Latest Case Studies/ Field Note

Building Pathogen Monitoring Networks Across Kenya

Growing up in a farming household in Homa Bay, a rural town in western Kenya along Lake Victoria, Dr. Samuel Oyola was often sick. So were his four older siblings and their parents. “We called it malaria—but we called everything malaria if you had a fever,” he remembers with a laugh.

Diagnoses were frequently catch-alls in Homa Bay. Few doctors served the community, with access to even fewer diagnostic tools. So it might be natural that when Dr. Oyola went to Egerton University in Njoro, he soon became interested in studying pathogens.

He studied next at the University of Brussels in Belgium, and then the University of Cambridge, United Kingdom, where he earned his PhD in molecular and cellular biology. Eventually, he developed and applied genomic technologies to pinpoint genetic variations in—what else?—malaria parasite populations.

Now Dr. Oyola, 44, a senior scientist at the International Livestock Research Institute (ILRI) in Nairobi and the only living member of his childhood family, has turned his skills and attention to Covid-19 and serving his community.

He leads a program supported by the Pandemic Prevention Institute and The Rockefeller Foundation to set up a comprehensive network of Surveillance and Response Teams in all 47 of Kenya’s counties, and support expansion of in-country genomic surveillance efforts throughout East Africa. The teams coordinate sample collection and transport to ILRI labs for near real-time genomic analysis of SARS-CoV-2 emerging variants.

Surveillance & Response Team working in Lokichar, Turkana County

“This network enables us to establish direct connection with the field for the delivery of viable samples, allowing for accurate genomic analysis and efficient and timely access to information,” he says. Within a period of six months, the newly trained team at ILRI has analyzed over 30,000 Covid-19 samples and sequenced over 3,000 SARS-CoV-2 whole genomes which are now deposited at the GISAID international database for global access.

Speed is crucial in any effort to contain a future pandemic so that public health officials and decisionmakers can make rapid and informed decisions, including where to focus limited resources. Beyond speed, these networks set the foundation for a clinical sampling system that can be used to monitor re-emerging and emerging pathogens.

At the same time, Dr. Oyola is working to train technologists from 11 other African countries in the use of genomic and bioinformatic tools, supporting East African nations to expand genomic surveillance capabilities.

Work Critical for Kenya, East Africa, and the World

“The work that Dr. Oyola and his team do both in Kenya and also regionally helps strengthen our global ability to prevent or mitigate future pandemics,” says Dr. Rick Bright, CEO of the Pandemic Prevention Institute and a Senior Vice President of The Rockefeller Foundation. “We must figuratively link hands across the globe, as Dr. Oyola is doing across Kenya, to connect data and turn it into actionable insights – stopping pandemics in their tracks and saving lives.”

Dr. Oyola (left) and his team at ILRI

The Pandemic Prevention Institute works with global experts to help connect, analyze, and translate both traditional and non-traditional data—from clinical sequencing to environmental, consumer and mobility tracking—with the goal of creating actionable insights that trigger an early warning system and allows decisionmakers to make evidence-based choices and invest in tailored solutions that save lives.

Dr. Oyola agrees on the importance of a global network linked by trust, and is certain the ILRI work is important not only for Kenya, but for East Africa and the world. “The virus is actively mutating,” he says. “No one knows what it is doing within a population, or will do next. Every piece of data we generate, we deposit into an international data base, open to the world, so it can help others.”

Dr. Oyola (left) works with a genomic sequencing team member

Great Strides in Less Than a Year

ILRI has significant experience supporting the Kenyan government and East African pastoralist communities with detecting animal spillover events. This has resulted in strong ties with country departments of health, building the foundation for Dr Oyola’s engagements to date.

So far, 27 counties have formed Surveillance and Response Teams, a leap from the three or four counties that were able to sequence samples in a timely fashion when the program began less than a year ago, in June 2021. It is a process that requires engaging with local Ministry of Health officials and then identifying team members and connecting them to a courier system. Dr. Oyola intends to have at least made contact with all of Kenya’s 47 counties by year’s end. They also check for other pathogens, including those associated with Rift Valley Fever.

Turkana County in Kenya’s far northwest desert region, has been the most difficult network to establish to date, Dr. Oyola said. In addition to being a remote and vast county, much of the Turkana population of just over 1 million is pastoralists, so they relocate their homes two or three times a year according to the rainy seasons. The newly formed response teams move with the communities, equipped with reagents supplied by ILRI.

The teams then work with a courier service that collects samples in the evening, travels through the night to reach a central depot at midday the following day, and then delivers to Dr. Oyola’s lab that evening. “It is about 15 hours from when the field teams collect the samples to when we receive them,” he says.

Spurred by Covid-19 Challenges, Dr. Oyola Dreams for the Future

Frederick Sanger, who like Dr. Oyola studied at the University of Cambridge early in his career, sequenced the first ever complete genome in 1977, identifying a virus that infects E. coli and winning the Nobel Prize three years later. Often called the “father of genomics,” Sanger’s work touched off decades of innovation that have led to steady improvement in sequencing techniques and abilities. But the skills and tools were often inequitably distributed across the globe, and equilibrium disrupted by Covid-19.

Dr. Samuel Oyola

In Kenya too, the impetus to set up the Surveillance and Response Teams began with Covid-19. “When the pandemic started, the first Kenyan samples were taken to South Africa, and it took almost a month for the Kenyan government to receive the results and declare Covid-19 was here,” says Dr. Oyola.

“That’s when the government started to take stock of the labs in the country. They found that our lab had the capability, and we were quickly able to repurpose some of our work. I assembled our team of nine and we started to diagnose. Then in early 2021, when we started hearing of variants, the government came to us again. And now we are sequencing.”

Dr. Oyola knows there is much more work to do. “One year from now, I would like to have given training to many more people, while simultaneously making advances in both tools and our protocols,” he says. “In five years, I would like to see a us at a point where many different countries have this training and can be confident in their ability to sequence a genome and use genomics as a critical tool for pandemic preparedness.”

Dr. Oyola’s desire to scale this throughout Kenya and beyond depends on funding. “That is the only limit,” he says. “There are many people out there who want training to develop these skills. And the long-term benefit to the world will be enormous.”

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