Spatial and Temporal Epidemiology of SARS-CoV-2 Virus Lineages in Teesside, UK, in 2020: Effects of Socio-Economic Deprivation, Weather, and Lockdown on Lineage Dynamics

Background SARS-CoV-2 emerged in the UK in January 2020. The UK government introduced control measures including national ‘lockdowns’ and local ‘tiers’ in England to control virus transmission. As the outbreak continued, new variants were detected through two national monitoring programmes that conducted genomic sequencing. This study aimed to determine the effects of weather, demographic features, and national and local COVID-19 restrictions on positive PCR tests at a sub-regional scale. Methods We examined the spatial and temporal patterns of COVID-19 in the Teesside sub-region of the UK, from January to December 2020, capturing the first two waves of the epidemic. We used a combination of disease mapping and mixed-effect modelling to analyse the total positive tests, and those of the eight most common virus lineages, in response to potential infection risk factors: socio-economic deprivation, population size, temperature, rainfall, government interventions, and a government restaurant subsidy (“Eat Out to Help Out”). Results Total positive tests of SARS-CoV-2 were decreased by temperature and the first national lockdown (the only one to include school closures), while deprivation, population, the second national lockdown, and the local tiered interventions were associated with increased cases. The restaurant subsidy and rainfall had no apparent effect. The relationships between positive tests and covariates varied greatly between lineages, likely due to the strong heterogeneity in their spatial and temporal distributions. Cases during the second wave appeared to be higher in areas that recorded fewer first-wave cases, however, an additional model showed the number of first-wave cases was not predictive of second-wave cases. Discussion National and local government interventions appeared to be ineffective at the sub-regional level if they did not include school closures. Examination of viral lineages at the sub-regional scale was less useful in terms of investigating covariate associations but may be more useful for tracking spread within communities. Our study highlights the importance of understanding the effects of government interventions in local and regional contexts, and the importance of applying local restrictions appropriately within such settings. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This research was funded under COG-UK; this is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) [grant code: MC\_PC\_19027], and Genome Research Limited, operating as the Wellcome Sanger Institute. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Covid-19 Genomics UK Consortium (COG-UK) I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors