A Simulation of a COVID-19 Epidemic Based on a Deterministic SEIR Model

Solutions to SIR/SEIR epidemic models with exponential series: Numerical and non numerical approaches

This study revisits the mathematical SIR/SEIR epidemic models, aiming to introduce novel exponential-type series solutions. Beyond standard non-dimensionalization, we implement a successful rescaling technique that reduces the parameter count in classical epidemiology. Consequently, solutions for the SIR model are determined solely by the basic reproduction number and initial infected fractions. Similarly, the SEIR model requires only the transmission-to-recovery ratio and initial exposed fractions. We present both numerical and non numerical solutions, alongside elucidating the limitations on the existence of exponential-type series solutions. Our analysis reveals that these solutions are valid under two key conditions: endemic situations and early epidemic stages, where the basic reproduction number is close to one. We graphically illustrate the range of physical parameters guaranteeing the existence of non numerical exponential series solutions. However, for epidemic/pandemic outbreaks with significantly higher reproduction numbers, achieving complete convergence of the exponential series across the entire physical domain becomes impossible. In such cases, we divide the exponential series solution into two zones: from initial time to peak time and from peak time to the final epidemic time. For the first zone, where convergence is slow, we successfully employ Padé approximants to accelerate the convergence of the series. This accelerated solution is then smoothly joined to the second zone solution once the peak time is identified within the first region. The presented non numerical solutions are envisioned to serve as valuable benchmarks for testing and enhancing other numerical approaches used to solve epidemic models and their variants.

Neural parameter calibration and uncertainty quantification for epidemic forecasting

The recent COVID-19 pandemic has thrown the importance of accurately forecasting contagion dynamics and learning infection parameters into sharp focus. At the same time, effective policy-making requires knowledge of the uncertainty on such predictions, in order, for instance, to be able to ready hospitals and intensive care units for a worst-case scenario without needlessly wasting resources. In this work, we apply a novel and powerful computational method to the problem of learning probability densities on contagion parameters and providing uncertainty quantification for pandemic projections. Using a neural network, we calibrate an ODE model to data of the spread of COVID-19 in Berlin in 2020, achieving both a significantly more accurate calibration and prediction than Markov-Chain Monte Carlo (MCMC)-based sampling schemes. The uncertainties on our predictions provide meaningful confidence intervals e.g. on infection figures and hospitalisation rates, while training and running the neural scheme takes minutes where MCMC takes hours. We show convergence of our method to the true posterior on a simplified SIR model of epidemics, and also demonstrate our method's learning capabilities on a reduced dataset, where a complex model is learned from a small number of compartments for which data is available.

Overcoming bias in estimating epidemiological parameters with realistic history-dependent disease spread dynamics

Epidemiological parameters such as the reproduction number, latent period, and infectious period provide crucial information about the spread of infectious diseases and directly inform intervention strategies. These parameters have generally been estimated by mathematical models that involve an unrealistic assumption of history-independent dynamics for simplicity. This assumes that the chance of becoming infectious during the latent period or recovering during the infectious period remains constant, whereas in reality, these chances vary over time. Here, we find that conventional approaches with this assumption cause serious bias in epidemiological parameter estimation. To address this bias, we developed a Bayesian inference method by adopting more realistic history-dependent disease dynamics. Our method more accurately and precisely estimates the reproduction number than the conventional approaches solely from confirmed cases data, which are easy to obtain through testing. It also revealed how the infectious period distribution changed throughout the COVID-19 pandemic during 2020 in South Korea. We also provide a user-friendly package, IONISE, that automates this method.

Holistic One Health Surveillance Framework: Synergizing Environmental, Animal, and Human Determinants for Enhanced Infectious Disease Management

Recent pandemics, including the COVID-19 outbreak, have brought up growing concerns about transmission of zoonotic diseases from animals to humans. This highlights the requirement for a novel approach to discern and address the escalating health threats. The One Health paradigm has been developed as a responsive strategy to confront forthcoming outbreaks through early warning, highlighting the interconnectedness of humans, animals, and their environment. The system employs several innovative methods such as the use of advanced technology, global collaboration, and data-driven decision-making to come up with an extraordinary solution for improving worldwide disease responses. This Review deliberates environmental, animal, and human factors that influence disease risk, analyzes the challenges and advantages inherent in using the One Health surveillance system, and demonstrates how these can be empowered by Big Data and Artificial Intelligence. The Holistic One Health Surveillance Framework presented herein holds the potential to revolutionize our capacity to monitor, understand, and mitigate the impact of infectious diseases on global populations.

Ontology-based taxonomical analysis of experimentally verified natural and laboratory human coronavirus hosts and its implication for COVID-19 virus origination and transmission

To fully understand COVID-19, it is critical to study all possible hosts of SARS-CoV-2 (the pathogen of COVID-19). In this work, we collected, annotated, and performed ontology-based taxonomical analysis of all the reported and verified hosts for all human coronaviruses including SARS-CoV, MERS-CoV, SARS-CoV-2, HCoV-229E, HCoV-NL63, HCoV-OC43, and HCoV-HKU1. A total of 37 natural hosts and 19 laboratory animal hosts of human coronaviruses were identified based on experimental evidence. Our analysis found that all the verified susceptible natural and laboratory animals belong to therian mammals. Specifically, these 37 natural therian hosts include one wildlife marsupial mammal (i.e., Virginia opossum) and 36 Eutheria mammals (a.k.a. placental mammals). The 19 laboratory animal hosts are also classified as therian mammals. The mouse models with genetically modified human ACE2 or DPP4 were more susceptible to virulent human coronaviruses with clear symptoms, suggesting the critical role of ACE2 and DPP4 to coronavirus virulence. Coronaviruses became more virulent and adaptive in the mouse hosts after a series of viral passages in the mice, providing clue to the possible coronavirus origination. The Huanan Seafood Wholesale Market animals identified early in the COVID-19 outbreak were also systematically analyzed as possible COVID-19 hosts. To support knowledge standardization and query, the annotated host knowledge was modeled and represented in the Coronavirus Infectious Disease Ontology (CIDO). Based on our and others' findings, we further propose a MOVIE model (i.e., Multiple-Organism viral Variations and Immune Evasion) to address how viral variations in therian animal hosts and the host immune evasion might have led to dynamic COVID-19 pandemic outcomes.

