• Kemri scanned the spike protein of the local SARS-CoV-2 genomes for amino acid changes including the N501Y mutation that is shared by both variants of concern.
• The scientists identified a single sequence containing an N501Y mutation from a 43-year-old asymptomatic individual from Lamu in August.
The two Covid-19 variants identified in the United Kingdom and South Africa are yet to be found in Kenya.
But the Kenya Medical Research Institute said Wednesday that some of the Kenyan SARS-CoV-2 genomes have mutations whose significance is yet to be fully understood.
A virus variant is detected by changes in the RNA (virus’ genetic material) sequence. RNA sequence changes may result in a change of the protein structure of the virus if they change the amino acid sequence.
Kemri scanned the spike protein of the local SARS-CoV-2 genomes for amino acid changes including the N501Y mutation that is shared by both variants of concern.
The scientists identified a single sequence containing an N501Y mutation from a 43-year-old asymptomatic individual from Lamu in August.
According to the experts, the significance of this is uncertain, since subsequent sampling does not suggest that viruses with this mutation have expanded.
“We observed 12 new lineages at low frequency but have not expanded locally to give rise to many cases. We are sequencing samples from October to present and going forward we propose surveillance of 50 samples each week from across the various testing laboratories and ports of entry to monitor for new variants and will report our findings on a monthly basis.”
Kemri previously sequenced 294 genomes sampled from the coastal region and Nairobi and identified 10 circulating SARS-CoV-2 lineages in Kenya between March and June last year.
Additional sequencing of 205 genomes sampled from the coastal region between June and October 2020 identified 16 circulating lineages.
“We plan to sequence approximately 400 samples between January and the end of February 2021 across multiple sites in Kenya and provide a monthly report,” Kemri said in a statement.
“At KEMRI-Kilifi, we have continued to undertake SARS-CoV-2 genome sequencing mostly from samples diagnosed in our laboratory as part of the national testing effort. These samples are received from all six coastal Kenya counties namely, Kilifi, Taita Taveta, Tana River, Mombasa, Kwale and Lamu.”
Last month, Kenya shelved a plan to restrict all flights from the UK over reports of the mutant Covid-19 strain. The government instead issued stricter measures to passengers jetting in from the UK.
Already, Kenyan scientists have increased surveillance of the coronavirus after the new mutations were reported.
“We have very strict travel measures with the UK which the US and the Europeans did not have. We are carefully observing every passenger travelling from there,” Health CS Mutahi Kagwe said.
The WHO had reported that the virus was mutating at a ‘much slower rate’ than seasonal influenza, but officials from the UK said the mutation of the virus was allowing it to spread more easily.
The discovery of the new strain sowed new panic in a pandemic that has killed more than 1.7 million people worldwide. Initial reports indicate the new strain spreads faster but does not appear to be deadlier than the original virus.
It is not clear whether the rapid spread was due to mutation or people’s laxity in protecting themselves.
(edited by o. owino)