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; Alessandra Lochen; Cian Ryan; Katie Wrenn; María 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
, Alessandra Lochen
, Cian Ryan
, Katie Wrenn
, María Saavedra-Campos

Zahidul Abedin, Isaac Florence, Paul Cleary, Richard Elson, Roberto Vivancos, Iain R. Lake^*

^*Corresponding author for this work

Field Service - Outbreak Surveillance & JSAT

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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
Pages (from-to)	6-10
Number of pages	5
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

Bibliographical note

Funding Information: IRL is part supported by the Health Protection Research Unit (NIHR HPRU) in Emergency Preparedness and Response at King’s College London in partnership with UK Health Security Agency and collaboration with the University of East Anglia. RV is part supported by the NIHR HPRU in Emerging and Zoonotic Infections and the NIHR HPRU in Gastrointestinal Infections, both at the University of Liverpool. The views expressed in this article are those of the author(s) and are not necessarily those of UK Health Security Agency, the Department of Health and Social Care, the National Health Service, the National Institute for Health Research, the London School of Hygiene and Tropical Medicine or the University of East Anglia.

Open Access: This is an open-access article distributed under the terms of the Creative Commons Attribution (CC BY 4.0) Licence. You may share and adapt the material, but must give appropriate credit to the source, provide a link to the licence and indicate if changes were made.

Publisher Copyright: This article is copyright of the authors or their affiliated institutions, 2022.

Citation: Blomquist Paula B, Bridgen Jessica, Bray Neil, O’Connell Anne Marie, West Daniel, Groves Natalie, Gallagher Eileen, Utsi Lara, Jarvis Christopher I, Hardstaff Jo L, Byers Chloe, Metelmann Soeren, Simons David, Zaidi Asad, Twohig Katherine A, Savagar Bethan, Løchen Alessandra, Ryan Cian, Wrenn Katie, Saavedra-Campos
María, Abedin Zahidul, Florence Isaac, Cleary Paul, Elson Richard, Vivancos Roberto, Lake Iain R. 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. Euro Surveill. 2022;27(11):pii=2200143.

DOI: https://doi.org/10.2807/1560-7917.ES.2022.27.11.2200143

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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., Lochen, 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), 6-10. 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.",

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 Alessandra Lochen and Cian Ryan and Katie Wrenn and Mar{\'i}a Saavedra-Campos and Zahidul Abedin and Isaac Florence and Paul Cleary and Richard Elson and Roberto Vivancos and Lake, \{Iain R.\}",

note = "Funding Information: IRL is part supported by the Health Protection Research Unit (NIHR HPRU) in Emergency Preparedness and Response at King{\textquoteright}s College London in partnership with UK Health Security Agency and collaboration with the University of East Anglia. RV is part supported by the NIHR HPRU in Emerging and Zoonotic Infections and the NIHR HPRU in Gastrointestinal Infections, both at the University of Liverpool. The views expressed in this article are those of the author(s) and are not necessarily those of UK Health Security Agency, the Department of Health and Social Care, the National Health Service, the National Institute for Health Research, the London School of Hygiene and Tropical Medicine or the University of East Anglia. Open Access: This is an open-access article distributed under the terms of the Creative Commons Attribution (CC BY 4.0) Licence. You may share and adapt the material, but must give appropriate credit to the source, provide a link to the licence and indicate if changes were made. Publisher Copyright: This article is copyright of the authors or their affiliated institutions, 2022. Citation: Blomquist Paula B, Bridgen Jessica, Bray Neil, O{\textquoteright}Connell Anne Marie, West Daniel, Groves Natalie, Gallagher Eileen, Utsi Lara, Jarvis Christopher I, Hardstaff Jo L, Byers Chloe, Metelmann Soeren, Simons David, Zaidi Asad, Twohig Katherine A, Savagar Bethan, L{\o}chen Alessandra, Ryan Cian, Wrenn Katie, Saavedra-Campos Mar{\'i}a, Abedin Zahidul, Florence Isaac, Cleary Paul, Elson Richard, Vivancos Roberto, Lake Iain R. 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. Euro Surveill. 2022;27(11):pii=2200143. DOI: https://doi.org/10.2807/1560-7917.ES.2022.27.11.2200143",

year = "2022",

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

language = "English",

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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, Lochen, 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, pp. 6-10. https://doi.org/10.2807/1560-7917.ES.2022.27.11.2200143

TY - JOUR

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 - Lochen, Alessandra

AU - Ryan, Cian

AU - Wrenn, Katie

AU - Saavedra-Campos, María

AU - Abedin, Zahidul

AU - Florence, Isaac

AU - Cleary, Paul

AU - Elson, Richard

AU - Vivancos, Roberto

AU - Lake, Iain R.

N1 - Funding Information: IRL is part supported by the Health Protection Research Unit (NIHR HPRU) in Emergency Preparedness and Response at King’s College London in partnership with UK Health Security Agency and collaboration with the University of East Anglia. RV is part supported by the NIHR HPRU in Emerging and Zoonotic Infections and the NIHR HPRU in Gastrointestinal Infections, both at the University of Liverpool. The views expressed in this article are those of the author(s) and are not necessarily those of UK Health Security Agency, the Department of Health and Social Care, the National Health Service, the National Institute for Health Research, the London School of Hygiene and Tropical Medicine or the University of East Anglia. Open Access: This is an open-access article distributed under the terms of the Creative Commons Attribution (CC BY 4.0) Licence. You may share and adapt the material, but must give appropriate credit to the source, provide a link to the licence and indicate if changes were made. Publisher Copyright: This article is copyright of the authors or their affiliated institutions, 2022. Citation: Blomquist Paula B, Bridgen Jessica, Bray Neil, O’Connell Anne Marie, West Daniel, Groves Natalie, Gallagher Eileen, Utsi Lara, Jarvis Christopher I, Hardstaff Jo L, Byers Chloe, Metelmann Soeren, Simons David, Zaidi Asad, Twohig Katherine A, Savagar Bethan, Løchen Alessandra, Ryan Cian, Wrenn Katie, Saavedra-Campos María, Abedin Zahidul, Florence Isaac, Cleary Paul, Elson Richard, Vivancos Roberto, Lake Iain R. 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. Euro Surveill. 2022;27(11):pii=2200143. DOI: https://doi.org/10.2807/1560-7917.ES.2022.27.11.2200143

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.

UR - https://www.scopus.com/pages/publications/85126702104

U2 - 10.2807/1560-7917.ES.2022.27.11.2200143

DO - 10.2807/1560-7917.ES.2022.27.11.2200143

M3 - Article

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AN - SCOPUS:85126702104

SN - 1025-496X

VL - 27

SP - 6

EP - 10

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

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Bibliographical note

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