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

Paula B. Blomquist, Jessica Bridgen, Neil Bray, Anne Marie O'Connell, Daniel West, Natalie Groves, Eileen Gallagher, Lara Utsi, Christopher I. Jarvis, Jo L. Hardstaff, Chloe Byers, Soeren Metelmann, David Simons, Asad Zaidi, Katherine A. Twohig, Bethan Savagar, Allesandra Løchen, Cian Ryan, Katie Wrenn, Maria Saavedra-CamposZahidul Abedin, Isaac Florence, Paul Cleary, Richard Elson, Roberto Vivancos, Iain R. Lake

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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.
Original languageEnglish
Article number2200143
Issue number11
Publication statusPublished - 17 Mar 2022


  • SARS-CoV-2
  • disease surveillance
  • s-gene target failure
  • COVD-19
  • public health
  • Omicron

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