The Botswana Covid variant, described by experts as the worst strain ever, has all the worrying mutations from previous versions of the virus, plus many more that could make it the most infectious and vaccine-resistant one so far.
The super strain has acquired the mutations of Delta, which made that variant so transmissible that it became world-dominant in months.
And the new variant also includes the vaccine-resistant alterations seen on Beta — another strain of concern that emerged in South Africa and was thought to be best at escaping the immune system until now.
It also contains a drop-out mutation that helped the Alpha variant take off in the UK last winter. In total, the new super strain has 32 mutations on its spike protein, more than any variant before it and twice as many as Delta.
It contains two unique alterations on a specific part of the spike which help viruses open the door to human cells.
All warning signs suggest it will become world-dominant in months but scientists have cautioned they have not confirmed any of the effects of the mutations in a laboratory.
South Africa’s population has very high levels of natural immunity and seems to be spreading with ease, which UK experts think may allow it to easily infect former Covid patients.
But there is no rise in hospitalisations in the region, which raises hopes it could be a milder Covid iteration.
Here is everything we know about the variant so far:
The Botswana variant has around 50 mutations and more than 30 of them are on the spike protein. The current crop of vaccines trigger the body to recognise the version of the spike protein from older versions of the virus. But the mutations may make the spike protein look so different that the body’s immune system struggles to recognise it and fight it off. And three of the spike mutations (H665Y, N679K, P681H) help it enter the body’s cells more easily. Meanwhile, it is missing a membrane protein (NSP6) which was seen in earlier iterations of the virus, which experts think could make it more infectious. And it has two mutations (R203K and G204R) that have been present in all variants of concern so far and have been linked with infectiousness
What is so concerning about the variant?
Experts say it is the ‘worst variant they have ever seen’ and are alarmed by the number of mutations it carries.
The variant — which the World Health Organization has named Omicron — has 32 mutations on the spike protein — the most ever recorded and twice as many as the currently dominant Delta strain.
Experts fear the changes could make the vaccines 40 per cent less effective in a best-case scenario.
This is because so many of the changes on B.1.1.529 are on the virus’s spike protein.
The current crop of vaccines trigger the body to recognise the version of the spike from older versions of the virus.
But because the spike protein looks so different on the new strain, the body’s immune system may struggle to recognise it and fight it off.
It also includes mutations found on the Delta variant that allow it to spread more easily.
Experts warn they won’t know how much more infectious the virus is for at least two weeks and may not know its impact on Covid hospitalisations and deaths for up to six weeks.
What mutations does the variant have?
The Botswana variant has more than 50 mutations and more than 30 of them are on the spike protein.
It carries mutations P681H and N679K which are ‘rarely seen together’ and could make it yet more jab resistant.
These two mutations, along with H655Y, may also make it easier for the virus to sneak into the body’s cells.
And the mutation N501Y may make the strain more transmissible and was previously seen on the Kent ‘Alpha’ variant and Beta among others.
Two other mutations (R203K and G204R) could make the virus more infectious, while a mutation that is missing from this variant (NSP6) could increase its transmissibility.
It also carries mutations K417N and E484A that are similar to those on the South African ‘Beta’ variant that made it better able to dodge vaccines.
But it also has the N440K, found on Delta, and S477N, on the New York variant — which was linked with a surge of cases in the state in March — that has been linked to antibody escape.
Other mutations it has include G446S, T478K, Q493K, G496S, Q498R and Y505H, although their significance is not yet clear.
Will it affect Christmas in the UK?
Experts said it will be weeks until they know how worrying the new variant is, so it is not yet clear what extra steps might need to be taken in the run up to Christmas.
The only restrictions brought in by the Government so far has been to add six countries to the red list.
But Professor Adam Finn, a member of the Joint Committee on Vaccination and Immunisation (JCVI), said new restrictions cannot be ruled out.
He told ITV’s Good Morning Britain: ‘On the one hand, I don’t want to induce unnecessary anxiety in people, but on the other hand, I think we all need to be ready for the possibility of a change in the restrictions.’
