WHO to assess new highly mutated Covid-19 variant as countries ramp up health checks

Meeting will determine if B.1.1.529 variant warrants a designation as one of ‘interest’ or of ‘concern.’

Countries around the world are responding to news of a new coronavirus variant carrying an unusually large number of mutations. Photograph: Michele Spatari/AFP/Getty Images

Guardian- The World Health Organization will meet on Friday to assess a new variant detected in South Africa that is feared to be the worst Covid-19 variant yet identified.

The meeting will determine if the B.1.1.529 variant should be designated a variant of “interest” or of “concern”. The variant, which was identified on Tuesday, initially attracted attention because it carries an “extremely high number” of mutations.

Some world leaders have hastily responded by issuing new precautions and travel restrictions, while markets around the world saw falls sparked by the uncertainty.

Indian health officials on Friday put states on alert, asking them to carry out “rigorous screening and testing” of travellers who had arrived from South Africa, Botswana and Hong Kong, and to trace and test their contacts.

Health secretary Rajesh Bhushan urged all states to ensure that samples from Covid-positive travellers were swiftly sent to genome sequencing labs for testing.

Singapore, a major transit hub, said on Friday it would restrict arrivals from South Africa and countries nearby. All non-Singaporean or non-permanent residents with recent travel history to Botswana, Eswatini, Lesotho, Mozambique, Namibia, South Africa, and Zimbabwe will be denied entry or transit through Singapore, its health ministry said.

Italy announced a similar entry ban on Friday. “Our scientists are studying the new B.1.1.529 variant. In the meantime, we will adopt the greatest possible caution,” health minister Roberto Speranza said.

Japan, too, will clamp down on border controls for visitors from South Africa and five other African countries, the Jiji news service reported.

A health worker administers a nasal swab at a Testaro Covid-19 mobile testing site in Johannesburg.
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New Zealand is also closely monitoring global advice on the new variant, the ministry of health said. The deputy prime minister, Grant Robertson, said the new variant was “a real wake-up call for all of us, that this pandemic is still going” and reiterated the need to continue with caution.

Dr Maria Van Kerkhove, WHO’s technical lead on Covid-19, said in a press briefing on Thursday: “We don’t know very much about this [variant] yet. What we do know is that this variant has a large number of mutations. And the concern is that when you have so many mutations, it can have an impact on how the virus behaves.”

The infectious disease epidemiologist said that researchers would meet to “understand where these mutations are and what this potentially may mean” in terms of whether it is more transmissible or has potential to evade immunity.

A high number of mutations does not necessarily make a variant more transmissible. In August, similar concerns emerged about a variant in South Africa, known as C.1.2, but it was never listed as a variant of interest or concern. In Japan, some experts believe the country’s pronounced fall in cases was down to mutations that drove it towards “natural extinction”.

At the meeting the WHO may decide whether or not to give the B.1.1.529 variant a name from the Greek alphabet. If it does, it is likely to be named Nu, the next available letter.

England announced it was temporarily banning flights from South Africa, Namibia, Botswana, Zimbabwe, Lesotho and Eswatini from midnight on Friday, and that returning travellers from those destinations would have to quarantine. Israel has followed suit, saying it will ban its citizens from travelling to southern Africa.

UK civil service sources said the variant, which is feared to be more transmissible and has the potential to evade immunity, posed “a potentially significant threat to the vaccine programme which we have to protect at all costs”.

Britain’s health secretary, Sajid Javid, confirmed the UK Health Security Agency (UKHSA) was investigating, saying “more data is needed but we’re taking precautions now” in a tweet late on Thursday.

UKHSA chief executive Jenny Harries said: “This is the most significant variant we have encountered to date and urgent research is under way to learn more about its transmissibility, severity and vaccine-susceptibility.”

Scotland confirmed late on Thursday that all arrivals from South Africa, Namibia, Lesotho, Botswana, Eswatini and Zimbabwe will be required to self-isolate and take two PCR tests from midday on Friday, while anyone arriving after 4am on Saturday will need to stay at a managed quarantine hotel.

Australia’s health minister, Greg Hunt, said it was investigating and would swiftly close its borders to travellers from the African nation if the WHO were to classify it as a major new variant. “If the medical advice is that we need to change, we won’t hesitate,” he told reporters on Friday morning.

South Africa’s Foreign Ministry said Britain’s decision to ban flights from the nation “seems to have been rushed” voicing concerns over the potential damage to tourism and business in both countries.

