Estimating transmission dynamics of SARS-CoV-2 at different intraspatial levels in an institutional outbreak
Introduction: Large, localised outbreaks of COVID-19 have been repeatedly reported in high-density residential institutions. Understanding the transmission dynamics will inform outbreak response and the design of living environments that are more resilient to future outbreaks. Methods: We developed...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-09-01
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| Series: | Epidemics |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1755436522000597 |
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| author | Shihui Jin Borame Lee Dickens Amy ML Quek Mikael Hartman Paul Anantharajah Tambyah Raymond Chee Seong Seet Alex R. Cook |
| author_facet | Shihui Jin Borame Lee Dickens Amy ML Quek Mikael Hartman Paul Anantharajah Tambyah Raymond Chee Seong Seet Alex R. Cook |
| author_sort | Shihui Jin |
| collection | DOAJ |
| description | Introduction: Large, localised outbreaks of COVID-19 have been repeatedly reported in high-density residential institutions. Understanding the transmission dynamics will inform outbreak response and the design of living environments that are more resilient to future outbreaks. Methods: We developed an individual-based, multilevel transmission dynamics model using case, serology and symptom data from a 60-day cluster randomised trial of prophylaxes in a densely populated foreign worker dormitory in Singapore. Using Bayesian data augmentation, we estimated the basic reproduction number and the contribution that within-room, between-level and across-block transmission made to it, and the prevalence of infection over the study period across different spatial levels. We then simulated the impact of changing the building layouts in terms of floors and blocks on outbreak size. Results: We found that the basic reproduction number was 2.76 averaged over the different putative prophylaxes, with substantial contributions due to transmission beyond the residents’ rooms. By the end of ~60 days of follow up, prevalence was 64.4 % (95 % credible interval 64.2–64.6 %). Future outbreak sizes could feasibly be halved by reducing the density to include additional housing blocks, or taller buildings, while retaining the overall number of men in the complex. Discussion: The methods discussed can potentially be utilised to estimate transmission dynamics at any high-density accommodation site with the availability of case and serology data. The restructuring of infrastructure to reduce the number of residents per room can dramatically slow down epidemics, and therefore should be considered by policymakers as a long-term intervention. |
| first_indexed | 2024-04-11T21:06:08Z |
| format | Article |
| id | doaj.art-a3356e01f4794d2abca7f2bed654f551 |
| institution | Directory Open Access Journal |
| issn | 1755-4365 |
| language | English |
| last_indexed | 2024-04-11T21:06:08Z |
| publishDate | 2022-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Epidemics |
| spelling | doaj.art-a3356e01f4794d2abca7f2bed654f5512022-12-22T04:03:21ZengElsevierEpidemics1755-43652022-09-0140100617Estimating transmission dynamics of SARS-CoV-2 at different intraspatial levels in an institutional outbreakShihui Jin0Borame Lee Dickens1Amy ML Quek2Mikael Hartman3Paul Anantharajah Tambyah4Raymond Chee Seong Seet5Alex R. Cook6Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore; Department of Statistics and Data Science, National University of Singapore, SingaporeSaw Swee Hock School of Public Health, National University of Singapore and National University Health System, SingaporeDepartment of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Division of Neurology, Department of Medicine, National University Hospital, SingaporeSaw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore; Department of Surgery, National University of Singapore, SingaporeDepartment of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, SingaporeDepartment of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Division of Neurology, Department of Medicine, National University Hospital, SingaporeSaw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore; Department of Statistics and Data Science, National University of Singapore, Singapore; Correspondence to: #10-01 Tahir Foundation Building, 12 Science Drive 2, 117549, Singapore.Introduction: Large, localised outbreaks of COVID-19 have been repeatedly reported in high-density residential institutions. Understanding the transmission dynamics will inform outbreak response and the design of living environments that are more resilient to future outbreaks. Methods: We developed an individual-based, multilevel transmission dynamics model using case, serology and symptom data from a 60-day cluster randomised trial of prophylaxes in a densely populated foreign worker dormitory in Singapore. Using Bayesian data augmentation, we estimated the basic reproduction number and the contribution that within-room, between-level and across-block transmission made to it, and the prevalence of infection over the study period across different spatial levels. We then simulated the impact of changing the building layouts in terms of floors and blocks on outbreak size. Results: We found that the basic reproduction number was 2.76 averaged over the different putative prophylaxes, with substantial contributions due to transmission beyond the residents’ rooms. By the end of ~60 days of follow up, prevalence was 64.4 % (95 % credible interval 64.2–64.6 %). Future outbreak sizes could feasibly be halved by reducing the density to include additional housing blocks, or taller buildings, while retaining the overall number of men in the complex. Discussion: The methods discussed can potentially be utilised to estimate transmission dynamics at any high-density accommodation site with the availability of case and serology data. The restructuring of infrastructure to reduce the number of residents per room can dramatically slow down epidemics, and therefore should be considered by policymakers as a long-term intervention.http://www.sciencedirect.com/science/article/pii/S1755436522000597Data augmentationTransmission dynamicsOutbreak modellingMigrant workersSARS-CoV-2 |
| spellingShingle | Shihui Jin Borame Lee Dickens Amy ML Quek Mikael Hartman Paul Anantharajah Tambyah Raymond Chee Seong Seet Alex R. Cook Estimating transmission dynamics of SARS-CoV-2 at different intraspatial levels in an institutional outbreak Epidemics Data augmentation Transmission dynamics Outbreak modelling Migrant workers SARS-CoV-2 |
| title | Estimating transmission dynamics of SARS-CoV-2 at different intraspatial levels in an institutional outbreak |
| title_full | Estimating transmission dynamics of SARS-CoV-2 at different intraspatial levels in an institutional outbreak |
| title_fullStr | Estimating transmission dynamics of SARS-CoV-2 at different intraspatial levels in an institutional outbreak |
| title_full_unstemmed | Estimating transmission dynamics of SARS-CoV-2 at different intraspatial levels in an institutional outbreak |
| title_short | Estimating transmission dynamics of SARS-CoV-2 at different intraspatial levels in an institutional outbreak |
| title_sort | estimating transmission dynamics of sars cov 2 at different intraspatial levels in an institutional outbreak |
| topic | Data augmentation Transmission dynamics Outbreak modelling Migrant workers SARS-CoV-2 |
| url | http://www.sciencedirect.com/science/article/pii/S1755436522000597 |
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