Extending the R number by applying hyperparameters of Log Gaussian Cox process models in an epidemiological context to provide insights into COVID-19 positivity in the City of Edinburgh and in students residing at Edinburgh University

Laxton, M. R. , Nightingale, G., Lindgren, F., Sivakumaran, A. and Othieno, R. (2023) Extending the R number by applying hyperparameters of Log Gaussian Cox process models in an epidemiological context to provide insights into COVID-19 positivity in the City of Edinburgh and in students residing at Edinburgh University. PLoS ONE, 18(11), e0291348. (doi: 10.1371/journal.pone.0291348) (PMID:37988358) (PMCID:PMC10662770)

Abstract

The impact of the COVID-19 pandemic on University students has been a topic of fiery debate and of public health research. This study demonstrates the use of a combination of spatiotemporal epidemiological models to describe the trends in COVID-19 positive cases on spatial, temporal and spatiotemporal scales. In addition, this study proposes new epidemiological metrics to describe the connectivity between observed positivity; an analogous metric to the R number in conventional epidemiology. The proposed indices, Rspatial, Rspatiotemporal and Rscaling will aim to improve the characterisation of the spread of infectious disease beyond that of the COVID-19 framework and as a result inform relevant public health policy. Apart from demonstrating the application of the novel epidemiological indices, the key findings in this study are: firstly, there were some Intermediate Zones in Edinburgh with noticeably high levels of COVID-19 positivity, and that the first outbreak during the study period was observed in Dalry and Fountainbridge. Secondly, the estimation of the distance over which the COVID-19 counts at the halls of residence are spatially correlated (or related to each other) was found to be 0.19km (0.13km to 0.27km) and is denoted by the index, Rspatial. This estimate is useful for public health policy in this setting, especially with contact tracing. Thirdly, the study indicates that the association between the surrounding community level of COVID-19 positivity (Intermediate Zones in Edinburgh) and that of the University of Edinburgh’s halls of residence was not statistically significant. Fourthly, this study reveals that relatively high levels of COVID-19 positivity were observed for halls for which higher COVID-19 fines were issued (Spearman’s correlation coefficient = 0.34), and separately, for halls which were non-ensuite relatively to those which were not (Spearman’s correlation coefficient = 0.16). Finally, Intermediate Zones with the highest positivity were associated with student residences that experienced relatively high COVID-19 positivity (Spearman’s correlation coefficient = 0.27).

• Item Type: Articles
• Additional Information: Funding: Funding was obtained by GN from the Edinburgh Futures Institute only for the analysis of the data. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Laxton, Megan

Creator Roles

Laxton, M.: Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Visualization, Writing – original draft, Writing – review and editing

• Authors: Laxton, M. R., Nightingale, G., Lindgren, F., Sivakumaran, A., and Othieno, R.
• College/School: College of Science and Engineering > School of Mathematics and Statistics
• Journal Name: PLoS ONE
• Publisher: Public Library of Science
• ISSN: 1932-6203
• ISSN (Online): 1932-6203
• Copyright Holders: Copyright: © 2023 Laxton et al.
• First Published: First published in PLoS ONE 18(11): e0291348
• Publisher Policy: Reproduced under a Creative Commons licence