@article{5ce25565a3834a3f9c2349b3e3e91608,
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 Justin O'Grady and Page, {Andrew J.} and {The COVID-19 Genomics UK (COG-UK) Consortium}",
note = "Data availability statement: The data that support the findings of this study are available at Wellcome Sanger Institute COVID–19 Genomic Surveillance (https://covid19.sanger.ac.uk/lineages/raw). ",
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",
}