Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

Abstract

SARS-CoV-2 variants of concern (VOCs) arise against the backdrop of increasingly heterogeneous human connectivity and population immunity. Through a large-scale phylodynamic analysis of 115,622 Omicron genomes, we identified >6,000 independent introductions of the antigenically distinct virus into England and reconstructed the dispersal history of resulting local transmission. Travel restrictions on southern Africa did not reduce BA.1 importation intensity as secondary hubs became major exporters. We explored potential drivers of BA.1 spread across England and discovered an early period during which viral lineage movements mainly occurred between larger cities, followed by a multi-focal spatial expansion shaped by shorter distance mobility patterns. We also found evidence that disease incidence impacted human commuting behaviours around major travel hubs. Our results offer a detailed characterisation of processes that drive the invasion of an emerging VOC across multiple spatial scales and provide unique insights on the interplay between disease spread and human mobility. Highlights Over 6,000 introductions ignited the epidemic wave of Omicron BA.1 in England Importations prior to international travel restrictions were responsible for majority of local BA.1 infections but importations continued from sources other than southern Africa Human mobility at regional and local spatial scales shaped dissemination and growth of BA.1 Changes in human commuting patterns are associated with higher case incidence in travel hubs across England