Inside the lab hunting for Disease X – the next pandemic

It all starts with a fever. It’s the first signal that an outbreak of disease could be moving silently through the population.

At a health centre in a busy area of the Senegalese capital, Dakar, no cases of dengue had been detected before 2023. In the following nine months, more than 200 cases were spotted. The illness had always been there – in homes and clinics, people were developing the warning signs of intense pain in the joints and bones that lend the mosquito-borne disease its nickname of “breakbone fever”. But these cases were invisible until a surveillance site, set up by the Institut Pasteur de Dakar (IPD), brought them under the microscope.

Although it was founded almost 100 years ago and became known for medical testing and research, it is only in the past couple of years that the institute has grown to become the control room of a network of listening posts dotted across 11 West African countries, primed to spot clusters of disease before they spill out into uncontrollable outbreaks. It is trying to expand these efforts further across Africa, in the face of deep funding cuts from rich countries, as many shift their resources towards defence spending.

At the more than 40 surveillance sites making up this network, health workers take swabs from the nose or throat of any patient who comes in with a temperature higher than 37.5C.

Whether it’s dengue, Ebola or more commonplace viruses like flu, they all share this symptom. “So the fever is the entry point,” says Dr Boubacar Diallo, who leads the lab’s outbreak response unit. Along with a host of other symptoms, it triggers an investigation which takes the patient’s swab on a journey from their local clinic to Institut Pasteur’s labs. There, millions or billions of copies of genetic material from the swab are made. This allows them to be studied to see if they match up with the genetic material of the virus suspected to be causing the infection

At the more than 40 surveillance sites making up this network, health workers take swabs from the nose or throat of any patient who comes in with a temperature higher than 37.5C.

Whether it’s dengue, Ebola or more commonplace viruses like flu, they all share this symptom. “So the fever is the entry point,” says Dr Boubacar Diallo, who leads the lab’s outbreak response unit. Along with a host of other symptoms, it triggers an investigation which takes the patient’s swab on a journey from their local clinic to Institut Pasteur’s labs. There, millions or billions of copies of genetic material from the swab are made. This allows them to be studied to see if they match up with the genetic material of the virus suspected to be causing the infection.

The results go back to the clinics that are caring for the patients, and anything concerning is reported to the Ministry of Health. Pretty much every time, the sample will either be negative or test positive for a known virus. But the lab is also on the hunt for unfamiliar microbes that could alert them to what’s known as Disease X – a new, currently unknown bug that could spark the next pandemic.

They even monitor animals in some areas, trying to spot diseases and quarantine them before they spread to humans. A recent outbreak of Rift Valley fever was spotted when groups of infected sheep and goats began to have miscarriages.

In Senegal, as in many countries in the region, disease outbreaks were for years a puzzle that could take months of an illness ripping through a community before the specific virus or bacteria was detected and action taken to stop its spread. The later it’s spotted, the harder it is to contain, with countries then needing to wait for international organisations like the United Nations and big charities to fly in with help.

Now, with cuts to global aid thinning that help out, the institute is hoping its disease-tracking efforts can help the region spot pathogens and respond to them faster without relying on outside support

The first time Dr Diallo heard of the institute, he had been parachuted by the World Health Organisation (WHO) into the middle of the deadly West African Ebola outbreak beginning in 2014. It lasted two years, cost more than 10,000 lives and ground economies to a halt.

When he arrived in Guinea, where the outbreak started, as part of the first investigation team, “it was a panic. I’ve seen houses closed, everyone died. We had a lot of colleagues that got infected and died. And at that time there was no vaccine.”

Dr Diallo ended up staying in the forest region for two and a half years. One man, a doctor who arrived with a small suitcase containing a mini laboratory, stands out in his memory. He came in the day and by nightfall he had confirmed what other institutions had been struggling to – that the samples they’d collected from sick patients with high fevers, vomiting and bleeding were indeed Ebola.

The man, Dr Ousmane Faye, was from the IPD, in whose corridors Dr Diallo – a rangy figure in a sharp checked blazer and a black beret – now stands as he recounts the story.

But the virus had started spreading four months before that detection. “Many people died before we detected. And we don’t want that to happen. If we don’t want that to happen, we need to put in a surveillance system that can help countries to capture when we have the first signal.”

While that experience sowed the seeds, it was in fact another Ebola outbreak in 2018 that finally led Dr Diallo to this lab. He was still working for the WHO when the Democratic Republic of the Congo (DRC)’s ninth recorded outbreak of the deadly haemorrhagic virus started, followed swiftly by its tenth.

