Spatio-temporal transmissibility and dispersion of SARS-CoV-2 variants and sub-variants of concern in England

The SARS-CoV-2 pandemic was characterised by continual emergence of variants. For improved future pandemic preparedness it is important to understand whether each successive variant has been more infectious and more widely spread. In this paper, we used genetic sequencing data from the COVID-19 Genomics UK Consortium in England and robust statistical models to quantify the transmissibility advantage and spatial heterogeneity of successive SARS-CoV-2 variants and their sub-variants circulating between September 2020 and December 2022. Our results show that each variant was progressively more transmissible and more heterogeneously spread. Alpha was 10-40% more transmissible than B.1.177, Delta was 40-100% more transmissible than Alpha, and Omicron was 80-120% more transmissible than the Delta variant. Progressive variants were also more spatially heterogeneous: Alpha was mostly clustered in London and Southeast England, Delta was less clustered and prevalent in both Northwest and Southeast England, while Omicron was dispersed across the country over the first six weeks of transmission. Sub-variants of the same clade didnt differ in transmissibility or spatial spread. Our method provides a tool for analysis of variant surveillance data, translatable across pathogens and settings, that can capture an emerging variant early and as part of the pandemic preparedness strategy.