And when asked what the situation would mean for the UK around the festive period, Health Secretary Sajid Javid said Plan B measures — including mandatory face masks and work from home guidance — would be brought in if needed to control infection rates.
Is it a variant of concern?
The World Health Organization has classified the virus as a ‘variant of concern’, the label given to the highest-risk strains.
This means WHO experts have concluded its mutations allow it to spread faster, cause more severe illness or hamper the protection from vaccines.
Where has the variant been detected so far?
The variant has so far been spotted in five nations: South Africa, Botswana, Hong Kong, Israel and Belgium.
Most cases have been spotted in Gauteng, a province in north east South Africa where Johannesburg is based.
The first case was uploaded to international variant database GISAID by Hong Kong and was spotted in someone who travelled to the country from South Africa.
No cases have been seen in the UK. But scientists do not sequence every positive Covid sample in the UK and not everyone who catches the virus will take a test.
This means there could be people infected with the variant in Britain.
What is the UK doing about the variant?
The Health Secretary announced last night six countries would be added to the red list from midday on Friday November 26.
The red-listed countries are: South Africa, Botswana, Eswatini, Lesotho, Namibia and Zimbabwe. This means all direct flights from these countries to the UK are banned.
Anyone arriving in England between midday today and 4am on Sunday from these countries — or who has been in the countries in the 10 previous days — must complete a passenger locator form, quarantine at home and should take a PCR test.
Anyone arriving from these countries after 4am on Sunday must stay in a managed quarantine hotel for 10 days and take a Covid test on or before the second day of their stay, as well as another test on or after day eight.
And the UK Health Security Agency classified B.1.1.529 as a Variant Under Investigation, which means it has worrying mutations.
Experts will now conduct a risk assessment and may increase its ranking to Variant of Concern if it is confirmed to be more infectious, cause more severe illness or make vaccines and medicines less effective.
Where did B.1.1.529 first emerge?
The first case was uploaded to international variant database GISAID by Hong Kong on November 23. The person carrying the new variant was travelling to the country from South Africa.
The UK was the first country to identify that the virus could be a threat and alerted other nations.
Since then, 77 cases have been confirmed in South Africa, two in Hong Kong and three in Botswana.
Health chiefs in Israel today announced it had one confirmed and two suspected B.1.1.529 cases, while there are two suspected cases in Belgium.
Experts believe the strain may have originated in Botswana, but continental Africa does not sequence many positive samples, so it may never be known where the variant first emerged.
Professor Francois Balloux, a geneticist at University College London, told MailOnline the virus likely emerged in a lingering infection in an immunocompromised patient, possibly someone with undiagnosed AIDS.
In patients with weakened immune systems infections can linger for months because the body is unable to fight it off. This gives the virus time to acquire mutations that allow it to get around the body’s defences.
Will I be protected if I have a booster?
Scientists have warned the new strain could make Covid vaccines 40 per cent less effective.
But they said emergence of the mutant variant makes it even more important to get a booster jab the minute people become eligible for one.
The vaccines trigger neutralising antibodies, which is the best protection available against the new variant. So the more of these antibodies a person has the better, experts said.
Health Secretary Sajid Javid said: ‘The booster jab was already important before we knew about this variant – but now, it could not be more important.’
When will we know more about the variant?
Data on how transmissible the new variant is and its effect on hospitalisations and deaths is still weeks away.
The UK has offered help to South Africa, where most of the cases are concentrated, to gather this information and believe they will know more about transmissibility in two to three weeks.
But it may be four to six weeks until they know more about hospitalisations and deaths.
What is the variant called?
The strain was scientifically named as B.1.1.529 on November 24, one day after it was spotted in Hong Kong, but has not yet been given a name based on letters of the Greek alphabet.
The variants given an official name so far include Alpha, Beta, Delta and Gamma.
Experts at the World Health Organization are holding emergency meetings about the variant today, during which it is expected to be named. It could be called the ‘Nu’ variant.