Posted January 14, 2021 1:18 pm by

NAIROBI, Kenya, Jan 14 – The Kenya Medical and Research Institute (KEMRI) has affirmed that none of the COVID-19 variants of concern identified in the United Kingdom or South Africa have been detected in the country.

KEMRI however, said that some of the Kenyan COVID-19 genomes had mutations whose significance is yet to be fully understood.

The scientists from the KEMRI’s Centre for Virus Research (CVR) and Centre for Geographic Medicine Research-Coast (CGMR-C) in collaboration with the National Public Health Laboratory (NPHL) working closely with County teams sequenced 294 genomes sampled from the coastal region and Nairobi and identified 10 circulating COVID-19 Lineages in Kenya between March and June 2020.

Additional sequencing of 205 genomes sampled from the coastal region between June and October 2020 identified 16 circulating lineages.

“This successful sequencing for the novel corona irus in Kenya is a significant milestone in the response to the pandemic in Kenya and the entire World, as this will strengthen surveillance for tracking mutations of the virus and aid in the tracing of the sources of community infections,” Prof. Yeri Kombe, Director General KEMRI said.

Viruses acquire changes in their genetic sequence over time.  Genetic sequences can therefore provide insights on person to person transmission, which can be visualized by drawing of genetic trees based on changes in the genetic sequence.

This can provide additional estimates of the rate of spread of the virus which is useful where case surveillance and tracing is sparse.  Furthermore, whole genome sequence data allows researchers to adapt testing reagents for new mutations in the virus to reduce false negative rates.

Has Kenya seen the new SARS-CoV-2 variants of concern (VOC) yet?

In a report released this week, none of the lineages that are described as “variants of concern” (B.1.1.7/501Y.V1 and B.1.351/501Y.V2) were detected in the current data set. This includes 20 samples collected from October which coincide with the start of the 2nd wave.

The UK variant of concern (lineage B.1.1.7/501Y.V1) was first observed in the UK on 20-Sept-2020. This variant has a unique set of 14 amino acid changes across the genome.

“From the data we have so far, we do not find evidence of this variant in Kenya before October 2020. We will need more sequencing covering the period October 2020 to January 2021 to conclude on the local status of these variants. Given the widespread global transmission of this lineage, there is a significant risk of its eventual introduction to Kenya,” indicated Read More…