The night after Alfred Jusson buried his first Ebola victim he had a nightmare: the corpse sat on the edge of his bed, blood dripping from her nostrils. When he got up to run away, she chased him.

Three months ago, Jusson had never heard of Ebola, one of the world's most lethal viruses. Now he volunteers to collect corpses, a job that puts him at the frontline of battle as the disease is spread by contact with bodily fluids.

"Sometimes when I think of it at home when I'm alone, I become scared. It's not easy to just [handle] a dead body like that," the 22-year-old said one evening after carrying out four burials in Kailahun, the remote, forested district at the heart of Sierra Leone's Ebola outbreak. Malaria, cholera and tuberculosis – endemic diseases that fell tens of thousands annually in Sierra Leone – used to be the illnesses that filled Jusson's days as he worked in his parents' tiny, dusty pharmacy and dreamed of one day becoming a doctor. In his spare time, he worked on the family's farm, saving and studying every day, until he was able to sit pre-university exams in December.

Then in March, weeks away from Jusson getting his results, Ebola erupted in neighbouring Guinea. It arrived in Liberia in April, then Sierra Leone the next month. Unlike previous outbreaks, the disease has mushroomed in the capitals of all three countries, killing more than 1,900 people. Nigeria and Senegal have recorded cases.

"The outbreaks are racing ahead of the control efforts in these countries," said World Health Organisation (WHO) chief Margaret Chan. The WHO says more than 20,000 could eventually be infected in an outbreak that in the best case scenario will continue for six more months.

Everything from surgical gloves to ambulances is in short supply, but Ebola's real lethality may lie in the fear and isolation it spawns. One morning, residents in Kailahun woke up to find their only bank closed. Those with cars fled. Life did slowly pick up again, but a state of emergency in July shut down schools. Soldiers poured in to quarantine entire communities and, in these lush farming hills, trade slowed to a trickle.

In desperation, 20 young men signed up for the burial teams, each paid $100 (£61) a month for the task. "Hunger is killing more people than Ebola," said Abraham Kamara, 21, a fellow digger. They work to rigorous standards enforced by the Red Cross, but pay a heavy price.

Medical staff working with Médecins sans Frontières put on their protective gear before entering an isolation area at the Ebola treatment centre in Kailahun. Photograph: Reuters

"When I'm passing, people I know say, 'don't come near me'!" Jusson said. He looked skyward for a moment before continuing: "I try to explain to them. If we don't volunteer to do this, there'll be nobody to bury the dead bodies because all of us will be infected."

The burial team's battle for acceptance is a reflection of a wider struggle. Amid fear, confusion and conflicting public health messages surrounding west Africa's first recorded encounter with Ebola, Kailahun and its surrounding chiefdoms must make decisions that will be vindicated by time or become tragic missteps.

"What would people do if they had 10 people in their neighbourhood dying every day?" said Barry Hewlett, a medical anthropologist who has worked in three outbreaks in central Africa. "Would they trust the government; which news station would they trust; would they try to flee their neighbourhood?"

Some communities have encircled themselves with denial and trenches, violently blocking outsiders from coming in; others have overturned long-ingrained traditions to accommodate bewildering advice on identifying and isolating infected people that can result in victims facing a lonely death in a clinic far from home.

"Ebola kills!" was the initial motto of a belated nationwide campaign, a stark tone which may have dissuaded some sick people from coming forward to face that truth. The scramble for containment meant counselling was sidelined, an oversight that has boomeranged with vicious consequences.

Lacking Knowledge

"To me, empathy is the place to start with Ebola. You're asking people to accept they're probably going to die in a few days' time. [You're] telling families to say goodbye to relatives they are never going to have human contact with again," said Raphael Frankfurter, director of the Wellbody Alliance, a medical charity based in Kono, where Sierra Leone's first case was recorded. "There's a misconception that when people don't comply with public health messages, it's because they're ignorant or lacking knowledge."

