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
This article has been Reviewed by the following groups
Discuss this preprint
Start a discussion What are Sciety discussions?Listed in
- Evaluated articles (ScreenIT)
Abstract
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.
Article activity feed
-
-
SciScore for 10.1101/2022.02.05.22269279: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Notwithstanding these caveats, four main conclusions can be drawn from our analyses. First, there was considerable spatio-temporal variation in positive SARS-CoV-2 tests across the region. Middlesbrough has the most ethnically diverse communities on Teesside with an ethnic minority population of 27.2% (29). There is a well-established …
SciScore for 10.1101/2022.02.05.22269279: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Notwithstanding these caveats, four main conclusions can be drawn from our analyses. First, there was considerable spatio-temporal variation in positive SARS-CoV-2 tests across the region. Middlesbrough has the most ethnically diverse communities on Teesside with an ethnic minority population of 27.2% (29). There is a well-established link between risk of serious disease from SARS-CoV-2 with both ethnicity (30) and deprivation (22). However, separating the possible contributions of ethnicity and deprivation on Teesside is difficult as we do not have information on the ethnic status of the individuals subject to PCR testing. Furthermore, whilst deprivation, population density, and ‘urbanness’ are strongly related, analysis of COVID-19 in Norfolk indicates that they can have independent contributions to levels of disease (31). Second, there was variation in the extent to which cases appeared spatially and temporally. Many of the more urban postcodes recorded cases earlier and records tended to expand in different directions from these foci with time. The lineages had all been recorded elsewhere in the UK before they appeared emerged on Teesside suggesting that lineages were introduced rather than arising locally. Indeed, B.1.177 emerged in Spain during summer 2020 before rapidly spreading across Europe (32). Teesside urban centres (TS1 to TS6), which function as a local transport and population hubs, may have played a role in the initiation and local spread of cases. Third, Gov...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
-
