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. A study of the evolution of the SARS-CoV-2 virus in England between September 2020 and June 2021 finds that interventions capable of containing previous variants were insufficient to stop the more transmissible Alpha and Delta variants.
【저자키워드】 SARS-CoV-2, viral infection, Epidemiology, Evolutionary genetics, 【초록키워드】 COVID-19, Evolution, coronavirus, lockdown, variant, Delta, B.1.617.2, SARS-CoV-2 virus, Intervention, Local, severe acute respiratory syndrome Coronavirus, virus, Genomics, variants, Transmissibility, Surveillance, SARS-CoV-2 genome, Lineage, Alpha, epidemiological, Alpha variant, E484K mutation, respiratory, genomic, England, Delta variants, Analysis, leads, followed by, acute respiratory syndrome, acute respiratory syndrome coronavirus, acute respiratory syndrome coronavirus 2, SARS-CoV-2 genomes, proportions, National, jump, English, peaked, unlikely, introduced, suppressed, reveal, sustained, exceeded, declined, eliminated, the SARS-CoV-2 virus, 【제목키워드】 Epidemic, the SARS-CoV-2,