Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021

The COVID-19 Genomics UK (COG-UK) Consortium

doi:10.1017/S0950268822001285

Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021

The COVID-19 Genomics UK (COG-UK) Consortium

Department of Medicine
University of Nottingham
University of Cambridge
University of Portsmouth
Cardiff University
Public Health Wales
University of Birmingham
Nuffield Department of Medicine
King's College London
EaStCHEM School of Chemistry, University of Edinburgh
Guy’s and St Thomas’ NHS Foundation Trust
Wellcome Sanger Institute
UK Health Security Agency
University College London (UCL)
University College London Hospitals NHS Foundation Trust
Cambridge University Hospitals NHS Foundation Trust
University of Southampton
University Hospital Southampton NHS Foundation Trust
University College London
St. George's University of London
University of Brighton
St George’s University Hospitals NHS Foundation Trust
MRC-University of Glasgow Centre for Virus Research
Queen's University Belfast
Blackpool Teaching Hospitals NHS Foundation Trust
Hull University Teaching Hospitals NHS Trust
University Hospitals Dorset NHS Foundation Trust
University Hospitals Sussex NHS Foundation Trust
University of Exeter
Belfast Health & Social Care Trust
East Kent Hospitals University NHS Foundation Trust
University of Kent
Northumbria University
University of Oxford
University of Sheffield
Portsmouth Hospitals University NHS Trust
NHS Lothian
NHS Greater Glasgow and Clyde
Quadram Institute
University of East Anglia
Hampshire Hospitals NHS Foundation Trust
Royal Free NHS Trust
South Tees Hospitals NHS Foundation Trust
Public Health Scotland
Health Services Laboratories
Heartlands Hospital
University of Liverpool
Imperial College London
MRC Biostatistics Unit
Buckinghamshire Healthcare NHS Trust
Newcastle upon Tyne Hospitals NHS Foundation Trust
University of St Andrews
Imperial College Healthcare NHS Trust
South West London Pathology
Betsi Cadwaladr University Health Board
University of Glasgow
Norfolk County Council
Great Ormond Street Hospital for Children NHS Foundation Trust
Cardiff & Vale University Health Board
Norfolk and Norwich University Hospitals NHS Foundation Trust
Royal Brompton and Harefield NHS Foundation Trust
The Queen Elizabeth Hospital King’s Lynn NHS Foundation Trust
Whittington Health NHS Trust
Barking, Havering and Redbridge University Hospitals NHS Trust
Bournemouth University
Queens Medical Centre
University Hospitals of Leicester NHS Trust
County Durham and Darlington NHS Foundation Trust
Kettering General Hospital
Barts Health NHS Trust
Maidstone and Tunbridge Wells NHS Trust
Royal Oldham Hospital
North Cumbria Integrated Care NHS Foundation Trust
North Tees and Hartlepool NHS Foundation Trust
Northern Lincolnshire & Goole NHS Foundation Trust
University Hospitals Birmingham NHS Foundation Trust
Royal Devon and Exeter NHS Foundation Trust
Swansea University
Sheffield Teaching Hospitals NHS Foundation Trust
Public Health Agency
Northumbria Healthcare NHS Foundation Trust
East Suffolk and North Essex NHS Foundation Trust
East Sussex Healthcare NHS Trust
Gateshead Health NHS Foundation Trust
Isle of Wight NHS Trust
King’s College Hospital NHS Foundation Trust
Liverpool Clinical Laboratories
Manchester University NHS Foundation Trust
North Middlesex University Hospital NHS Trust
Southwest Pathology Services
Royal Marsden NHS Foundation Trust
Royal Wolverhampton Hospitals NHS Trust
Watford General Hospital
Guy's and St. Thomas' Biomedical Research Centre
Newcastle University

