Ian Crozier had been Ebola-free for two months when the virus reappeared. An American specialist in infectious diseases, Crozier had contracted Ebola in September 2014 while volunteering for the World Health Organisation (WHO) in Kenema, Sierra Leone. He is not sure how exactly he came into contact with the virus – in the Ebola treatment units (ETUs) the virus, like death, was everywhere, and hundreds of health workers got sick. But he remembers being transferred to Emory University Hospital in Atlanta, after coming down with the fever and headache that announce the infection.

Once it enters the body, the Ebola virus starts replicating uncontrollably, causing diarrhoea, vomiting, internal bleeding and, in some cases, organ failure. Crozier's case was severe, and life-threatening: as the virus ravaged his body, he fell unconscious and was put on a respirator and dialysis to keep him alive.

Crozier, 45, spent 40 days at Emory recovering. When he was discharged, he was still in a bad way. He'd suffered neurological complications and had to learn to walk again. Although his blood and urine tests came back Ebola-free, his body ached and he felt constantly exhausted. Yet, as Crozier left the hospital to recuperate at his parents' house in Phoenix, he was grateful to be alive.

So when, nine weeks later, he began having problems with his vision, Crozier initially didn't think much of it. Ebola is known to affect the eyes during the acute phase of the infection (red eyes are an early symptom; some patients' eyes bleed), and there had been reports of survivors having inflammation inside the eye, 
a condition called uveitis. Crozier went to see an ophthalmologist: other than some internal scarring, likely from his initial hospitalisation, everything was normal.

Then, a month later, his eye got worse. Crozier felt a burning pain in his left eye, and his vision began to deteriorate rapidly. After running comprehensive tests, the clinical team at Emory diagnosed him with uveitis and increasing pressure inside his eye. As the days passed and his condition worsened, they prescribed corticosteroids, but to little effect. Crozier was going blind. Then it started getting even stranger: one morning, Crozier went into the bathroom and took in his reflection – although he'd thinned out in hospital, he is still broad and tall, 195cm, with a light beard and mop of short brown hair. In the mirror, he saw something startling: his left eye had changed colour. While his right eye remained sky blue, his left was now an alien, milky green.

The change was mystifying. Although some viruses – most notably herpes simplex – are known to hide in the eye after infection, there were no recorded cases of that happening with Ebola. The closest was a single case, from the 70s, with a patient infected with Marburg, a related filovirus.

Crozier's doctors decided to do a test. They inserted a needle into his eye and extracted a small amount of fluid, sending it to infectious-disease specialists in the lab. The test came back positive: Crozier's eye was swarming with live Ebola virus.

The Emory team was stunned. "Nobody really thought about it being live virus. We had prepared for it, but none of us expected it," recalls Crozier. "It was an interesting phenomenon," says Steven Yeh, the ophthalmologist who extracted Crozier's sample. "On the other hand, not knowing how the virus was going to behave – especially in the face of Crozier's deteriorating condition – was challenging." Yeh's team debated a course of treatment. Although they had taken the proper precautions, they also couldn't be sure that they hadn't been exposed. Yeh spent the next three weeks avoiding contact with his wife and infant son. (A later test of Crozier's eye surface and tear fluid came back negative.) Meanwhile, the medical team settled on a higher dose of steroids and an experimental antiviral drug administered to Crozier's eye.

Mercifully, it worked. Over the following weeks, Crozier's symptoms gradually cleared. His eye turned blue again and his vision slowly returned. As it did, Crozier began to have questions. "While my eye was going blind, I was fascinated by the science going on," Crozier says. Now he was thinking of his former patients in Sierra Leone. From fairly early on in the outbreak, anecdotal reports had emerged of survivors struggling with "post-Ebola syndrome" – symptoms ranging from vision loss to hearing loss, joint pains, headaches and memory loss. There were even some rare reports of survivors dying suddenly. Could it be that they too still had the virus inside them? Or was it something else entirely?

Ebola is not a new disease. The first case was recorded in Zaire in 1976. But, until recently, it was extremely rare: outbreaks have typically been small and remote, the largest only a few hundred cases. They occur in rural African communities with little to no healthcare infrastructure. The virus, a Biosesafety Level 4 agent (the highest rating for fatal pathogens) is astonishingly infectious. A drop of blood can contain tens of millions of particles, a virulence only matched by its ruthlessness. Depending on the strain and outbreak, 50 to 90 per cent of Ebola patients die.

