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Register a new userAssessing the effectiveness of regional physical distancing measures of COVID-19 in rural regions of British Columbia
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We study the effects of physical distancing measures for the spread of COVID-19 in regional areas within British Columbia, using the reported cases of the five provincial Health Authorities. Building on the Bayesian epidemiological model of Anderson et al. (2020), we propose a hierarchical Bayesian model with time-varying regional parameters to account for the relative reduction in contact due to physical distancing and increased testing from March to December of 2020. In the absence of COVID-19 variants and vaccinations during this period, we examine the regionalized basic reproduction number, modelled prevalence, fraction of normal contacts, proportion of anticipated cases, and we observed significant differences between the provincial-wide and regional models.
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We analysed publicly available data on place of occurrence of COVID-19 deaths from national statistical agencies in the UK between March 9 2020 and February 28 2021. We introduce a modified Weibull model that describes the deaths due to COVID-19 at a national and place of occurrence level. We observe similar trends in the UK where deaths due to COVID-19 first peak in Homes, followed by Hospitals and Care Homes 1-2 weeks later in the first and second waves. This is in line with the infectious period of the disease, indicating a possible transmission vehicle between the settings. Our results show that the first wave is characterised by fast growth and a slow reduction after the peak in deaths due to COVID-19. The second and third waves have the converse property, with slow growth and a rapid decrease from the peak. This difference may result from behavioural changes in the population (social distancing, masks, etc). Finally, we introduce a double logistic model to describe the dynamic proportion of COVID-19 deaths occurring in each setting. This analysis reveals that the proportion of COVID-19 deaths occurring in Care Homes increases from the start of the pandemic and past the peak in total number of COVID-19 deaths in the first wave. After the catastrophic impact in the first wave, the proportion of COVID-19 deaths occurring in Care Homes gradually decreased from is maximum after the first wave indicating residence were better protected in the second and third waves compared to the first.
With a two-layer contact-dispersion model and data in China, we analyze the cost-effectiveness of three types of antiepidemic measures for COVID-19: regular epidemiological control, local social interaction control, and inter-city travel restriction. We find that: 1) intercity travel restriction has minimal or even negative effect compared to the other two at the national level; 2) the time of reaching turning point is independent of the current number of cases, and only related to the enforcement stringency of epidemiological control and social interaction control measures; 3) strong enforcement at the early stage is the only opportunity to maximize both antiepidemic effectiveness and cost-effectiveness; 4) mediocre stringency of social interaction measures is the worst choice. Subsequently, we cluster countries/regions into four groups based on their control measures and provide situation assessment and policy suggestions for each group.
Following the emergence of a novel coronavirus (SARS-CoV-2) and its spread outside of China, Europe has experienced large epidemics. In response, many European countries have implemented unprecedented non-pharmaceutical interventions including case isolation, the closure of schools and universities, banning of mass gatherings and/or public events, and most recently, wide-scale social distancing including local and national lockdowns. In this technical update, we extend a semi-mechanistic Bayesian hierarchical model that infers the impact of these interventions and estimates the number of infections over time. Our methods assume that changes in the reproductive number - a measure of transmission - are an immediate response to these interventions being implemented rather than broader gradual changes in behaviour. Our model estimates these changes by calculating backwards from temporal data on observed to estimate the number of infections and rate of transmission that occurred several weeks prior, allowing for a probabilistic time lag between infection and death. In this update we extend our original model [Flaxman, Mishra, Gandy et al 2020, Report #13, Imperial College London] to include (a) population saturation effects, (b) prior uncertainty on the infection fatality ratio, (c) a more balanced prior on intervention effects and (d) partial pooling of the lockdown intervention covariate. We also (e) included another 3 countries (Greece, the Netherlands and Portugal). The model code is available at https://github.com/ImperialCollegeLondon/covid19model/ We are now reporting the results of our updated model online at https://mrc-ide.github.io/covid19estimates/ We estimated parameters jointly for all M=14 countries in a single hierarchical model. Inference is performed in the probabilistic programming language Stan using an adaptive Hamiltonian Monte Carlo (HMC) sampler.
Large-scale testing is considered key to assess the state of the current COVID-19 pandemic. Yet, the link between the reported case numbers and the true state of the pandemic remains elusive. We develop mathematical models based on competing hypotheses regarding this link, thereby providing different prevalence estimates based on case numbers, and validate them by predicting SARS-CoV-2-attributed death rate trajectories. Assuming that individuals were tested based solely on a predefined risk of being infectious implies the absolute case numbers reflect the prevalence, but turned out to be a poor predictor, consistently overestimating growth rates at the beginning of two COVID-19 epidemic waves. In contrast, assuming that testing capacity is fully exploited performs better. This leads to using the percent-positive rate as a more robust indicator of epidemic dynamics, however we find it is subject to a saturation phenomenon that needs to be accounted for as the number of tests becomes larger.
We review epidemiological models for the propagation of the COVID-19 pandemic during the early months of the outbreak: from February to May 2020. The aim is to propose a methodological review that highlights the following characteristics: (i) the epidemic propagation models, (ii) the modeling of intervention strategies, (iii) the models and estimation procedures of the epidemic parameters and (iv) the characteristics of the data used. We finally selected 80 articles from open access databases based on criteria such as the theoretical background, the reproducibility, the incorporation of interventions strategies, etc. It mainly resulted to phenomenological, compartmental and individual-level models. A digital companion including an online sheet, a Kibana interface and a markdown document is proposed. Finally, this work provides an opportunity to witness how the scientific community reacted to this unique situation.
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