From Ebola to swine flu to HIV/Aids, viruses borne by animals have caused some of the most devastating epidemics in history. What will come next? In Sierra Leone, Joe Shute joins the scientists working to find Disease X – a virus that is as yet undiscovered, but which could have the potential to ravage populations. Photographs by Simon Townsley

The caves surrounding the village of Gbentu in northern Sierra Leone are held sacred in local culture. Kings have been laid to rest here, and tributes stowed deep within the crevasses. For centuries, in times of death or crisis, tribal elders have tramped through the jungle to hold secret rituals in the darkness.

Tonight, however, it is a dozen or so Sierra Leonean scientists in blue scrubs and gumboots who trudge through the gloom. As we approach, a chorus of nervous-sounding coughs echoes down the line. The head of the village, known as the paramount chief, has instructed us to clear our throats when we arrive at the caves to activate a spell he has conjured to help protect us against the poisonous snakes that reside here.

As their assistants (recruits from the village) use machetes to hack a clearing, the scientists put on the ghostly white full personal-protection suits that strike fear into the hearts of so many in this disease-ravaged part of west Africa, which between 2014 and 2016 suffered the worst Ebola outbreak in history – resulting in 11,325 deaths. Mist nets – mesh used to capture bats and birds – are unfurled across the various mouths of the caves. And then, we wait: loitering among belching frogs and whining mosquitoes as the jungle canopy is swallowed into night. 

Gradually, plumes of bats rise like smoke from the caves. Those that get caught in the nets snarl and thrash about. Avoiding their snapping fangs, scientists disentangle the bats and pass them to a team seated around a plastic picnic table converted into a makeshift field laboratory. Under torchlight the bats are weighed and measured, and subjected to oral and rectal swabs, with blood samples taken from the veins laced through their wings. The test tubes are placed in a mobile freezer before the bats are released back into the night air; now carrying the scent of chlorine disinfectant intermingled with rich earth. 

By the end of the evening the scientists have tested some 21 bats; insect-eating ones from the Hipposideros genus. The hope, if you can call it that, is that one of them may turn out to be harbouring what is a sort of holy grail to virus hunters: the next deadly pathogen that could sweep across the globe. In July this same team discovered an entirely new strain of the Ebola virus among bats captured in the neighbouring district of Bombali. It is gruelling and potentially lethal work. But the ambition prevails that by locating new diseases in the wild they can prevent epidemics before they spread to humans. ‘I realise the seriousness of what we are doing,’ says one of the virus hunters, Edwin Lavalie, a 29-year-old specialist in ecology. ‘But at the same time I know we are contributing to something global. That is where my energy comes from.’

Monkeys, bats and rodents all harbour viruses capable of jumping the species barrier

Photo: Simon Townsley

The virus hunters of Sierra Leone are part of an international network known as Predict, launched with $200 million funding from USAID (the United States Agency for International Development) and currently operating in more than 30 countries. The project has amassed tens of thousands of samples for analysis and discovered more than 900 new viruses. Predict is a forerunner of the more ambitious Global Virome Project – a 10-year plan to identify as many as possible of the estimated 1.6 million unknown viruses in birds and mammals. Of these, it is thought between 600,000 and 800,000 are zoonotic, meaning they have the potential to jump from animals to people. Earlier this year the World Health Organization (WHO) announced it was sufficiently concerned about what was lurking in the wild to include something called ‘Disease X’ in its global strategy plan, representing an as yet undiscovered pathogen with the potential to spark a pandemic.

There is a classic equation devised by the scientists Robert May and Roy Anderson to assess the lifespan of an epidemic. Virulence, contacts and the length of time for which people are infectious are the three factors that determine what is called ‘the basic reproductive rate’ – how far and fast the epidemic will spread. When a two-year-old boy fell ill and died from Ebola in the isolated Guinea village of Meliandou around Christmas 2013, the disease spread like wildfire over west Africa’s porous borders. While the exact source of the virus – the Zaire strain of Ebola – has never been confirmed, shortly before falling ill the boy was seen playing near a tree infested with bats. By the following spring, the disease had become rampant in Guinea, Sierra Leone and Liberia, and it later spread to Lagos in Nigeria (although it was curtailed before it could take hold among the city’s 21 million inhabitants). 

