Spatial Growth Rate of Emerging SARS-CoV-2 Lineages in England, September 2020–December 2021

  1. M.R. Smallman-Raynor
  2. A.D. Cliff
  3. The COVID-19 Genomics UK (COG-UK) Consortium

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

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    Data analysis was performed in Minitab®17 (Minitab Inc., Pennsylvania) and data mapping in QGIS 3.10.14-A Coruña (QGIS.org) using Local Authority Districts (May 2021) UK and Regions (December 2020) EN shapefiles from the Office for National Statistics (ONS) [22].
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    Subject to these caveats, we have identified four AY lineages (AY.4.2, AY.43, AY.98 and AY.120 ) for which the rate of spatial growth exceeded the aggregate rate for the Delta variant. These lineages had been detected in all (AY.4.2, AY.43 and AY.98 ) or most (AY.120 ) of the local authority areas under investigation, and each had been associated with considerably more than 10,000 detections (Table 1). Table 2 summarizes the global status of these four lineages as of 9 January 2022. With the exception of the AY.43 lineage, which was prevalent in a number of European countries and associated with >267,000 detections worldwide, the majority of detections of these lineages originated from the United Kingdom. Our findings for the AY.4.2 and AY.43 lineages are consistent with their respective designations by the UK Health Security Agency as a distinct variant under investigation (VUI-21OCT-01) and a variant of concern [32, 33]. Preliminary investigations have indicated the AY.4.2 lineage to be associated with a higher growth rate and a higher household secondary attack rate, but with no significant reduction in vaccine effectiveness, as compared to the parent lineage [32, 34]. It remains to be established, however, whether the higher growth rate is due to enhanced transmissibility or is context-dependent [32, 35, 36]. Similarly, the status of the AY.43 lineage in terms of transmission advantage and/or immune escape remains to be determined, although further investigation is merite...

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  2. Version published to 10.1101/2022.02.02.22270110 on medRxiv
  3. Version published to 10.1017/s0950268822001285