A new viral surveillance system in West Africa is showing the world how to prevent the next pandemic
Scientists from the US and West Africa have teamed up to build a better public health network that can quickly detect and respond to emerging viral threats.
As night fell on July 20th, 2014, genomicist Christian Happi was at home with his family in Lagos, Nigeria when he received a phone call he would never forget. There was a suspected case of Ebola in Lagos: a diplomat who’d flown in from Liberia with a fever. Blood and urine samples from the man were waiting for Happi in his lab.
Happi felt chilled. Lagos is Africa’s largest city, home to about 25 million people, with a busy seaport and airport. He started to imagine how the deadly and contagious disease, if confirmed, might spread to half the city’s population.
Within an hour, Happi was in the car, speeding through the dark to his lab. By 6 am the following morning, he and his assistant had the first case of Ebola in Nigeria using a PCR test. Happi immediately contacted the Lagos State Ministry of Health and together, they began tracking down everyone who’d been on the patient’s flight. They identified 20 cases and isolated everyone who’d been exposed. Eight of the 20 patients died, but the spread of the disease in Nigeria stopped there.
However, in other parts of , Ebola was spreading, infecting nearly 29,000 people and killing more than 11,000 before the outbreak was contained in 2016. Although public health officials and healthcare workers responded deftly to the outbreak, local communities lacked the public health infrastructure, such as low-cost diagnostic tests, needed for rapid responses. In addition, the exchange of health data between local clinics and national and public health officials from the World Health Organization (WHO) happened on paper, making timely responses to outbreaks nearly impossible. While Happi and his colleagues in Lagos helped avert a crisis in Nigeria with their rapid, on-the-ground diagnostic capabilities — saving possibly tens of thousands of lives — in Guinea, Ebola infections multiplied as public health officials sent patient samples out of the country for sequencing and waited up to to get results.
On October 20th, 2014, as Ebola continued to spread in Guinea and in neighboring Liberia and Sierra Leone, WHO Nigeria free of Ebola. Happi says it was the first time genomics work in Africa had been used for public health surveillance. The experience made him more certain than ever that viral genomic data, when shared quickly and widely, could transform public health.
As the Ebola epidemic began to wane, talked more urgently with his longtime collaborator Pardis Sabeti, a computational geneticist at the ӳý of MIT and Harvard, about an idea they had been discussing for years: building an early-warning system in Africa that could prevent future epidemics, even pandemics. Sabeti and her lab had also responded quickly to Ebola in 2014, working with hospitals and government officials in Sierra Leone to sequence viral genomes from patients and make the data available to local communities.
Happi and Sabeti wanted to use the same infectious disease surveillance principles they had followed in 2014 to build a network of experts and diagnostic and sequencing centers in Africa that would act as sentinels, quickly detecting and reporting local clusters of viral infections before they morphed into larger outbreaks. They called the idea Sentinel.
“Technological advances in genomics and data sciences have the potential to transform how we think about detecting and treating deadly and pervasive diseases like Ebola,” Sabeti said. “Partnering with researchers on the ground to reach communities where they are is absolutely critical to making that a reality.”
“We learned a lot from Ebola,” Happi said. “We started thinking how if you act fast, if you have the right tools, the right platform, and you’re accurate about what you’re detecting, you could really beat an epidemic. You could save lives.”
A new model
Formally launched in early 2020, is a new model of pathogen surveillance that its leaders say could be used anywhere in the world. The project is a collaboration between the ӳý and the African Center of Excellence for Genomics of Infectious Diseases (ACEGID) at Redeemer’s University outside Lagos in Nigeria, where Happi is a professor of molecular biology and genomics. Supported by the , Sentinel uses cutting-edge tools for pathogen detection developed at ӳý and builds data analysis expertise and digital infrastructure in West Africa. The project connects local clinics and hospitals with scientists at genomics hubs and government health officials, all tracking infections at the local and regional levels.
Today, Sentinel has established sites at ACEGID as well as four hospitals in Nigeria and one in Sierra Leone, and has laid the groundwork for more in Senegal and Liberia. Rural clinics use rapid, low-cost tests to detect a few common pathogens. Hospitals with laboratories use pathogen detection technology developed by Sabeti’s group that scans samples for a panel of additional pathogens. Public health officials monitor infections and communicate between sites and the regional genomics hubs.
The Sentinel team has also trained more than 1,600 scientists from all 54 African countries in genomics, diagnostics, and bioinformatics. This year, they will open a new genome center at ACEGID that will train scientists from across Africa and sequence viruses in a state-of-the-art lab with advanced biosafety.
The Sentinel team put an early version of their system to the test in 2020 to respond to COVID-19 and again in 2022 for Mpox surveillance and response efforts. Those early tests showed that their framework could be adapted rapidly to respond to new viruses.
