New COVID variant emerges in southern Africa

Anastasia Tsirtsakis

26/11/2021 4:43:29 PM

B.1.1.529 has double the mutations of Delta and fuelled a rapid rise in cases in South Africa. What could it mean for vaccine-induced immunity?

A man undergoing a PCR test.
Around 100 cases of the variant B.1.1.529 have been confirmed in South Africa so far. Photo: AAP

When vaccination became a tool for countries around the world in the fight against COVID-19, many breathed a collective sigh of relief. In conjunction with other public health measures, a possible end to the pandemic was thought to be in the sight.
But experts have been warning that lagging vaccination rates around the world – either due to inequity or hesitancy – could result in new viral mutations. Now that prediction may be coming to fruition.
B.1.1.529, a new strain of coronavirus identified in Botswana earlier this month, is being branded the ‘worst’ one yet.
Around 100 cases have been confirmed in South Africa, with some scientists attributing the variant to the country’s rapid rise in cases, particularly among young people and in schools. The country’s cases went up from 868 on 23 November to 2465 on 25 November.
Scientists, who are working rapidly to determine the characteristics of the variant, have found the spike protein varies significantly from that of the original strain, which has been used to develop the current vaccines in circulation.
Due to a number of mutations – potentially more than double those found in the highly infectious Delta strain – there are concerns B.1.1.529 could evade antibodies created by either vaccination or natural infection.
While more than 2.8 million South Africans have recovered from COVID-19 infection since the start of the pandemic, just 24% of the population is fully vaccinated.
The World Health Organization’s (WHO) working group on virus evolution scheduled an emergency meeting to discuss the variant on Friday.
In the meantime, as an early precautionary measure, the UK has announced a temporary ban on flights from South Africa, as well as Botswana, Namibia, Zimbabwe, Lesotho and Eswatini. Returned travellers from the six destinations are also being directed to quarantine in a hotel.
While a number of unknowns remain about the variant, the UK’s Health Secretary Sajid Javid said the significant number of mutations identified has raised some alarm.
‘That would suggest that it may well be more transmissible and the current vaccines that we have may well be less effective,’ he said.
So far, the variant has only been detected in Botswana, South Africa and in travellers from South Africa to Hong Kong.
Scientists have identified 50 mutations overall in B.1.1.529. The spike protein alone has 32 mutations, while the receptor binding domain has 10 mutations compared to just two found in the Delta variant.
As well as the possibility of the variant evading vaccine-induced antibodies, computer modelling suggests it has the potential to evade immunity from T cells.
While it is likely to take weeks to gather all information about the new variant’s characteristics, Professor Tulio de Oliveira, Director of South Africa’s Centre for Epidemic Response and Innovation, says the emerging data has him very worried.
He estimates that about 90% of new cases in the region of Gauteng, where Johannesburg is located, have been caused by the new variant. But preliminary results from genotyping tests suggest that the variant could be spreading even wider.
‘This variant did surprise us,’ Professor de Oliveira said. ‘It has a big jump on evolution [and] many more mutations than we expected.
‘The one piece of good news is that it can be detected by a PCR test.’
The variant has raised some concern for Australia as it eases restrictions, with international travel now back on the table.
However, Federal Health Minister Greg Hunt, who was briefed by Chief Medical Officer Paul Kelly and Department of Health Secretary Professor Brendan Murphy on Friday morning, said there will be no change to Australia’s international border policy at this stage – although he did not rule it out entirely. 
‘At this point in time there’s very little traffic directly between South Africa and Australia,’ he said.
‘We also happen to be very, very highly vaccinated now … 92.1% of the 16-plus population.
‘But we will continue to be flexible and when tough decisions need to be made, we haven’t shied away in the past and we won’t shy away in the future.’
The most recent repatriation flight from South Africa to Australia arrived almost two weeks ago, with returning travellers being directed through the quarantine facility in Howard Springs in the Northern Territory.
Minister Hunt said local health officials are working with the WHO and international partners to investigate the new variant.
Ewan Birney, Deputy Director-General of the European Molecular Biology Laboratory, said that early evidence from genomic surveillance ‘is a serious cause for concern’ and that ‘early action is far better than late action’.
‘It may turn out that this variant is not as large a threat as Alpha and Delta, but the potential consequences of not acting on the possibility it could be are serious,’ he said.
The WHO currently has B.1.1.529 listed as a ‘variant under monitoring’. If determined to be a variant of concern, it is likely to be assigned the Greek letter ‘Nu’.
Dr Richard Lessells, an infectious disease physician at University of KwaZulu-Natal in South Africa, stressed that there is still a lot that is yet to be understood about the variant.
‘It gives us concern that this variant may already be circulating quite widely in the country [but] the really key question comes around disease severity,’ he said.
‘Now we need to do the work to understand the significance of this variant and what it means for the response to the pandemic.’
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