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Lineage-specific growth of SARS-CoV-2 B.1.1.7 during the English national lockdown

A new SARS-CoV-2 lineage termed B.1.1.7 (known as VOC202012/01 by Public Health England) was first observed in the U.K. on September 20 in Kent [1]. It has since spread to at least 244/317 English local authorities (based on genome sequencing data until December 13), with a particularly high prevalence in the South East of England, and contributes an ever increasing share of cases locally and nationally. This indicates increased transmissibility relative to other circulating lineages which is estimated to be 1.5-1.7 fold [2-4]. A particular concern is B.1.1.7’s rise during the period of English lockdown between November 5 and December 2 2020, during which SARS-CoV-2 case numbers were generally contracting. It is therefore an urgent question whether the relative B.1.1.7 growth was enabled by biologically increased transmissibility or whether it was facilitated by local failure of lockdown compliance.

Here we test these hypotheses using a hierarchical Bayesian model of lineage-specific spatiotemporal prevalence and R values of B.1.1.7 and other SARS-CoV-2 lineages (Methods). The model is fit to publicly available daily PCR testing data for each of 382 lower tier local authorities (LTLAs) across the U.K. during the period of September 1 to December 22, 2020, as well as aggregated weekly genome surveillance data from 317 English LTLAs (a total of 44,418 viral genomes) from COG-UK covering the period from September 21 to December 13, 2020.

We specifically investigate lineage-specific temporal R values during the period of the English lockdown. The analysis reveals that the B.1.1.7 lineage grew (R>1), while other lineages shrank (R<1) in 200/244 LTLAs. The rate at which other SARS-CoV-2 lineages contracted was similar across areas regardless of the presence of B.1.1.7, providing strong evidence that B.1.1.7 was repeatedly capable of expanding despite lockdown measures sufficient to suppress other SARS-CoV-2 lineages.


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