“We often don’t pay much attention to surveillance of infectious diseases until there’s an outbreak, and it’s a really overlooked aspect of global health,” said , the operational director of the US contingent of Sentinel and Sabeti’s senior advisor. Ozonoff is also an associate professor of pediatrics at Harvard Medical School and a scientist at Boston Children’s Hospital. He joined the team in 2022 after two decades of experience with public health surveillance of all kinds — cancer, occupational health, HIV/AIDS, influenza, SARS-CoV-1 — because he was excited by the potential Sentinel had to impact the lives of people around the world.
“Sentinel is more than just a short-lived research program in West Africa,” he said. “This is how we should be conducting surveillance. It’s a call to the world to say, ‘We need to do surveillance before there’s an outbreak, not after.’”
Happi adds that Sentinel is important for pandemic prevention in an increasingly connected world. “It can take only 36 hours for a virus that is emerging in a very remote place to find itself in New York or Paris — they are just a few flights away,” Happi said. “Through Sentinel, we are creating a world that is equitable. We are creating a platform that helps those that are at higher risk, where the pathogens are, not only to protect Africa, but to protect the world.”
Building a network
When Ebola struck West Africa in 2014, Sabeti and Happi had already been thinking about the possibility of on-the-ground pathogen surveillance for years. Since 2007, they’d been studying Lassa fever, an often deadly illness caused by infection with the Lassa virus, which is endemic in West Africa. They and their teams soon discovered that diseases such as Lassa fever that were once considered “emerging” had, in fact, been circulating undetected in local populations because hospitals didn’t have the right tools to diagnose them. Their work would later reveal that the Lassa virus had likely been circulating in West Africa for at least 500 years.
The results of their Lassa work rattled Happi and Sabeti. They began envisioning a new hub-and-spoke pathogen surveillance — one that centered on long-term partnerships between local health clinics and their communities, supported by diagnostics at regional genomics hubs. They hoped that better diagnostic capabilities would help build trust in healthcare and make people with illnesses more willing to visit clinics and hospitals, which would further help stop disease spread. They also recognized the potential global impact this model could have, by preventing local viral threats from ballooning into global ones.
In 2013, Happi and Sabeti applied to the World Bank for support to establish a genomic center of excellence in Nigeria. Their hope was to begin building local expertise and trust between communities and healthcare clinics that would bolster new diagnostic hubs. And in March of 2014, as Ebola started spreading throughout West Africa, ACEGID was born: a genomic research center at Redeemer’s University that quickly seeded a network of African partners. In collaboration with the ӳý and other research and public health partners, the team began laying the foundation for Sentinel.
CRISPR diagnostics
Sentinel consists of three distinct layers of technology to detect viral infections: low-cost tests that can identify common pathogens in local clinics with few resources; hospital-based screening panels to diagnose illnesses not covered by the low-cost tests; and finally, genomics centers that can sequence and analyze viral genomes to identify new viruses and monitor the evolution of known ones.
“Once we realized how widespread these viruses were, and how they were circulating under the radar, we knew we’d need better diagnostics that were rapid and sensitive and could be deployed anywhere,” said Sabeti. “And knowing that viruses are always emerging and are continually evolving, we wanted to develop tools that we could easily adapt to new pathogens and their variants.”
Even before launching Sentinel, Sabeti’s lab began developing the technologies needed for the first two layers in partnership with Feng Zhang’s lab at the ӳý. As the first point of defense, Sabeti’s team created SHINE, or Streamlined Highlighting of Infections to Navigate Epidemics, a sensitive and low-cost paper strip test that uses CRISPR to test patient samples for the presence of a specific virus and generates results in less than an hour. SHINE doesn’t require expensive equipment or reagents and can be used in the field and in small clinics.
The Sabeti lab also partnered with Paul Blainey’s lab at the ӳý to develop Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN), an approach that can be deployed in hospital labs. It uses CRISPR and microfluidic technology to perform thousands of tests at once. This allows scientists to scan multiple samples for a panel of up to 96 viruses simultaneously, and can provide results in a few hours.
For each new piece of technology, Sabeti’s and Happi’s labs worked with local scientists to make sure that whatever they built was well-suited to a setting with very different resources than a lab in Cambridge, Massachusetts.
“A lot of times, outbreaks happen in areas where folks don’t have access to lab testing and don’t have a way to get there,” said Chelsea l’Anson, one of Sentinel’s project managers at the ӳý. “We’re trying to develop these technologies that will work for people who need them the most.”
“Pardis and Christian have created an environment where we can collaborate closely with our colleagues in West Africa, which gives us a deep understanding of what the current system looks like and where tools can fill in the gaps,” said Colby Wilkason, ӳý’s program manager for Sentinel. “This environment has enabled us to integrate detection and surveillance innovations into the public health system and strengthen local capacity in areas most needed.”
In March 2020, just one month after Happi and Sabeti officially launched Sentinel, WHO declared COVID-19 an international pandemic. Sooner than planned, Sentinel would be put to the test.
