Abstract
The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.
Highlights
We use the dense genomic surveillance generated by the COVID-19 Genomics UK Consortium to
E reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021
L sub-epidemics that peaked in the early autumn of 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage
Summary
Parallel to the elimination of many formerly dominant SARS-CoV-2 lineages, a number of new variants were imported or emerged (Figure 4a) These include the VOCs B.1.351/Beta, P.1/Gamma, which carry the spike variant N501Y found in B.1.1.7/Alpha and a similar pair of mutations (K417N/T, E484K) each shown to reduce the binding affinity of antibodies from vaccine derived or convalescent sera. During the second national lockdown, Alpha grew despite falling numbers for other lineages and, Delta took hold in April and May when cases of Alpha were declining The fact that such growth was initially masked by the falling cases of dominant lineages highlights the need for dense genomic surveillance and rapid analysis to devise optimal and timely control strategies. Phylogenetic analysis of nCoV-2019 genomes. (2020). at
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