Epidemiology: Tracking the evolution and spread of SARS-CoV-2 in England

The rise and fall of 71 different SARS-CoV-2 lineages in England between September 2020 and June 2021, tracked by a study published in Nature, demonstrates the role of different variants during the course of the COVID-19 pandemic. In particular, the data show how, unlike other viral lineages, the Alpha variant spread during the second lockdown in autumn 2020, and how the Delta variant became dominant in the summer of 2021. The findings highlight the interplay between SARS-CoV-2 evolution and different lockdown measures in shaping the course of this pandemic.

The SARS-CoV-2 virus accumulates approximately 24 point mutations per year; characterizing new variants is an important tool for monitoring the spread of the virus and predicting what might happen in the future. To reconstruct the dynamics of the COVID-19 epidemic in the UK, Moritz Gerstung and colleagues used 280,000 viral samples sequenced by the COVID-19 Genomics UK (COG-UK) Consortium for the purpose of genomic surveillance to study the growth and spread of different SARS-CoV-2 variants in 315 English local authorities.

The rise of the more transmissible Alpha variant was associated with soaring infections in early winter of 2020, the authors report. The prominence of the Alpha variant increased when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. However, this variant was shown to be suppressed by the stringent third national lockdown in early 2021. By early summer 2021, the Delta variant became dominant, constituting approximately 98% of sampled SARS-CoV-2 genomes at the end of June. Delta variant cases continued to rise in the first two weeks of July 2021, as restrictions were relaxed, even though more than 90% of adults in England had antibodies against SARS-CoV-2 and close to 70% had received two doses of vaccination. Alpha variant cases were falling during this period. Other countries with high vaccination coverage may also experience rising cases when restrictions are lifted, the authors suggest.