Kenyan scientists make breakthrough on Covid-19 genetics

Written By: Margaret Kalekye
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Kemri is already banking on its herbal medicine Zedupex for management of the deadly virus.

For the first time, Kenyan scientists have successfully sequenced genomes of SARS-CoV-2, the virus responsible for the global Covid-19 pandemic, obtaining important information about the genetic composition of viral strains in 122 of the confirmed cases in Kenya.

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The results of the genome sequencing for the Covid-19 cases in Kenya were released Wednesday by scientists from Kenya Medical Research Institute (KEMRI).

Genome sequencing allows for the compilation of the most comprehensive information about an organism’s genetic makeup.

The scientists using advanced next-generation sequencing methods are now able to track and compare viral mutations to understand the origins of imported strains and to discover if any novel strains are emerging locally.

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“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, Director-General KEMRI said.

According to the study, Covid-19 infections detected and confirmed in the country in March were largely imported.

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The report that was deposited in the Gene Bank indicates that there were at least nine separate importations of SARS-CoV-2 into the country prior to 30th April 2020 based on a proportion of sequenced cases.

“This is based on genetic sequencing of a proportion of SARS-CoV-2 (n=122) samples collected from cases that circulated in Kenya between 12th March and 30th April 2020”, read the report.

Local transmissions

The report, first of its kind in Kenya further shows that SARS-CoV-2 viruses circulating in the country do not differ from viruses circulating elsewhere in the world and provides evidence for local transmissions in Mombasa County, with clusters of infections showing local transmission following these introductions.

The report also shows evidence of transmission between Nairobi and Mombasa prior to the introduction of restrictions on movement into and out of these counties.

It further reveals that there are clusters of infections showing local transmission following these introductions.

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 analyzed 122 samples from the selected cases to gain a comprehensive understanding of the variations of the virus that are present in the country.

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The report that was deposited in the Gene Bank indicates that there were at least nine separate importations of SARS-CoV-2 into the country prior to 30th April 2020 based on a proportion of sequenced cases.

The report further suggests infections detected and confirmed in March 2020 were largely from virus importation into the country.

“This is based on genetic sequencing of a proportion of SARS-CoV-2 (n=122) samples collected from cases that circulated in Kenya between 12th March and 30th April 2020”, read the report.

Further sequencing will be used to describe the pattern of continuing spread both within communities and between counties across the country.

Additional sequencing could also provide information on infections that have been missed and guide testing strategies

According to the scientists, 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.

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This can provide additional estimates of the rate of spread of the virus which is useful where case surveillance and tracing is sparse”

New mutations

Furthermore, whole-genome sequence data allows researchers to adapt testing reagents for new mutations in the virus to reduce false-negative rates.

Sequencing of additional SARS-CoV-2 genomes in Kenya provides a more detailed picture of local transmission patterns.

The researchers note that additional sampling going forward in time will also help researchers build a more complete tree to infer transmission patterns within local outbreaks and continue to monitor for evidence of transmission between geographical locations.

They will be able to estimate from the genetic distance between sequences how many infections may have been missed. This will be useful in guiding future testing strategy.

The collaborative team has also developed the required capacity within Kenya for monitoring the genetic sequence of SARS-CoV-2 viruses circulating in the country and urges the scaling up of capacity across the country to generate a SARS-CoV-2 genetic sequence library to support and guide public health control measures.

 

 

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