January 4, 2021

expert reaction to the South African variant

Several journalists have asked us about the South African variant of SARS-CoV-2, so here are some comments from scientists.

Dr Julian W Tang, Honorary Associate Professor/Clinical Virologist at the University of Leicester, said:

“The South African variant (B.1.351 or 501Y.V2) differs significantly from the UK B.1.1.7(variant) in several ways that may impact on vaccine effectiveness.

“Both variants share the N501Y mutation in the viral S gene which lies in the receptor binding domain (RBD) – where the virus binds to the host cell – and where vaccine-induced antibodies bind to the virus.  But the South African variant has two more mutations – E484K and K417N – in this RBD region that are absent in the UK variant. These two additional mutations may interfere more with vaccine effectiveness in the South African variant than in the UK variant.

“This does not mean that the existing COVID-19 vaccines will not work at all, just that the antibodies induced by the current vaccines may not bind and neutralise the South African variant as well as it would the other circulating viruses – including the UK variant.

“Even if the South African variant becomes more widespread and dominant, the mRNA (Pfizer-BioNTech and Moderna) and adenovirus-vectored (Oxford-Astrazeneca and Russian Sputnik V) vaccines can be modified to be more close-fitting and effective against this variant in a few months.

“Meanwhile, most of us believe that the existing vaccines are likely to work to some extent to reduce infection/ transmission rates and severe disease against both the UK and South African variants – as the various mutations have not altered the S protein shape that the current vaccine induced antibodies will not bind at all.”

Prof Francois Balloux, Professor of Computational Systems Biology and Director, UCL Genetics Institute, University College London, said:

“The ‘South African variant’ carries a mutation in the spike protein called E484K, which is not present in the ‘UK strain’. The E484K mutation has been shown to reduce antibody recognition. As such, it helps the virus SARS-CoV-2 to bypass immune protection provided by prior infection or vaccination. It is not anticipated that this mutation is sufficient for the ‘South African’ variant to bypass the protection provided by current vaccines. It’s possible that new variants will affect the efficacy of the covid vaccines, but we shouldn’t make that assumption yet about the South African one.”

Prof Lawrence S. Young, Virologist and Professor of Molecular Oncology, Warwick Medical School, University of Warwick, said:

“The South African virus variant was recently reported in a preprint ahead of formal publication.  The variant has multiple spike mutations and emerged in a major metropolitan area in South Africa following the first wave of the epidemic and then spread to multiple locations within two other neighbouring provinces.  It has rapidly spread become the dominant virus variant in the Eastern and Western Cape provinces.

“The South African variant has 3 mutations at key sites in the receptor binding domain (K417N, E484K and N501Y) of the spike gene.  Two of these (E484K and N501Y) are within the receptor-binding motif (RBM), the main functional motif that forms the interface with the human ACE2 receptor.  The N501Y mutation is the same as that found in the UK virus variant.  These changes are consistent with both these variants being more infectious (transmissible) but we don’t know whether they will affect the disease severity. While changes in the UK variant are unlikely to impact the effectiveness of current vaccines, the accumulation of more spike mutations in the South African variant are more of a concern and could lead to some escape from immune protection.

“Variants of SARS-CoV-2 have been around since the beginning of the pandemic and are a product of the natural process by which viruses develop and adapt to their hosts as they replicate.  Most of these mutations have no effect on the behaviour of the virus but very occasionally they can improve the ability of the virus to infect and/or become more resistant to the body’s immune response.  Many thousands of these mutations have already been identified in isolates of the virus with around 4000 spike mutations being found in different viruses from around the world.  The UK and South African virus variants have changes in the spike gene consistent with the possibility that they are more infectious. 

“But the standard measures to restrict transmission (hands, face, space) will prevent infection with this variant.  Along with improved surveillance (testing, tracing and isolating) and expediating the roll out of the vaccine, these measures will prevent transmission of this variant and any others that will arise. 

“The move to harsher levels of restriction across the country is inevitable.  It is essential that we do everything possible to prevent the South African variant from spreading to the UK population.  Quarantine measures and restricting travel from and to South Africa are imperative.”

Dr Simon Clarke, Associate Professor in Cellular Microbiology at the University of Reading, said:

“The variant found in South Africa which is now also seen in the UK, is another mutated version of the coronavirus which is causing significant problems.

“The South African variant has a number additional mutations including changes to some of the virus’ spike protein which are concerning. They cause more extensive alteration of the spike protein than the changes in the Kent variant and may make the virus less susceptible to the immune response triggered by the vaccines. 

“While it is more infectious, it currently remains unclear whether it causes a more severe form of the disease.  Moreover, the South African variant is a more difficult virus to track as it lacks some mutations in the spike found in the Kent virus which make it easily detectable by the PCR test used by the NHS.”

Prof James Naismith, Director of the Rosalind Franklin Institute, and University of Oxford, said:

“Viruses mutate and new strains will emerge. The so-called South African strain has a number of changes, and scientists are working flat out to understand their significance. Some of the changes are quite significant and thus scientists are paying a lot of attention. We do not yet know enough to say more than this. 

“For the general public, I would say think about our human nature. Many of us like a good scare and horror stories are part and parcel of human culture, which means such things get a lot of coverage.  However a drumbeat of nightmare scenarios about this new variant does nothing but create anxiety because too little is known and there is nothing we can do about it at the moment.  Prolonged anxiety is far from enjoyable and leads to mental illness.  I would say there are many much more positive things we can do.

“We can support scientists to work on the new variants and keep other research efforts to treat the disease going (don’t stop funding covid19 science just yet).  We can all help if we redouble our efforts to wash our hands, wear a mask and socially distance.  The faster and further the vaccine is rolled out, the quicker the end to this nightmare.  We can all help each other through kindness and understanding, many are grieving, others are financially very stretched and other are very lonely.  We can help by not amplifying or spreading doomsday scenarios or spreading magical thinking or nonsense information. 

“And we need to have a proper informed debate: further social restrictions are required if we wish to avoid overloading the NHS before the vaccines stop spread.  Those who advocate reducing social restrictions really should make clear the costs in lives of their policy.  In our democracy we elect politicians, not scientists, to take decisions. We expect politicians to make decisions based on facts, not fantasy.”

All our previous output on this subject can be seen at this weblink:

www.sciencemediacentre.org/tag/covid-19

Declared interests

None received.