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Register a new userModelling remote epidemic transmission in Western Australia and implications for pandemic response
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We develop an agent-based model of disease transmission in remote communities in Western Australia. Despite extreme isolation, we show that the movement of people amongst a large number of small but isolated communities has the effect of causing transmission to spread quickly. Significant movement between remote communities, and regional and urban centres allows for infection to quickly spread to and then among these remote communities. Our conclusions are based on two characteristic features of remote communities in Western Australia: (1) high mobility of people amongst these communities, and (2) relatively high proportion of travellers from very small communities to major population centres. In models of infection initiated in the state capital, Perth, these remote communities are collectively and uniquely vulnerable. Our model and analysis does not account for possibly heightened impact due to preexisting conditions, such additional assumptions would only make the projections of this model more dire. We advocate stringent monitoring and control of movement to prevent significant impact on the indigenous population of Western Australia.
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There is a continuing debate on relative benefits of various mitigation and suppression strategies aimed to control the spread of COVID-19. Here we report the results of agent-based modelling using a fine-grained computational simulation of the ongoing COVID-19 pandemic in Australia. This model is calibrated to match key characteristics of COVID-19 transmission. An important calibration outcome is the age-dependent fraction of symptomatic cases, with this fraction for children found to be one-fifth of such fraction for adults. We apply the model to compare several intervention strategies, including restrictions on international air travel, case isolation, home quarantine, social distancing with varying levels of compliance, and school closures. School closures are not found to bring decisive benefits, unless coupled with high level of social distancing compliance. We report several trade-offs, and an important transition across the levels of social distancing compliance, in the range between 70% and 80% levels, with compliance at the 90% level found to control the disease within 13--14 weeks, when coupled with effective case isolation and international travel restrictions.
In late 2019, a novel coronavirus, the SARS-CoV-2 outbreak was identified in Wuhan, China and later spread to every corner of the globe. Whilst the number of infection-induced deaths in Ghana, West Africa are minimal when compared with the rest of the world, the impact on the local health service is still significant. Compartmental models are a useful framework for investigating transmission of diseases in societies. To understand how the infection will spread and how to limit the outbreak. We have developed a modified SEIR compartmental model with nine compartments (CoVCom9) to describe the dynamics of SARS-CoV-2 transmission in Ghana. We have carried out a detailed mathematical analysis of the CoVCom9, including the derivation of the basic reproduction number, $mathcal{R}_{0}$. In particular, we have shown that the disease-free equilibrium is globally asymptotically stable when $mathcal{R}_{0}<1$ via a candidate Lyapunov function. Using the SARS-CoV-2 reported data for confirmed-positive cases and deaths from March 13 to August 10, 2020, we have parametrised the CoVCom9 model. The results of this fit show good agreement with data. We used Latin hypercube sampling-rank correlation coefficient (LHS-PRCC) to investigate the uncertainty and sensitivity of $mathcal{R}_{0}$ since the results derived are significant in controlling the spread of SARS-CoV-2. We estimate that over this five month period, the basic reproduction number is given by $mathcal{R}_{0} = 3.110$, with the 95% confidence interval being $2.042 leq mathcal{R}_0 leq 3.240$, and the mean value being $mathcal{R}_{0}=2.623$. Of the 32 parameters in the model, we find that just six have a significant influence on $mathcal{R}_{0}$, these include the rate of testing, where an increasing testing rate contributes to the reduction of $mathcal{R}_{0}$.
Some of the key questions of interest during the COVID-19 pandemic (and all outbreaks) include: where did the disease start, how is it spreading, who is at risk, and how to control the spread. There are a large number of complex factors driving the spread of pandemics, and, as a result, multiple modeling techniques play an increasingly important role in shaping public policy and decision making. As different countries and regions go through phases of the pandemic, the questions and data availability also changes. Especially of interest is aligning model development and data collection to support response efforts at each stage of the pandemic. The COVID-19 pandemic has been unprecedented in terms of real-time collection and dissemination of a number of diverse datasets, ranging from disease outcomes, to mobility, behaviors, and socio-economic factors. The data sets have been critical from the perspective of disease modeling and analytics to support policymakers in real-time. In this overview article, we survey the data landscape around COVID-19, with a focus on how such datasets have aided modeling and response through different stages so far in the pandemic. We also discuss some of the current challenges and the needs that will arise as we plan our way out of the pandemic.
As of July 2021, there is a continuing outbreak of the B.1.617.2 (Delta) variant of SARS-CoV-2 in Sydney, Australia. The outbreak is of major concern as the Delta variant is estimated to have twice the reproductive number to previous variants that circulated in Australia in 2020, which is worsened by low levels of acquired immunity in the population. Using a re-calibrated agent-based model, we explored a feasible range of non-pharmaceutical interventions, in terms of both mitigation (case isolation, home quarantine) and suppression (school closures, social distancing). Our nowcasting modelling indicated that the level of social distancing currently attained in Sydney is inadequate for the outbreak control. A counter-factual analysis suggested that if 80% of agents comply with social distancing, then at least a month is needed for the new daily cases to reduce from their peak to below ten. A small reduction in social distancing compliance to 70% lengthens this period to 45 days.
The spread of an epidemic process is considered in the context of a spatial SIR stochastic model that includes a parameter $0le ple 1$ that assigns weights $p$ and $1- p$ to global and local infective contacts respectively. The model was previously studied by other authors in different contexts. In this work we characterized the behavior of the system around the threshold for epidemic spreading. We first used a deterministic approximation of the stochastic model and checked the existence of a threshold value of $p$ for exponential epidemic spread. An analytical expression, which defines a function of the quotient $alpha$ between the transmission and recovery rates, is obtained to approximate this threshold. We then performed different analyses based on intensive stochastic simulations and found that this expression is also a good estimate for a similar threshold value of $p$ obtained in the stochastic model. The dynamics of the average number of infected individuals and the average size of outbreaks show a behavior across the threshold that is well described by the deterministic approximation. The distributions of the outbreak sizes at the threshold present common features for all the cases considered corresponding to different values of $alpha>1$. These features are otherwise already known to hold for the standard stochastic SIR model at its threshold, $alpha=1$: (i) the probability of having an outbreak of size $n$ goes asymptotically as $n^{-3/2}$ for an infinite system, (ii) the maximal size of an outbreak scales as $N^{2/3}$ for a finite system of size $N$.
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