Sequencing of SARS-CoV-2 - first update

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.

In the context of the recently identified new variant (SARS-CoV-2 VOC 202012/01) reported by the UK, and the urgent need to assess the extent to which it is circulating in EU/EEA countries, the document incudes a section on sampling approaches. Particular priority at this time (i.e. during early 2021) should be given to sequencing of isolates from the following cases: those with epidemiological links to areas known to be affected, those occurring as part of sudden increases or unusual distributions of cases, reinfections and monoclonal antibody treatment failures, and those for which there is evidence of S-gene ‘drop out’ in PCR testing. When assays for specific detection of this variant become available, they can be used for screening for samples to be sequenced.