Matters haven't been helped by years of mistrust as successive governments failed to deliver health services. Kailahun has just four ambulances for almost half a million residents. Yet the outbreak which has killed more than all 26 previous episodes combined need never have spiralled out of control.

"It's not rocket science," said David Heymann, who was part of the team that first identified the virus near the Democratic Republic of Congo's Ebola river in 1976. "If I'd been told then it would become a global public health emergency, my reaction would have been, that's very unfortunate, because we know exactly how to stop outbreaks in rural areas."

Those methods are being implemented on a scrubby hill in Kailahun, the site of Médecins Sans Frontières' biggest ever field hospital. But the 80 beds aren't enough, and the organisation says expanding without more boots on the ground will endanger staff and patients. Fear is also hobbling efforts. Survival rates hover around 50% if early treatment is sought, but of the 1,038 Ebola patients seen by MSF across three countries, only 241 have survived.

A Médecins sans Frontières medical worker, wearing protective clothing at an Ebola treatment facility in Kailahun. Photograph: Carl De Souza/AFP/Getty Images

As they scour villages deep in the tropical forests, the burial team rely on spaceman-like suits for protection. If a bag of flour were poured over them, the suits should prevent even one grain touching their skin. But once the job is done, these very suits become a danger – they have to be removed without a grain of that flour getting on them.

"The truth is, no one in [the capital] Freetown wanted to come here and do this job," said Daniel James, the Red Cross team leader in Kailahun, as he prepared to lead the burial team one morning. "Eventually my colleagues said, 'you're from Kailahun, you go.'"

For the second time in his life, James found himself burying corpses in Kailahun. The first had been when the district was at the heart of the 11-year civil war which ended in 2002. "The boys are brave, but I can see they're scared sometimes," he said, pointing to the diggers.

Jusson arrived late, held back by the daily lecture from his mother as he set off for work. "Forget about this job," she had pleaded. "Qualified doctors and nurses have been dying. So who are you, that you think you're not going to die if you're doing this?" More than 240 frontliners have been infected during this outbreak, the highest rate ever. When Jusson tried to reassure his mother, she switched tactics. Even if he didn't care about dying, she said, the pharmacy's trade had dwindled because customers were scared when he approached.

"Tell her you've been trained, it's a job now," Nickson Haruna, an 18-year-old colleague, advised Jusson.

The youngest of the so-called burial boys is 17-year-old Andrew Neyuma. "I want to kick Ebola out of this country," he said, to nods from the others. "Our population is already very small and Ebola wants to reduce it? No way!"

On the streets, many believe Ebola was spread by local politicians to decimate the Kissi population ahead of elections, or that foreigners are using it as a way to harvest body parts.

In part, the rumours are fuelled by the fact relatives rarely ever see those who succumb in hospitals as their bodies are doused in bleach, sealed in anonymous plastic bags and hurriedly buried to halt further contagion. After several attacks, the burial boys began chlorinating the bodies then opening windows, if possible, so loved ones could watch what was happening inside. All of the burial team dread one day being called to a burial in their own villages.

In theory, one of the three burial teams is always on standby. In practice, there aren't enough cars or manpower to deal with the number of cases. Today one team is dispatched to the treatment centre, where there is a backlog of corpses waiting to be buried.

Sierra Leonese burial team members are disinfected after loading the bodies of Ebola victims onto a truck at the Médecins sans Frontières facility in Kailahun. Photograph: Carl De Souza/AFP/Getty Images

The other team has to decide between two alerts in the community. Dia village is 15 miles away – which translates into nearly two hours' drive through the potholed forest roads. The second village is further, and they want to go there first to avoid returning well after midnight. But residents in Dia have been known to bury corpses if the burial team don't arrive quickly, a practice that periodically re-ignites new chains of infections. The team chooses Dia. Their two 4x4s slither up muddy banks overgrown with elephant grass on either side. A wall of forest green, broken only by tiny red flowers, orange cocoa leaves and sudden clearings of rice paddies unfurls for miles eastward into Liberia.