The impact of non-pharmaceutical interventions on the spread of COVID-19 in Saudi Arabia: Simulation approach

Objectives

This paper aims to measure the impact of the implemented nonpharmaceutical interventions (NPIs) in the Kingdom of Saudi Arabia (KSA) during the pandemic using simulation modeling.

Methods

To measure the impact of NPI, a hybrid agent-based and system dynamics simulation model was built and validated. Data were collected prospectively on a weekly basis. The core epidemiological model is based on a complex Susceptible-Exposed-Infectious-Recovered and Dead model of epidemic dynamics. Reverse engineering was performed on a weekly basis throughout the study period as a mean for model validation which reported on four outcomes: total cases, active cases, ICU cases, and deaths cases. To measure the impact of each NPI, the observed values of active and total cases were captured and compared to the projected values of active and total cases from the simulation. To measure the impact of each NPI, the study period was divided into rounds of incubation periods (cycles of 14 days each). The behavioral change of the spread of the disease was interpreted as the impact of NPIs that occurred at the beginning of the cycle. The behavioral change was measured by the change in the initial reproduction rate (R0).

Results

After 18 weeks of the reverse engineering process, the model achieved a 0.4 % difference in total cases for prediction at the end of the study period. The results estimated that NPIs led to 64 % change in The R0. Our breakdown analysis of the impact of each NPI indicates that banning going to schools had the greatest impact on the infection reproduction rate (24 %).

Conclusion

We used hybrid simulation modeling to measure the impact of NPIs taken by the KSA government. The finding further supports the notion that early NPIs adoption can effectively limit the spread of COVID-19. It also supports using simulation for building mathematical modeling for epidemiological scenarios.

On-site airborne pathogen detection for infection risk mitigation

Human-infecting pathogens that transmit through the air pose a significant threat to public health. As a prominent instance, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that caused the COVID-19 pandemic has affected the world in an unprecedented manner over the past few years. Despite the dissipating pandemic gloom, the lessons we have learned in dealing with pathogen-laden aerosols should be thoroughly reviewed because the airborne transmission risk may have been grossly underestimated. From a bioanalytical chemistry perspective, on-site airborne pathogen detection can be an effective non-pharmaceutic intervention (NPI) strategy, with on-site airborne pathogen detection and early-stage infection risk evaluation reducing the spread of disease and enabling life-saving decisions to be made. In light of this, we summarize the recent advances in highly efficient pathogen-laden aerosol sampling approaches, bioanalytical sensing technologies, and the prospects for airborne pathogen exposure measurement and evidence-based transmission interventions. We also discuss open challenges facing general bioaerosols detection, such as handling complex aerosol samples, improving sensitivity for airborne pathogen quantification, and establishing a risk assessment system with high spatiotemporal resolution for mitigating airborne transmission risks. This review provides a multidisciplinary outlook for future opportunities to improve the on-site airborne pathogen detection techniques, thereby enhancing the preparedness for more on-site bioaerosols measurement scenarios, such as monitoring high-risk pathogens on airplanes, weaponized pathogen aerosols, influenza variants at the workplace, and pollutant correlated with sick building syndromes.

Analytical tool for COVID-19 using an SIR model equivalent to the chain reaction equation of infection

Insights from data analysis of existing cases are important to prevent future outbreaks of coronavirus disease 2019 (COVID-19). Although mathematical models are expected to be useful for this purpose, the adequacy of reproducibility of these models is difficult to confirm because they are based on hypotheses. For example, using the time variation of the parameter of the basic reproduction number for the time variation of complex data on the number of infected persons is a change of expression and does not capture the substance of the problem. We previously showed that the simplest Susceptible, Infected, Recovered (SIR) model alone, without any complex models, exhibits acceptable reproducibility. By clarifying the rationale for this reproducibility, quantifiable characteristics regarding the infection spread, such as the duration of the pandemic and the mechanism of occurrence of several large waves, can be uncovered and this can contribute to countermeasures. Here, we show this method equals the chain reaction equation for infection, allowing the parameters (infection rate, population) of the mathematical models to be extracted from the data. Once a model that reproduces the actual situation is determined, much of the information becomes apparent. As an example, we present three characteristics of the spread of infection effective in controlling COVID-19: the time of onset of infection, the rapidity of the spread, and the time to acquisition of herd immunity. Acquiring this information is likely to increase the predictive accuracy of the model.

A comparative study of compartmental models for COVID-19 transmission in Ontario, Canada

The number of confirmed COVID-19 cases reached over 1.3 million in Ontario, Canada by June 4, 2022. The continued spread of the virus underlying COVID-19 has been spurred by the emergence of variants since the initial outbreak in December, 2019. Much attention has thus been devoted to tracking and modelling the transmission of COVID-19. Compartmental models are commonly used to mimic epidemic transmission mechanisms and are easy to understand. Their performance in real-world settings, however, needs to be more thoroughly assessed. In this comparative study, we examine five compartmental models-four existing ones and an extended model that we propose-and analyze their ability to describe COVID-19 transmission in Ontario from January 2022 to June 2022.

