Enhancing epidemiological surveillance of the emergence of the SARS-CoV-2 Omicron variant using spike gene target failure data, England, 15 November to 31 December 2021

When SARS-CoV-2 Omicron emerged in 2021, S gene target failure enabled differentiation between Omicron and the dominant Delta variant. In England, where S gene target surveillance (SGTS) was already established, this led to rapid identification (within ca 3 days of sample collection) of possible Omicron cases, alongside real-time surveillance and modelling of Omicron growth. SGTS was key to public health action (including case identification and incident management), and we share applied insights on how and when to use SGTS.

Automated summary

When SARS-CoV-2 Omicron emerged, the failure of the S gene target provided a way to differentiate it from the dominant Delta variant. In England, where S gene target surveillance was already in place, this led to quick identification of potential Omicron cases and real-time monitoring of its growth. The use of S gene target surveillance played a crucial role in public health measures, including case identification and incident management, and we provide practical insights on its application.