HAT outbreak in East African region is associated with specific foci (Hide, 1999). These foci are considered potential areas where the risk of infection with the disease and disease transmission may be high (Figure 3). Moreover, HAT foci expanded and contracted over time as tsetse fly distribution and human activities changed (Welburn and Maudlin, 1999). Human activities and the factors affecting vector distribution over time might give an insight into the characteristics of HAT foci. Therefore, disease outbreak at foci, necessitates a transmission cycle by efficient tsetse fly and suitable habitats that support the fly population and the presence of mammalian hosts. In South Sudan active HAT foci due to T. b. gambiense have been described in the Greater Equatoria region bordering the CAR, the DRC, and Uganda; whereas, the HAT caused by T. b. rhodesiense was reported from Akobo County of Jonglei State bordering Gambella in Ethiopia, although since 1984 no cases were reported (Ruiz-Postigo et al., 2012) despite the presence of G. f. fuscipes and G. tachinoides.

Repeated epidemics of HAT due to T. b. gambiense in South Sudan were observed periodically in foci found within a belt bordering the CAR, the DRC and Uganda (Moore and Richer, 2001). One of the most important episodes of HAT outbreaks in 1950s in the South Sudan occurred when Yambio in Western Equatoria State was designated as the centre of the New Zande Development Scheme (NZDS) in 1946. This event was one of the unique situations in Africa in which agricultural developments triggered  massive  population  movement.

People moved and settled in high density in the Centre of the NZDS where many G. palpalis infested streams and HAT active foci present. The surrounding HAT-epidemic villages created conditions favorable for HAT in urban areas (Simo et al., 2006).

Following the signing of the Addis Ababa Peace Accord in 1972, the repatriation of South Sudanese refugees from endemic HAT areas of Uganda to South Sudan and the massive movements of the internally displaced Ugandan citizens to Nimule might be the cause of HAT outbreak in Nimule in 1970s (Palmer et al., 2014). Resurgence of HAT in 1970’s in the former Western and Eastern Equatoria Provinces had prompted an intervention for control programme by bilateral Belgian Sudanese Trypanosomiasis programme (BSTP). Between 1974 and 1978 HAT control activities were maintained through external assistance from WHO and BSTP. Hence, a reduction in the cases of HAT revealed in the mids-1980, both Li-Rangu and Juba Teaching Hospitals became reference centers for HAT, but later on it deteriorated due to eruption of the second civil war in 1983 (Ruiz-Postigo et al., 2012).

In the late 1980’sand 1990’s HAT control programmes and activities had collapsed. Consequently, by 1997 HAT re-emerged with prevalence rates as high as 19% in South-western Communities of South Sudan bordering DRC (Ford, 2007). By 1990, 4 out of 5 health facilities in the country were shut (Palmer et al., 2014).Consequently, HAT outbreaks occurred in the HAT already known foci in the South-western part of the county bordering CAR and DRC (Moore et al., 1999). Furthermore, HAT resurgence surfaced as renown epidemic in the Southern Sudan in 1997 (Hide, 1999).

Subsequent to the signing of the CPA in 2005, a relative peace and stability prevailed in South Sudan where HAT control activities carried out by the Ministry of Health (MoH) and Non-governmental Organizations (NGOs). The MoH and the NGOs planned control activities and as a result there was a significant decrease in number of reporting cases (Ruiz-Postigo et al., 2012).

In post-CPA era, the NGOs that were instrumental in HAT control programme withdrew leading to increasing HAT cases between the years 2000 and 2010. This was due to cessation of HAT control activities and reduction of health facilities after 2006 (Ruiz-Postigo et al., 2012).

Currently, the low HAT cases in South Sudan do not suggest that HAT foci do not exist. All the HAT ancient foci in Yambio and Tambura Counties in Western Equatoria State, Yei River and Morobo Counties in Central Equatoria State, Torit and Magwi Counties as well as Nimule Payam of Eastern Equatoria State may be active. No reported cases of HAT from the Raga historic foci in the Raga County of Western Bahr El Ghazal State were realized. This might be attributed to numerous factors including ecological factors and vegetation cover. HAT high risk correlates with areas of high infection,  and so do areas of low risk with low infection. High risk also occurs in areas with low population densities, and low risk is also found in areas with high population densities (Ford et al., 2006). Disease risk is high in population with low density due to higher fly-host contact ratios; whereas the risk is low in dense population due to low fly-host contact ratios. There is a high disease risk when a new population moves into a population with high infection.

Social conflicts play a role in infectious diseases outbreaks and have long been recognized as determinants of infectious disease risk. The close association between the temporal occurrences of HAT outbreaks and  civil  conflicts  is  not  a  new  scenario  in South Sudan. There is an association between conflict and infectious disease, especially in the foci where civil conflicts still persist (Ford, 2007). The temporal occurrences of outbreaks for both T. b. rhodesiense and T. b. gambiense sub-species are associated with times of conflicts in south eastern Uganda (Ford, 2007). All of the HAT epidemics and outbreaks in South Sudan were observed during the era of political upheavals, instability and civil disturbance (Duku, 1979). With the eruption of the first civil war in the Sudan, enormous and unceasing population dislodgment across the country occurred. The movement of population to the regions where HAT foci prevailed  and  repatriated  back  to their  homeland could explain HAT outbreaks and expansion of the local HAT reservoir. Proliferation of the HAT in Uganda was attributed to refugee movements and interaction with infected regions of the southern Sudan (Ford et al., 2006). Repatriation of the refugees had eventually increased HAT transmission potential in two ways: first the refugees from the endemic foci might pose the risk of infection to the few natives who did not leave their home land during the long years of conflict, secondly the vegetation and the new tsetse fly habitat that had grown during their absence became a potential risk since they might have made the environment suitable for tsetse fly (Ford, 2007). The later scenario increased HAT transmission potential by affecting directly a number of parameters in the HAT transmission leading to the increasing of  HAT transmission  potential  (Ford,  2007); this might have contributed in the HAT cases in 1970’s.

The current review indicates that previously infected known Gambian HAT foci may still be active and can pose infection risk in South Sudan. Only Raga HAT historic foci remain without infection. No new cases of Rhodesian HAT are reported in South Sudan, though cattle are imported from Uganda which could warrant precautionary measures. Further studies on molecular parasitology and epidemiology are needed to confirm the elimination of infection or re-establish the endemic status of Raga, Akobo and Pachalla HAT foci in South Sudan.

The authors have not declared any conflict of interests.