Population-Level Immunity for Transient Suppression of COVID-19 Waves in Japan from April 2021 to September 2022

Multiple COVID-19 waves have been observed worldwide, with varying numbers of positive cases. Population-level immunity can partly explain a transient suppression of epidemic waves, including immunity acquired after vaccination strategies. In this study, we aimed to estimate population-level immunity in 47 Japanese prefectures during the three waves from April 2021 to September 2022. For each wave, characterized by the predominant variants, namely, Delta, Omicron, and BA.5, the estimated rates of population-level immunity in the 10-64-years age group, wherein the most positive cases were observed, were 20%, 35%, and 45%, respectively. The number of infected cases in the BA.5 wave was inversely associated with the vaccination rates for the second and third injections. We employed machine learning to replicate positive cases in three Japanese prefectures to validate the reliability of our model for population-level immunity. Using interpolation based on machine learning, we estimated the impact of behavioral factors and vaccination on the fifth wave of new positive cases that occurred during the Tokyo 2020 Olympic Games. Our computational results highlighted the critical role of population-level immunity, such as vaccination, in infection suppression. These findings underscore the importance of estimating and monitoring population-level immunity to predict the number of infected cases in future waves. Such estimations that combine numerical derivation and machine learning are of utmost significance for effective management of medical resources, including the vaccination strategy.

Mobility data shows effectiveness of control strategies for COVID-19 in remote, sparse and diffuse populations

Data that is collected at the individual-level from mobile phones is typically aggregated to the population-level for privacy reasons. If we are interested in answering questions regarding the mean, or working with groups appropriately modeled by a continuum, then this data is immediately informative. However, coupling such data regarding a population to a model that requires information at the individual-level raises a number of complexities. This is the case if we aim to characterize human mobility and simulate the spatial and geographical spread of a disease by dealing in discrete, absolute numbers. In this work, we highlight the hurdles faced and outline how they can be overcome to effectively leverage the specific dataset: Google COVID-19 Aggregated Mobility Research Dataset (GAMRD). Using a case study of Western Australia, which has many sparsely populated regions with incomplete data, we firstly demonstrate how to overcome these challenges to approximate absolute flow of people around a transport network from the aggregated data. Overlaying this evolving mobility network with a compartmental model for disease that incorporated vaccination status we run simulations and draw meaningful conclusions about the spread of COVID-19 throughout the state without de-anonymizing the data. We can see that towns in the Pilbara region are highly vulnerable to an outbreak originating in Perth. Further, we show that regional restrictions on travel are not enough to stop the spread of the virus from reaching regional Western Australia. The methods explained in this paper can be therefore used to analyze disease outbreaks in similarly sparse populations. We demonstrate that using this data appropriately can be used to inform public health policies and have an impact in pandemic responses.

Direct numerical solutions of the SIR and SEIR models via the Dirichlet series approach

Compartment models are implemented to understand the dynamic of a system. To analyze the models, a numerical tool is required. This manuscript presents an alternative numerical tool for the SIR and SEIR models. The same idea could be applied to other compartment models. The result starts with transforming the SIR model to an equivalent differential equation. The Dirichlet series satisfying the differential equation leads to an alternative numerical method to obtain the model's solutions. The derived Dirichlet solution not only matches the numerical solution obtained by the fourth-order Runge-Kutta method (RK-4), but it also carries the long-run behavior of the system. The SIR solutions obtained by the RK-4 method, an approximated analytical solution, and the Dirichlet series approximants are graphically compared. The Dirichlet series approximants order 15 and the RK-4 method are almost perfectly matched with the mean square error less than 2 × 10-5. A specific Dirichlet series is considered in the case of the SEIR model. The process to obtain a numerical solution is done in the similar way. The graphical comparisons of the solutions achieved by the Dirichlet series approximants order 20 and the RK-4 method show that both methods produce almost the same solution. The mean square errors of the Dirichlet series approximants order 20 in this case are less than 1.2 × 10-4.

A simulation of undiagnosed population and excess mortality during the COVID-19 pandemic

Whereas the extent of outbreak of COVID-19 is usually accessed via the number of reported cases and the number of patients succumbed to the disease, the officially recorded overall excess mortality numbers during the pandemic waves, which are significant and often followed the rise and fall of the pandemic waves, put a question mark on the above methodology. Gradually it has been recognized that estimating the size of the undiagnosed population (which includes asymptomatic cases and symptomatic cases but not reported) is also crucial. Here we used the classical mathematical SEIR model having an additional compartment, that is the undiagnosed group in addition to the susceptible, exposed, diagnosed, recovered and deceased groups, to link the undiagnosed COVID-19 cases to the reported excess mortality numbers and thereby try to know the actual size of the disease outbreak. The developed model wase successfully applied to relevant COVID-19 waves in USA (initial months of 2020), South Africa (mid of 2021) and Russia (2020–21) when a large discrepancy between the reported COVID-19 mortality and the overall excess mortality had been noticed.

Value of information analysis for pandemic response: intensive care unit preparedness at the onset of COVID-19

BACKGROUND

During the early stages of the COVID-19 pandemic, there was considerable uncertainty surrounding epidemiological and clinical aspects of SARS-CoV-2. Governments around the world, starting from varying levels of pandemic preparedness, needed to make decisions about how to respond to SARS-CoV-2 with only limited information about transmission rates, disease severity and the likely effectiveness of public health interventions. In the face of such uncertainties, formal approaches to quantifying the value of information can help decision makers to prioritise research efforts.

METHODS

In this study we use Value of Information (VoI) analysis to quantify the likely benefit associated with reducing three key uncertainties present in the early stages of the COVID-19 pandemic: the basic reproduction number ([Formula: see text]), case severity (CS), and the relative infectiousness of children compared to adults (CI). The specific decision problem we consider is the optimal level of investment in intensive care unit (ICU) beds. Our analysis incorporates mathematical models of disease transmission and clinical pathways in order to estimate ICU demand and disease outcomes across a range of scenarios.

RESULTS

We found that VoI analysis enabled us to estimate the relative benefit of resolving different uncertainties about epidemiological and clinical aspects of SARS-CoV-2. Given the initial beliefs of an expert, obtaining more information about case severity had the highest parameter value of information, followed by the basic reproduction number [Formula: see text]. Resolving uncertainty about the relative infectiousness of children did not affect the decision about the number of ICU beds to be purchased for any COVID-19 outbreak scenarios defined by these three parameters.

