Africa’s Covid experts build early warning systems for the next pandemic

As scientists in Africa track Covid patterns and stay alert to new variants, they are also building the technological infrastructure to spot – and hopefully avert – the next pandemic.

At Dakar’s Pasteur Institute in Senegal researchers have developed a new system to stay in daily contact with clinics in 23 regions across the country. At the end of every day, after taking their samples, the clinics send in information online about the kind of symptoms, such as fever, that they have identified in patients.

The Covid-19 pandemic has lent added urgency. The scheme started with three centres just over five years ago, and now has sites in each region of Senegal. It plans to go up to 79 sites, with one across each district. Then the scheme will be expanded into three neighbouring countries: Cape Verde, Gambia, and Guinea Bissau.

Dr Joe Fitchett of the Pasteur Institute says: “We want to respond effectively to the next outbreak, and if you respond to that outbreak in a swift and smart way, you prevent it from becoming an epidemic, and ultimately escalating to a pandemic.”

Known as the One Million Fevers project, the centres already track over 200,000 people a year with the ambition to reach a million or more. The fevers can indicate common malaria, coughs and colds, but also rarer diseases. “We have a list of dangerous pathogens that we are looking out for and we detect here all the time and we go out and stop the outbreak,” Fitchett says.

The Covid pandemic and related lockdowns have interrupted many routine immunisation campaigns and laboratory surveillance programmes.

“The pandemic speeds or enables certain things and it impedes and slows down others,” Fitchett says. “Whilst at the high level it shines a spotlight on the importance of the health sector, in practice there’s only a certain number of scientists and health workers and experts who can deliver this programme without immediate training.”

Nevertheless, the pandemic has sharpened interest and investment on disease surveillance in Africa, says senior advisor to the Africa Centres for Disease Control and Prevention, (Africa CDC), Dr Ebere Okereke.

The use of electronic health records has come on in leaps and bounds across the continent in the past two years, she says. “Traditionally in Africa we are still predominantly dependent on paper, which by definition is slow.”

But new computerised systems including the use of QR codes have changed that. “Rather than the person in the clinic waiting until the end of the day, the week or the month to collate everything… they can input information in real time into an electronic system, which is constantly able to aggregate, analyse and interpret.”

Covid-19 is in large part responsible, Okereke says. “Because we’ve had to try and deliver an adult vaccination programme, which for a lot of countries is the only adult vaccination programme they’ve ever delivered routinely, systems have had to be set up to record the vaccination.” Previously, only young children and pregnant women’s records were routinely kept in many countries, she says.

It’s not just data systems that have improved on the continent, but the science itself.

AFP via Getty Images

The early detection of the Beta and Omicron coronavirus variants in South Africa has highlighted the importance of genomic surveillance in identifying variants quickly, tracking their transmission around the globe and helping authorities to make quick public health decisions.

In Africa, there are over 500 scientists working in 30 countries involved in sequencing, according to the South Africa-based Human Heredity and Health in Africa (H3Africa) initiative, which aims to create and support a pan-continental network of laboratories conducting research in genomic sciences.

While Africa still lags the rest of the world in sequencing, such developments will allow the “mapping of outbreaks of tuberculosis and other diseases through genetic sequencing at pace and across boundaries,” says Okereke, describing these developments as “the promised land that Covid has brought closer for Africa”.


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