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 dynamicsuse asterix (*) to get italics

E.D. Moss, S.P. Rushton, P. Baker, M. Bashton, M.R. Crown, R.N. dos Santos, A. Nelson, S.J. O’Brien, Z. Richards, R.A. Sanderson, W.C. Yew, G.R. Young, C.M. McCann, D.L. SmithPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

2024

<h4>Background</h4> <p>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.</p> <h4>Methods</h4> <p>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").</p> <h4>Results</h4> <p>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.</p> <h4>Discussion</h4> <p>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.</p>

https://doi.org/10.25405/data.ncl.23815077You should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https://

https://doi.org/10.25405/data.ncl.23815077You should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https://

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COVID-19, variant, spatio-temporal models, non-pharmaceutical interventions, local transmission

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Epidemiology, Microbiology of infections, One Health, Viruses

Cyril Caminade [cyril.caminade@liverpool.ac.uk] suggested: My apologies, too busy and I already have other reviews to do., Cyril Caminade [cyril.caminade@liverpool.ac.uk] suggested: A few potential reviewers:, Cyril Caminade [cyril.caminade@liverpool.ac.uk] suggested: Francesco Sera - francesco.sera@lshtm.ac.uk, Cyril Caminade [cyril.caminade@liverpool.ac.uk] suggested: Liam Brierley - Liam.Brierley@liverpool.ac.uk, Cyril Caminade [cyril.caminade@liverpool.ac.uk] suggested: Maaike VanGerwen - maaike.vangerwen@mountsinai.org, Cyril Caminade [cyril.caminade@liverpool.ac.uk] suggested: Weilang Tang - twl-sxyz@163.com, Kevin Jean [kevin.jean@lecnam.net] suggested: Cher Jean-François, , Kevin Jean [kevin.jean@lecnam.net] suggested: Merci pour cette proposition, mais je suis dans une période très chargée (avec notamment une audition à préparer mais je crois que tu es au courant !) et j'ai peur de ne pas pouvoir reviewer ce papier dans un temps raisonnable. , Kevin Jean [kevin.jean@lecnam.net] suggested: Je te suggères de contacter des membres de l'équipe de Simon Cauchemez qui ont réalisé un travail proche (https://pubmed.ncbi.nlm.nih.gov/35476520/):, Kevin Jean [kevin.jean@lecnam.net] suggested: juliette.paireau@pasteur.fr, Kevin Jean [kevin.jean@lecnam.net] suggested: "Nathanael HOZÉ" <nathanael.hoze@pasteur.fr>, Kevin Jean [kevin.jean@lecnam.net] suggested: Amitiés, Kevin Jean [kevin.jean@lecnam.net] suggested: Kévin, Liam Brierley [liam.brierley@liverpool.ac.uk] suggested: Thank you for the invitation to review this manuscript. At this time I'm unable to commit to reviewing, but you may try contacting the following:, Liam Brierley [liam.brierley@liverpool.ac.uk] suggested: Andrew Hayward (a.hayward@ucl.ac.uk), Liam Brierley [liam.brierley@liverpool.ac.uk] suggested: Garyfallos Konstantinoudis (g.konstantinoudis@imperial.ac.uk), Samuel Alizon suggested: Désolé, trop de revues en ce moment (et je tente d'arrêter les infections respiratoires). , Samuel Alizon suggested: Éventuellement Bastien Reyné <bastien.reyne@ird.fr> pourrait être intéressé No need for them to be recommenders of PCIInfections. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct

2023-08-08 15:28:11

Jean-Francois Guégan

Samuel Alizon, Anonymous, Olivier Supplisson