South Sudan, newest nation
A South Sudan flag is prepared for South Sudan's Independence Day celebrations in Juba

The Centres for Disease Control and Prevention (CDC) in Atlanta, Georgia, sent an emergency response team to rural southern Sudan in May to try and assess a mysterious illness seen in children in the region. But despite their preparation, most of the doctors and scientists said they were deeply affected by their first encounter with 'nodding syndrome'. "Actually seeing it out in the community was overwhelming and distressing," Bunga, a member of the U.S team told reporters. "The burden of the disease looked really high." he added.

Nodding syndrome is a poorly understood and seemingly growing problem in eastern Africa, where it is particularly affecting communities in South Sudan and northern Uganda, but has also previously struck parts of Tanzania.

In South Sudan, which achieved political independence from the North on July 9, "it's affecting thousands of children," says Abdinasir Abubakar, a physician for the World Health Organization (WHO) based in South Sudan who coordinated the recent CDC trip. "Of course, the question is whether this syndrome is spreading to new communities."

With the continent's newest county facing problems such as refugees and Internationally Displaced people and poverty, the Nodding Syndrome epidemic might be too much for the government to cope with, as it lacks both resources and expertise.

"Nodding syndrome cannot be left with the nascent government in South Sudan," says Martin Opoka, an epidemiologist with the WHO's eastern Mediterranean regional office in Cairo. "They will certainly need assistance from the international community."

Nodding syndrome is one such enigma. Most children it strikes are aged between 5 and 15. It impairs both physical growth and cognitive development.

One of the primary physical signs of the syndrome, head nodding - often brought on by eating, and sometimes by cold - occurs when abnormal brain activity causes a brief lapse in neck muscle tone, causing the head to fall forwards.

Electroencephalograms conducted by CDC investigators and others have shown subtler, sub-clinical seizures in many children, and some magnetic resonance imaging scans have revealed brain atrophy and damage to the hippocampus and to supportive brain cells known as glia.

After the first seizures have occurred and the children have been diagnosed with the disease, scientists have warned that in the majority of cases, the children's health will keep on degrading.

As a result of the seizures, many struggle to eat, which in the most severe cases, results in malnutrition, further putting the children at risk.

They are also prone to accidents such as drowning and burning and many stop attending school, become isolated and cut off from their own community because of fears of contagion.

The condition was first documented in 1962 in southern Tanzania but its incidence now seems to be rising rapidly in South Sudan (see map) and in a non-contiguous area of northern Uganda where, in late 2009, the ministry of health reported that more than 2,000 children were affected.

According to the CDC the poorest children are the most susceptible.

As it struggles to find the root cause of the syndrome, the organisation is now considering whether population displacements and associated chemical exposures during wartime could have played a part, in the development of the disease, as it insist that genetics alone cannot explain the rapid emergence of so many cases.

CDC noted that in one village the team visited almost every family had an affected child.

Investigators have wondered whether Onchocerca volvulus, the blackfly-borne parasite that is best known for causing river blindness, might be the culprit as the CDC's work in northern Uganda showed a higher prevalence of nodding in children whose blood samples revealed infection with the parasite.

However, after a recent study in Tanzania failed to confirm the previous finding, Andrea Winkler, first author on the study said "We could not establish any hint that Onchocerca volvulus is actually going into the brain." "But what we cannot exclude is that there is an autoimmune mechanism going on."

The CDC team is now investigating whether deficiency of vitamin B6, or pyridoxine - which is common in children with nodding syndrome - could be the cause.