CONCLUSION

For the scenarios where the value of information was high enough to justify monitoring, if CS and [Formula: see text] are known, management actions will not change when we learn about child infectiousness. VoI is an important tool for understanding the importance of each disease factor during outbreak preparedness and can help to prioritise the allocation of resources for relevant information.

Cost-effectiveness analysis of COVID-19 screening strategy under China's dynamic zero-case policy

This study aims to optimize the COVID-19 screening strategies under China's dynamic zero-case policy through cost-effectiveness analysis. A total of 9 screening strategies with different screening frequencies and combinations of detection methods were designed. A stochastic agent-based model was used to simulate the progress of the COVID-19 outbreak in scenario I (close contacts were promptly quarantined) and scenario II (close contacts were not promptly quarantined). The primary outcomes included the number of infections, number of close contacts, number of deaths, the duration of the epidemic, and duration of movement restriction. Net monetary benefit (NMB) and the incremental cost-benefit ratio were used to compare the cost-effectiveness of different screening strategies. The results indicated that under China's COVID-19 dynamic zero-case policy, high-frequency screening can help contain the spread of the epidemic, reduce the size and burden of the epidemic, and is cost-effective. Mass antigen testing is not cost-effective compared with mass nucleic acid testing in the same screening frequency. It would be more cost-effective to use AT as a supplemental screening tool when NAT capacity is insufficient or when outbreaks are spreading very rapidly.

Mechanistic modeling of viral particle production

Viral systems such as wild-type viruses, viral vectors, and virus-like particles are essential components of modern biotechnology and medicine. Despite their importance, the commercial-scale production of viral systems remains highly inefficient for multiple reasons. Computational strategies are a promising avenue for improving process development, optimization, and control, but require a mathematical description of the system. This article reviews mechanistic modeling strategies for the production of viral particles, both at the cellular and bioreactor scales. In many cases, techniques and models from adjacent fields such as epidemiology and wild-type viral infection kinetics can be adapted to construct a suitable process model. These process models can then be employed for various purposes such as in-silico testing of novel process operating strategies and/or advanced process control.

Real-time estimation and forecasting of COVID-19 cases and hospitalizations in Wisconsin HERC regions for public health decision making processes

BACKGROUND

The spread of the COVID-19 (SARS-CoV-2) and the surging number of cases across the United States have resulted in full hospitals and exhausted health care workers. Limited availability and questionable reliability of the data make outbreak prediction and resource planning difficult. Any estimates or forecasts are subject to high uncertainty and low accuracy to measure such components. The aim of this study is to apply, automate, and assess a Bayesian time series model for the real-time estimation and forecasting of COVID-19 cases and number of hospitalizations in Wisconsin healthcare emergency readiness coalition (HERC) regions.

METHODS

This study makes use of the publicly available Wisconsin COVID-19 historical data by county. Cases and effective time-varying reproduction number [Formula: see text] by the HERC region over time are estimated using Bayesian latent variable models. Hospitalizations are estimated by the HERC region over time using a Bayesian regression model. Cases, effective Rt, and hospitalizations are forecasted over a 1-day, 3-day, and 7-day time horizon using the last 28 days of data, and the 20%, 50%, and 90% Bayesian credible intervals of the forecasts are calculated. The frequentist coverage probability is compared to the Bayesian credible level to evaluate performance.

RESULTS

For cases and effective [Formula: see text], all three time horizons outperform the three credible levels of the forecast. For hospitalizations, all three time horizons outperform the 20% and 50% credible intervals of the forecast. On the contrary, the 1-day and 3-day periods underperform the 90% credible intervals. Questions about uncertainty quantification should be re-calculated using the frequentist coverage probability of the Bayesian credible interval based on observed data for all three metrics.

CONCLUSIONS

We present an approach to automate the real-time estimation and forecasting of cases and hospitalizations and corresponding uncertainty using publicly available data. The models were able to infer short-term trends consistent with reported values at the HERC region level. Additionally, the models were able to accurately forecast and estimate the uncertainty of the measurements. This study can help identify the most affected regions and major outbreaks in the near future. The workflow can be adapted to other geographic regions, states, and even countries where decision-making processes are supported in real-time by the proposed modeling system.

Simulating wood companies development considering the effect of ethical marketing

Dedicating oneself to a greater good is one of the secret ingredients to business success in an evolving and highly interconnected markets environment. For wood companies, this is even more needed to face the overwhelming ongoing environmental crisis affecting business practices and customers' behavior in general. To build solid reputation and increase one's presence on competing markets, wood companies should not only care about products competitiveness, but also customers' perception, environmental awareness and ethical marketing. In this article, we simulated the effect of ethical commerce on wood companies' reputation using a modified competitive and cooperative model based on differential equations considering wood type, products categories and companies brand score or reputation as function of their commitment to social and environmental causes. The qualitative analysis and results of numerical experiment show that, focusing on sharing values, and building strong relationship with customers are highly important for long-term development. Moreover, reducing environmental impact by shifting production strategy towards man-made materials could meet today customers' demands for ethically and environmentally aware manufactured wood products.

