Detection of SARS-CoV-2 P681H Spike Protein Variant in ACEGID Lab, Nigeria.

As viruses replicate and transfer from person to person, changes (mutations) can occur in these viruses. These mutations can lead to new variants of the virus being formed. Mutations can also either be a meaningless tweak or the virus alters itself in such a way that it can spread more easily and cause more infections.

In December 2020, reports of a new variant of the Covid19 virus (SARS-CoV-2) were made by scientists in the United Kingdom. This new variant- called the “lineage B.1.1.7” has been associated with more rapid spread and a rise in the number of COVID-19 cases in some areas in the UK.

The new variant is said to have acquired mutations, many of which are on the gene that encodes the spike protein on the surface of the virus, through which it binds to and enters human cells.

Following the report of the new variant in the UK, we did a quick retrospective analysis of samples recently sequenced at our lab (ACEGID) and identified two Covid virus sequences that share the same mutation in the spike protein (P681H) in common with the B.1.1.7 lineage, but none of the other unique mutations of B.1.1.7. These sequences were found in two samples collected on the 3rd of August & 9th of October 2020 from individuals in Osun State, Nigeria.

Multiple alignment of SARS-CoV-2 reference genome with genomes from Osun state, Nigeria and the United Kingdom. Only two genomes (highlighted in yellow) in Nigeria (Osun state) have been seen to have the P681H mutation so far. This non-synonymous mutation is found in the B.1.1.7 lineage (highlighted in red) and can also be found in other UK lineages such as the B.1.255 (highlighted in purple).

At the moment, only about 1% of the genomes from the samples we analyzed in Nigeria share any of the spike protein-altering mutations from the UK variant. We haven’t observed a rapid rise in Nigeria and don’t have enough evidence to indicate that this new variant is contributing to increased transmission of the virus in Nigeria. However, this might change in the next few weeks when we sequence more samples from the newly reported surge of covid-19 in Nigeria.

In as much as the full effect of this mutation isn’t known yet and is still being studied, the main concern will be whether this new variant shows any difference in the severity of illness and speed of spread.

However, a new variant doesn’t alter the effectiveness of precautionary measures like hand washing, sanitizers, and social distancing. Please adhere to these safety precautions.

Read the official report, and find out more on the science behind this finding here. 

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