Livestock scientists to help Kenya identity Covid-19 variants

April 13, 2021 Newsroom

Livestock scientists at the International Livestock Research Institute are poised to contribute to the fight against Covid-19 pandemic in Kenya.

Through a request from the government, the institute’s laboratories in Nairobi, equipment and experts, will sequence the entire genome of SARS-CoV-2 circulating in the country.

SARS-CoV-2 is the virus that causes Covid-19 and monitoring the different variants that emerge in the country’s population or arrive from outside borders is critical in managing the pandemic.

In what the scientists term as ‘genomic surveillance’, the institute will provide important information about which strains of the virus make people sicker, or are more easily transmitted, and in the long run, help ensure the right vaccines and diagnostic tests are used.

This comes at a time when genomic testing capabilities are still low in Kenya. So far, only KEMRI-Wellcome Trust (Kilifi) has generated the available sequencing data.

But monitoring of the variant strains are ongoing.

The CGIAR Research Program on Livestock has redirected $700,000 of its funding to support the effort by the ILRI team.

“There’s a moral aspect to it,” said Ulf Magnusson from the Swedish University of Agricultural Sciences and head of the animal health activities within the CGIAR Research Program on Livestock.

“We felt that if you have the skills, the personnel and the equipment, and the Kenyan government asks you to help, there’s a moral imperative to do so,” Magnusson said.

“This is a global emergency.”

Swabs taken from positive-testing patients in Kenyan hospitals will be sent to the institute’s lab.

Samuel Oyola, senior scientist at ILRI and his team will then isolate the coronavirus genetic material, amplify it, and use NextSeq high-throughout DNA sequencing equipment to decode the genes and learn more about the virus.

“Once we have the genetic readout of the virus, we are able to analyse it and compare it to the original form of the virus, and see the parts of the genome that have mutated or changed and then relate them to what is known about the consequences of such mutations,” said Oyola.

The strains circulating in Africa may well be different to those in other parts of the world since the virus is continuously mutating, Oyola says.

“We are putting in place something that will help us monitor in near real time how this pathogen is evolving in the country,” added Oyola.

This is particularly important, he said, as the current leading vaccines developed against Covid-19 rely on our immune systems recognizing one single protein associated with the virus, called the spike protein. If mutations change the structure of that protein in the virus, our immune systems may no longer be able to ‘see’ the virus so well, rendering the vaccine less effective.

Repurposing some of the institute’s veterinary research capacity and animal health scientists to respond to a global public health emergency is ‘a prime example of the ‘One Health’ approach in action,’ said Bernard Bett, an ILRI senior scientist, who specialises in animal and human health and leads the One Health Research, Education and Outreach Centre in Africa (OHRECA).

Zoonotic diseases such as Covid-19, which ‘spillover’ from animals to humans and vice versa, demand a highly coordinated multidisciplinary effort to control their spread and understand their effects.

Although Kenya had made some success combating the virus in the early days of the pandemic with curfews and shutdowns. Vaccinations have begun, but President Uhuru Kenyatta announced on March 26 that the country is now ‘squarely in the grip of a third wave of the pandemic.’

Daily case numbers are expected to reach 3000 over the next month, around seven people are dying every day – the highest death rate since the start of the pandemic – and hospitalizations are spiking, Kenyatta said.

“The stress the pandemic is placing on our health system is unparalleled.”

That makes the genomic surveillance even more timely.

‘The work demonstrates how ILRI can be nimble and pivot support to the Kenyan government on issues of national and global importance like COVID-19,’

“We’re happy to be able to play our part in fighting the pandemic in Kenya,” said Jimmy Smith, the Director-General of ILRI.

Genome sequencing may also pay dividends once the current pandemic is over. Spending months monitoring SARS-CoV-2 will further strengthen ILRI’s expertise at genomic surveillance, says Magnusson. ‘It will help to create a critical mass of people doing this in Africa,’ he says: people with a skillset that may be critical for picking up the next pandemic.