Tamba Morris, 28, the skinny local health co-ordinator wearing black rubber gloves, greets the team with a look of relief. The first death in Dia was a month ago. He waited two days until angry villagers besieged his house. "The body was rotting in this heat, the smell was too much. So I called together some youths, and we did our best to do a safe burial," he said.

No one in Dia believes Mami Lamy – the woman they have come to bury – had Ebola, says Tamba Yussufu, a village elder wearing a faded T-shirt. "But we're not medical practitioners, so when those who are tell us this is the way to do it, we accept it."

Yussufu forbade Lamy's grieving family from washing her body, as is customary. But three men approach nervously as the team gets ready. If they can't do burials the traditional way, can they at least stand at a distance and say a prayer over the body?

Many specialists believe unrecorded rural outbreaks – both before and after the virus was identified in 1976 – may have burnt themselves out as people adapted naturally after centuries of living in hostile environments. When medical anthropologist Hewlett reviewed the first recorded outbreak in DRC he found that locals had isolated those with the illness, monitored traffic into their village and modified their burial practices. Still, for many, long-trusted herbalists offer a better choice than strangers in a hospital miles from home. "Nobody wants to be viewed as disease carriers rather than human beings," said Frankfurter.

International teams have started training local volunteers in how to keep safe. The volunteers then return to their own communities. But in a climate of fear simple miscommunications have had unexpected results. Residents in one village were told not to shake hands in greeting as it could spread the illness. They took on board the advice, but for weeks machete-wielding youths inexplicably barred health workers from coming into the village. "I'd go and I'd wave, just to try to break the ice, and they'd throw stones at me," said one international health worker. A team of locals were eventually uncovered the problem: the community considered waving was a form of greeting.

Dripping sweat

In this climate, the burial teams never know what reception awaits them in each village. Today they get dressed under the silent gaze of encircling residents. All are dripping sweat inside their suits by the time they've finished. Two dogs doze in afternoon heat. Shaded by a tree in front of Mami Lamy's house, women sifting rice in palm frond baskets scuttle out of the way as the team approach.

"We have to finish this in 30 minutes because of the heat," James says, his voice muffled through the layers.

A woman stands by the gate of the government hospital under the rain in Kailahun. Photograph: Carl De Souza/AFP/Getty Images

In the dim light of her tiny home, Lamy looks like one of the rice-sifters taking a short nap. She wears a pink flowered shirt, and white head-wrap. The team begin spraying a concentrated chlorine solution. They spray before each step. They spray the window, and open it. They turn her body. One arm is lifted, sprayed. Then the other. The red flowered blanket covering her is pulled down, sprayed as each inch is rolled down. The smell of chlorine fills the air.

In slow motion, James leans over the woman's body and takes a swab from her mouth. Holding the sample with two fingers, he drops it into a bag.

Visibly exhausted, goggles fogging up with each breath, the team lift the body, place it in a body bag, spray, seal the bag, spray again, and repeat the whole process. At last they emerge carrying the body. A wail shatters the silence.

The crying descends into angry confrontation at the freshly-dug gravesite on the village outskirts. The locals who have dug the grave refuse to pour in the mould. If the job is so unsafe, one man shouts, gesturing at the workers now stripped down to blue aprons, why haven't they been paid too?

It takes some 45 minutes to resolve the dispute, and that's a success. Two days ago, villagers stood on the side of the road calling out "Don't bring Ebola here!" and hurled stones at the team. Once, the worst day Jusson recalls of countless burials, they lugged a bagged corpse for two miles through the forest to a gravesite.

At 10pm that night, James was back in the fluorescent-lit glow of his office. On his to-do list: ordering more supplies, getting a broken car repaired and scheduling a visit to the police station. One of the boys had just called to say his flatmates had kicked him out, a discrimination now punishable by law.

But there was good news elsewhere. A friend who had avoided Jusson for weeks called to say he was starting to "believe" his work now. Could they meet sometime so he could explain how to avoid falling sick?