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; David K. Jackson; William L. Hamilton; Catherine Moore; Fiona Rogan; Derek J. Fairley; Husam Osman; David A. Simpson; James P. McKenna; Ben Temperton; Helen Adams; Marc Fuchs; Julia Miskelly; Thomas Davis; Anna Casey; Christopher R. Jones; Stephen Bridgett; Salman Goudarzi; Sophie Jones; Sarah Taylor; Tanya Curran; Tim Wyatt; Timofey Skvortsov; Declan T. Bradley; Jonathan Moore; Jack C.D. Lee; Zoltan Molnar; Kate Johnson; Leanne J. Murray; Darren R. Murray; Chris Baxter; Deborah Lavin; Arun Mariappan; Clara Radulescu; Aditi Singh; Miao Tang; Kathleen A. Williamson; Carol Scott; 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

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, David K. Jackson, William L. Hamilton, Catherine Moore, Fiona Rogan, Derek J. Fairley, Husam Osman, David A. SimpsonJames P. McKenna, Ben Temperton, Helen Adams, Marc Fuchs, Julia Miskelly, Thomas Davis, Anna Casey, Christopher R. Jones, Stephen Bridgett, Salman Goudarzi, Sophie Jones, Sarah Taylor, Tanya Curran, Tim Wyatt, Timofey Skvortsov, Declan T. Bradley, Jonathan Moore, Jack C.D. Lee, Zoltan Molnar, Kate Johnson, Leanne J. Murray, Darren R. Murray, Chris Baxter, Deborah Lavin, Arun Mariappan, Clara Radulescu, Aditi Singh, Miao Tang, Kathleen A. Williamson, Carol Scott, The COVID-19 Genomics UK (COG-UK) Consortium

^*Corresponding author for this work

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

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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

ASJC Scopus subject areas

Epidemiology
Infectious Diseases

UN SDGs

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

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Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020–December 2021
Copyright 2022 the authors. This is an open access article published under a Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited.
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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., Jackson, D. K., Hamilton, W. L., Moore, C., Rogan, F., Fairley, D. J., Osman, H., ... The COVID-19 Genomics UK (COG-UK) Consortium (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

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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 Jackson, {David K.} and Hamilton, {William L.} and Catherine Moore and Fiona Rogan and Fairley, {Derek J.} and Husam Osman and Simpson, {David A.} and McKenna, {James P.} and Ben Temperton and Helen Adams and Marc Fuchs and Julia Miskelly and Thomas Davis and Anna Casey and Jones, {Christopher R.} and Stephen Bridgett and Salman Goudarzi and Sophie Jones and Sarah Taylor and Tanya Curran and Tim Wyatt and Timofey Skvortsov and Bradley, {Declan T.} and Jonathan Moore and Lee, {Jack C.D.} and Zoltan Molnar and Kate Johnson and Murray, {Leanne J.} and Murray, {Darren R.} and Chris Baxter and Deborah Lavin and Arun Mariappan and Clara Radulescu and Aditi Singh and Miao Tang and Williamson, {Kathleen A.} and Carol Scott and {The COVID-19 Genomics UK (COG-UK) Consortium}",

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, Jackson, DK, Hamilton, WL, Moore, C, Rogan, F, Fairley, DJ, Osman, H, Simpson, DA, McKenna, JP, Temperton, B, Adams, H, Fuchs, M, Miskelly, J, Davis, T, Casey, A, Jones, CR, Bridgett, S, Goudarzi, S, Jones, S, Taylor, S, Curran, T, Wyatt, T, Skvortsov, T, Bradley, DT, Moore, J, Lee, JCD, Molnar, Z, Johnson, K, Murray, LJ, Murray, DR, Baxter, C, Lavin, D, Mariappan, A, Radulescu, C, Singh, A, Tang, M, Williamson, KA, Scott, C & The COVID-19 Genomics UK (COG-UK) Consortium 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 - Jackson, David K.

AU - Hamilton, William L.

AU - Moore, Catherine

AU - Rogan, Fiona

AU - Fairley, Derek J.

AU - Osman, Husam

AU - Simpson, David A.

AU - McKenna, James P.

AU - Temperton, Ben

AU - Adams, Helen

AU - Fuchs, Marc

AU - Miskelly, Julia

AU - Davis, Thomas

AU - Casey, Anna

AU - Jones, Christopher R.

AU - Bridgett, Stephen

AU - Goudarzi, Salman

AU - Jones, Sophie

AU - Taylor, Sarah

AU - Curran, Tanya

AU - Wyatt, Tim

AU - Skvortsov, Timofey

AU - Bradley, Declan T.

AU - Moore, Jonathan

AU - Lee, Jack C.D.

AU - Molnar, Zoltan

AU - Johnson, Kate

AU - Murray, Leanne J.

AU - Murray, Darren R.

AU - Baxter, Chris

AU - Lavin, Deborah

AU - Mariappan, Arun

AU - Radulescu, Clara

AU - Singh, Aditi

AU - Tang, Miao

AU - Williamson, Kathleen A.

AU - Scott, Carol

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

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

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

ASJC Scopus subject areas

UN SDGs

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