Test run
In February of 2020, when it was clear that COVID-19 was spreading around the world, Sentinel teams began distributing SARS-CoV-2 PCR tests to hospitals in Nigeria, Sierra Leone, and Senegal. And in early March, Happi’s lab sequenced the first SARS-CoV-2 genome in Africa and .
CARMEN and SHINE, which the Sabeti lab had originally designed to detect viral hemorrhagic fevers such as Ebola in West African countries, suddenly had a new purpose: detecting SARS-CoV-2. The Sentinel team had intended to spend their first two or three years developing tools and conducting research, but it was clear communities needed tests immediately. Sabeti’s lab quickly pivoted and, within months, had adapted CARMEN and SHINE to detect SARS-CoV-2, which were soon deployed in Nigeria.
Happi’s team, meanwhile, quickly started training scientists from other African countries, flying them into Nigeria to learn how to sequence SARS-CoV-2 genomes to track viral evolution and detect new variants. Throughout the pandemic, they trained more than 1,600 people from 38 countries who returned home with continued support from Happi’s team. When researchers who had trained in Nigeria couldn’t get their own sequencers to run properly in Côte d’Ivoire, for example, two members of Happi’s team flew in to help them identify roadblocks. Within two weeks, the Institut Pasteur de Côte d’Ivoire shared 700 new genome sequences with the world.
“That was Sentinel in action,” Happi said. “It was a process we’d only dreamed of, and then COVID demonstrated its power, and it showed.”
In 2022, Happi’s team also redirected energy to respond to an outbreak of Mpox, a viral disease that had begun to spread mostly around Europe and the Americas, though it has been endemic in West Africa for years. ACEGID collected and sequenced Mpox genomes from cases from around West Africa to better understand the underlying networks driving transmission in the region. Happi also led a workshop to train other researchers to analyze the genomic data and respond to Mpox outbreaks in their own communities.
Empowering a generation
After two and a half years of testing an early version of its framework with COVID-19, Sentinel is now implementing more general pathogen surveillance, focusing on those that Nigerian leaders determined would be most important in their country. Last year, the team started using CARMEN in Sentinel hub sites in Nigeria and Sierra Leone to detect respiratory viruses including SARS-CoV-2, other coronaviruses, and influenza viruses. This year they began testing for 19 bloodborne pathogens such as Ebola, yellow fever, Lassa, and HIV.
Sentinel is also developing a SHINE test to detect Lassa virus in rural clinics in Nigeria, where there are currently no FDA-approved diagnostics for the disease. The Irrua Specialist Teaching Hospital, a long-standing center for diagnosing and treating Lassa fever in a rural area about 300 kilometers outside of Lagos, is now field-testing the SHINE test for widespread use across all Sentinel sites in Nigeria during seasonal peaks of Lassa infection.
In addition to detection tools, Sentinel also refined a suite of surveillance tools called Lookout, developed by for the team. Lookout overlays multiple data sources, including epidemiological, clinical, and behavioral data from patients, so clinicians and local government officials can visualize local trends in disease transmission and send reports to hospitals with CARMEN diagnostic capabilities to help spot epidemics early.
Lookout has been implemented in the Sentinel sites in Nigeria and later this year will roll out at the Sierra Leone site, the Kenema Government Hospital, which was one of the leading responders to the 2014-2016 Ebola outbreak.
“These are people on the frontlines,” Happi said. “We’re empowering them to be more effective at the job they do on a daily basis.”
And in the fall, Sentinel will help unveil a new state-of-the-art genome center at Redeemer’s University staffed by locally trained Nigerian scientists. It will contain laboratories equipped to sequence and study pathogens such as Lassa virus and Ebola virus, and includes biosafety level 3 capabilities. Typically, this kind of analysis occurs in major urban centers such as Lagos, but the new lab will relocate these tools closer to the point of the source of outbreaks, enabling more timely responses. The new hub will also contain an educational center where scientists from all over Africa can receive training.
The newly designed genome center at ACEGID, which will open later this year.
Lab facilities at ACEGID’s new genome center.
Sabeti, who hosted intense training programs for African scientists in her own lab at ӳý for many years before ACEGID got on its feet, has watched these capacity-building programs become a mainstay for scientists in Africa. “Education is how you build community and a shared culture,” she said. “Now all 54 countries in Africa have ACEGID alumni and have a community of front-line researchers working together across the continent. That’s astonishing.”
Ozonoff, Sentinel’s operational director, hopes that one day, their model may even extend to other parts of the world where a pandemic-causing pathogen is likely to emerge, such as Central and South America or Southeast Asia.
“We’re trying to offer a blueprint, almost a template,” he said. “If other people have the relationships and resources to put that framework into action in other parts of the world, that would be amazing.”
In Nigeria, Sentinel's hub and spoke model consists of the hub — ACEGID at Redeemer's University — and four sites around the country.
