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1. 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.

Author

Blomquist PB, Bridgen J, Bray N, O'Connell AM, West D, Groves N, Gallagher E, Utsi L, Jarvis CI, Hardstaff JL, Byers C, Metelmann S, Simons D, Zaidi A, Twohig KA, Savagar B, Løchen A, Ryan C, Wrenn K, Saavedra-Campos M, Abedin Z, Florence I, Cleary P, Elson R, Vivancos R, and Lake IR

Subjects
Humans, Membrane Glycoproteins genetics, Spike Glycoprotein, Coronavirus genetics, Viral Envelope Proteins genetics, COVID-19 epidemiology, SARS-CoV-2 genetics
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.

Published
2022
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