As a result, gathering data on Ebola is extraordinarily difficult. Much of what we do understand comes from laboratory testing, performed on macaques. Despite 40 years of trying, nobody has identified the virus's reservoir – where it hides between outbreaks. (Fruit bats are one suspect, but no one has ever cultured a live virus from a bat, and some experts dispute the bat theory.) There are disputes about how Ebola works in the body. And there is almost zero data on survivors. Prior to this outbreak, only two controlled studies had been published: one tracking 29 survivors of a 1995 outbreak in the Democratic Republic Of Congo (formerly Zaire), and another of 70 survivors of a 2000 outbreak in Uganda. "The largest outbreak that we have ever had was 425 cases for the entire outbreak, and that had 60 per cent case fatality, so you only have around 200 survivors," says Daniel Bausch, a tropical-disease expert at Tulane University and a lead Ebola expert for the WHO. "And I think it is largely true that the international community felt that once we had stemmed transmission, our job was pretty much done. People had exhausted their time and money and energy, and went home."

That started to change in December 2013. The largest Ebola outbreak in history began with the death of a two-year-old boy in Meliandou, Guinea, near the borders with Liberia and Sierra Leone. For months, the virus tore through the West African bush, infecting more than 28,000 people and killing more than 11,000. (The true number, when accounting for those who died at home, is likely even higher.)

The estimated 17,000 people who have survived make up the largest data source on Ebola in history. Understanding their survival, and their strange complications, are vital to anticipating the next outbreak – and perhaps even to developing treatments.

The John F Kennedy Hospital in Monrovia, the capital of Liberia, looks out on a slum, and beyond that the Atlantic Ocean. It's a large hospital, but like much of the capital – which remains scarred after decades of civil war – is in poor condition. Rusting barbed wire lines the drives leading up to the entrance. The corridors are barely tiled, and some lie in darkness. On the second floor, however, is a modern, well-equipped clinic marked PREVAIL. It's here that the US National Institutes of Health is running the largest ever study into Ebola survivors. On a Monday morning in January 2016, more than a dozen patients in plastic chairs lined the corridor; just a few of the 1,500 survivors and 6,000 controls that PREVAIL will study over the next five years. In doing so, PREVAIL – and smaller studies in Sierra Leone 
and Guinea – hopes to transform our understanding of the virus.

The in-country lead on the PREVAIL study is a Liberian epidemiologist called Mosoka Fallah. He has a strong brow, large hands and a preference for loud shirts. "The most common thing at the moment are joint and body pains. A large number have eye complaints; some of them have hearing impairments," he says. "The key is that we will be able to separate that by looking at the controls, to unpack what is there in the general population. It's a big challenge."

Using advanced imaging equipment previously only available in modern western clinics, PREVAIL is documenting the strange effects Ebola can have inside the eye. "It has been surprising how broad the destruction in the eye from the Ebola virus has been," says Allen Eghrari, an ophthalmology professor at Johns Hopkins medical school. Eghrari runs the eye study at PREVAIL alongside Rachel Bishop, an ophthalmologist with the NIH. Some, like Crozier, have uveitis; others develop cataracts or are going blind. "We're seeing patterns of change in the retina that haven't been seen 
before," explains Bishop. "Some of them look like you've taken a sponge, got it damp and then pulled it apart – all those little holes. This is quite bizarre. This is not a signature of any other disease we see." "And we've found in some patients we couldn't pinpoint a problem in the eye exam. What we are now appreciating is there is a whole neurological component to Ebola. Clearly, it affects what goes on in the brain."

Ebola virus disease has a devastating impact on the brain. Some patients hallucinate; others suffer strokes or fall into comas. In the ETUs, that often meant death. "When they went into a coma, they just stopped treating them and they died, because most of the time all they could do was oral rehydration," says Avindra Nath, the lead neurological investigator on PREVAIL's study.

Nath became involved after PREVAIL noticed survivors having difficulties following instructions. So in summer 2015, Nath flew to Monrovia to assess six patients. "Every single one of them had neurological manifestations," he says.

