Human African trypanosomiasis (HAT) also known as sleeping sickness, is only endemic in South Sudan within the WHO Eastern Mediterranean Region. Foci of T.b. gambiense occur in Equatoria Region a belt bordering the Central African Republic, Democratic Republic of the Congo and Uganda. In South Sudan, Western Equatoria is the most affected state, followed by Central Equatoria and Eastern Equatoria states. Historically, cases of T. b. rhodesiense were anecdotally reported in Eastern Equatoria (Torit County) and Jonglei (Akobo County), but there is no recent evidence of cases being reported there.
Nine counties are endemic for the disease, namely Tambura, Ezo, Yambio, Maridi, Mundri, Juba, Yei, Kajo Keji and Magwi. The number of people at-risk of HAT is estimated at 1.4 million.
Large epidemics of HAT have periodically occurred in South Sudan since the early 20th century. When outbreaks occur, large-scale control reduces number of cases but when the program scales down disease resurgence occurs. After the latest epidemic registered in the mid-1990s control programs were re-initiated by a number of international non-governmental organizations in several counties.
In 2001, eflornithine started to be used as first line treatment for HAT stage II patients due to its safer profile compared to melarsoprol. However, its administration involves an important workload for the four intravenous infusions over 14 days. In 2010, the eflornithine monotherapy has been replaced by new treatment protocol, based on a combination of eflornithine (twice a day intravenously over 7 days) and nifurtimox (three times a day orally over 10 days) which significantly decreases the workload and shortens the admission period for patients.
In April 2009, eflornithine in combination with nifurtimox was included in the WHO essential medicine list for treatment of stage two T. b. gambienseWHO established a six-month emergency intervention in 2004 in Tambura and Ezo counties due to absence of implementing partners in the area and the weak capacity of public health facilities to respond to the arising needs.
In 2006, nine out of the ten HAT treatment centers in South Sudan were run by international NGOs and one by the Ministry of Health (MoH). In 2010, only two international NGOs, are supporting HAT activities in Lui and Nimule hospitals; four hospitals are run by MoH in Juba, Yambio, Yei and Tambura; and four health facilities have stopped their activities in Source Yubu, Ezo, Maridi and Kajo Keji.
WHO provides technical support to MoH and implementing partners, trains staff involved in control of the disease and provides reagents and anti-trypanosome medicines free of charge for all HAT centers thanks to a Public-Private-Partnership with drug producers such as Bayer and Sanofi-aventis.