Kemri researchers release their analysis of coronavirus strains

Wednesday June 03 2020

A researcher at work in a Kemri laboratory. 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). PHOTO | WACHIRA MWANGI NATION MEDIA GROUP


The coronavirus strain that is circulating and causing infection in the country is not different from the strains of the virus circulating elsewhere in the world.

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

At least nine strains of the novel coronavirus are circulating in Kenya.

However, the strain of the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that is circulating and causing infection in the country is not different from others circulating elsewhere in the world.

SARS-CoV-2 is the strain of coronavirus that causes coronavirus disease 2019 (Covid-19). From the findings, the team of scientists drawn 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) and County teams analyzed 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.

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 the laboratory.


“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.

The team led by Dr Isabella Oyier a senior researcher and head of bioscience at the Kemri-Wellcome Trust Kilifi collected 102 samples in the Coast region and 20 samples from Nairobi from symptomatic and asymptomatic cases whose samples were collected by the respective county rapid response teams. Other members of the team include research scientists Dr George Githinji and Dr Charles Nyaigoti.

Those incomplete or with errors were removed from the analysis. The final selection of 78 global sequences were combined with 122 sequences from Kenya.

“Our analysis supports the statements from the ministry that there is evidence of local transmission in Mombasa County. A large majority of the samples are from Mombasa County, and this what we have reported on since we are the designated testing centre for the Coast region,” Dr Benjamin Tsofa, Deputy Director in charge of the Kemri’s Centre for Geographic Medicine Research-Coast.

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 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.

“We see evidence of ongoing local transmission based on few genomic changes that will require further investigations and from the evidence of increased number of recent cases, the epidemic is entrenched in Kenya,” he said.

Put simply, Dr Tsofa added, the virus is already well adapted to infect humans including Kenyans.

Genome sequencing involves revealing the order of bases present in the entire genome of an organism. Whole-genome sequencing (WGS) is the analysis of the entire DNA fingerprint sequence of a cell at a single time, providing the most comprehensive characterisation of the genome. Genome sequencing is important because it has potential to inform on the pattern of transmission patterns between person to person, within communities and households, and even between larger geographical regions such as counties, and continents.

One such pool is the Global Initiative on Sharing All Influenza Data (GISAID), 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.

“It complements our testing capacity in several ways, for example, providing information on infections that have been missed, complement our virus detection in terms of assessment of mutations that might make a testing kit less sensitive,” said Dr Isabella Oyier.

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

In their analysis, they observed that the strains circulating in Kenya are the same as the ones observed elsewhere in the world.

If the SARS-CoV-2 circulating in Kenya is the same as the strains circulating elsewhere in the world, why aren't many Kenyans falling ill or dying like the rest of the world?

“The sequence data we have tells us how similar the viruses are globally. It does not tell us about the manifestation of the disease in individuals since this depends on a number of factors relating to the individual,” explained Dr Oyier, adding that there is no evidence that the virus was circulating in the country before March.

“We have assembled the genomes and we will be piecing together the data we have with epidemiological data to get a full spectrum of the epidemic and to boost testing, modelling, and public health measures,” she noted.

There’s information that only strains L & S of the virus are circulating globally but only strain L is more virulent. Last week, the World Health Organisation Regional-Director for Africa Dr Matshidiso Moeti during a weekly virtual webinar what the scientific world was seeing is said that only strains L & S-types of the virus are circulating globally but only strain L is more virulent. Two strains of the new coronavirus are spreading around the world, according to an analysis of 103 cases.

The team at Peking University in Beijing found common mutations at two locations on the genome at these two regions: 72 were considered to be the “L-type” and 29 were classed “S-type”.

A separate analysis published in March by the Journal National Science Review suggests that the L-type was derived from the older S-type which likely emerged around the time the virus jumped from animals to humans. The second emerged soon after that, says the team. Although both strains are involved in the current global outbreak, the fact that the L-type is more prevalent suggests that it is “more aggressive” than the S-type, the team said.

So then we asked the team at Kemri if their groundbreaking analysis shows any mutation of the virus circulating in Kenya.

“There are known and expected mutations in the virus. The virus is new to the human body and we are still learning about it. Whole-genome sequencing will allow us to keep abreast of any changes in the viruses circulating within our communities,” said Dr Oyier.

By identifying chains of transmission and assigned cases to clusters of infection Genome sequencing is an important way of managing emerging infections. 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 also only realise that 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.

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.

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 and like all pathogens undergo [minor] changes over course of a pandemic, and sequencing helps keep track of these changes, Prof Sam Kariuki a microbiologist and Director, Research & Development, Kemri 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.