On a sunny day in Lapul village in Pader district, northern Uganda, 13-year-old Nancy Lamwaka lies on the dirt, her ankles shackled to the branch of a mango tree as her younger siblings play happily around her.

"It hurts to see a human being tied to a tree like an animal," says her mother, Grace Akumu, who helplessly watches Nancy, face down on the ground, her hands on her head and her eyes closed as flies swarm around her. "A human being should be free to move about, to get fresh air, and then do whatever he or she wants. [But] this is the only way we can help her."

The disease Nancy is afflicted with has no scientific name. Baffled medical experts have dubbed it nodding disease as it causes its victims – usually children aged between five and 15 – to repeatedly droop their heads. This is often accompanied by violent seizures, convulsions and staring spells, where the child will appear non-responsive. Sometimes they lose consciousness. Some victims suffer mental deterioration. Most are malnourished and stunted in their growth.

The illness is having a tragic impact on the Pader, Lamwo and Kitgum districts of northern Uganda. At least 170 children have died, with more than 3,000 affected in the area, the World Health Organisation (WHO) estimates. The figures are likely to be higher because not all cases are reported.

"The nodding syndrome is a serious public health problem, with psychological, social and economic consequences," says Dr Charles Okot, the organisation's country advisor in Uganda. The situation is so grim that the WHO and the Centers for Disease Control and Prevention, a US federal agency, are hoping to hold a conference on the disease in July, attended by medical experts from around the world.

But while this mystery killer threatens a whole generation in these villages, much of the world has been focused on northern Uganda's other blight, the fugitive warlord Joseph Kony and his Lord's Resistance Army (LRA). A film by the US-based charity Invisible Children has been viewed more than 100 million times online. Kony's reign of terror in northern Uganda has ended, but nodding disease continues to haunt the villages. Nancy's father, Michael Odongkara, a peasant farmer who lives in a thatched grass hut with his family, is bemused at all the fuss over the film when his eldest daughter is wasting away before his eyes.

"It hurts us when the government and then the international community puts more attention on the Kony issue while we're suffering with the disease here," says Mr Odongkara. "It's very hard for us to take care of the children. It's all well and good if they can flush out the [LRA] rebels from wherever they are, but the most important thing for now is that this disease is tackled."

Before Nancy's symptoms worsened, she was a "good girl, humble and hardworking", says Mr Odongkara, 30. "She used to be the one taking care of her siblings." He and his wife noticed something was wrong in 2004. Saliva poured uncontrollably from her mouth. Her lips swelled. Soon, Nancy started nodding after being given food. "She'd get seizures and all of her body would start shaking," recalls Mr Odongkara. "At that time we didn't think it was anything apart from epilepsy."

Initially, that is what the doctors through too. But by 2008 the once energetic girl had stopped talking. Her parents took her to the Gulu Referral Hospital, about 50 miles away, where medics told them Nancy had nodding disease. "We hadn't heard about it at all," says Mr Odongkara. "The doctors told us they weren't certain about the disease, that they were still doing investigations."

Four years later, there is still no cure for nodding disease, and its cause remains unknown. It is believed to have been first reported in northern Uganda between 1995 and 1998. There have also been cases in Tanzania and Liberia.

"Associations between nodding syndrome and onchocerciasis [river blindness] have been described in many of the places that have reported nodding syndrome, but no scientific proof linking it as the cause of nodding syndrome has been established," says Dr Okot. "Studies conducted in Uganda so far have ruled out more that 30 potential etiological factors including infectious, chemical and environmental."

But James Tumwine, professor of pediatrics and child health in the School of Medicine, Makerere University, in Kampala, is convinced there is a link with river blindness, and is fighting for more resources to help the affected youngsters.

"We are not making much progress in finding the cause," he told The Independent. "There is a concerted effort by the Ministry of Health to bring together all the scientists involved in the process. We need to go back to the drawing board and [examine] all the facts."

As the search for the cause and cure goes on, Nancy continues to suffer. What terrifies her parents more than the nodding is that she will wander into the bush in a zombie-like state and become lost, or fall into the nearby river and drown. Nancy's hands and bald head are already scarred after she fell on to the fireplace during a seizure.

Last year, in a desperate attempt to protect her, her parents began securing her to the tree opposite the family's home with an old green mosquito net. Now she's shackled most days from 7am until 6pm. "Three days ago when we left her [alone] we found her near the river," says her mother.

Nancy has been prescribed the anti-epileptic drug sodium valproate, currently considered the best treatment, though it is much more expensive than the usual anti-epileptics, such as Carbamazepine. The drug is helping to control the attacks and Nancy is starting to show small signs of improvement. Her parents say she can hear, and she gestures when she needs food and water.

The Ugandan government has set up screening and treatment centres in the three affected districts. "You must all prepare to take drugs when I return to [wage] war against it in the next financial year," President Yoweri Museveni said recently at the launch of one of the centres. "We will defeat the disease."

But although the government has pledged to provide the anti-epileptic drugs to children with nodding disease, getting them to the few clinics is sometimes too much of an expense for poor families in this impoverished area.

Mr Odongkara wants financial assistance from the government and more awareness from the West. His wife is six months pregnant. Another child developing nodding disease would be the family's worst nightmare.

"It worries me a lot. We're not certain of her [Nancy's] survival," Grace Akumu says. "By this time Nancy should be in primary five and she can't do small things in the home like even fetch water. It hurts me so much and all my hope is gone, but I'm praying to God."

Q&A: Nodding disease

By Richard Hall

Q: Who is affected?

A: The condition only affects children, typically between the ages of five and 15. Reported cases are currently restricted to small regions in South Sudan, Tanzania, and northern Uganda. There are currently no accurate statistics regarding the number affected by the disease, but the World Health Organisation says a total of 3,097 suspected cases and 170 deaths have been reported in Uganda. Thousands of children in South Sudan are also sufferers.

Q: What are the symptoms?

A: Those affected suffer from uncontrollable spasms, stunted physical and mental growth and nodding of the head. Nodding often begins when the children are presented with food, or when they feel cold. The disease has led to deaths, but these are mostly due to indirect causes such as malnutrition, drowning, burns and accidents. Investigations to date reveal that the syndrome is not transmissible person to person.

Q: What are the causes?

A: Doctors do not yet know the cause, but one theory being pursued is a link with the black fly-borne parasite that causes river blindness. Investigators say they plan to do genetic testing on skin samples taken from the children to try to establish a link. Researchers have also observed a deficiency of vitamin B6 in the populations where the disease is prevalent.

Q: What is the treatment?