Modeling Consequences of COVID-19 and Assessing Its Epidemiological Parameters: A System Dynamics Approach

In 2020, coronavirus (COVID-19) was declared a global pandemic and it remains prevalent today. A necessity to model the transmission of the virus has emerged as a result of COVID-19's exceedingly contagious characteristics and its rapid propagation throughout the world. Assessing the incidence of infection could enable policymakers to identify measures to halt the pandemic and gauge the required capacity of healthcare centers. Therefore, modeling the susceptibility, exposure, infection, and recovery in relation to the COVID-19 pandemic is crucial for the adoption of interventions by regulatory authorities. Fundamental factors, such as the infection rate, mortality rate, and recovery rate, must be considered in order to accurately represent the behavior of the pandemic using mathematical models. The difficulty in creating a mathematical model is in identifying the real model variables. Parameters might vary significantly across models, which can result in variations in the simulation results because projections primarily rely on a particular dataset. The purpose of this work was to establish a susceptible-exposed-infected-recovered (SEIR) model describing the propagation of the COVID-19 outbreak throughout the Kingdom of Saudi Arabia (KSA). The goal of this study was to derive the essential COVID-19 epidemiological factors from actual data. System dynamics modeling and design of experiment approaches were used to determine the most appropriate combination of epidemiological parameters and the influence of COVID-19. This study investigates how epidemiological variables such as seasonal amplitude, social awareness impact, and waning time can be adapted to correctly estimate COVID-19 scenarios such as the number of infected persons on a daily basis in KSA. This model can also be utilized to ascertain how stress (or hospital capacity) affects the percentage of hospitalizations and the number of deaths. Additionally, the results of this study can be used to establish policies or strategies for monitoring or restricting COVID-19 in Saudi Arabia.

Deaths from undetected COVID-19 infections as a fraction of COVID-19 deaths can be used for early detection of an upcoming epidemic wave

With countries across the world facing repeated epidemic waves, it becomes critical to monitor, mitigate and prevent subsequent waves. Common indicators like active case numbers may not be sensitive enough in the presence of systemic inefficiencies like insufficient testing or contact tracing. Test positivity rates are sensitive to testing strategies and cannot estimate the extent of undetected cases. Reproductive numbers estimated from logarithms of new incidences are inaccurate in dynamic scenarios and not sensitive enough to capture changes in efficiencies. Systemic fatigue results in lower testing, inefficient tracing and quarantining thereby precipitating the onset of the epidemic wave. We propose a novel indicator for detecting the slippage of test-trace efficiency based on the number of deaths/hospitalizations resulting from known and hitherto unknown infections. This can also be used to forecast an epidemic wave that is advanced or exacerbated due to a drop in efficiency in situations where the testing has come down drastically and contact tracing is virtually nil as is prevalent currently. Using a modified SEIRD epidemic simulator we show that (i) Ratio of deaths/hospitalizations from an undetected infection to total deaths converges to a measure of systemic test-trace inefficiency. (ii) This index forecasts the slippage in efficiency earlier than other known metrics. (iii) Mitigation triggered by this index helps reduce peak active caseload and eventual deaths. Deaths/hospitalizations accurately track the systemic inefficiencies and detect latent cases. Based on these results we make a strong case that administrations use this metric in the ensemble of indicators. Further, hospitals may need to be mandated to distinctly register deaths/hospitalizations due to previously undetected infections. Thus the proposed metric is an ideal indicator of an epidemic wave that poses the least socio-economic cost while keeping the surveillance robust during periods of pandemic fatigue.

A probabilistic epidemiological model for infectious diseases: The case of COVID-19 at global-level

This study has developed a probabilistic epidemiological model a few weeks after the World Health Organization declared COVID-19 a pandemic (based on the little data available at that time). The aim was to assess relative risks for future scenarios and evaluate the effectiveness of different management actions for 1 year ahead. We quantified, categorized, and ranked the risks for scenarios such as business as usual, and moderate and strong mitigation. We estimated that, in the absence of interventions, COVID-19 would have a 100% risk of explosion (i.e., more than 25% infections in the world population) and 34% (2.6 billion) of the world population would have been infected until the end of simulation. We analyzed the suitability of model scenarios by comparing actual values against estimated values for the first 6 weeks of the simulation period. The results proved to be more suitable with a business-as-usual scenario in Asia and moderate mitigation in the other continents. If everything went on like this, we would have 55% risk of explosion and 22% (1.7 billion) of the world population would have been infected. Strong mitigation actions in all continents could reduce these numbers to, 7% and 3% (223 million), respectively. Although the results were based on the data available in March 2020, both the model and probabilistic approach proved to be practicable and could be a basis for risk assessment in future pandemic episodes with unknown virus, especially in the early stages, when data and literature are scarce.

Toward an efficient approximate analytical solution for 4-compartment COVID-19 fractional mathematical model

With the recent trend in the spread of coronavirus disease 2019 (Covid-19), there is a need for an accurate approximate analytical solution from which several intrinsic features of COVID-19 dynamics can be extracted. This study proposes a time-fractional model for the SEIR COVID-19 mathematical model to predict the trend of COVID-19 epidemic in China. The efficient approximate analytical solution of multistage optimal homotopy asymptotic method (MOHAM) is used to solve the model for a closed-form series solution and mathematical representation of COVID-19 model which is indeed a field where MOHAM has not been applied. The equilibrium points and basic reproduction number ( R 0 ) are obtained and the local stability analysis is carried out on the model. The behaviour of the pandemic is studied based on the data obtained from the World Health Organization. We show on tables and graphs the performance, behaviour, and mathematical representation of the various fractional-order of the model. The study aimed to expand the application areas of fractional-order analysis. The results indicate that the infected class decreases gradually until 14 October 2021, and it will still decrease slightly if people are being vaccinated. Lastly, we carried out the implementation using Maple software 2021a.

Adapting a Physical Earthquake-Aftershock Model to Simulate the Spread of COVID-19

There exists a need for a simple, deterministic, scalable, and accurate model that captures the dominant physics of pandemic propagation. We propose such a model by adapting a physical earthquake/aftershock model to COVID-19. The aftershock model revealed the physical basis for the statistical Epidemic Type Aftershock Sequence (ETAS) model as a highly non-linear diffusion process, thus permitting a grafting of the underlying physical equations into a formulation for calculating infection pressure propagation in a pandemic-type model. Our model shows that the COVID-19 pandemic propagates through an analogous porous media with hydraulic properties approximating beach sand and water. Model results show good correlations with reported cumulative infections for all cases studied. In alphabetical order, these include Austria, Belgium, Brazil, France, Germany, Italy, New Zealand, Melbourne (AU), Spain, Sweden, Switzerland, the UK, and the USA. Importantly, the model is predominantly controlled by one parameter (α), which modulates the societal recovery from the spread of the virus. The obtained recovery times for the different pandemic waves vary considerably from country to country and are reflected in the temporal evolution of registered infections. These results provide an intuition-based approach to designing and implementing mitigation measures, with predictive capabilities for various mitigation scenarios.

