Background: In this study we are evaluating the potential impact of the current COVID-19-induced delay in Community Directed Treatment with ivermectin (CDTi) on the onchocerciasis elimination targets in Ghana. This has become necessary because, in response to the current COVID-19 pandemic, the World Health Organization (WHO) has stated that community-based surveys, active case-finding activities and mass treatment campaigns for neglected tropical diseases (NTDs) such as onchocerciasis be postponed until further notice. Though this decision was necessary to help curb the spread of the COVID-19 pandemic, there is the risk of losing the gains of interruption or elimination of onchocerciasis transmission set forth in the recent WHO roadmap on Neglected Tropical Diseases (NTDs) for the period 2021–2030. The study will be carried out in 6 communities of the Wenchi, Banda and Tain districts of the Bono Region of Ghana. These communities are currently mesoendemic for onchocerciasis, with biannual mass drug administration programmes since 2010. Currently, these programmes have been suspended in compliance with the WHO recommendation to temporarily suspend all such activities. We, therefore, propose to investigate microfilarial intensity and prevalence of onchocerciasis in the study communities in Ghana prior to CDTi interruption (via transmission modelling), and (empirically) before CDTi resumption and after 6 months following resumption, and compare with modelled data on infection trends with and without interruption. The safe piloting of CDTi resumption in the study communities will be done using optimal mitigation strategies identified by modelling and in collaboration with the National NTD programme. Data analyses will be done using R and the EPIONCHO-IBM model (which also uses R). The study will use EPIONCHO-IBM to predict the prevalence and intensity of Onchocerca volvulus infection before the COVID-19 induced interruption, evaluate the duration of the interruption, and measure empirically the prevalence and intensity of infection at the restart of the programme and 6 months later. The study will then use transmission modelling to determine the best mitigation strategies and make policy and implementation recommendations to the national NTD control programme, government and other stakeholders to enable planning and implementation necessary to mitigate the impact of delays in CDTi and sustain programmatic gains