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Covid: New heavily mutated variant B.1.1.529 in South Africa raises concern


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So, what do we know?

The variant is called B.1.1.529 and is likely to be given a Greek code-name (like the Alpha and Delta variants) by the World Health Organization on Friday.

 

It is also incredibly heavily mutated. Prof Tulio de Oliveira, the director of the Centre for Epidemic Response and Innovation in South Africa, said there was an "unusual constellation of mutations" and that it was "very different" to other variants that have circulated.

"This variant did surprise us, it has a big jump on evolution [and] many more mutations that we expected," he said.

In a media briefing Prof de Oliveira said there were 50 mutations overall and more than 30 on the spike protein, which is the target of most vaccines and the key the virus uses to unlock the doorway into our body's cells.

Zooming in even further to the receptor binding domain (that's the part of the virus that makes first contact with our body's cells), it has 10 mutations compared to just two for the Delta variant that swept the world.

This level of mutation has most likely come from a single patient who was unable to beat the virus.

A lot of mutation doesn't automatically mean: bad. It is important to know what those mutations are actually doing.

 

But the concern is this virus is now radically different to the original that emerged in Wuhan, China. That means vaccines, which were designed using the original strain, may not be as effective.

Some of the mutations have been seen before in other variants, which gives some insight their likely role in this variant.

For example N501Y seems to make it easier for a coronavirus to spread. There are others in there that make it harder for antibodies to recognise the virus and might make vaccines less effective, but there are others that are completely new.

Prof Richard Lessells, from the University of KwaZulu-Natal in South Africa, said: "They give us concern this virus might have enhanced transmissibility, enhanced ability to spread from person to person, but might also be able to get around parts of the immune system."

There have been many examples of variants that have seemed scary on paper, but came to nothing. The Beta variant was at the top of people's concerns at the beginning of the year because it was the best at escaping the immune system. But in the end it was the faster-spreading Delta that took over the world.

Prof Ravi Gupta, from the University of Cambridge, said: "Beta was all immune escape and nothing else, Delta had infectivity and modest immune escape, this potentially has both to high degrees."

Scientific studies in the laboratory will yield give a clearer picture, but answers will come more quickly from monitoring the virus in the real world.

It is still early to draw clear conclusions, but there are already signs that are causing worry.

There have been 77 fully confirmed cases in Gauteng province in South Africa, four cases in Botswana and one in Hong Kong (which is directly linked to travel from South Africa).

However, there are clues the variant has spread even more widely.

This variant seems to give quirky results (known as an S-gene dropout) in the standard tests and that can be used to track the variant without doing a full genetic analysis.

That suggests 90% of cases in Gauteng may already be this variant and it "may already be present in most provinces" in South Africa.

But this does not tell us whether it spreads faster than Delta, is any more severe or to what extent it can evade the immune protection that comes from vaccination.

It also does not tell us how well the variant will spread in countries with much higher vaccination rates than the 24% of South Africa that is fully vaccinated, although large numbers of people in the country have had Covid.

So for now we are left with a variant that raises significant concerns despite huge holes in our knowledge, and is one that needs to be watched closely and asks deep questions about what to do and when. The lesson of the pandemic is you can't always wait until you have all the answers.

 
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New COVID-19 variant: Govt issues alert over South African strain; 10 points to know

The Union Health Ministry, on November 25, issued an alert for the B.1.1.529 variant of coronavirus, which was detected in South Africa.

The Union Health Ministry, on November 25, issued an alert for the B.1.1.529 variant of coronavirus, which was detected in South Africa. The ministry directed states and Union Territories (UTs) to ensure “rigorous screening and testing” of all international travellers landing in India from countries that are ‘at risk’.

 
 

Confirmed cases of the new variant have been reported from South Africa, Hong Kong and Botswana.

In a letter to all states and UTs, Union Health Secretary Rajesh Bhushan wrote, "This variant is reported to have a significantly high number of mutations, and thus, has serious public health implications for the country, in view of recently relaxed visa restrictions and opening up of international travel."

Here are 10 key points you need to know about B.1.1.529 variant of Covid-19

1. South African scientists have confirmed nearly 100 cases of B.1.1.529 but the variant has also been identified in Botswana and Hong Kong. The case identified in Hong Kong is a traveller from South Africa. The variant was first spotted in Botswana and only 10 cases have been confirmed via genomic sequencing so far.

2. “Although the data are limited, our experts are working overtime with all the established surveillance systems to understand the new variant and what the potential implications could be,” South Africa’s National Institute of Communicable Diseases said in a statement.

3. South Africa was the first country to detect the Beta variant last year. Beta is one of the only four labelled “of concern” by the WHO because it is comparatively more contagious and COVID-19 vaccines work less well against it.

4. South African Health Minister Joe Phaahla noted it was too early to say that whether the government would impose tougher restrictions in response to the newly discovered variant.

5. Director of Center for Epidemic Response and Innovation (CERI) Tulio de Oliviera also appealed to billionaires like Jeff Bezos, Bill Gates, Elon Musk, Dr. Pat Soon-Shiong and Warren Buffett as well as global institutions like World Bank and IMF to support Africa and South Africa financially in their fight against COVID-19 variants.

6. Australian government has said it is investigating the newly identified variant spreading in South Africa. The government has also warned that it may close borders to travellers from the African nations if risks from the new strain rise.

7. UK Secretary of State for Health and Social Care Sajid Javid tweeted, “COVID-19 UPDATE: UKHSA is investigating a new variant. More data is needed but we’re taking precautions now. From noon tomorrow, six African countries will be added to the red list, flights will be temporarily banned, and UK travellers must quarantine.”

8. Imperial College London epidemiologist Neil Ferguson said B.1.1529 has an “unprecedented” number of mutations in the spike protein and is driving a recent rapid increase in the number of cases in South Africa.

9. UK Health Security Agency has also expressed its concern about the newly identified variant of the novel coronavirus spreading in South Africa that could make vaccination less effective. The agency said this variant has a spike protein that is different from the one in the original coronavirus on which the vaccines are based.

10. The WHO has designated four variants of the novel coronavirus as “variants of concern” – Alpha or the UK variant (B.1.17), Beta or the South African variant (B.1.351), Gamma or the Brazil variant (P.1) and Delta or the Indian variant (B.1.617.2).

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Belgium reports Europe's first case of new COVID-19 variant

The new COVID-19 variant identified in southern Africa led to investors dump riskier assets across markets with European stocks falling the most since July while emerging markets slumped.

Belgium has detected the first case of the new coronavirus variant which was first found in South Africa, a virologist said on Friday.

 
 

Marc Van Ranst, whose laboratory works closely with Belgium's public health body Sciensano, said on Twitter that the variant was found in a traveller returning in Belgium from Egypt on Nov 11. The person developed the first symptoms on Nov. 22, the virologist said.

The new COVID-19 variant identified in southern Africa led to investors dump riskier assets across markets with European stocks falling the most since July while emerging markets slumped.

Earlier today, Israel also identified its first case of the new COVID-19 variant. “The variant discovered in southern African states has been identified in Israel,” the Israeli health ministry said.

The B.1.1.529 variant has been detected in relatively small numbers in Botswana, Hong Kong and South Africa but the authorities are perturbed by its high number of mutations that could evade the body’s immune response and become more transmissible.

World Health Organization’s Technical Advisory Group on Virus Evolution (TAG-VE) earlier today announced that it will meet to discuss whether this variant should be classified as a variant of interest or a variant of concern.

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