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In its new roadmap for neglected tropical diseases, the World Health Organization proposes three important strategic shifts: (i) Stronger accountability which shifting from process to impact indicators; (ii) Intensified cross-cutting approaches; and (iii) Stronger country ownership. In this paper we discuss the implementation of these three strategies in the setting of a high onchocerciasis disease burden in South Sudan.“,”In its new roadmap for neglected tropical diseases, the World Health Organization proposes three important strategic shifts: (i) Stronger accountability which shifting from process to impact indicators; (ii) Intensified cross-cutting approaches; and (iii) Stronger country ownership. In this paper we discuss the implementation of these three strategies in the setting of a high onchocerciasis disease burden in South Sudan.