The ECDC Communicable Disease Threats Report (CDTR) is a weekly bulletin for epidemiologists and health professionals on active public health threats. This issue of the CDTR covers covers the period 12-18 September, and includes updates on Ebola, malaria, botulism, avian influenza A(H9N2), influenza A(H5), respiratory virus epidemiology in the EU/.EEA, West Nile virus infections, chikungunya, dengue, Crimean-Congo haemorrhagic fever, Vibrio, measles, and expert deployments.