During the epidemic James Bangura was the lead surveillance officer for the government in Sierra Leone. The 39-year-old – whose brother is the former Celtic striker Mohamed Bangura – lost numerous colleagues, including his mentor, the viral haemorrhagic fever specialist Dr Sheikh Humarr Khan. Bangura broke the news to Dr Khan that he had contracted the disease, and as a contact himself was forced to go into self-quarantine for 21 days. He would be quarantined three more times, after other colleagues died, and opted to live in an entirely separate part of the house from his wife and two children. Every night he would douse himself in chlorine and wonder if the virus had somehow made it into his body.

Bangura was awarded a presidential silver medal for his work during the outbreak, and is now Predict’s project coordinator in Sierra Leone. The virus hunters on his team – graduates in their 20s and 30s – all bear their own trauma. While the outlook of previous generations of Sierra Leoneans was shaped by the civil war that raged between 1991 and 2002, theirs has been shaped by disease. One Predict scientist, Marilyn Kanu, 29, who worked on the wards in an Ebola treatment centre, lost 21 relatives during the outbreak. Her colleague Mohammed Turay remembers visiting a close friend in one of the centres. ‘I promised him on his deathbed that I would do everything I could to fight this battle,’ the 28-year-old recalls quietly.

Since being established two years ago, the Predict team in Sierra Leone has taken some 49,000 samples from bats, rodents, primates and livestock in more than 30 sites around the country. As well as developing its core team of scientists – who are almost entirely homegrown – the project is also developing a network of 70 trained health officers around the country. ‘It’s a capacity that is really being built from scratch,’ Bangura says. ‘What we learnt during the outbreak is that as soon as we got the community involved we had a breakthrough.’ While Bangura was initially persuaded to join the project to pinpoint the exact method by which Ebola transmits to humans in the wild (something that has never been achieved), he cannot help but contemplate its wider scope. ‘Ebola we know, but I am also concerned about which other viruses out there have the potential to claim lives like Ebola did. I am so worried about what will be next.’

Virus hunting is a relatively modern preoccupation, pioneered in the mid-to-late 20th century by scientists such as Peter Piot (director of the London School of Hygiene & Tropical Medicine) and Karl Johnson, who first identified the Ebola virus in 1976. In his autobiography, No Time To Lose, Piot recalls huge risks taken in Zaire while travelling in decrepit transport planes, and near non-existent biosafety protocols. On one occasion, while working in Belgium, he received a thermos containing two vials of blood samples infected with Ebola, which had been transported from Zaire in carry-on luggage on a commercial flight. He opened it to find one had broken, leaving a mix of blood and icy slush. Regardless, he reached in wearing only thin latex gloves to fish out the intact test tube. During this cavalier era of discovery, scientists would sneak viral trophies home from epidemics, code-named ‘flying VIP’ – vial-in-pocket.

The samples taken by James Bangura’s team are stored in the field at minus-80C before being transferred to a specialist infectious-diseases laboratory in the university city of Makeni, established in partnership with Cambridge University. Laboratory manager Dr Raoul Emeric Wadoum gives me a tour of the facility, pointing out, among other things, a £200,000 specialist genome-sequencing machine. The feeling of powerlessness in the face of such a dreadful epidemic has, he says, led to a massive upsurge in students graduating in public health at the university: from 13 in 2014 to 67 last year. His laboratory colleague Moinya Ruth Coomber was the person who confirmed the first Ebola case in Sierra Leone. ‘That moment was just huge for me,’ says the 32-year-old mother-of-two. ‘At first I was thinking of my family. But then I thought of my country.’

All the domestic-livestock samples taken by the Predict team are analysed in Makeni, but those from wild animals are shipped out to the University of California, Davis and Columbia University in New York. In July this year, researchers confirmed the discovery of two new viruses in bats in Myanmar. They belong to the coronavirus family, which includes two pathogens already featured in serious outbreaks: severe acute respiratory syndrome (SARS), which spread worldwide in 2003, infecting about 8,000 people; and Middle East Respiratory Syndrome (MERS), first identified in 2012, which has a 35 per cent mortality rate.

The discovery of the Bombali virus in free-tailed bats is the first time a strain of Ebola has been confirmed prior to an outbreak. It is not yet known to what extent it could mutate. ‘Viruses surprise us all the time,’ says Professor Tracey Goldstein, the co-principal lead on pathogen detection for Predict at UC Davis. She points to extrapolated figures that suggest there may be a staggering 3,200 different types of coronavirus harboured in bats alone. ‘Keeping your eyes on understanding what might be coming up ahead and testing and learning from these viruses once we have found them is critically important.’

