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Kemri uses biotech to trace Covid-19’s trail in the country

Thursday April 23 2020

Kenya Medical Research Institute

Staff at the Kenya Medical Research Institute in Nairobi work on a virus project, on April 7, 2020. PHOTO | EVANS HABIL | NATION MEDIA GROUP 

ELIZABETH MERAB
By ELIZABETH MERAB
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When you hear of Charles Darwin, the mind quickly drifts to the theory of evolution as the scientist is best known for his contributions to this science.

Today, this concept can be applied to anything that evolves, including viruses.

Forty days after reporting its first confirmed case of the novel coronavirus, Kenya has joined the global race to trace Covid-19 with genomics after posting the DNA of the virus circulating in the country.

The Ministry of Health is expected to receive the results from the Kenya Medical Research Institute (Kemri) which has analysed 28 sets of genomes.

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

“We have fully sequenced 28 genomes whose results we will be sharing with the health CS today. We also intend to deposit them in the gene bank,” said Professor, Tropical Microbiology and Dircetor, Research & Development, KEMRI.

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

The first use of this kind of fingerprinting, more formally known as genomic epidemiology, was to trace the source of anthrax used in the 2001 anthrax letter attacks in the US.

In South Africa similar techniques were used to identify the source of a 2017-2018 listeriosis outbreak.

TRANSMISSION CHAINS

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 the virus.

A good share, like the 26-year-old asymptomatic patient in Homa Bay County, also only realise they have the virus after undertaking 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 understanding the new disease and in the research and development of diagnostic kits, drugs, and vaccines.

MUTATION

Usually, viruses, like all pathogens, undergo [minor] changes over course of a pandemic, and sequencing helps keep track of these changes, Pro Kariuki 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.

The first two SARS-CoV-2 virus sequences from the African continent were published by ACEGID in Ede, Nigeria, and INRB in Kinshasa, Democratic Republic of the Congo, in early March.

The two labs have played significant roles in research on and fighting Ebola.

In an opinion piece published by The Conversation Africa, Bioinformatician Niema Moshiri, says current results indicate that the SARS-CoV-2 virus appears to be mutating more slowly than the seasonal flu which may allow scientists to develop a vaccine.

CHINA'S CASE

As early as two weeks after cases of a strange pneumonia-like sickness was reported in Wuhan, a city in China, scientists in the country did the first genome sequencing of the virus causing the sickness.

Within a week, they had done five genome sequences of the virus identities as SARS-CoV-2—a new coronavirus.

Since then over 10,00 genome sequences have been done as the virus, which causes a highly infectious and deadly disease called Covid-19, spreads fast across the globe.

“Essentially, genetic sequencing decodes the exact information that makes up an individual or any living thing like a virus. The genes are the blueprint of information on a virus make-up which tells us the genes that make up an organism and their exact information and what makes them unique," says Prof Thumbi Ndung'u, a South Africa-based HIV researcher.

"Based on this information, one can design diagnostic tests that specifically identify the virus,  one can design specific antiviral drugs and vaccines to prevent infection."

USEFULNESS

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.

GISAID is 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 are used for the development of diagnostic tests and vaccines.

In South Africa, the National Bioinformatics Institute (SANBI) collaborated with the National Institute for Communicable Disease (NICD) to produce the first SARS-CoV-2 viral genome collected in South Africa.

Soon after this the Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP) published five further genomes.

Worldwide, genomic surveillance techniques are proving useful in tracking the spread of Covid-19 and South Africa is well-positioned to adopt them within its public health system response.