“I was deployed to be the incidence manager for that outbreak, which was the most challenging outbreak ever because it was in an insecure area,” he says. “I lost five of my colleagues.”

The outbreak had got into a rebel fighters’ camp. Dr Diallo and his colleagues had to make the decision to treat infected colonels from the M23 armed group and train them how to safely bury their dead, without informing the national army.

A close colleague from Cameroon was sitting in the hospital having meetings with his team when the shooting started.

“I myself came to take the body,” Dr Diallo says. While some international donors had to leave the country, his team stayed. “We said we will never run,” he says, meaning until the outbreak is under control.

It made him realise he needed to lead from the continent, not from the WHO in Geneva or the US Centers for Disease Control (CDC) in Atlanta.

“Why can’t we prepare countries to be better prepared instead of waiting for outbreaks?” Dr Diallo had asked himself. “So that’s why I’m here today.”

In many ways, things have improved since then. Though during a monkeypox (Mpox) outbreak in DRC this year, according to Africa CDC, after aid cuts meant testing of suspected cases halved from 60 per cent to roughly 30 per cent, IPD sent mobile labs to ensure this figure didn’t fall further.

When Guinea faced a new attack of Ebola in 2021, a lot of the health workers responding had been trained by the Institut Pasteur. This year in Sierra Leone, during another Mpox outbreak, Dr Diallo andhis team sent mobile labs in trucks to help with the response, “because they only had one lab in the country”.

“We came today. At night, we are open’” says Dr Diallo. “Now, that one [is] really working very well. A month after they requested to have another mobile lab, which is just a suitcase.” These labs contain all the equipment needed to run tests to confirm a patient is infected and what virus they are dealing with.

‘“We have at least four suitcases. We can deploy that any time and everywhere.

The network still has many blind spots, though. Even in Senegal, where it started and where the most surveillance sites are housed, “we are not covering the entire country yet, “ Dr Diallo says.

And it has come under strain. Despite being one of the first responders, once the 2014 West African Ebola outbreak started to spread, the IPD faced a lot of logistical challenges when it came to shipping samples for hundreds or thousands of miles, delaying the process of confirming and containing it.

Now, rather than receiving samples from across Africa, the IPD is the laboratory hub for West Africa while labs in Cameroon and Uganda have become regional hubs for central, and eastern and southern African countries respectively. But all of this requires money. At the moment IPD still relies heavily on grants, but its ambition is to become more self-sufficient by using the data it gathers to develop and sell tests and vaccines.

Head of the Africa CDC, Dr Jean Kaseya, tells The Independent that the institute started to manufacture the yellow fever vaccine, “almost 100 years ago. A long time before seeing that in China, in Russia.” But, he says, “unfair treatment of the Western countries to Africa” meant the IPD was not supplying the vaccine to the continent; rather, the bulk of supplies comes from France and Russia.

“Our partners didn’t support this institute to extend the capacity. But today we are working on that,” he says. He thinks countries giving grants to such work should see them not as charity but as an investment.

The biggest source of funding to the IPD currently is The Global Fund, which has so far fallen almost $7bn short of its target of raising $18bn (roughly £14bn) for the next three years. The UK’s contribution amounts to a cut of 15 per cent. If the fund misses its target, it will have to prioritise, with life-saving work usually first in line to be protected – things like HIV and TB drugs and malaria bed nets, though deaths as a result of the cuts have been recorded nevertheless. The IPD’s work hangs in the balance.

The institute’s chief executive, Dr Ibrahima Socé Fall, is keen to stress what’s at stake. “I always tell the media in Europe that the best epidemiologists are in Africa, because the epidemiologists in Europe are sitting in hospitals and in laboratories.” But outbreaks happen in often hard-to-reach communities. You need systems working on the ground in affected countries to “rapidly detect and respond to outbreaks to prevent pandemics,” Dr Fall says.

In The Gambia, for example, lack of resources meant no disease outbreak had ever been detected by its national laboratory up to January 2023. The IPD visited for two weeks with materials and training. By September, the country’s own lab had detected a chikungunya outbreak for the first time in its history.

“That’s why the role of Institut Pasteur is crucial in the term of health security,” Dr Fall says. “Because when you have an outbreak somewhere in the world, it can be anywhere because of travel.”

The UK’s Foreign, Commonwealth and Development Office is giving £10m to the institute from next January to fund more disease surveillance centres in West Africa. But at the same time, the UK is cutting its wider funding intended to tackle the diseases being monitored, including malaria, as well as funding that helps countries develop their own health systems to become self-reliant.