Research output: Contribution to journal › Article › peer-review

10 Scopus citations

Abstract

This paper uses a robust method of spatial epidemiological analysis to assess the spatial growth rate of multiple lineages of SARS-CoV-2 in the local authority areas of England, September 2020-December 2021. Using the genomic surveillance records of the COVID-19 Genomics UK (COG-UK) Consortium, the analysis identifies a substantial (7.6-fold) difference in the average rate of spatial growth of 37 sample lineages, from the slowest (Delta AY.4.3) to the fastest (Omicron BA.1). Spatial growth of the Omicron (B.1.1.529 and BA) variant was found to be 2.81× faster than the Delta (B.1.617.2 and AY) variant and 3.76× faster than the Alpha (B.1.1.7 and Q) variant. In addition to AY.4.2 (a designated variant under investigation, VUI-21OCT-01), three Delta sublineages (AY.43, AY.98 and AY.120) were found to display a statistically faster rate of spatial growth than the parent lineage and would seem to merit further investigation. We suggest that the monitoring of spatial growth rates is a potentially valuable adjunct to outbreak response procedures for emerging SARS-CoV-2 variants in a defined population.

Original language	English
Article number	e145
Journal	Epidemiology and Infection
Volume	150
DOIs	https://doi.org/10.1017/S0950268822001285
State	Published - 20 Jul 2022
Externally published	Yes

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SDG 3 Good Health and Well-being

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10.1017/S0950268822001285

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@article{797dde92150240df8afdcae50e9d58ab,

title = "Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021",

abstract = "This paper uses a robust method of spatial epidemiological analysis to assess the spatial growth rate of multiple lineages of SARS-CoV-2 in the local authority areas of England, September 2020-December 2021. Using the genomic surveillance records of the COVID-19 Genomics UK (COG-UK) Consortium, the analysis identifies a substantial (7.6-fold) difference in the average rate of spatial growth of 37 sample lineages, from the slowest (Delta AY.4.3) to the fastest (Omicron BA.1). Spatial growth of the Omicron (B.1.1.529 and BA) variant was found to be 2.81× faster than the Delta (B.1.617.2 and AY) variant and 3.76× faster than the Alpha (B.1.1.7 and Q) variant. In addition to AY.4.2 (a designated variant under investigation, VUI-21OCT-01), three Delta sublineages (AY.43, AY.98 and AY.120) were found to display a statistically faster rate of spatial growth than the parent lineage and would seem to merit further investigation. We suggest that the monitoring of spatial growth rates is a potentially valuable adjunct to outbreak response procedures for emerging SARS-CoV-2 variants in a defined population.",

author = "\{The COVID-19 Genomics UK (COG-UK) Consortium\} and Smallman-Raynor, \{M. R.\} and Cliff, \{A. D.\} and Robson, \{Samuel C.\} and Connor, \{Thomas R.\} and Loman, \{Nicholas J.\} and Tanya Golubchik and \{Martinez Nunez\}, \{Rocio T.\} and David Bonsall and Andrew Rambaut and Snell, \{Luke B.\} and Rich Livett and Catherine Ludden and Sally Corden and Eleni Nastouli and Gaia Nebbia and Ian Johnston and Katrina Lythgoe and Torok, \{M. Estee\} and Goodfellow, \{Ian G.\} and Prieto, \{Jacqui A.\} and Kordo Saeed and Jackson, \{David K.\} and Catherine Houlihan and Dan Frampton and Hamilton, \{William L.\} and Witney, \{Adam A.\} and Giselda Bucca and Pope, \{Cassie F.\} and Catherine Moore and Thomson, \{Emma C.\} and Harrison, \{Ewan M.\} and Smith, \{Colin P.\} and Fiona Rogan and Beckwith, \{Shaun M.\} and Abigail Murray and Dawn Singleton and Kirstine Eastick and Sheridan, \{Liz A.\} and Paul Randell and Jackson, \{Leigh M.\} and Ariani, \{Cristina V.\} and S{\'o}nia Gon{\c c}alves and Fairley, \{Derek J.\} and Loose, \{Matthew W.\} and Joanne Watkins and Samuel Moses and Sam Nicholls and Matthew Bull and Roberto Amato and Smith, \{Darren L.\}",

year = "2022",

month = jul,

day = "20",

doi = "10.1017/S0950268822001285",

language = "Ingl{\'e}s",

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journal = "Epidemiology and Infection",

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T1 - Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021

AU - The COVID-19 Genomics UK (COG-UK) Consortium

AU - Smallman-Raynor, M. R.

AU - Cliff, A. D.

AU - Robson, Samuel C.

AU - Connor, Thomas R.