Foreign minister Naledi Pandor said South Africa would engage with British authorities to try to get them to reconsider their decision.

Markets took a hit on Friday, with world stocks heading for a 0.7% fall – their largest weekly drop in nearly two months, Reuters reported.

South Africa’s rand fell 1%, Japan’s Nikkei was down 2.4% and Australian shares fell 0.6% in early trade, as did US crude futures. S&P 500 futures fell 0.4%, while the Australian and New Zealand dollars dropped to three-month lows.

“The trigger was news of this Covid variant …and the uncertainty as to what this means,” said Ray Attrill, head of FX strategy at National Australia Bank in Sydney. “You shoot first and ask questions later when this sort of news erupts.”

On Thursday, South Africa’s health minister Dr Joe Phaahla said the new variant could be driving a recent “exponential rise” in cases in Gauteng, a north-eastern province home to the city of Johannesburg.

B.1.1.529 is thought to contain a total of 32 unusual mutations to the spike protein, the part of the virus that most vaccines use to prime the immune system against Covid.

Penny Moore, a virologist at the University of Witwatersrand in Johannesburg, whose lab is assessing the variant, said: “We’re flying at warp speed.” She said there were anecdotal reports of reinfections but that it was too early to draw any conclusions.

Professor Tulio de Oliveira, director of South Africa’s centre for epidemic response and innovation, said the news was “really worrisome at the mutational level” and described the variant as being “of great concern”.

Variants of concern, such as Delta, show increased transmissibility, virulence or change in clinical disease, and a decreased effectiveness of public health and social measures. Variants of interest are those shown to cause community transmission in multiple clusters, and which have been detected in multiple countries, but have not yet necessarily proven to be more virulent or transmissible.

An infectious diseases specialist at the University of KwaZulu-Natal in Durban, Dr Richard Lessells, said the number of mutations “might affect how well the virus is neutralised” and may give the virus enhanced transmissibility.

South Africa has confirmed about 100 cases as B.1.1.529 but the variant has also been found in Botswana and Hong Kong, with the Hong Kong case a traveller from South Africa.

The significance of the variant so far remains unknown, with the coming days and weeks key to determining its severity.

“It will take a few weeks for us to understand what impact this variant has,” Kerkhove of the WHO said, adding the variant is “under monitoring” and “something to watch”.

Ewan Birney, the deputy director general of the European Molecular Biology Laboratory and a member of Spi-M, which advises the UK government, said it posed a risk of worsening the pandemic.

He urged countries not to repeat the mistake of failing to act quickly. “What we’ve learned from the other situations like this – some have turned out OK and some haven’t – is that whilst we’re [investigating] you have to be reasonably paranoid,” he said.

The 32 mutations in the spike protein is about double the number associated with the Delta variant. Mutations of this kind can affect the virus’s ability to infect cells and spread, but also make it harder for immune cells to attack the pathogen.

However, Africa Centers for Disease Control and Prevention chief John Nkengasong urged for caution. “There are so many variants out there but some of them are of no consequence on the trajectory of the epidemic,” he told a news conference on Thursday.

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Flights from six countries will be banned as officials review travel measures after scientists voice concern over variant

A health worker administers a nasal swab at a Testaro Covid-19 mobile testing site in Johannesburg.
A health worker administers a nasal swab at a Covid-19 mobile testing site in Johannesburg. Photograph: Bloomberg/Getty Images

Flights from southern Africa will be banned, with six countries placed under England’s red list travel restrictions, after scientists raised the alarm over what is feared to be the worst Covid-19 variant yet identified.

Whitehall sources said the B.1.1.529 variant, which is feared to be more transmissible and has the potential to evade immunity, posed “a potentially significant threat to the vaccine programme which we have to protect at all costs”.

Hundreds of people who have recently returned from South Africa, where the variant was detected, and neighbouring countries are expected to be tracked down and offered tests in an effort to avoid the new variant entering the UK.

Dr Tom Peacock of Imperial College London said the variant ‘could be of real concern’ but may just be an ‘odd cluster’
Scientists warn of new Covid variant with high number of mutations

The variant, which was identified on Tuesday, initially caused concern because it carries an “extremely high number” of mutations meaning that the spike protein looks different from the version that vaccines were designed to target. The latest data, presented by South African scientists on Thursday, revealed that the variant also appears to be more transmissible and is already present in provinces throughout the country.