Coronavirus disease 2019 epidemic prediction in Shanghai under the "dynamic zero-COVID policy" using time-dependent SEAIQR model

It's urgently needed to assess the COVID-19 epidemic under the "dynamic zero-COVID policy" in China, which provides a scientific basis for evaluating the effectiveness of this strategy in COVID-19 control. Here, we developed a time-dependent susceptible-exposed-asymptomatic-infected-quarantined-removed (SEAIQR) model with stage-specific interventions based on recent Shanghai epidemic data, considering a large number of asymptomatic infectious, the changing parameters, and control procedures. The data collected from March 1st, 2022 to April 15th, 2022 were used to fit the model, and the data of subsequent 7 days and 14 days were used to evaluate the model performance of forecasting. We then calculated the effective regeneration number (R _t) and analyzed the sensitivity of different measures scenarios. Asymptomatic infectious accounts for the vast majority of the outbreaks in Shanghai, and Pudong is the district with the most positive cases. The peak of newly confirmed cases and newly asymptomatic infectious predicted by the SEAIQR model would appear on April 13th, 2022, with 1963 and 28,502 cases, respectively, and zero community transmission may be achieved in early to mid-May. The prediction errors for newly confirmed cases were considered to be reasonable, and newly asymptomatic infectious were considered to be good between April 16th to 22nd and reasonable between April 16th to 29th. The final ranges of cumulative confirmed cases and cumulative asymptomatic infectious predicted in this round of the epidemic were 26,477 ∼ 47,749 and 402,254 ∼ 730,176, respectively. At the beginning of the outbreak, R _t was 6.69. Since the implementation of comprehensive control, R _t showed a gradual downward trend, dropping to below 1.0 on April 15th, 2022. With the early implementation of control measures and the improvement of quarantine rate, recovery rate, and immunity threshold, the peak number of infections will continue to decrease, whereas the earlier the control is implemented, the earlier the turning point of the epidemic will arrive. The proposed time-dependent SEAIQR dynamic model fits and forecasts the epidemic well, which can provide a reference for decision making of the "dynamic zero-COVID policy".

Strain-stream model of epidemic spread in application to COVID-19

ABSTRACT

The recently developed model of the epidemic spread of two virus strains in a closed population is generalized to the situation typical for the couple of strains delta and omicron, when there is a high probability of omicron infection soon enough after recovering from delta infection. This model can be considered as a kind of combination of SIR and SIS models for the case of competition of two strains of the same virus with different contagiousness in a population. The obtained equations and results can be directly implemented for practical calculations of the replacement of strains of the SARS-CoV-2 virus. A comparison between the estimated replacement time and the corresponding statistics shows reasonable agreement.

Modelling the Effect of Vaccination Program and Inter-state Travel in the Spread of COVID-19 in Malaysia

A modified version of the SEIR model with the effects of vaccination and inter-state movement is proposed to simulate the spread of COVID-19 in Malaysia. A mathematical analysis of the proposed model was performed to derive the basic reproduction number. To enhance the model's forecasting capabilities, the model parameters were estimated using the Nelder-Mead simplex method by fitting the model outputs to the observed data. Our results showed a good fit between the model outputs and available data, where the model was then able to perform short-term predictions. In line with the rapid vaccination program, our model predicted that the COVID-19 cases in the country would decrease by the end of August. Furthermore, our findings indicated that relaxing travel restrictions from a highly vaccinated region to a low vaccinated region would result in an epidemic outbreak.

A swarm-optimizer-assisted simulation and prediction model for emerging infectious diseases based on SEIR

Mechanism-driven models based on transmission dynamics and statistic models driven by public health data are two main methods for simulating and predicting emerging infectious diseases. In this paper, we intend to combine these two methods to develop a more comprehensive model for the simulation and prediction of emerging infectious diseases. First, we combine a standard epidemic dynamic, the susceptible–exposed–infected–recovered (SEIR) model with population migration. This model can provide a biological spread process for emerging infectious diseases. Second, to determine suitable parameters for the model, we propose a data-driven approach, in which the public health data and population migration data are assembled. Moreover, an objective function is defined to minimize the error based on these data. Third, based on the proposed model, we further develop a swarm-optimizer-assisted simulation and prediction method, which contains two modules. In the first module, we use a level-based learning swarm optimizer to optimize the parameters required in the epidemic mechanism. In the second module, the optimized parameters are used to predicate the spread of emerging infectious diseases. Finally, various experiments are conducted to validate the effectiveness of the proposed model and method.

Infectious Disease Modeling with Socio-Viral Behavioral Aspects-Lessons Learned from the Spread of SARS-CoV-2 in a University

When it comes to understanding the spread of COVID-19, recent studies have shown that pathogens can be transmitted in two ways: direct contact and airborne pathogens. While the former is strongly related to the distancing behavior of people in society, the latter are associated with the length of the period in which the airborne pathogens remain active. Considering those facts, we constructed a compartmental model with a time-dependent transmission rate that incorporates the two sources of infection. This paper provides an analytical and numerical study of the model that validates trivial insights related to disease spread in a responsive society. As a case study, we applied the model to the COVID-19 spread data from a university environment, namely, the Institut Teknologi Bandung, Indonesia, during its early reopening stage, with a constant number of students. The results show a significant fit between the rendered model and the recorded cases of infections. The extrapolated trajectories indicate the resurgence of cases as students' interaction distance approaches its natural level. The assessment of several strategies is undertaken in this study in order to assist with the school reopening process.