AU - Loman, Nicholas J.

AU - Golubchik, Tanya

AU - Martinez Nunez, Rocio T.

AU - Bonsall, David

AU - Rambaut, Andrew

AU - Snell, Luke B.

AU - Livett, Rich

AU - Ludden, Catherine

AU - Corden, Sally

AU - Nastouli, Eleni

AU - Nebbia, Gaia

AU - Johnston, Ian

AU - Lythgoe, Katrina

AU - Torok, M. Estee

AU - Goodfellow, Ian G.

AU - Prieto, Jacqui A.

AU - Saeed, Kordo

AU - Jackson, David K.

AU - Houlihan, Catherine

AU - Frampton, Dan

AU - Hamilton, William L.

AU - Witney, Adam A.

AU - Bucca, Giselda

AU - Pope, Cassie F.

AU - Moore, Catherine

AU - Thomson, Emma C.

AU - Harrison, Ewan M.

AU - Smith, Colin P.

AU - Rogan, Fiona

AU - Beckwith, Shaun M.

AU - Murray, Abigail

AU - Singleton, Dawn

AU - Eastick, Kirstine

AU - Sheridan, Liz A.

AU - Randell, Paul

AU - Jackson, Leigh M.

AU - Ariani, Cristina V.

AU - Gonçalves, Sónia

AU - Fairley, Derek J.

AU - Loose, Matthew W.

AU - Watkins, Joanne

AU - Moses, Samuel

AU - Nicholls, Sam

AU - Bull, Matthew

AU - Amato, Roberto

AU - Smith, Darren L.

PY - 2022/7/20

Y1 - 2022/7/20

N2 - This paper uses a robust method of spatial epidemiological analysis to assess the spatial growth rate of multiple lineages of SARS-CoV-2 in the local authority areas of England, September 2020-December 2021. Using the genomic surveillance records of the COVID-19 Genomics UK (COG-UK) Consortium, the analysis identifies a substantial (7.6-fold) difference in the average rate of spatial growth of 37 sample lineages, from the slowest (Delta AY.4.3) to the fastest (Omicron BA.1). Spatial growth of the Omicron (B.1.1.529 and BA) variant was found to be 2.81× faster than the Delta (B.1.617.2 and AY) variant and 3.76× faster than the Alpha (B.1.1.7 and Q) variant. In addition to AY.4.2 (a designated variant under investigation, VUI-21OCT-01), three Delta sublineages (AY.43, AY.98 and AY.120) were found to display a statistically faster rate of spatial growth than the parent lineage and would seem to merit further investigation. We suggest that the monitoring of spatial growth rates is a potentially valuable adjunct to outbreak response procedures for emerging SARS-CoV-2 variants in a defined population.

AB - This paper uses a robust method of spatial epidemiological analysis to assess the spatial growth rate of multiple lineages of SARS-CoV-2 in the local authority areas of England, September 2020-December 2021. Using the genomic surveillance records of the COVID-19 Genomics UK (COG-UK) Consortium, the analysis identifies a substantial (7.6-fold) difference in the average rate of spatial growth of 37 sample lineages, from the slowest (Delta AY.4.3) to the fastest (Omicron BA.1). Spatial growth of the Omicron (B.1.1.529 and BA) variant was found to be 2.81× faster than the Delta (B.1.617.2 and AY) variant and 3.76× faster than the Alpha (B.1.1.7 and Q) variant. In addition to AY.4.2 (a designated variant under investigation, VUI-21OCT-01), three Delta sublineages (AY.43, AY.98 and AY.120) were found to display a statistically faster rate of spatial growth than the parent lineage and would seem to merit further investigation. We suggest that the monitoring of spatial growth rates is a potentially valuable adjunct to outbreak response procedures for emerging SARS-CoV-2 variants in a defined population.

UR - https://www.scopus.com/pages/publications/85135596528

U2 - 10.1017/S0950268822001285

DO - 10.1017/S0950268822001285

M3 - Artículo

C2 - 35855577

AN - SCOPUS:85135596528

SN - 0950-2688

VL - 150

JO - Epidemiology and Infection

JF - Epidemiology and Infection

M1 - e145

ER -

Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021

Abstract

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