As well as placing South Africa, Namibia, Lesotho, Botswana, Eswatini and Zimbabwe on England’s travel red list and banning flights from Friday, officials are reviewing a number of travel measures including whether there should be a limited reintroduction of the use of PCR tests for arrivals. Travellers who test positive will be strongly encouraged to take a PCR so that their results can be sequenced to test for variants. The Scottish government later confirmed all arrivals from the six countries will be required to self-isolate and take two PCR tests from midday on Friday, while anyone arriving after 4am on Saturday will need to stay at a managed quarantine hotel. There are no direct flights from any of the countries into Scotland.

Israel also announced it will ban its citizens from travelling to southern Africa – covering the same six countries as well as Mozambique – and barring the entry of foreign travellers from the region.

Announcing the move, the health secretary, Sajid Javid, said: “We’ve always been clear that we will take action to protect the progress that we have made.

“Our scientists are deeply concerned about this variant. I’m concerned, of course, that’s one of the reasons we have taken this action.”

He said that more work was needed to understand how concerning the variant is, adding: “From what we do know there’s a significant number of mutations, perhaps double the number of mutations that we have seen in the Delta variant.

“That would suggest that it may well be more transmissible and the current vaccines that we have may well be less effective.”

Ewan Birney, the deputy director general of the European Molecular Biology Laboratory and a member of Spi-M, which advises the UK government, said it posed a risk of worsening the pandemic.

He urged countries not to repeat the mistake of failing to act quickly. “What we’ve learned from the other situations like this – some have turned out OK and some haven’t – is that whilst we’re [investigating] you have to be reasonably paranoid,” he said.

The new variant was identified after a surge of cases in Gauteng, an urban area containing Pretoria and Johannesburg. Initially the cluster of cases, centred on a university, was assumed to be because of an increase in socialising.

However, this week the variant was identified as a potential cause of the increase. The first detected cases of the variant were collected in Botswana on 11 November and a case has also been found in Hong Kong – a 36-year-old man who tested positive while in quarantine after a trip to South Africa.

In the past 48 hours, South African scientists reviewed PCR test data from the Gauteng region and discovered the variant appeared to be behind the increase in cases, having risen to account for about 90% of cases in a matter of weeks. At a national level, South Africa’s daily number of infections hit 1,200 on Wednesday, up from 106 earlier in the month.

Speaking at a hastily called news conference on Thursday, the virologist Tulio de Oliveira said: “We can see very early signs that this lineage has rapidly increased in prevalence in Gauteng and may already be present in most provinces.”

Prof Anne von Gottberg, a clinical microbiologist and head of respiratory diseases at the National Institute of Communicable Diseases in South Africa, said there were now about 100 cases confirmed through full sequencing of samples, up from just 10 reported on Wednesday, and signs of community transmission.

Prof Richard Lessells, an infectious diseases specialist at the University of KwaZulu-Natal in Durban, said the coming days and weeks would be key to determining the severity of the variant. “At the beginning of a resurgence we sometimes get fooled into thinking everything is a milder disease, and that can be because it’s initially spreading in younger age groups, so we have to see as the spread becomes more generalised whether we are seeing cases of more severe disease,” he said.

“What gives us some concerns [is] that this variant might not just have enhanced transmissibility, so spreads more efficiently, but might also be able to get around parts of the immune system and the protection we have in our immune system,” he added.

Birney and other UK scientists called for new controls to be brought in immediately, saying that it would be preferable to reverse measures if the variant was found to be less of a concern than feared following further investigation.

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Until now, England no longer had any countries on the red list imposing quarantine on travellers arriving from abroad. People who are not fully vaccinated must test negative before flying and arrange two PCR tests on arrival. Those who are fully vaccinated need to have a Covid test within two days of landing.

The World Health Organization said it was “closely monitoring” the reported variant and was expected to convene a technical meeting on Friday to determine if it should be designated a variant of “interest” or of “concern”.

A No 10 spokesperson said: “We have one of the largest genomic sequencing programmes here in the UK that allows us to spot and track variants as they emerge and, as we have done throughout the pandemic, we will continue to keep an eye and keep this particular variant under investigation.”

Asked whether more travel restrictions would be needed before Christmas as a result of the variant, the spokesperson said: “If we believe we need to take action we will, but we will continue to monitor this variant and other variants in the same way that we have done throughout the pandemic.”

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WORLD STATS

Coronavirus Cases:

260,452,193

Deaths:

5,202,433

Recovered:

235,410,873
Highlighted in green
= all cases have recovered from the infection