The World Health Organization Regional Office for Africa (WHO AFRO), in accordance with recommendations from various WHO committees, has developed three flagship programmes to support Member States in the African region to prepare for, detect and respond to public health emergencies. They are the result of extensive consultations with more than 30 African government ministers, technical actors, partners across the continent as well as regional institutions such as the Africa Centres for Disease Control and Prevention (Africa CDC), whose contributions have shaped the priority activities. This report provides the second quarterly summary of progress in implementing the flagship programmes.