Quantitative Biology

Epidemic models play a key role in understanding and responding to the emerging COVID-19 pandemic. Widely used compartmental models are static and are of limited use to evaluate intervention strategies with the emerging pandemic. Applying the technology of data assimilation, we propose a Bayesian updating approach for estimating epidemiological parameters using observable information for the purpose of assessing the impacts of different intervention strategies. We adopt a concise renewal model and propose new parameters by disentangling the reduction of instantaneous reproduction number Rt into mitigation and suppression factors for quantifying intervention impacts at a finer granularity. Then we developed a data assimilation framework for estimating these parameters including constructing an observation function and developing a Bayesian updating scheme. A statistical analysis framework is then built to quantify the impact of intervention strategies by monitoring the evolution of these estimated parameters. By Investigating the impacts of intervention measures of European countries, the United States and Wuhan with the framework, we reveal the effects of interventions in these countries and the resurgence risk in the USA.

Forecasting models have been influential in shaping decision-making in the COVID-19 pandemic. However, there is concern that their predictions may have been misleading. Here, we dissect the predictions made by four models for the daily COVID-19 death counts between March 25 and June 5 in New York state, as well as the predictions of ICU bed utilisation made by the influential IHME model. We evaluated the accuracy of the point estimates and the accuracy of the uncertainty estimates of the model predictions. First, we compared the "ground truth" data sources on daily deaths against which these models were trained. Three different data sources were used by these models, and these had substantial differences in recorded daily death counts. Two additional data sources that we examined also provided different death counts per day. For accuracy of prediction, all models fared very poorly. Only 10.2% of the predictions fell within 10% of their training ground truth, irrespective of distance into the future. For accurate assessment of uncertainty, only one model matched relatively well the nominal 95% coverage, but that model did not start predictions until April 16, thus had no impact on early, major decisions. For ICU bed utilisation, the IHME model was highly inaccurate; the point estimates only started to match ground truth after the pandemic wave had started to wane. We conclude that trustworthy models require trustworthy input data to be trained upon. Moreover, models need to be subjected to prespecified real time performance tests, before their results are provided to policy makers and public health officials.

In a pandemic like Covid-19, there are many countries of lower-earning cannot provide a complete locked-down within the duration of the detected case. The locked-down may result in famine throughout the region of underdeveloped countries after the outbreak. So, a conjectural setup of an epidemic has been studied by applying specific period of locked-down (30 days) in 5 different scenarios. The stochastic approach to the SEIR (Susceptible, Exposed, Infected and Recovered) model has been used to evaluate the dynamics and the effects of locked-down. It is observed that there exist a suitable period to apply locked-down where more susceptible escape from the infection. The effect of the early (as soon as the infected case detected) and late (with respect to the estimated peak of detected cases for no locked-down) implementation of the locked-down has also been studied and found that the late implementation of locked-down will take the least time to end the epidemic. The CFR (Case Fatality Rate) has also been found to be varied from 7.55 to 8.02 for all the considered scenarios.

In this paper, we introduce a new control-theoretic paradigm for mitigating the spread of a virus. To this end, our discrete-time controller, aims to reduce the number of new daily deaths, and consequently, the cumulative number of deaths. In contrast to much of the existing literature, we do not rely on a potentially complex virus transmission model whose equations must be customized to the "particulars" of the pandemic at hand. For new viruses such as Covid-19, the epidemiology driving the modelling process may not be well known and model estimation with limited data may be unreliable. With this motivation in mind, the new paradigm described here is data-driven and, to a large extent, we avoid modelling difficulties by concentrating on just two key quantities which are common to pandemics: the doubling time, denoted by d(k) and the peak day denoted by θ(k) . Our numerical studies to date suggest that our appealingly simple model can provide a reasonable fit to real data. Given that time is of the essence during the ongoing global health crisis, the intent of this paper is to introduce this new paradigm to control practitioners and describe a number of new research directions suggested by our current results.

The ongoing Coronavirus Disease 2019 (COVID-19) pandemic threatens the health of humans and causes great economic losses. Predictive modelling and forecasting the epidemic trends are essential for developing countermeasures to mitigate this pandemic. We develop a network model, where each node represents an individual and the edges represent contacts between individuals where the infection can spread. The individuals are classified based on the number of contacts they have each day (their node degrees) and their infection status. The transmission network model was respectively fitted to the reported data for the COVID-19 epidemic in Wuhan (China), Toronto (Canada), and the Italian Republic using a Markov Chain Monte Carlo (MCMC) optimization algorithm. Our model fits all three regions well with narrow confidence intervals and could be adapted to simulate other megacities or regions. The model projections on the role of containment strategies can help inform public health authorities to plan control measures.

