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

Smallman-Raynor, M. R., Cliff, A. D., Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg, McCann, Clare and The (COG-UK) Consortium, (2022) Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020–December 2021. Epidemiology and Infection, 150. e145. ISSN 0950-2688

spatial-growth-rate-of-emerging-sars-cov-2-lineages-in-england-september-2020-december-2021.pdf - Published Version
Available under License Creative Commons Attribution 4.0.

Download (930kB) | Preview
Official URL:


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.

Item Type: Article
Additional Information: Matthew Bashton, Andrew Nelson, Clare McCann, Greg Young and Darren Smith are members of the COVID-19 Genomics UK consortium.
Uncontrolled Keywords: COVID-19/epidemiology, Disease Outbreaks, England/epidemiology, Humans, SARS-CoV-2/genetics
Subjects: A300 Clinical Medicine
B100 Anatomy, Physiology and Pathology
Department: Faculties > Health and Life Sciences > Applied Sciences
Depositing User: Rachel Branson
Date Deposited: 22 Feb 2023 09:38
Last Modified: 22 Feb 2023 10:12

Actions (login required)

View Item View Item


Downloads per month over past year

View more statistics