The mystery deepened in October, when Pauline Cafferkey, 40, a Scottish nurse who had recovered from Ebola ten months earlier, was rushed back to the isolation unit at London's Royal Free Hospital. Cafferkey had contracted Ebola in December 2014 while volunteering in Sierra Leone. Now she was admitted with neurological complications, which her doctors soon identified as viral meningitis. After taking blood tests and spinal fluid, they too were shocked: Cafferkey had live Ebola virus hiding in her central nervous system. "This is an unprecedented situation," Michael Jacobs, Cafferkey's clinician, told a press conference at the time. (Cafferkey and her doctors declined WIRED's interview requests.) "We have no doubt that the virus re-emerged around the brain and spinal column... We detected a low level of virus in the blood as well."

With the help of an experimental viral treatment, Cafferkey began 
to stabilise. Her case stunned the medical community all over again. Why wasn't this happening to other survivors – or was it? "Pauline Cafferkey and Ian Crozier were extremely sick during their illness," Bausch says. "And almost certainly, if they were being treated in West Africa wouldn't have survived. So are some of the things we're seeing in people like Ian and Pauline happening in West Africa and we're just not noticing? Or are we noticing them in these people, because they never would have survived?"

There have been isolated reports of survivors dying in West Africa. Notably, Dennis Khakie, a Liberian survivor, died suddenly in September 2014 after suffering from seizures, according to a family member. Survivor groups 
share stories of strange deaths. "We hear about the odd cases of people dying suddenly, and we're not really sure why. Some of that may be neurological," Crozier says.

However, such cases are rare, and – like so much in West Africa – gathering data is difficult. Survivors such as Khakie could be suffering complications similar to Cafferkey's, but it could equally be an unrelated illness, or lingering damage from the initial infection. In July 2015, Crozier experienced an epileptic seizure which 
his neurologists concluded was a result of brain damage sustained during his infection (tests show his spinal fluid is Ebola-free). He now takes anti-epileptic medication. "If these survivors developed something like meningitis, and they did 
not have access to high-level care, it's possible they could die quite quickly without anyone being able to describe it," says Barbara Knust, an immunologist at the US Centers For Disease Control and Prevention.

PREVAIL will soon begin testing survivors' spinal fluid for traces of the virus. Doing so won't be easy: it is invasive and requires precautions against the risk of being exposed to the virus. But if successful, they will prove Cafferkey and Crozier aren't outliers.

Mosoka Fallah grew up in West Point, one of the poorest slums in Monrovia, which lies on a sand spit jutting out into the ocean. (West Point was devastated by ebola. At the height of the outbreak, the army quarantined the entire slum for several days after the panic-stricken looting of healthcare clinics.) Fallah has always been interested in science. In the 90s, he was trying to start university, when the civil war came. "If I wasn't running for my life, I was trying to go back to school," Fallah says. He got a job in food distribution with USAID, and after 11 years earned a degree in chemistry. With support from a friend, he was able to study immunology at the University of Kentucky and earned a PhD at Harvard. He had just moved back to Liberia when Ebola arrived.

With Liberia having so few home-grown doctors – less than 200 in a country of 4.2 million – Fallah threw himself into the crisis, tracing cases and organising the public-health response. Since the outbreak has died down, Fallah has become a champion for survivors, providing financial support or helping those with complications to get treatment or find work. ("Whenever a survivor has a problem, they call Dr Fallah," one survivor told WIRED.)

One of Fallah's biggest challenges has been combating the stigma that Ebola survivors face. Many returned from the ETUs only to be chased out of their homes. Market sellers found that people would refuse to touch their produce. Many were abandoned by their husbands or wives.

The stigma extends to healthcare workers. During the outbreak, doctors and nurses were disproportionately affected. Hundreds across West Africa died. As a result, even with the outbreak over, survivors have gone to their clinic only to be turned away. Some are admitted, only to be labelled "special patients" and told they will be charged $50 (£34) a night – an impossible sum in a country where the average income is around $1 per day – and have to leave.

Theophilus Faiyah was working as a physician's assistant when he contracted Ebola. He caught the virus in November 2014 while treating the son of a colleague whose entire family had been infected. Six died. 
Fortunately, Faiyah identified his own symptoms early and isolated himself from his wife and son, who avoided contracting the disease. But after leaving the ETU, he was forced out of his home and developed joint pains. "Sometimes, to dress. I have to sit down in a chair," he says.

Faiyah met fellow survivors who were struggling with post-Ebola syndrome and being refused care. "The nurses feel that when they do the treatment they will contract the virus," he says.

