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. 2022 Mar;27(11):2200143.
doi: 10.2807/1560-7917.ES.2022.27.11.2200143.

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  1 , Jessica Bridgen  1 , Neil Bray  1 , Anne Marie O'Connell  1 , Daniel West  2 , Natalie Groves  2 , Eileen Gallagher  2 , Lara Utsi  1 , Christopher I Jarvis  1   3 , Jo L Hardstaff  1 , Chloe Byers  1 , Soeren Metelmann  1 , David Simons  1 , Asad Zaidi  2 , Katherine A Twohig  2 , Bethan Savagar  1 , Alessandra Løchen  1 , Cian Ryan  1 , Katie Wrenn  1 , María Saavedra-Campos  1 , Zahidul Abedin  1 , Isaac Florence  2 , Paul Cleary  1 , Richard Elson  1   4 , Roberto Vivancos  1 , Iain R Lake  1   4
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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

Paula B Blomquist et al. Euro Surveill. 2022 Mar.

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.

Keywords: COVD-19; Omicron; SARS-CoV-2; disease surveillance; public health; s-gene target failure.

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Conflict of interest statement

Conflict of interest: None declared.

Figures

Figure 1
Figure 1
Turnaround time between specimen date and notification, COVID-19 screening, PCR vs sequencing, England, samples submitted 19–30 December 2021 (n = 138,764 samples)
Figure 2
Figure 2
COVID-19 cases with S gene target failure, England, 15 November–31 December 2021 (n = 937,155)
See this image and copyright information in PMC

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