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-Campos; Zahidul Abedin; Isaac Florence; Paul Cleary; Richard Elson; Roberto Vivancos; Iain R. Lake

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, 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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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.

Original language	English
Article number	2200143
Journal	Eurosurveillance
Volume	27
Issue number	11
DOIs	https://doi.org/10.2807/1560-7917.ES.2022.27.11.2200143
Publication status	Published - 17 Mar 2022

Keywords

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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.2807/1560-7917.ES.2022.27.11.2200143Licence: CC BY

Accepted_ManuscriptAccepted author manuscript, 346 KBLicence: CC BY

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Blomquist, P. B., Bridgen, J., Bray, N., O'Connell, A. M., West, D., Groves, N., Gallagher, E., Utsi, L., Jarvis, C. I., Hardstaff, J. L., Byers, C., Metelmann, S., Simons, D., Zaidi, A., Twohig, K. A., Savagar, B., Løchen, A., Ryan, C., Wrenn, K., ... Lake, I. R. (2022). 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. Eurosurveillance, 27(11), Article 2200143. https://doi.org/10.2807/1560-7917.ES.2022.27.11.2200143

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title = "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",

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 = "SARS-CoV-2, disease surveillance, s-gene target failure, COVD-19, public health, Omicron",

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

year = "2022",

month = mar,

day = "17",

doi = "10.2807/1560-7917.ES.2022.27.11.2200143",

language = "English",

volume = "27",

journal = "Eurosurveillance",

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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 & Lake, IR 2022, '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', Eurosurveillance, vol. 27, no. 11, 2200143. https://doi.org/10.2807/1560-7917.ES.2022.27.11.2200143

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T1 - 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

AU - Blomquist, Paula B.

AU - Bridgen, Jessica

AU - Bray, Neil

AU - O'Connell, Anne Marie

AU - West, Daniel

AU - Groves, Natalie

AU - Gallagher, Eileen

AU - Utsi, Lara

AU - Jarvis, Christopher I.

AU - Hardstaff, Jo L.

AU - Byers, Chloe

AU - Metelmann, Soeren

AU - Simons, David

AU - Zaidi, Asad

AU - Twohig, Katherine A.

AU - Savagar, Bethan

AU - Løchen, Allesandra

AU - Ryan, Cian

AU - Wrenn, Katie

AU - Saavedra-Campos, Maria

AU - Abedin, Zahidul

AU - Florence, Isaac

AU - Cleary, Paul

AU - Elson, Richard

AU - Vivancos, Roberto

AU - Lake, Iain R.

PY - 2022/3/17

Y1 - 2022/3/17

N2 - 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.

AB - 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.

KW - SARS-CoV-2

KW - disease surveillance

KW - s-gene target failure

KW - COVD-19

KW - public health

KW - Omicron

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U2 - 10.2807/1560-7917.ES.2022.27.11.2200143

DO - 10.2807/1560-7917.ES.2022.27.11.2200143

M3 - Article

SN - 1560-7917

VL - 27

JO - Eurosurveillance

JF - Eurosurveillance

IS - 11

M1 - 2200143

ER -

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

Abstract

Keywords

UN SDGs

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