A friend introduced him to Fallah, and together they hatched a plan for a survivors clinic. Faiyah now helps to run a dedicated ambulance service for Ebola survivors in Monrovia and the surrounding Montserrado County. 
Ambulance may not be the right word: a converted 4x4, the vehicle contains 
a bed and enough first-aid supplies for basic care. "We visit each of the four sectors on a particular day," he says. "Every Friday and Saturday are for pregnant women. We visit their homes."

Prenatal care, he explains, is very important. Ebola is catastrophic to pregnant women: almost all those unfortunate enough to contract the virus miscarry. The rare cases who do make it to full term can suffer stillbirths; evidence suggests that babies can contract the virus while in the womb.

Faiyah is concerned about female survivors. Many women find that after leaving the ETU, they no longer menstruate – some haven't had a period for more than a year. And, although the data is thin, anecdotal reports suggest that survivors who later become pregnant may have high levels of birth complications. "We have had about 17 patients who have given birth – only eight women have had a live baby," he says. "Most of them will be four months pregnant, call us, and say ‘I am bleeding' and have a miscarriage." "Lots of the female survivors who have become pregnant are having a worse outcome: stillbirth, miscarriages," says Fallah. His team has begun testing breast milk and the placenta for Ebola persistence. It's too early to be sure, he stresses – birth mortality in Liberia is much higher than in the UK, and as such any findings will require extensive, controlled study. But it's another anxiety to add to a long list.

To survive Ebola is to have experienced death. The virus preys on kindness: people who become infected invariably do so while caring for a loved one – mopping up infected vomit or diarrhoea, or burying the dead. Hear enough stories and they start to sound like echoes.

When Henry Tony was in the hospital, he hallucinated about schools of fish surrounding him. "They were attacking me, drawing blood. I was fighting, fighting, fighting," he recalls. A mechanic, Tony contracted Ebola from his wife, Melletta. The day after he buried her, he came down with a fever. On the day he was admitted to the ETU, five patients filled the beds around him – every one of them passed away. "When they all die around you, you lose hope," he says. Weeks later, he was discharged, he discovered his two-month-old son had died while he was in the unit.

Patrick Faley caught Ebola at the height of the epidemic, when the hospitals couldn't cope. He was piled into an ambulance with three other men, vomiting and passing blood. They prayed in the blistering heat as the ambulance waited outside JFK Hospital for beds to clear. "Fortunately for me, and unfortunately for some family, two people died," he says. All four men were admitted. Only Faley survived. When he was discharged, his father came for him. "But I could not see happiness in his face," he says. "Unfortunately for me, I made my eight-month-old son also come down with the virus." Faley sobs gently as he remembers how his son died.

Faley and Tony now head the Liberia Ebola Survivors Network, which tracks survivors across the country. Each district helps connect those having problems to reach doctors. They struggle with one of the biggest ethical challenges: how to inform survivors about the risks without further contributing to stigma.

One afternoon in January, Tony gathered a group of survivors at the Emergency Operations Centre, a low prefab building opposite Liberia's Ministry of Health. Set up at the height of the outbreak, the building now serves as the hub for survivors and for NGOs still in the country. In a grey conference room, representatives from the Ministry Of Health, WHO, Médecins Sans Frontières (MSF), and other groups sat as the survivors told stories: of stigma, of their friends getting sick and in some cases dying. Some raised Ian Crozier and Pauline Cafferkey and the sense of anxiety they felt.

Amadou Koné, an elderly survivor wearing a black and yellow T-shirt and jeans, stood to speak. "Whenever I am called a ‘special case', I feel so low," he said. "It creates psychological problems for us." The survivors around him murmured in agreement. "If we still have the virus inside us, tell us!"

PREVAIL hopes to publish its first findings this spring. As the initial information from other studies have been published, a picture is emerging. The eye, the brain and the reproductive organs are immune-privileged sites: areas inside which the immune response is repressed, in order to stop the body from attacking its own cells. "For example, the nervous system has a blood-brain barrier, which acts to keep pathogens out," explains Knust. "But when you're critically ill with Ebola, it could be that the virus is gaining entry. But once the person has recovered, that blood-brain barrier may be built up again, so that the immune cells cannot go in to neutralise it." In most cases, the immune system drives any persistent virus from these sites – but it's uncertain how long the virus can persist. In October 2015, Knust co-authored a study that found Ebola ribonucleic acid (RNA) present in male survivors' semen up to nine months after recovery.

