A day in life of Kenya’s COVID-19 genomic sequencing team

Inside the Kenya Medical Research Institute genome sequencing laboratory in Kilifi, a town on Kenya’s Indian Ocean coast, a team of seven scientists process and analyse samples to monitor the COVID-19 variants and detect possible variants of concern.

The laboratory is part of a network of 12 reference laboratories across Africa with advanced genome sequencing programmes that support to neighbouring countries with limited or no capacity to conduct these analyses.

Before COVID-19 struck, the laboratory produced about 300 genome sequences in a year, solely for use in research projects. With the pandemic, it has widened focus to serve immediate public health needs. The laboratory increased its sequencing work to support Kenya and five other countries, there was an urgent need for more supplies and more personnel. The original three-person team was overwhelmed.

The hours are long, and each day is different. “It takes us three days to turn a COVID-19 sample into a sequence,” says Eddidah Moraa, a research assistant at the laboratory. “Each day involves a different set of steps we have to go through to prepare the samples for sequencing.”

At its busiest during the pandemic, it peaked at 600 samples weekly.

“Oh! That was a hard time, that week,” remembers Khadija Said, a research officer on the genome surveillance team. “There was so much pressure.”

World Health Organization (WHO) provided financial support to the laboratory to hire two additional technicians. The Organization also helped procure reagents, which are needed to prepare samples for sequencing. Over the past two years, WHO has also facilitated agreements between countries and arranged logistics for laboratories sending their samples to Kenya for analysis.

The physical process of sequencing samples is only half the task. “One of the most important steps is to change the RNA into DNA so our sequencing machines can read the sample. We also have to make sure there’s enough of the virus remaining in the sample to draw out the genetic information we need,” explains Said.

The team analyses mutations in the virus and determines if the changes are a cause for concern. They also look for trends, to understand where the variants are circulating, when and if the variants are affecting specific groups of people.

When the sequences are complete, they appear on a computer screen in green text as a series of letters that are indecipherable to the untrained eye.
“It’s just a simple file, that’s the whole idea,” Said points out as she scrolls through them keenly.

The laboratory invested in additional sequencing machines, increasing its capacity from 24 sequences in a week to 700. It also designated three freezers exclusively for the storage of COVID-19 samples from within and outside of Kenya. Since April 2020, the team have created more than 8000 genome sequences, two-thirds of which were from within Kenya.

For Dr George Githinji, who leads the genomic surveillance team at the laboratory, it doesn’t matter from where the samples arrive. “We just come every day and do our research,” he says. “Some days, we have a lot more work than others.”
Dr Githinji points out that the most important aspect of sequencing is consistency. “That’s how we recognize when the virus has changed in a meaningful way.”

Supporting Kenya and other countries with sequencing adds more work to the technicians’ already full plates, but they don’t mind.
For Said, she’s happy to play her part: “It’s fulfilling when we’re getting samples from other places. They trust us.”

Dr Githinji notes the laboratory’s role in training technicians from other countries. He says he is proud of their contribution in “building capacity for the world.”

As the sun makes its way below the horizon, the team remains in the lab with their eyes fixed on their research. They still have several more tasks before their 12-hour shift ends.