Optimization of restricted insecticide/acaricide application protocol for tsetse and tick-borne disease control in south-eastern Uganda Abstract Tsetse and tick-borne diseases (TTBDs) constrain integration of livestock and crop production and human health in Sub-Saharan Africa aggravating hunger and poverty in this region. Improving livelihoods in this region requires enhancing livestock production by developing and using cheap and environmentally benign TTBD control methods. To set stage to determining the smallest proportion of the village cattle herd that needs to be sprayed by restricting insecticides to the legs, bellies and ears (RAP) to control TTBDs, the burden and spatial distribution of African trypanosomes and T.parva in crop-livestock production systems in south-eastern Uganda was determined. The actual cost of applying RAP for TTBD control was undertaken to guide future on-scale TTBD control. Cluster sampling was used to select 57 villages in Tororo district, blood samples taken from cattle in all selected villages, screened for T.parva and trypanosomes by a suite of molecular techniques. To determine preintervention Trypanosome species and T.parva prevalences, risk factors and their confidence intervals, generalised estimating equation (GEE) models were completed in R statistical software v 3.0.2 (R). A 20 village sequence was randomly selected from baseline villages by setting the inter-village distance at 2 km2 and trypanosome prevalence at 15% in R. Villages were randomised to 5 treatment regimens; cattle therein ear-tagged, treated with diminazene diaceturate (DA) and followed for 18 months. Cattle in regimens 2-4 received monthly graded RAP (25, 50 and 75 % of village cattle herd sprayed respectively) while those in regimen 5 were dewormed once every 3 months. Tsetse apparent density was monitored by pyramidal traps at 161 locations in the district. Blood samples taken fourteen days post DA treatment and once every three months were screened as above. The effect of RAP on trypanosome and T.parva prevalence was assessed by mixed binary outcome and Poisson random effect modelling in R and STATA V12.1 respectively. Spatial analyses were done on the spatial analyst extension of ArcMap v10.1 while the total cost calculation and straight line methodologies were used to determine the actual cost of RAP application. Pre-intervention trypanosome species prevalence was 15.3 % (95 % CI; 12.2-19.1) while that of T.parva was 5.3 %. Trypanosome and T.parva herd level prevalences were greatly clustered in different villages. RAP was associated with low risk of infection with trypanosomes and T.parva. However there was no explicit dose-response between graded RAP and Trypanosome or T.parva prevalence. RAP (p; 0.001) and village locations (p; 0.001) were the best predictors of infection with trypanosome infections. The actual cost of RAP was US$ 6.89 per animal per year; comparable to the cost (US$ 5.69) of 4 curative doses of trypanocides per animal per year and; higher than previously reported because past RAP cost calculations excluded planning and organisational overheads. These results are discussed with reference to future on-scale and farmer-led RAP application for TTBD control. Key words: African trypanosomiasis, Collateral benefits, Direct costs, Indirect costs, ITS1-PCR, Restricted insecticide application protocol (RAP), Tick-borne diseases (TBDs), T.parva, p-104based PCR, Tsetse density, Tororo District