Understanding how long the virus can persist will be crucial in preventing rare but dangerous cases of sexual transmission. On the wall of the MSF's survivors' clinic in Monrovia, a poster warns survivors to wear condoms for three months. It has been since crossed out for a "six", then a "12".

On January 14, 2016, Mosoka Fallah rode out to Paynesville, a poor neighbourhood on the outskirts of Monrovia, to visit Nathan Gbotoe. It was a significant day: on the radio, the newscaster announced that the WHO had declared Liberia free of Ebola. The news was met with little fanfare. Liberia had already been declared Ebola-free twice, only for new cases to emerge. "The first time it ended was in May. There was 
a big celebration," said Fallah. "Then in September, a less big celebration." This time, they were being more cautious. "There will be a small ceremony," he allowed.

Gbotoe's house lay down a dirt track, in a group of small brick houses. Many had tin or tarp roofs, none had running water. Chickens pecked through rubbish in the grass; to reach the house, Fallah stepped across a single plank of wood laid across a thin stream. Fallah ducked into the main room, which was unlit and bereft of furniture beside some plastic chairs and a pram languishing in the corner.

Gbotoe and his ten-year-old son Abraham are, at the time of writing, the last cases of Ebola in Liberia. There was a third: Gbotoe's 15-year-old son, Nathan Jr, who died in the ETU.

The house belongs to Nathan Sr's brother. The family moved in a few weeks ago. At the old one, he says, the memories of his son became too much to bear. Gbotoe is a plumber, but since his case was on television his clients won't see him. "Dr Fallah has been helping me. So far, he alone," he says.

Gbotoe represents another mystery about Ebola: investigators don't know how he contracted the disease. After tracing Nathan Jr's contacts, and sequencing the virus's RNA, the evidence pointed at Ophelia, his mother. Ophelia's brother had died in August 2014; afterwards, she became sick and miscarried, Fallah says. Serological testing showed Ebola antibodies in her bloodstream – she may have had survived Ebola and somehow passed the virus on to the family months later. "The evidence points to female-to-male transmission," Fallah says. If so, it would be the first recorded case. "Ebola is like a black hole," Fallah says later. "What we know is so small. We're discovering things every day. It's going to transform the science. Before, we only looked at persistence in semen and the testes. Now we think it's in the eyes. Now we think it's in the brain. We thought the blood-brain barrier could not be breached. Now we are wondering about the uterus. And it's going to take even more science to understand the mechanism, to understand the consequences."

There are glimmers of hope. Scientists are working with survivors' antibodies to develop treatments, and in January, Merck announced plans to manufacture 300,000 copies of its VSV-EBOV vaccine, which has shown promising 
results in trials. But vigilance is needed. The WHO has warned of further 
flare-ups, likely from sexual transmission by survivors. "We probably will have small blips," Bausch says. "We hope they won't snowball into anything large. Everybody's tired and wants this damn thing to go away now. But the problem is when it goes away, the resources go away."

Aid budgets are already stretched thin. In February, the WHO declared a new global emergency: the Zika virus outbreak in South America, linked to childbirth defects. "I think we have a general ADD as a society, even in the medical world," Crozier says. "That's unavoidable, just because new things keep popping up, right? And they will continue to. We've seen that happen during the course of this outbreak: after a little excitement, people stopped paying attention months ago." "A big fear for all of us trying to assist the survivors – and I guess that includes me – is that we'll forget about them. And that means we'll have failed. Because dealing with what's happening to these survivors has a great deal to do with some complex questions. The kind of things that build systemic capacity that stops this happening in this scope again."

Back in Paynesville, Fallah checked up on Gbotoe, and asked after Abraham. Ophelia needs medical treatment for a separate condition, and they're struggling for money – their belongings, like so many, were burned.

He looks weary. Outside, Abraham ran in the grass; the rest of his family hid from the heat on the porch outside. “In my prayers, I pray that it won’t come back.”

As he left, Fallah took a picture on his phones – he's going to see if he can get the family some money from an NGO – and told Gbotoe to come to PREVAIL the following week. "This is one family," he said. "It's a drop in the ocean." Then he strode back to his car, late for another survivors' meeting.

That night, after the sun set over Monrovia, the World Health Organisation retracted its statement from that morning. A new case of Ebola had been discovered in Sierra Leone.

Oliver Franklin-Wallis is assistant editor of WIRED

This article was originally published by WIRED UK