The time-varying reproduction (Rt) provides a real-time estimate of pathogen transmissibility and may be influenced by exogenous factors such as mobility and mitigation measures which are not directly related to epidemiology parameters and observations. Meanwhile, evaluating the impacts of these factors is vital for policy makers to propose and adjust containment strategies. Here, we developed a Bayesian regression framework, EpiRegress, to provide Rt estimates and assess impacts of diverse factors on virus transmission, utilising daily case counts, mobility, and policy data. To demonstrate the method’s utility, we used simulations as well as data in four regions from the Western Pacific with periods of low COVID-19 incidence, namely: New South Wales, Australia; New Zealand; Singapore; and Taiwan, China. We found that imported cases had a limited contribution on the overall epidemic dynamics but may degrade the quality of the Rt estimate if not explicitly accounted for. We additionally demonstrated EpiRegress’s capability in nowcasting disease transmissibility before contemporaneous cases diagnosis. The approach was proved flexible enough to respond to periods of atypical local transmission during epidemic lulls and to periods of mass community transmission. Furthermore, in epidemics where travel restrictions are present, it is able to distinguish the influence of imported cases.
Introduction COVID-19 transmission within overcrowded migrant worker dormitories is an ongoing global issue. Many countries have implemented extensive control measures to prevent the entire migrant worker population from becoming infected. Here, we explore case count outcomes when utilising lockdown and testing under different testing measures and transmissibility settings. Methods We built a mathematical model which estimates transmission across 10 different blocks with 1000 individuals per block under different parameter combinations and testing conditions over the period of 1 month. We vary parameters including differences in block connectivity, underlying recovered proportion at the time of intervention, case importation rates and testing protocols using either PCR or rapid antigen testing. Results We estimate that in a relatively transmissible environment, fortnightly PCR testing at a relatively low initial recovered proportion at 40%, low connectivity where 10% of contacts occurred outside of the infected individuals’ block and high importation rate of per day, results in an average of 39 (95%Interval: 9–121) new COVID-19 cases after one month of observation. Similar results were observed for weekly rapid antigen testing at 33 (9–95) cases. Interpretation Our findings support the need for either fortnightly PCR testing or weekly rapid antigen testing in high population density environments such as migrant worker dormitories. Repeated mass testing is highly effective, preventing localized site outbreaks and reducing the need for site wide lockdowns or other extensive social distancing measures within and outside of dormitories. Funding This research is supported by DEMOS funding from Saw Swee Hock School of Public Health, National University of Singapore, the COVID-19 grant under Singapore's National Medical Research Council Centre Grant Programme – the Singapore Population Health Improvement Centre (NMRC/CG/C026/2017_NUHS) and COVID-19 Research Fund (COVID19RF-004).
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