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Fellowships Bring Enhanced Genomic Sequencing Skills to Africa

When the Covid-19 pandemic began, only a single lab in Malawi was working to sample SARS-CoV-2 viruses in this country of 19.55 million people. Only four people were working in that lab. One of them was technologist Lucious Chabuka.

“On a normal day, I was at work by 6 a.m. and tried to leave by 8 p.m.” recalls the 37-year-old father of two. “After a few weeks, we started going to other labs and training them on how to test for SARS-CoV-2. As people returned to the country from South Africa, we collected samples at the border. We had about 500 clinical specimens coming in every day for the four of us to analyze.”

The work was nonstop. “There were times when I worked through the night,” Lucious says. “I had no weekends. When I finally went home, my family was really worried. I slept apart from them in my own room.”

Malawi has persevered through three Covid-19 surges, in January, July and December of 2021. Throughout those waves, dedicated lab technicians like Lucious helped the country diagnose more than 85,000 cases.

His team also led the nation’s genomic sequencing efforts, shedding light on virus variants that impacted Malawi. A more specialized process, genomic sequencing requires additional investments in infrastructure, technology, training and workforce capacity, along with advanced data analytics skillsets.

To date, Malawi has sequenced and shared more than 1,100 SARS-CoV-2 genomes with the global community through GISAID.

Lucious training in South Africa

But Lucious says those figures, as in many other parts of the world, can be misleading. The lab where he worked as an employee of the Public Health Institute of Malawi is in the capital city of Lilongwe, in the middle of the country.

In the north and the south, there is little to no sequencing being done.

— Lucious Chabuka

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.

CERI Already Helping Transform Disease Tracking in Africa

CERI is a new organization, backed by an initial $4.5 million in funding from The Rockefeller Foundation’s Pandemic Prevention Institute, that is already leading work to expand pathogen surveillance capability across the African continent.

Map of Malawi

By improving pathogen surveillance and clinical diagnosis, CERI’s work will advance the treatment, diagnosis and prevention of human disease, enhance biomedical discovery, and generate additional economic opportunities for Africa. Just two months after its September 2021 launch, its scientists detected the Omicron variant and worked with South African authorities to alert the world.

“Africa has a long history of responding to epidemics, and it’s important that we harness this expertise, coupled with pathogen genomic surveillance capabilities, to counter Covid-19, make progress against other existing epidemics, and prevent future outbreaks,” said Prof Tulio de Oliveira, CERI’s director.

CERI trains scientists in South Africa during intensive fellowships

“At the Pandemic Prevention Institute, we recognize the value of pathogen genomic surveillance in detecting and understanding disease outbreaks,” said Dr. Rick Bright, the Institute’s Chief Executive Officer. We also understand the value of strengthening local knowledge and capabilities to improve access to this critical information, he added, “and that is why we are honored to support this transformational initiative to build genomic surveillance capabilities in coordination with other global stakeholders.”

CERI is part of a larger effort to ramp up genome sequencing throughout Africa, including the Network for Genomic Surveillance in South Africa and the Africa CDC’s Institute for Pathogen Genomics. The Pandemic Prevention Institute believes improved disease tracking—through genomic sequencing labs, routine disease surveillance, and environmental and other monitoring modalities—has the potential to revolutionize public health, transforming responses to other major health threats beyond Covid-19, including tuberculosis, malaria, dengue, and other emerging and re-emerging diseases.

CERI is training lab technologists from 21 African countries

Meeting Malawi’s Challenges

Malawi’s health system, while under-resourced, is no stranger to diseases that threaten the health of the population. The country has also faced health crises prior to Covid-19. Malawi has only two physicians per 100,000 people and the average life expectancy is 39 years. About a million adults are living with HIV/AIDS, and about a million children have been orphaned by the disease, according to the U.N. The country also declared an outbreak of polio this year, and faces routine health threats like hepatitis A, malaria, rabies, schistosomiasis and typhoid.

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.”