This technical guidance aims to provide guidelines to laboratories and relevant stakeholders in the European Union (EU), European Economic Area (EEA) and other countries in the WHO European region in making decisions on establishing sequencing capacities and capabilities, in making decisions on which technologies to use and/or in deciding on the role of sequencing for SARS-CoV-2 diagnostics, research, outbreak investigations and surveillance. It addresses the most used sequencing technologies and their applications and proposes a central standardisation process to analyse and report the findings of SARS-CoV-2 genetic characterisations.