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

Authors: Smallman-Raynor, M. R.;

Cliff, A. D.;

Rambaut, Andrew ;

Templeton, Kate E. ;

O'Toole, Áine Niamh ;

Colquhoun, Rachel M. ;

Hill, Verity ;

Jackson, Ben ;

McCrone, JT;

Medd, Nathan;

Scher, Emily;

Keatley, Jon-Paul;

Balcazar, Carlos E.;

Gallagher, Michael D.;

Maloney, Daniel;

Stanton, Thomas D;

Williamson, Kathleen

Source: Epidemiology and Infection

Full text

: https://doi.org/10.1017/S0950268822001285

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.

Rights

© The Author(s), 2022. Published by Cambridge University Press. This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited.

Cite as

Smallman-Raynor, M., Cliff, A., Rambaut, A., Templeton, K., O'Toole, Á., Colquhoun, R., Hill, V., Jackson, B., McCrone, J., Medd, N., Scher, E., Keatley, J., Balcazar, C., Gallagher, M., Maloney, D., Stanton, T. & Williamson, K. 2022, 'Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020–December 2021', Epidemiology and Infection, 150, pp. 1-13, article no: e145. https://doi.org/10.1017/S0950268822001285

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DOI: https://doi.org/10.1017/S0950268822001285

Repository URI: https://www.research.ed.ac.uk/en/publications/eb3c5cef-d8fd-4183-8547-7882a772a62e