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 con...
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2024-09-01
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| author | Moss, E.D. Rushton, S.P. Baker, P. Bashton, M. Crown, M.R. dos Santos, R.N. Nelson, A. O’Brien, S.J. Richards, Z. Sanderson, R.A. Yew, W.C. Young, G.R. McCann, C.M. Smith, D.L. |
| author_facet | Moss, E.D. Rushton, S.P. Baker, P. Bashton, M. Crown, M.R. dos Santos, R.N. Nelson, A. O’Brien, S.J. Richards, Z. Sanderson, R.A. Yew, W.C. Young, G.R. McCann, C.M. Smith, D.L. |
| author_sort | Moss, E.D. |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-e732b683e0534a34a933f0e13c975e4a |
| institution | Kabale University |
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| language | English |
| publishDate | 2024-09-01 |
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| spelling | doaj-art-e732b683e0534a34a933f0e13c975e4a2025-02-07T10:17:17ZengPeer Community InPeer Community Journal2804-38712024-09-01410.24072/pcjournal.46110.24072/pcjournal.461Spatial 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 Moss, E.D.0https://orcid.org/0000-0001-8821-8984Rushton, S.P.1https://orcid.org/0000-0001-8443-5228Baker, P.2https://orcid.org/0000-0001-8529-2417Bashton, M.3https://orcid.org/0000-0002-6847-1525Crown, M.R.4dos Santos, R.N.5Nelson, A.6O’Brien, S.J.7https://orcid.org/0000-0003-2896-8999Richards, Z.8Sanderson, R.A.9https://orcid.org/0000-0002-9580-4751Yew, W.C.10Young, G.R.11McCann, C.M.12Smith, D.L.13https://orcid.org/0000-0003-4925-467XPopulation Health Sciences Institute, Newcastle University – Newcastle upon Tyne, UKSchool of Natural and Environmental Sciences, Newcastle University – Newcastle upon Tyne, UKSouth Tees Hospitals NHS Foundation Trust – Newcastle upon Tyne, UKHub for Biotechnology in the Built Environment, Northumbria University – Newcastle upon Tyne, UKHub for Biotechnology in the Built Environment, Northumbria University – Newcastle upon Tyne, UKDepartment of Applied Sciences, Northumbria University – Newcastle upon Tyne, UKDepartment of Applied Sciences, Northumbria University – Newcastle upon Tyne, UKSchool of Natural and Environmental Sciences, Newcastle University – Newcastle upon Tyne, UKDepartment of Applied Sciences, Northumbria University – Newcastle upon Tyne, UKSchool of Natural and Environmental Sciences, Newcastle University – Newcastle upon Tyne, UKDepartment of Applied Sciences, Northumbria University – Newcastle upon Tyne, UKHub for Biotechnology in the Built Environment, Northumbria University – Newcastle upon Tyne, UKHub for Biotechnology in the Built Environment, Northumbria University – Newcastle upon Tyne, UKHub for Biotechnology in the Built Environment, Northumbria University – Newcastle upon Tyne, UKBackground: 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. https://peercommunityjournal.org/articles/10.24072/pcjournal.461/COVID-19, variant, autoregressive model, non-pharmaceutical interventions, local restrictions |
| spellingShingle | Moss, E.D. Rushton, S.P. Baker, P. Bashton, M. Crown, M.R. dos Santos, R.N. Nelson, A. O’Brien, S.J. Richards, Z. Sanderson, R.A. Yew, W.C. Young, G.R. McCann, C.M. Smith, D.L. 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 Peer Community Journal COVID-19, variant, autoregressive model, non-pharmaceutical interventions, local restrictions |
| title | 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
|
| title_full | 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
|
| title_fullStr | 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
|
| title_full_unstemmed | 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
|
| title_short | 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
|
| title_sort | 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 |
| topic | COVID-19, variant, autoregressive model, non-pharmaceutical interventions, local restrictions |
| url | https://peercommunityjournal.org/articles/10.24072/pcjournal.461/ |
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