorded in the last day.

                  Gladys Mutele | about 11 hours ago
                  JOHANNESBURG - South Africa has reported a record increase in coronavirus cases with 14,046 new cases detected in the past 24-hours.

                  This brings the total number of infections in the country to 954,258 since the start of the outbreak in March.

                  On Wednesday, the health ministry said it was concerned as this indicated that the virus continued to spread exponentially.

                  Health Minister Zweli Mkhize said the rate of the spread was much faster than the first wave, whose peak would be surpassed in the coming days.


                  This pushes the national COVID-19 related death toll to 25,657 with the most deaths recorded in the Western Cape, followed by Eastern Cape and KwaZulu-Natal.



                  (Okieman comment: I am pretty sure that the Western Cape, Eastern Cape and KwaZulu-Natal are the areas in South Africa where the new variant of Covid-19 has been found to be the most widespread.)


                  • #11

                    South Africa has reported a staggering 14,046 in new confirmed cases in the last 24-hours alone.

                    Thando Kubheka & Kaylynn Palm | about 6 hours ago
                    CAPE TOWN/JOHANNESBURG - The Western Cape Health Department is frantically trying to provide more beds for COVID-19 patients as the new variant of the virus tears through the nation like wildfire.

                    The province currently has the highest number of active cases and authorities say they're seeing around 570 hospital admissions across private and public facilities every single day.

                    The province suggested earlier this week that the peak would likely hit in the first week of January but that could change.

                    Western Cape Health's Sadiq Karrim said the rate of increase of new infections was alarming.

                    “Cases are still exponentially increasing and that’s why we’re trying to quickly bring online additional beds into the service platform. It’s hard to say at the moment when that peak is going to be, whether it’s early or mid-January, but at the moment we’re till noting a very exponential rise in our cases and hospitalisations.”




                    • #12
                      COVID-19 in SA: Western Cape could ask for military help
                      Wednesday 23 December 2020 - 5:21am

                      CAPE TOWN - Western Cape health authorities are looking to the South African military for help, amid the second wave of COVID-19 infections.

                      Hospitals across the province are under severe strain with health workers pleading for some form of reprieve. Coronavirus cases among health workers continue to spike, while their families, too, are being infected.

                      Private hospitals are also under pressure with patients being diverted to state hospitals and vice versa.


                      (Okieman comment: There is also a video worth watching. It is the mention of a spike in health care workers which caught my eye.)


                      • #13
                        Another new coronavirus variant found in Nigeria, says Africa CDC

                        DECEMBER 24, 20207:56 AM UPDATED 5 HOURS AGO
                        By Reuters Staff

                        NAIROBI (Reuters) - Another new variant of the novel coronavirus seems to have emerged in Nigeria, the head of Africa’s disease control body said on Thursday, cautioning more investigation was needed.

                        The news comes after Britain and South Africa both reported new variants of the SARS-CoV-2 virus that appear to be more contagious, leading to new travel restrictions and turmoil in markets.

                        “It’s a separate lineage from the UK and the South African lineages,” John Nkengasong, director of the Africa Centres for Disease Control and Prevention (CDC) told an online news conference from Addis Ababa.



                        • #14

                          Covid-19: Looking for glimmers of hope in second wave – SA health policy expert Prof Whiteside

                          24th December 2020 by Melani Nathan

                          South Africa is in the vice grip of a second wave of the Covid-19 virus. After a year of social isolation, financial pressure, emotional turmoil and fear Covid-19 is delivering an even more devastating blow. A new strain of Sars CoV-2 has been identified. It spreads more easily and younger, healthy people are succumbing to the disease in hospitals, Discovery Health’s Covid-19 expert Dr Ronald Whelan recently told This second wave is being driven by the new variant and healthcare experts are expressing concern that the latest wave has a much steeper curve with more deaths and intensive care unit admissions. The Western Cape‘s healthcare system is buckling under the wave and private facilities are sending patients into the public sector.




                          • #15

                            Mkhize criticises travel bans, saying there is 'no evidence' new SA variant is more dangerous

                            Matthew SavidesNight news editor

                            24 December 2020 - 22:40

                            Health minister Dr Zweli Mkhize.
                            Image: theo jeptha

                            Health minister Dr Zweli Mkhize on Thursday moved to allay fears that the fast-spreading newly-identified Covid-19 variant circulating in SA was more dangerous than variants in other countries.

                            In a statement on Christmas Eve, Mkhize said that there was "no evidence" of this.

                            And, said Mkhize, the decision to ban international travel from South Africa was not in line with current scientific evidence.