Christian Happi at the African Centre of Excellence for Genomics of Infectious Diseases
Pius Utomi Ekpei / AFP via Getty Images
In late December, 2013, a 18-month-old boy in a small village in southern Guinea died two days after contracting a mysterious disease. By the middle of January, 2014, several members of his family fell ill with the same symptoms: fever, vomiting and black stools. Two months later the cause of the outbreak was identified: Ebola virus. The subsequent epidemic hit West Africa hard, infecting more than 28,000 people and killing 11,325. Cases were also reported in Italy, Spain, the UK and the US.
Christian Happi was the first person to diagnose a case of Ebola in Nigeria, and helped to sequence the virus. But Happi, a professor of molecular biology and genomics at the Redeemer’s University in Nigeria, was frustrated by how inadequate the response was. Hospitals were sharing information through paper, or Excel, if they even had electricity. “There was no coordination,” he says. “It was a big mess.”
Every week it took for information about new infections to be sent around, the more the virus was spreading. “I started thinking, how do we create a system that will make information available almost in real-time, so that those that are making decisions can be abreast of what is going on?” says Happi. He decided to create a system that could easily detect viruses, immediately tip off local authorities and halt an outbreak in its tracks.
Africa is no stranger to infectious diseases. An estimated 140 disease outbreaks are reported annually across Africa. Diseases such as Ebola, Lassa fever, Zika and West Nile virus all were first identified on the continent. On an index that ranks the countries vulnerable to outbreaks, 22 of the 25 most-vulnerable countries were in Africa. A rich viral biodiversity, combined with a weak surveillance system, a mushrooming population, and poor public health infrastructure means that any disease outbreak is ripe for spreading like wildfire across the continent, and the world.
Pardis Sabeti has worked with Happi for over two decades, studying infectious diseases such as Ebola and Lassa fever. (Happi refers to Sabeti, a computational biologist at the Broad Institute of Harvard and MIT, as his “academic better half”.) Having experienced firsthand how lethargic and uncoordinated the response to outbreaks was in Africa, they spent years discussing the idea of designing and implementing a better system. One that could quickly detect viral outbreaks, and sound the alarm to local health authorities almost instantly. Such a system could contain an outbreak, stem its spread and potentially prevent a pandemic.
In the early 2010s, Happi and Sabeti began to put in applications, and were rejected repeatedly for years. And then Ebola hit. It became starkly clear just how much the system like they were proposing was desperately needed. Finally, in May 2014, they were awarded a grant from the World Bank. Following the Ebola epidemic, they went to work at building their project, calling it Sentinel.
Sabeti and Happi have designed their own new diagnostics tests to spot pathogens. One of these is a simple, cheap paper strip test that can detect common viruses. Another can test for hundreds of viruses simultaneously, which could enable hospital lab staff to test patient samples for a whole range of viruses within a day, and previously unknown viruses within a week.
Part of the initiative will be setting up a rapid sharing system of data in real-time using mobile applications. In the case that a person in a remote rural village comes down with a viral disease, this can quickly be reported to local health authorities who can then take the necessary measures to contain it.
When word of a novel coronavirus outbreak spread, Happi and Sabeti sprung into action. It was the perfect trial run for Sentinel. They had diagnostic testing set up at their hospital sites in Nigeria, Sierra Leone and Senegal by early February – before any hospital in the US. They trained local healthcare workers, and Happi’s team is doing diagnostic testing for the 30 million people in Nigeria. Happi’s lab sequenced the first Covid-19 genome in Africa within 48 hours. Less than a decade ago, virus sequencing would have been done by labs abroad.
In the first phase of the project, which is set to last until 2025, the system is being piloted first in Nigeria. They will then move further afield, to countries like Guinea, Liberia, Senegal, Sierra Leone and the Democratic Republic of Congo. But the pandemic has meant that everything has had to speed up. “The timeline that we had set for ourselves, a five-year proposal to do this work, is definitely way too slow,” says Sabeti.
One of the goals of Sentinel is to train healthcare workers in Africa, so that Sentinel detection tools become part of their everyday life. Over the next five years, they plan to train 1,000 medical workers. Happi moved to the US to work at Harvard, but after a decade, he decided to return home to Africa, settling in Nigeria. He is passionate about empowering African scientists to take back control. “I see no reason why Africa shouldn’t be the leaders in the field of infectious disease prevention and innovation,” says Happi.
During the Ebola epidemic, researchers from Western countries flew in, collected thousands of samples and left. These experiences have left Happi wary of what is known as ‘parachute science’ – where scientists from other countries fly in and take whatever data they need to further their own research. He is all for collaboration with other countries, but that relationship must be symbiotic. “I believe in equity; I don’t believe in exploitation.” All the people from abroad who came to Africa to aid in the response to Ebola actually “left the country worse,” he says.
There are a lot of obstacles around Sentinel that must be rectified before it can fulfil its promise, says Chikwe Ihekweazu, director general of the Nigeria Centre for Disease Control. Prerequisites such as being able to transport samples while controlling temperatures, reliable internet access and security all need to be put in place.
But a system like Sentinel in a place like West Africa will be critical in saving lives, Ihekweazu says. “We live in the middle of the tropics, a dense ecology, the temperature is very hot, very high population density – it’s a perfect environment for viruses to spread.” And nobody in Africa wants to send samples across the world anymore, he says. “We want to do our science.”
Not only could an early-warning system for viral threats potentially curb a global outbreak, it will also mitigate the devastating impact these diseases have on African communities on a regular basis. At least 35 per cent of total deaths reported on the continent annually are due to infectious disease. “African people are very familiar – sadly – with infectious disease,” Sabeti says. “But that also means they’re very well poised and positioned to do this.”
Grace Browne is a science writer at WIRED. She tweets from @gracefbrowne
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