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 routine assessments of the growth of emerging SARS-CoV-2 lineages in a defined population.

Systematic surveillance of SARS-CoV-2 reveals dynamics of variant mutagenesis and transmission in a large urban population

“…Of the dominant VOCs, we noted that only a single variant was dominant at any time, as noted in other jurisdictions (Fig. 2, lower panel) 14,15 . We next assessed the transition between variants by calculating the crossover point when each subsequent dominant VOC became proportionally more of the tracked cases than the previous dominant VOC (Fig.…”

Systematic surveillance of SARS-CoV-2 reveals dynamics of variant mutagenesis and transmission in a large urban population

“…Of the dominant VOCs, we noted that only a single variant was dominant at any time, as noted in other jurisdictions (Fig. 2, lower panel) 14,15 . We next assessed the transition between variants by calculating the crossover point when each subsequent dominant VOC became proportionally more of the tracked cases than the previous dominant VOC (Fig.…”