December 23, 2020

expert reaction to South African variant of SARS-CoV-2, as mentioned by Matt Hancock at the Downing Street press briefing

Matt Hancock announced that two people in the UK who had returned from South Africa had a variant of SARS-CoV-2 from South Africa.

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

“The expansion of Tier 4 is a natural response to attempt to ring-fence the new UK B.1.1.7 (variant) virus that is spreading across South/Southeast England.

“A new virus variant ‘501.V2’ from South Africa has been identified in some COVID-19 cases in the UK recently.  This new South African variant is described in this presentation: https://www.scribd.com/document/488618010/Full-Presentation-by-SSAK-18-Dec, which cites a paper in Cell (Tyler N et al. 2020).

“The South African variant ‘501.V2’ is characterised by N501Y, E484K and K417N mutations in the S protein – so it shares the N501Y mutation with the UK variant, but the other two mutations are not found in the UK variant.  Similarly, the South African variant does not contain the 69-70del mutation that is found in the UK variant.

“The spread of this variant also seems to be focused in the south and southeast regions of South Africa, and also exhibits higher viral loads diagnostic swabs – which may make it more transmissible via aerosols produced during breathing and talking, etc.

“Ongoing studies in South Africa are being conducted to assess whether it causes more severe disease, whether it targets young people specifically (or whether this is a behavioural effect), and whether the COVID-19 vaccines in development will be effective against it.

“There is some suggestion that this South African variant may be driving a faster spreading second wave in South Africa that may be bigger than the first wave.”

Prof Jonathan Ball, Professor of Molecular Virology, University of Nottingham, said:

“The mutation that has cropped in Africa has been seen before, and we have no idea whether it impacts on virus transmissibility or immunity.  We need to study the impact of mutations on virus behaviour, but until we have performed those important experiments we should avoid panicking.  If we practice social distancing and limit interactions with others, then we will avoid spreading the virus, no matter what collection of mutations it has.”

Dr Andrew Preston, Reader in Microbial Pathogenesis, University of Bath, said:

“The ’South African’ variant is distinct from the UK variant, but both contain an unusually high number of mutations compared to other SARS-CoV-2 lineages.  Some of these mutations change the S protein, which is cause for concern.  Both contain the N501Y mutation but so do many other variants that do not appear to have increased transmission, so the picture is complex.  It is critical to act quickly to ring-fence a high-transmission infection to prevent it from becoming established, so the precautionary quarantine of those who may have come into contact with the SA variant is vital for this.  The importance of real-time genomic surveillance to understanding patterns of disease is evident.  The UK has used genomics throughout the pandemic and thus was well placed to identify the new variant early during its rise.  In other countries that do not have this capacity, it is quite possible that these variants are already in circulation, but currently unidentified.  It appears we are entering a particularly dangerous phase of this pandemic, making the effective roll out of the vaccines even more time-critical.”

Prof Lawrence Young, Professor of Molecular Oncology, Warwick Medical School, said:

“The South African virus variant was recently reported in a preprint¹ 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 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.  What these changes mean for the infectiousness of the variant virus (transmissibility) and its impact on disease severity remain unknown.

“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.”

1 https://www.krisp.org.za/publications.php?pubid=315

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