COVID-19 forecasting using new viral variants and vaccination effectiveness models

Recently, a high number of daily positive COVID-19 cases have been reported in regions with relatively high vaccination rates; hence, booster vaccination has become necessary. In addition, infections caused by the different variants and correlated factors have not been discussed in depth. With large variabilities and different co-factors, it is difficult to use conventional mathematical models to forecast the incidence of COVID-19. Machine learning based on long short-term memory was applied to forecasting the time series of new daily positive cases (DPC), serious cases, hospitalized cases, and deaths. Data acquired from regions with high rates of vaccination, such as Israel, were blended with the current data of other regions in Japan such that the effect of vaccination was considered in efficient manner. The protection provided by symptomatic infection was also considered in terms of the population effectiveness of vaccination as well as the vaccination protection waning effect and ratio and infectivity of different viral variants. To represent changes in public behavior, public mobility and interactions through social media were also included in the analysis. Comparing the observed and estimated new DPC in Tel Aviv, Israel, the parameters characterizing vaccination effectiveness and the waning protection from infection were well estimated; the vaccination effectiveness of the second dose after 5 months and the third dose after two weeks from infection by the delta variant were 0.24 and 0.95, respectively. Using the extracted parameters regarding vaccination effectiveness, DPC in three major prefectures of Japan were replicated. The key factor influencing the prevention of COVID-19 transmission is the vaccination effectiveness at the population level, which considers the waning protection from vaccination rather than the percentage of fully vaccinated people. The threshold of the efficiency at the population level was estimated as 0.3 in Tel Aviv and 0.4 in Tokyo, Osaka, and Aichi. Moreover, a weighting scheme associated with infectivity results in more accurate forecasting by the infectivity model of viral variants. Results indicate that vaccination effectiveness and infectivity of viral variants are important factors in future forecasting of DPC. Moreover, this study demonstrate a feasible way to project the effect of vaccination using data obtained from other country.

Intelligent Decision-Support System for Epidemiological Diagnostics. I. A Concept of Architecture Design

The problems of decision support for epidemiological diagnostics are investigated. The basis for supporting decision-making is mathematical tools for analyzing morbidity data, as well as modeling of epidemic processes. The current state of research in this area is analyzed. The features of decision-making in epidemiology and public health are formalized. Principles for the development of an intelligent information system for decision-making support for epidemiological diagnostics are proposed. A systemic model of the system, a model of the interaction of elements of the epidemiological diagnostics system and the interaction of logical components of the information system has been developed. Taking into account the identified features of these processes, the concept of the architecture of such an intelligent information system is proposed.

Fast screening framework for infection control scenario identification

Due to the emergence of the novel coronavirus disease, many recent studies have investigated prediction methods for infectious disease transmission. This paper proposes a framework to quickly screen infection control scenarios and identify the most effective scheme for reducing the number of infected individuals. Analytical methods, as typified by the SIR model, can conduct trial-and-error verification with low computational costs; however, they must be reformulated to introduce additional constraints, and thus are inappropriate for case studies considering detailed constraint parameters. In contrast, multi-agent system (MAS) simulators introduce detailed parameters but incur high computation costs per simulation, making them unsuitable for extracting effective measures. Therefore, we propose a framework that implements an MAS for constructing a training dataset, and then trains a support vector regression (SVR) model to obtain effective measure results. The proposed framework overcomes the weaknesses of conventional methods to produce effective control measure recommendations. The constructed SVR model was experimentally verified by comparing its performance on datasets with expected and unexpected outputs. Although datasets producing an unexpected output decreased the prediction accuracy, by removing randomness from the training dataset, the accuracy of the proposed method was still high in these cases. High-precision predictions of the MAS-based simulation output were obtained for both test datasets in under one second of the computational time. Furthermore, the experimental results establish that the proposed framework can obtain intuitively correct outputs for unknown inputs, and produces sufficiently high-precision prediction with lower computation costs than an existing method.

SEIR model with unreported infected population and dynamic parameters for the spread of COVID-19

Coronavirus disease 2019 (COVID-19) is a contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that can be transmitted through human interaction. In this paper, we present a Piecewise Susceptible-Exposed-Infectious-Unreported-Removed model for infectious diseases and discuss qualitatively and quantitatively. The parameters are explored by mathematical and statistical methods. Numerical simulations of these models are performed on COVID-19 US data and Python is used in the visualization of results. Outbreak factor is generated by piecewise model to explore the future trend of the US pandemic. Several error metrics are given to discuss the accuracy of the models. The main achievement of this paper is to propose the piecewise model and find the relationship between spread of pandemic and mitigation measures to control it by observing the results of numerical simulations. Performance analysis of piecewise model is presented based on COVID-19 data obtained by 'worldmeter'.

Dynamics of a stochastic SIRS epidemic model with standard incidence and vaccination

A stochastic SIRS epidemic model with vaccination is discussed. A new stochastic threshold $ R_0^s $ is determined. When the noise is very low ($ R_0^s < 1 $), the disease becomes extinct, and if $ R_0^s > 1 $, the disease persists. Furthermore, we show that the solution of the stochastic model oscillates around the endemic equilibrium point and the intensity of the fluctuation is proportional to the intensity of the white noise. Computer simulations are used to support our findings.

