KEMRI says new COVID-19 strain not yet in Kenya

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 have mutations whose significance is yet to be fully understood.

The scientists from 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 coronavirus 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.

According to experts, 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, 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 (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 the report.

Variants of Concern

Currently, there are two COVID-19 genetic variants that are of global concern. One was first identified in the United Kingdom and the other identified in South Africa (named B.1.351/501Y.V2).

A virus variant is detected by changes in the RNA sequence (virus’ genetic material). RNA sequence changes may result in a change of the protein structure of the virus if they change the amino acid sequence.

The RNA sequence changes in the two variants of concern share in common a change at amino acid position 501 on the immunogenic spike protein, which is abbreviated N501Y. Most RNA sequence changes do not lead to amino acid changes that significantly modify the virus properties (e.g. transmissibility, virulence) and such changes are not regarded as “variants of concern”.

There are several previous RNA sequence changes that have led to amino acid changes, but these have not been regarded as “variants of concern” because of limited spread compared with the UK or South African “variants of concern”.

To date, 11th January 2021, the two “variants of concern” Lineage B.1.1.7/501Y.V1 (first reported in the UK) and Lineage B.1.351/501Y.V2 (first reported from South Africa) have been reported in 47 and 11 countries respectively.

The UK variant, has not been reported in any African country yet, and the South African variant has now been reported in Botswana. However, genomic surveillance across Africa is very limited and therefore introduction and spread in Africa cannot be ruled out.

KEMRI has set out to sequence approximately 400 samples between January and the end of February 2021 across multiple sites in Kenya and will report their findings on a monthly basis.