Kemri releases Covid-19 analysis

The coronavirus strain that is circulating and causing infection in the country is not different from others circulating elsewhere in the world, the Kenya Medical Research Institute (Kemri) has said.

In a first of its kind report in the country, a team of scientists at Kemri have analysed a set of 122 strains of the SARS-CoV-2, the virus that causes the coronavirus disease (Covid-19).

By analysing the strains, the scientists say they obtained important information about the genetic composition of viral strains in 122 of the confirmed cases in Kenya.

Genome sequencing is ostensibly the process of determining the fingerprint of an organism which is done in a laboratory.


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) and County teams analysed 122 samples of the first 399 confirmed Covid-19 cases in the country to gain a comprehensive understanding of the variations of the virus that are present in the country.

“This successful sequencing for the novel coronavirus SARS-CoV-2 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, Kemri Director-General said.

The variation captured in these genomes, when compared to genomes sampled elsewhere, provides a fingerprint that might be associated with a particular virus and a patient with a particular cluster of transmission.


The scientists found at least nine separate importations of the SARS-CoV-2 virus into Kenya before April 30.

Further, early cases came from multiple importations into the country from Europe and Asia.

Genome sequencing involves revealing the order of bases present in the entire genome of an organism. One such pool is the GISAID’s SARS-CoV-2 genome sequence database, a German-based public-private partnership that provides public access to the most complete collection of genetic sequence data of influenza viruses and related clinical and epidemiological data through its database.

These genome sequences which are being pooled into several databases are vital for tracking how the virus mutates over time as it spreads and for the development of diagnostic tests and vaccines.

The Kenyan team Wednesday deposited the sequence data at GISAID Gene.


One important aspect of managing emerging infections is identifying chains of transmission and assigned cases to clusters of infection.

Reports are now emerging of situations where some Kenyans who have tested positive for the virus cannot retrace their footsteps and identify how they might have contracted Covid-19.

A good share also only realise that they have the virus after taking the test. To ensure that scientists can trace people’s contacts, stronger systems of disease surveillance are needed – ones that draw on genome sequencing.

Sequence data are essential to design and evaluate diagnostic tests, to track and trace the ongoing outbreak, and to identify potential intervention options.


Since the start of the Covid-19 outbreak, laboratories around the world have been generating viral genome sequence data that have been scrutinised by pools of researchers. This has enabled real-time progress in the understanding of the new disease and in the research and development of diagnostic kits, drugs, and vaccines.

Usually, viruses, like all pathogens, undergo [minor] changes over the course of a pandemic, and sequencing helps keep track of these changes, Prof Sam Kariuki, a microbiologist and the Kemri director of research and development explained.

“But so far no significant changes on this virus have been observed,” he added.

This sequencing makes Kenya the fourth African country to post the finger-print of the Covid-19 circulating in the continent.

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