Fellowships Bring Enhanced Genomic Sequencing Skills to Africa

Setting up more sequencing labs throughout Malawi is one of his dreams, and it seems closer to happening since he was selected to be one of more than 100 scientists from 21 countries as part of a continental training initiative coordinated by the Africa Centre for Disease Control.

The Pandemic Prevention Institute’s partner, the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University in South Africa, is a part of this effort, providing hands-on training to improve country capabilities to conduct end-to-end genomic surveillance. CERI is also working to make sure genomic sequencing goes beyond urban centers to reach more rural, remote areas, and to improve the time it takes to collect specimens, conduct testing and share the results with the scientific community, all crucial steps towards the goal of sustaining an early warning system to prevent future pandemics.

Following his intense short-term fellowship, Lucious was awarded a scholarship to complete a master’s degree in pathogenic genomics at Stellenbosch University. With this expertise, he will be able to work with the National Public Health Institute in Malawi to train others with the goal of sustainably expanding the country’s sequencing capacity with in-country expertise.

That said, the country has made immense progress in safeguarding the health of its population. Between 1990 and 2013, the Government of Malawi reduced maternal mortality by 53%, and since 2003, has reduced HIV/AIDS deaths and new HIV infections by 73% and 41% respectively. This is in large part due to the leadership of the government, global health partners, and committed Malawians like Chabuka.

CERI’s work to build and strengthen pathogen genomic surveillance capability throughout Africa is part of the Pandemic Prevention Institute’s vision of creating an interconnected network that connects and translates data into actionable insights to inform decisionmakers from nations to neighborhoods so they can play an effective role in rapidly detecting, responding to and containing pandemic threats. That work has already proved critical with the Omicron variant alert CERI sounded first to the World Health Organization and other global authorities.

Lucious is thrilled to be part of this team. When he was eight, he spent some time living with his brother, who was a medical doctor, and he became passionate about the work. Lucious’s brother urged him to work very hard in his science classes, “so I put all my efforts there.” When he applied to the College of Medicine at the University of Malawi, though, he was accepted in the medical technician track instead of the doctor training program.

“I was disappointed at first,” he recalls, “but then I grew to really love the work. We are very important because we find the real cause of the illness. The doctor is the one who tells the patient, but we are behind the scenes.”

After completing his initial fellowship with CERI in September 2021, Lucious got Covid himself two months later. He was at work when he realized he felt ill. His boss told him: “We’re too busy for you to have Covid!” He sequenced his own clinical swab and identified the culprit as the Omicron variant.

Now studying in South Africa, Chabuka misses his family and also the food, especially chambo, a fish dish from Lake Nyasa, often fried and curried, that is considered a delicacy. “I know I’m doing the right thing,” he says. “I am surrounded by people who are goal-oriented, I’m learning a lot from them and look forward to learning more.

“Still, I am eager to go back to Malawi because I have a lot of work to do there. We are way, way behind in sequencing in my country. I can teach my colleagues and we will be ready for whatever diseases might come.”