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Pathogen prevention

In Africa, detecting disease outbreaks before they become a global threat

Using genomic sequencing technologies, this hero is working to prevent the next pandemic.


While promoting my new pandemic book the last month, I’ve been telling audiences and interviewers that if we want to make COVID-19 the last pandemic, we need to combat infectious diseases the same way we fight fires.

Just like we have a robust system of fire alarms, firefighters, and fire hydrants to help detect and extinguish fires, we need to create an equally effective system to identify and respond to new disease outbreaks.

This firefighting comparison is also a useful way to understand the amazing work of Sofonias Tessema.

Officially, Sofonias is the program lead for the Africa Pathogen Genomics Initiative at the Africa Centers for Disease Control and Prevention or Africa CDC. But in firefighting terms you might think of him as a fire safety officer who is building a network of fire watchtowers and smoke detectors across Africa.

Instead of looking out for the first signs of a fire before it can spread, however, Sofonias is focused on quickly detecting deadly pathogens before they can grow into a global threat. And instead of using watchtowers and smoke detectors, he relies on powerful genomic sequencing technologies to spot disease outbreaks.

Genomic sequencing allows scientists to read the DNA and RNA of pathogens and understand what they are, how they spread from one person to another, and develop counter measures like vaccines. During COVID-19, this technology has been an invaluable tool for identifying new variants, tracking the evolution and spread of the virus, and guiding public health responses.

Advances in this technology have made it easier, faster, and cheaper to do genomic surveillance. Over the last two decades, the price of sequencing a full human genome has fallen dramatically. And one company, Oxford-Nanopore, has even developed a portable gene sequencer that can be operated with a laptop and no need for a lab, allowing health officials to conduct genetic testing in remote areas where outbreaks may occur.

As powerful as genomic sequencing technologies have become, many countries have not taken full advantage of them. Building genomic disease surveillance capacity presents challenges because it requires investments in labs, expensive equipment, and specially trained personnel. While the COVID-19 pandemic has sparked new interest in using genomic sequencing to improve disease surveillance, many parts of the world are still working to strengthen their capacity to use this critical technology.

In 2019, Sofonias joined the Africa CDC to establish a continent-wide genomic disease surveillance network. One of Sofonias’s first projects was to conduct an assessment to understand how many African nations were prepared to use this technology.

The results, Sofonias said, were shocking.

Of the African Union’s 55 member states, just seven had public health institutions with trained personnel and equipment to do genetic sequencing.

Given the scale of the job before them, Sofonias and his team had planned for a phased approach to help African nations build genomic surveillance capabilities. They had to acquire the technology, hire and train the technicians to operate them, and create the data systems so governments can analyze and share the genetic information and use it to inform public health decisions. Building this system would take time.

But the Africa CDC soon learned that time was a luxury they didn’t have. Within weeks of Sofonias joining the Africa CDC, the first cases of COVID-19 were detected in China. And two months later, the first cases were identified in African countries.

It’s hard to overstate the challenge before Sofonias and the Africa CDC. While genomic surveillance had been used during Ebola, Lassa fever, and cholera outbreaks, bringing this technology to scale posed many challenges in Africa, where many countries did not have the infrastructure or trained personnel to run these labs.

But this was just the kind of challenge Sofonias had always been eager to take on.

Born in Ethiopia, Sofonias grew up in a rural town where malaria was always a major threat. Seeing people die and suffer from the mosquito-borne disease got him interested in a career in public health. He earned a PhD in malaria genomics, an emerging field of research that uses genetic data of the malaria parasite to advance malaria eradication efforts. After graduate school, he was working as postdoctoral fellow at the University of California in San Francisco, where he was focused on how genomic data combined with mobile phone data could help researchers understand how malaria spreads from one country to another.

In 2019, when a call came from the Africa CDC asking if he would use his knowledge of genomic surveillance technologies to help Africa, he jumped at the opportunity. Sofonias saw the untapped potential of this new technology to make more informed public health decisions in Africa. And after years living abroad, he was also excited to return home to Ethiopia, where the Africa CDC is based.

Sofonias and his team scrambled to quickly build up Africa’s capacity to do genomic disease surveillance. The Africa CDC focused first on scaling up COVID-19 testing capabilities. At the beginning of the pandemic, only two African nations had the ability to perform PCR COVID tests, highly accurate tests that detect genetic material from the virus.

At the same time, his team worked to acquire next-generation sequencing technologies (NGS) for Africa. NGS technologies offer a more efficient, accurate, and cheaper way for researchers to track the slightest genetic changes in pathogens which may cause disease outbreaks. This effort received support from a group of public, private, and non-profit partners including the African Union, Illumina and Oxford Nanopore, which produce next-generation sequencing machines, the US Centers for Disease Control and our foundation.

Thanks to Sofonias and the rest of the Africa Pathogen Genomics Initiative team, 31 African nations now have the capability to do genetic sequencing for surveillance of COVID, malaria, cholera, Ebola, and other diseases.

Despite this progress, much remains to be done. Sofonias’s team faces challenges in bringing this technology to all African nations. Access to the equipment needed in the labs has been delayed because of global supply chain disruptions. Training enough lab technicians and data scientists to process and analyze the samples has been difficult. Finally, more coordination is needed between countries to share their genetic data and use it to inform collective health responses.

But every month, Sofonias’s team continues to strengthen and expand the system across the continent. The goal is to create a seamless, integrated network that includes laboratories at the community level, which can spot the first signs of an outbreak, perform genomic testing of pathogens, and analyze the results to guide a public health response.

“Our vision is bold. Our vision is optimistic. We always push forward and continue to work with the countries to show that this is actually feasible,” he said. “It really makes me hopeful that this technology can improve outbreak detection and response in Africa.”

Sofonias shared the progress and challenges of building a genomic disease surveillance network with a group of graduate students who participated in a recent Gates Notes Deep Dive on pandemic prevention.

Meet more of my heroes in the field