Spatio-temporal epidemiology of SARS-CoV-2 virus lineages in Teesside, UK, in 2020: effects of social deprivation, weather and lockdown on lineage dynamics (preprint)

ABSTRACT

Background SARS-CoV-2 emerged in the UK in January 2020 and spread rapidly in different communities. The UK Government introduced a series of measures including national 'lockdowns' and regional 'tiers' to control virus transmission. As the outbreak continued, new variants were detected through two national disease monitoring programmes. Longitudinal records of their emergence and spread provide information with which we investigate factors affecting disease spread and the effectiveness of interventions. Methods We analysed the spatio-temporal dynamics of positive tests for COVID-19 on Teesside, UK throughout 2020. We investigated putative risk factors for infection, specifically, socio-economic deprivation, weather, and government interventions (lockdown). We used a combination of disease mapping and mixed-effect modelling to investigate the dynamics of positive tests from two sampling strategies and the spread of particular variants of the virus as they emerged on Teesside. Results SARS-CoV-2 spread was related to the extent of social deprivation, lockdown interventions and weather conditions over the period of the study. Cases in the first wave appeared to be associated with the first lockdown, but interventions had less impact on the second wave. Conclusions There was spatial and temporal heterogeneity in the distribution of different lineages, with spread faster in some lineages than others and varying across the region. Positive tests within region appeared to be related to levels of socio-economic deprivation. The interventions appeared to have different effects in the two waves of disease, and were associated with reduced numbers of records in the first wave, but having no effect during the second.