A new variant of Covid-19 with over 30 spike mutations has been reported from southern Africa. On November 23, Dr. Tom Peacock, a virologist at Imperial College London, posted the details of the variant on github.com, noting that the “incredibly high amount of spike mutations suggest this could be of real concern (predicted escape from most known monoclonal antibodies)”
Assigned as B.1.1.529, the variant was first spotted in Botswana and the other circulating countries are Hong Kong and South Africa. According to The Guardian, only 10 cases have been confirmed by genomic sequencing.
Dr. Tom Peacock tweeted that the variant should be monitored due to its “horrific spike profile”.
Just spotted: very small cluster of variant associated with Southern Africa with very long branch length and really awful Spike mutation profile including RBD – K417N, N440K, G446S, S477N, T478K, E484A, Q493K, G496S, Q498R, N501Y, Y505Hhttps://t.co/kgA9c1hKDa
— Tom Peacock (@PeacockFlu) November 23, 2021
According to WHO, currently, only four variants of the coronavirus are designated as variants of concern – Alpha (lineage B.1.1.7, the so-called ‘UK variant’), Beta (lineage B.1.351, the so-called ‘South Africa variant’), Gamma (lineage P.1, the so-called ‘Brazil variant’) and Delta (lineage B.1.617.2).
“Worth emphasising this is at super low numbers right now in a region of Africa that is fairly well sampled, however, it very very much should be monitored due to that horrific spike profile (would take a guess that this would be worse antigenically than nearly anything else about),” Dr. Peacock said.
The mutation P681H seen in the new variant has also been reported in Alpha, Mu, some Gamma, and B.1.1.318 variants. The new variant also carries the N679K mutation which has been reported in many other variants. Dr. Peacock tweets: “This is the first time I’ve seen two of these mutations in a single variant”
The new variant also carries a mutation called N501Y which has been reported in other variants of concern. Studies have shown that this mutation helps the variant be more transmissible. It also allows the virus to readily bind to the human angiotensin-converting enzyme 2 (ACE2) receptors.
It also carries the P681H mutation, one of the commonly identified spike mutations in SARS CoV-2, which enhances the transmissibility of the virus. The D614G mutation which has been reported to increase virus infectivity was also seen in the new variant.
Dr. Divya Tej Sowpati from CSIR-Centre for Cellular and Molecular Biology said that only very few genomic sequences of the new variant are available and more studies are needed. “The variant is currently being monitored,” he says.