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expert comments about two SARS-CoV-2 variants, one in Botswana (B.1.1529) and one in the US (B.1.628)

There are reports of two emerging SARS-CoV-2 variants, one in Botswana (B.1.1529)* and one in the US (B.1.628)¥


On the B.1.1529 lineage in Botswana:

Prof Ewan Birney, Deputy Director General of EMBL and Director of EMBL’s European Bioinformatics Institute (EMBL-EBI), said:

“Early evidence from genomic surveillance in South Africa suggests that B.1.1.529 is a serious cause for concern. The South African surveillance and epidemiology groups should be commended for their timely data collection, analysis and transparency.

“Armed by our experience and understanding of the Alpha and Delta variants, we know 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.

“Measures to prevent this variant of concern from spreading include implementing appropriate quarantine and PCR testing measures and sequencing on international travel from Southern Africa and continue careful monitoring of the circulating SARS-CoV-2 variants. The international community should get drugs and vaccines to South Africa as soon as possible. All countries should remain vigilant and share SARS-CoV-2 genomes.”


Prof Ravi Gupta, Professor of Clinical Microbiology, University of Cambridge, said:

“B.1.1.529 has signatures of cumulative mutation indicating that it emerged in a chronic infection.

“B.1.1.529 does certainly look of significant concern based on mutations present.  Many have been shown to impact binding by neutralising antibodies, and some are known to increase the ability of virus to enter cells or to make them fuse together to allow cell-cell spread.”


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

“B.1.1529 is a new lineage that has been found in Botswana that carries an unusual constellation of mutations.  Given the large number of mutations it has accumulated apparently in a single burst, it likely evolved during a chronic infection of an immunocompromised person, possibly in an untreated HIV/AIDS patient.

“It is difficult to know what to make of the carriage of both P681H and N679K.  It is a combination we see only exceptionally rarely.  I suspect it is generally not ‘stable’, but it might be so, in combination with other mutations/deletions.

“I would definitely expect it to be poorly recognised by neutralising antibodies relative to Alpha or Delta.  It is difficult to predict how transmissible it may be at this stage.

“So far, four strains have been sequenced in a region of Sub-Saharan with reasonable surveillance in place.  It may be present in other parts of Africa.

“For the time being, it should be closely monitored and analysed, but there is no reason to get overly concerned, unless it starts going up in frequency in the near future.”


On the B.1.628 lineage in the US:

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

“B.1.628 has been shown to likely have emerged through an event of recombination rather than sequential accumulation of mutations and deletions.  All coronavirus tend to readily recombine between strains of the same species, and SARS-CoV-2 is likely no exception.

“There have been putative SARS-CoV-2 ‘recombinant strains’ identified before.  Though, this is the first time that there is evidence this happened in a lineage that has been reasonably successful.

“B.1.628 reached a global prevalence of ~0.5% globally during the summer of 2020, but is likely extinct by now.  There is no evidence it more transmissible, virulent or better at evading immune recognition than other SARS-CoV-2 lineages.”



* B.1.1529 lineage in Botswana:

¥ B.1.628 lineage in the US (preprint):


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


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