Kenya’s New Genomics Lab to Transform Environmental Surveillance in Polio Eradication Efforts

By Gideon Kirui

Kenya is set to step up its fight against polio with the launch of a state-of-the-art genomics sequencing laboratory at the Kenya Medical Research Institute (KEMRI). The facility, which promises faster and more precise detection of polioviruses, marks a major leap in environmental surveillance and positions the country at the frontline of Africa’s polio eradication drive.

The milestone was revealed on 26th August 2025 during a World Health Organization (WHO) documentary production exercise led by the organization’s communications officer, Ms. Genna Print. The photo story project captured moments of determination and resilience among the scientists, health workers, and sample collectors who form the backbone of Kenya’s surveillance efforts, showcasing their critical role in safeguarding communities from the threat of polio.

The laboratory, scheduled to be officially handed over to the Institute on 4th September 2025, is designed to complement clinical surveillance by decoding genetic material from sewage and wastewater samples collected across Kenya and the wider region. By sequencing these samples, researchers can identify polioviruses long before cases of paralysis appear, giving health authorities a crucial window to respond and contain potential outbreaks.

Speaking in an interview, WHO’s Global Polio Eradication Initiative (GPEI) Coordinator in Kenya, Dr. Charles Korir, underscored the growing importance of environmental surveillance, which has expanded rapidly in the past decade. The country now boasts twenty-four sites, up from just two in 2013, with the most recent additions being Jomo Kenyatta International Airport (JKIA) and Nakuru.

“Our Environmental Surveillance sites have played a very critical role in monitoring the spread of poliovirus. Last year, all five confirmed cases of variant polioviruses in the country were detected through environmental surveillance. This makes it a vital complement to Acute Flaccid Paralysis (AFP) surveillance” Dr. Korir said.

Until now, samples collected in Kenya had to be shipped to the U.S. Centres for Disease Control and Prevention in Atlanta for genetic sequencing, a process that took between three and six weeks before results could be shared. With the new laboratory, turnaround time will be cut to just one week. This not only ensures a faster response but also reduces costs at a time when funding is under pressure.

“During this eradication phase, timeliness is everything,” explained KEMRI’s Research Scientist and EPI Lab Technical Manager, Ms. Joanne Hassan. “With results available locally and much faster, the government can swiftly deploy teams to contain the virus and maintain Kenya’s polio-free status.”

The lab is also expected to strengthen the country’s role in the Global Polio Laboratory Network. According to KEMRI’s Director of Polio Lab and WHO-affiliated Research Scientist, Dr. Peter Borus, Kenya will soon be accredited to perform full sequencing and diagnostic work.

“The genomics sequencing lab is a major step forward in diagnostics. It means we can now carry out the entire process locally, from virus isolation to sequencing, and report on the nature of the viruses. This expansion will bring us in line with global standards by December 2025,” he said

The development of the film documentary has been made possible through collaboration between the Kenyan government, KEMRI, WHO, the WHO Regional Office Surveillance Unit, and the Gates Foundation. Dr. Korir described the project as the realization of a long-held dream for Kenya’s public health sector.

Behind this scientific progress, the activity also revealed the tireless work of sample collectors, who play a critical role in feeding the lab with the raw material it needs. Kibera Sub-County Disease Surveillance Coordinator, Mr. Samuel Muturi and the Community Health Promoter Mr. Peter Adoyo who are the sample collectors at the Kibera site both exuded pride in their contribution towards a safer community. However, while citing unfavourable weather conditions and insecurity as some of the challenges they face in their line of work, they appealed for enhanced support to overcome these obstacles and carry out their responsibility effectively.

The documentary further traced the journey of samples: from the point of collection, through transportation, reception at the laboratory, and processing. Each step, from isolation to intra-typic differentiation, is crucial in ensuring accurate results. With genomic sequencing, scientists can not only detect local circulation of polioviruses but also determine how long a strain has been present and even trace its geographic origin. Such intelligence is indispensable for planning public health interventions and blocking potential outbreaks.

As Kenya edges closer to the global goal of polio eradication, the new laboratory is both a scientific and symbolic milestone. It underscores the country’s growing capacity to lead in disease surveillance while honoring the often-unseen efforts of health workers who form the backbone of eradication programmes.

While the immediate priority remains polio, the laboratory’s impact could extend well beyond. According to Dr. Borus, the genomics technology can eventually be deployed to monitor other pathogens, giving Kenya an edge in detecting and responding to future outbreaks.

“For now, our urgent task is to eradicate polio,” he noted. “But in the future, this technology will strengthen our preparedness for other diseases as well.”

With Africa still vulnerable to cross-border outbreaks, the ability to detect, analyze, and respond quickly to viral threats has never been more critical. The genomics laboratory stands as a testament to Kenya’s commitment, not only to achieving a polio-free future but also to laying the foundation for stronger health security in the years to come.