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

M. R. Smallman-Raynor; A. D. Cliff; Samuel C. Robson; Thomas R. Connor; Nicholas J. Loman; Tanya Golubchik; Rocio T. Martinez Nunez; David Bonsall; Andrew Rambaut; Luke B. Snell; Rich Livett; Catherine Ludden; Sally Corden; Eleni Nastouli; Gaia Nebbia; Ian Johnston; Katrina Lythgoe; M. Estee Torok; Ian G. Goodfellow; Jacqui A. Prieto; Kordo Saeed; David K. Jackson; Catherine Houlihan; Dan Frampton; William L. Hamilton; Adam A. Witney; Giselda Bucca; Cassie F. Pope; Catherine Moore; Emma C. Thomson; Ewan M. Harrison; Colin P. Smith; Fiona Rogan; Shaun M. Beckwith; Abigail Murray; Dawn Singleton; Kirstine Eastick; Liz A. Sheridan; Paul Randell; Leigh M. Jackson; Cristina V. Ariani; Sónia Gonçalves; Derek J. Fairley; Matthew W. Loose; Joanne Watkins; Samuel Moses; Sam Nicholls; Matthew Bull; Sally Forrest; Jonathan Ball

doi:10.1017/s0950268822001285

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

M. R. Smallman-Raynor
, A. D. Cliff
, Samuel C. Robson
, Thomas R. Connor
, Nicholas J. Loman
, Tanya Golubchik
, Rocio T. Martinez Nunez
, David Bonsall
, Andrew Rambaut
, Luke B. Snell
, Rich Livett
, Catherine Ludden
, Sally Corden
, Eleni Nastouli
, Gaia Nebbia
, Ian Johnston
, Katrina Lythgoe
, M. Estee Torok
, Ian G. Goodfellow
, Jacqui A. Prieto

Kordo Saeed, David K. Jackson, Catherine Houlihan, Dan Frampton, William L. Hamilton, Adam A. Witney, Giselda Bucca, Cassie F. Pope, Catherine Moore, Emma C. Thomson, Ewan M. Harrison, Colin P. Smith, Fiona Rogan, Shaun M. Beckwith, Abigail Murray, Dawn Singleton, Kirstine Eastick, Liz A. Sheridan, Paul Randell, Leigh M. Jackson, Cristina V. Ariani, Sónia Gonçalves, Derek J. Fairley, Matthew W. Loose, Joanne Watkins, Samuel Moses, Sam Nicholls, Matthew Bull, Sally Forrest, Jonathan Ball

University of Nottingham
University of Cambridge
University of Portsmouth
Cardiff University
Public Health Wales
University of Birmingham
University of Oxford
King's College London
University of Edinburgh
Guy's and St Thomas' NHS Foundation Trust
Wellcome Sanger Institute
UK Health Security Agency
University College London
University College London Hospitals NHS Foundation Trust
Cambridge University Hospitals NHS Foundation Trust
University of Southampton
University Hospital Southampton NHS Foundation Trust
City 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 and Social Care Trust
East Kent Hospitals University NHS Foundation Trust
University of Kent

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

10 Citations (Scopus)

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
Publication status	Published - 20 Jul 2022
Externally published	Yes

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SDG 3 Good Health and Well-being

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10.1017/s0950268822001285Licence: CC BY

Cite this

Smallman-Raynor, M. R., Cliff, A. D., Robson, S. C., Connor, T. R., Loman, N. J., Golubchik, T., Martinez Nunez, R. T., Bonsall, D., Rambaut, A., Snell, L. B., Livett, R., Ludden, C., Corden, S., Nastouli, E., Nebbia, G., Johnston, I., Lythgoe, K., Torok, M. E., Goodfellow, I. G., ... Ball, J. (2022). Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021. Epidemiology and Infection, 150, Article e145. https://doi.org/10.1017/s0950268822001285

@article{87fb3b4fe4e34737b1e3b196a7815da5,

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 = "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 Sally Forrest and Jonathan Ball",

year = "2022",

month = jul,

day = "20",

doi = "10.1017/s0950268822001285",

language = "English",

volume = "150",

journal = "Epidemiology and Infection",

issn = "0950-2688",

publisher = "Cambridge University Press",

}

Smallman-Raynor, MR, Cliff, AD, Robson, SC, Connor, TR, Loman, NJ, Golubchik, T, Martinez Nunez, RT, Bonsall, D, Rambaut, A, Snell, LB, Livett, R, Ludden, C, Corden, S, Nastouli, E, Nebbia, G, Johnston, I, Lythgoe, K, Torok, ME, Goodfellow, IG, Prieto, JA, Saeed, K, Jackson, DK, Houlihan, C, Frampton, D, Hamilton, WL, Witney, AA, Bucca, G, Pope, CF, Moore, C, Thomson, EC, Harrison, EM, Smith, CP, Rogan, F, Beckwith, SM, Murray, A, Singleton, D, Eastick, K, Sheridan, LA, Randell, P, Jackson, LM, Ariani, CV, Gonçalves, S, Fairley, DJ, Loose, MW, Watkins, J, Moses, S, Nicholls, S, Bull, M, Forrest, S & Ball, J 2022, 'Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021', Epidemiology and Infection, vol. 150, e145. https://doi.org/10.1017/s0950268822001285

TY - JOUR

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

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 - Forrest, Sally

AU - Ball, Jonathan

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.

U2 - 10.1017/s0950268822001285

DO - 10.1017/s0950268822001285

M3 - Article

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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