Date/Time: 21 December 2020
Incident/Event title/Name: New SARS-CoV-2 variant with multiple spike protein mutations
Notification*: Alert Warning Activation Execution
From: Africa Centres for Disease Control and Prevention (Africa CDC) jointly with Africa Task Force for Coronavirus (AFTCOR)
To: African Union Member States
Africa is currently experiencing a sharp increase in the number of confirmed COVID-19 cases across Member States. Over the last few weeks, South Africa has also faced a rapid increase in the number of COVID-19 cases driven by a new SARS-CoV-2 lineage, the 501Y.V2, which show signs to be potentially more transmissible.
The Network for Genomics Surveillance in South Africa (NGS-SA), led by Prof. Tulio de Olivera, had identified a new variant of SARS-CoV2 that is driving the second wave of infections. The new variant is defined by multiple non-synonymous mutation in the spike (S) protein, of which three are on the receptor-binding domain (RBD). One of the most significant is an N501Y mutation in the receptor binding motif that bind to the human ACE2 receptor. In addition, the United Kingdom has recently identified a second new lineage of SARS-CoV-2, which contain the N501Y mutation but distinct from the South African variant. Further studies are ongoing to determine whether this lineage is more infectious and transmissible; or causes more severe illness; or evade the vaccination or a human immune response.
As of 21 December 2020, more than 300 genomes of the 501Y.V2 variant have been identified, all in South Africa. Preliminary analysis in South Africa (501Y.V2) and the UK (501Y) suggests that this variant is significantly more transmissible than previously circulating variants and potentially higher viral load in South Africa.
While research is ongoing to generate clear-cut evidence, these two lineages seem to spread faster, and this notification is being sent out to increase Member State awareness of the new variants from South Africa and the UK, which may spread and introduced to other Member States. Given that there is currently a lack of evidence to indicate the extent to which these new 501Y lineages are spread outside of South Africa or outside Europe, timely efforts to monitor, prevent and control its spread are needed, and include the following:
Africa CDC advise Member States and health authorities to:
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