Where once virus hunters took to pristine rainforest to locate disease, this is changing as human populations expand. Africa’s population is expected to double by 2050, exceeding more than 2 billion people. As people encroach ever further into the environment, the potential to encounter new viruses for which we have no natural immunity is huge.

At the Kabala School for the Blind, in the countryside outside the northern city of Kabala, Alpha Karoma comes tapping across the dusty playground towards the shade of a mango tree. The 34-year-old was blinded by measles at the age of 11 and is now a teacher at the school, which has 87 students in its boarding house. The school, he explains, was built in 1988 by US missionaries, but during the civil war rebels raided the area and executed villagers who tried to shelter here. The building was burnt down and rebuilt. Today the blue and white concrete is streaked with bat faeces; so too, the inside of the classroom. The culprits roost in their hundreds in the rusty corrugated-steel roof. ‘They are very noisy and cause a lot of mess,’ Karoma says. Occasionally he has tried to remove the bats and been bitten with sufficient force to draw blood. He assures the Predict team, who have arrived to take samples from the bats, that it is OK to sterilise a wound by simply pouring salt on it.

Many in rural Africa prefer traditional medicines to those introduced from the West. The local attachment to bushmeat is another challenge that authorities continue to come up against. Sorie Kamara, director of the livestock and veterinary services division at Sierra Leone’s Ministry of Agriculture, describes the consumption of bushmeat as a ‘serious problem’. The country’s markets were closed during the outbreak but are now once more doing a roaring trade selling tropical game including monkeys, chimpanzees, cane rats, bats and snakes. Bushmeat is entrenched in local culture and is often a vital form of subsistence, hence why the authorities are unwilling or unable to announce an outright ban. The health risks, however, are enormous. The HIV/Aids pandemic – which to date has killed 35 million and infected 70 million – started about a century ago in Cameroon when a chimpanzee virus was transmitted to a human who almost certainly killed, butchered or consumed it. ‘I am seriously worried for the future, about the diseases lurking in the bush,’ says Kamara, sitting in his office in Freetown. ‘We are making an imbalance in the ecosystem. Ebola caught us unawares, but there may be another far worse threat out there.’

Not all monkeys are a threat. This one is kept as pet by a local farmer Photo: Simon Townsley

James Bangura and his team attempt to work with bushmeat hunters and vendors, though he admits it is difficult to achieve any impact. For two mornings in a row we visit a normally thriving market stall on the concrete porch of a house in Kabala, and on both occasions there is no meat on show but a pungent antelope corpse, which we are offered for 100,000 leones (£9). Bangura suspects the hunters are hiding the rest until we leave. ‘It is very difficult to break through these barriers and beliefs. We try to educate communities about the dangers but some will respond, “We eat fruit bats and nothing has happened to us.”’

The virus hunters encounter suspicion wherever they go. A prevailing myth remains in rural parts of the country that the Ebola virus was either released intentionally or the product of a research project gone wrong. Many communities suffered a total breakdown of trust in healthcare professionals during the outbreak. In Guinea in September 2014, eight members of a team trying to raise awareness of Ebola were hacked to death by villagers wielding machetes and clubs.

The sight of people in white suits still evokes the dreaded burial teams who would remove corpses from homes to prevent traditional funerals, which are a key transmitter of disease, but also deeply important to families. In local culture – Christian and Muslim – bodies are washed by relatives at a moment when the virus is at its infectious peak. It is also common to lie over the corpse to connect with the spirits. In the Kissi tribe, a dead pregnant woman’s foetus must be cut out before she is laid to rest. During the outbreak, the WHO estimated that at least 20 per cent of new Ebola infections occurred as a result of such rituals. In Sierra Leone the teams removed more than 66,000 bodies to hastily created cemeteries. To prevent the further spread of the disease, all those who died in that time were interred in this manner. To this day nobody knows how they lost their lives; in many cases people don’t even know where their loved ones are buried.

Ebola survivor Margaret Kamara is one such example. The 39-year-old, who lives in the village of Yeli Sanda on the outskirts of Makeni city, lost 15 relatives in total, including her husband and four children. ‘I do not know where their graves are,’ she says. ‘I survived but have cried every day since. All the people who tried to help me have died.’ 

Burial grounds remain all over the country, slowly being reclaimed by the surrounding bush. Some of the graves bear just a number and the date they were buried. The name and the origin of whatever disease it was that killed them, known only unto God.