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European Centre for Disease Prevention and Control, Eurosurveillance, 11(27), 2022

DOI: 10.2807/1560-7917.es.2022.27.11.2200143

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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

Journal article published in 2022 by Paula B. Blomquist ORCID, Jessica Bridgen ORCID, Neil Bray, Anne Marie O’Connell, Daniel West, Natalie Groves ORCID, Eileen Gallagher, Lara Utsi ORCID, Christopher I. Jarvis ORCID, Jo L. Hardstaff ORCID, Chloe Byers ORCID, Soeren Metelmann ORCID, David Simons ORCID, Asad Zaidi ORCID, Katherine A. Twohig ORCID and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

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.