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The Programme has three core and interconnected pillars, conflict prevention, conflict management and post-conflict reconstruction and development, which address interventions at specific stages of the conflict life cycle. These intersect with two other ancillary programmes areas that address security and democratic governance. The impact of the two largely cross-cutting pillars on the different conflict levels highlights the necessary linkages between peace and security and democratic governance. COMESA has curved a niche on economic dimensions of conflict and as far as possible, it works in collaboration and cooperation with the AU and other RECs with shared membership. The ongoing programmes include:

Conflict Prevention: The Programme has established an early warning system, COMWARN, which is anchored on a composite index, the COMESA Peace and Prosperity Index (CPPI) that enables the programme to diagnostically project structural factors to conflict. The conflict prevention programme has also put in place a Committee of Elders for preventive diplomacy.

Democracy and Governance: This programme supports the consolidation of democracy in Member States including pre-election assessment missions and the observation of elections.

Conflict and Crisis Management: The programme deploys its Committee of Elders on preventive peace-making assignments as and when required.

Post-Conflict Reconstruction and Development: COMESA Trading for Peace project is implemented in countries that have emerged from conflict, using trade as a mechanism for peacebuilding.