In this paper, we introduce a novel modeling framework for incorporating fear of infection and frustration with social distancing into disease dynamics. We show that the resulting SEIR behavior-perception model has three principal modes of qualitative behavior---no outbreak, controlled outbreak, and uncontrolled outbreak. We also demonstrate that the model can produce transient and sustained waves of infection consistent with secondary outbreaks. We fit the model to cumulative COVID-19 case and mortality data from several regions. Our analysis suggests that regions which experience a significant decline after the first wave of infection, such as Canada and Israel, are more likely to contain secondary waves of infection, whereas regions which only achieve moderate success in mitigating the disease's spread initially, such as the United States, are likely to experience substantial secondary waves or uncontrolled outbreaks.

We derive both the finite and infinite population spatial replicator dynamics as the fluid limit of a stochastic cellular automaton. The infinite population spatial replicator is identical to the model used by Vickers and our derivation justifies the addition of a diffusion to the replicator. The finite population form generalizes the results by Durett and Levin on finite spatial replicator games. We study the differences in the two equations as they pertain to a one-dimensional rock-paper-scissors game.

This work is devoted to the study of a stochastic logistic growth model with and without the Allee effect. Such a model describes the evolution of a population under environmental stochastic fluctuations and is in the form of a stochastic differential equation driven by multiplicative Gaussian noise. With the help of the associated Fokker-Planck equation, we analyze the population extinction probability and the probability of reaching a large population size before reaching a small one. We further study the impact of the harvest rate, noise intensity, and the Allee effect on population evolution. The analysis and numerical experiments show that if the noise intensity and harvest rate are small, the population grows exponentially, and upon reaching the carrying capacity, the population size fluctuates around it. In the stochastic logistic-harvest model without the Allee effect, when noise intensity becomes small (or goes to zero), the stationary probability density becomes more acute and its maximum point approaches one. However, for large noise intensity and harvest rate, the population size fluctuates wildly and does not grow exponentially to the carrying capacity. So as far as biological meanings are concerned, we must catch at small values of noise intensity and harvest rate. Finally, we discuss the biological implications of our results.

A mathematical model for estimating the risk of airborne transmission of a respiratory infection such as COVID-19, is presented. The model employs basic concepts from fluid dynamics and incorporates the known scope of factors involved in the airborne transmission of such diseases. Simplicity in the mathematical form of the model is by design, so that it can serve not only as a common basis for scientific inquiry across disciplinary boundaries, but also be understandable by a broad audience outside science and academia. The caveats and limitations of the model are discussed in detail. The model is used to assess the protection from transmission afforded by face coverings made from a variety of fabrics. The reduction in transmission risk associated with increased physical distance between the host and susceptible is also quantified by coupling the model with available data on scalar dispersion in canonical flows. Finally, the effect of the level of physical activity (or exercise intensity) of the host and the susceptible in enhancing transmission risk, is also assessed.

This study describes the dynamics of COVID-19 deaths and infections via a Monte Carlo approach. The analyses include death's data from USA, Brazil, Mexico, UK, India and Russia, which comprise the four countries with the highest number of deaths/confirmed cases, as of Aug 07, 2020, according to the WHO. The Gompertz functions were fitted to the data of weekly averaged confirmed deaths per day by mapping the χ 2 values. The uncertainties, variances and covariances of the model parameters were calculated by propagation. The fitted functions for the average deaths per day for USA and India have an upward trend, with the former having a higher growth rate and quite huge uncertainties. For Mexico, UK and Russia, the fits are consistent with a slope down pattern. For Brazil we found a subtle trend down, but with significant uncertainties. The USA, UK and India data shown a first peak with a higher growth rate when compared to the second one, demonstrating the benefits of non-pharmaceutical interventions of sanitary measures and social distance flattening the curve. For USA, a third peak seems quite plausible, most likely related with the recent relaxation policies. Brazil's data are satisfactorily described by two highly overlapped Gompertz functions with similar growth rates, suggesting a two-steps process for the pandemic spreading. The 95% CI for the total number of deaths ( × 10 3 ) predicted by the model for Aug 31, 2020 are 160 to 220, 110 to 130, 59 to 62, 46.6 to 47.3, 54 to 63 and 16.0 to 16.7 for USA, Brazil, Mexico, UK, India and Russia, respectively. Our estimates for the prevalences of infections are in reasonable agreement with some preliminary reports from serological studies carried out in USA and Brazil. The method represents an effective framework to estimate the line-shape of the infection curves and the uncertainties of the relevant parameters based on the actual data.