Mathematical Modeling and Short-Term Forecasting of the COVID-19 Epidemic in Bulgaria: SEIRS Model with Vaccination

Data from the World Health Organization indicate that Bulgaria has the second-highest COVID-19 mortality rate in the world and the lowest vaccination rate in the European Union. In this context, to find the crucial epidemiological parameters that characterize the ongoing pandemic in Bulgaria, we introduce an extended SEIRS model with time-dependent coefficients. In addition to this, vaccination and vital dynamics are included in the model. We construct an appropriate Cauchy problem for a system of nonlinear ordinary differential equations and prove that its unique solution possesses some biologically reasonable features. Furthermore, we propose a numerical scheme and give an algorithm for the parameters identification in the obtained discrete problem. We show that the found values are close to the parameters values in the original differential problem. Based on the presented analysis, we develop a strategy for short-term prediction of the spread of the pandemic among the host population. The proposed model, as well as the methods and algorithms for parameters identification and forecasting, could be applied to COVID-19 data in every single country in the world.

Mathematical Modeling and Control of COVID-19 Using Super Twisting Sliding Mode and Nonlinear Techniques

Since the outbreak of the COVID-19 epidemic, several control strategies have been proposed. The rapid spread of COVID-19 globally, allied with the fact that COVID-19 is a serious threat to people's health and life, motivated many researchers around the world to investigate new methods and techniques to control its spread and offer treatment. Currently, the most effective approach to containing SARS-CoV-2 (COVID-19) and minimizing its impact on education and the economy remains a vaccination control strategy, however. In this paper, a modified version of the susceptible, exposed, infectious, and recovered (SEIR) model using vaccination control with a novel construct of active disturbance rejection control (ADRC) is thus used to generate a proper vaccination control scheme by rejecting those disturbances that might possibly affect the system. For the COVID-19 system, which has a unit relative degree, a new structure for the ADRC has been introduced by embedding the tracking differentiator (TD) in the control unit to obtain an error signal and its derivative. Two further novel nonlinear controllers, the nonlinear PID and a super twisting sliding mode (STC-SM) were also used with the TD to develop a new version of the nonlinear state error feedback (NLSEF), while a new nonlinear extended state observer (NLESO) was introduced to estimate the system state and total disturbance. The final simulation results show that the proposed methods achieve excellent performance compared to conventional active disturbance rejection controls.

Use of a modified SIR-V model to quantify the effect of vaccination strategies on hospital demand during the Covid-19 pandemic

A novel compartmental model that includes vaccination strategy, permanence in hospital wards and tracing of infected individuals has been implemented to forecast hospital overload caused by COVID-19 pandemics in Italy. The model parameters were calibrated according to available data on cases, hospital admissions, and number of deaths in Italy during the second wave, and were validated in the timeframe corresponding to the first successive wave where vaccination campaign was fully operational. This model allowed quantifying the decrease of hospital demand in Italy associated with the vaccination campaign. Clinical relevance This study provides evidence for the ability of deterministic SIR-based models to accurately forecast hospital demand dynamics, and support informed decisions regarding dimensioning of hospital personnel and technologies to respond to large-scale epidemics, even when vaccination campaigns are available.

A novel CO2-based demand-controlled ventilation strategy to limit the spread of COVID-19 in the indoor environment

Ventilation is of critical importance to containing COVID-19 contagion in indoor environments. Keeping the ventilation rate at high level is recommended by many guidelines to dilute virus-laden respiratory particles and mitigate airborne transmission risk. However, high ventilation rate will cause high energy use. Demand-controlled ventilation is a promising technology option for controlling indoor air quality in an energy-efficient manner. This paper proposes a novel CO2-based demand-controlled ventilation strategy to limit the spread of COVID-19 in indoor environments. First, the quantitative relationship is established between COVID-19 infection risk and average CO2 level. Then, a sufficient condition is proposed to ensure COVID-19 event reproduction number is less than 1 under a conservative consideration of the number of infectors. Finally, a ventilation control scheme is designed to make sure the above condition can be satisfied. Case studies of different indoor environments have been conducted on a testbed of a real ventilation system to validate the effectiveness of the proposed strategy. Results show that the proposed strategy can efficiently maintain the reproduction number less than 1 to limit COVID-19 contagion while saving about 30%-50% of energy compared with the fixed ventilation scheme. The proposed strategy offers more practical values compared with existing studies: it is applicable to scenarios where there are multiple infectors, and the number of infectors varies with time; it only requires CO2 sensors and does not require occupancy detection sensors. Since CO2 sensors are very mature and low-cost, the proposed strategy is suitable for mass deployment in most existing ventilation systems.

Optimal Control and Stability Analysis of an SEIR Model with Infectious Force in Latent Period

In this paper, an SEWIR epidemic model with the government control rate and infectious force in latent period is proposed. The conditions to the existence and uniqueness of disease-free and endemic equilibrium points in the SEWIR model are obtained. By using the Hurwitz criterion, the locally asymptotic stability of disease-free and endemic equilibrium points is proved. We show the global asymptotic stability of the disease-free equilibrium point by the construction of Lyapunov function and LaSalle invariance principle. The globally asymptotic stability of the endemic equilibrium is verified by numerical simulation. Several optimal control strategies are proposed on controlling infectious diseases.

Inter-Country COVID-19 Contagiousness Variation in Eight African Countries

The estimates of contiguousness parameters of an epidemic have been used for health-related policy and control measures such as non-pharmaceutical control interventions (NPIs). The estimates have varied by demographics, epidemic phase, and geographical region. Our aim was to estimate four contagiousness parameters: basic reproduction number (R₀), contact rate, removal rate, and infectious period of coronavirus disease 2019 (COVID-19) among eight African countries, namely Angola, Botswana, Egypt, Ethiopia, Malawi, Nigeria, South Africa, and Tunisia using Susceptible, Infectious, or Recovered (SIR) epidemic models for the period 1 January 2020 to 31 December 2021. For reference, we also estimated these parameters for three of COVID-19's most severely affected countries: Brazil, India, and the USA. The basic reproduction number, contact and remove rates, and infectious period ranged from 1.11 to 1.59, 0.53 to 1.0, 0.39 to 0.81; and 1.23 to 2.59 for the eight African countries. For the USA, Brazil, and India these were 1.94, 0.66, 0.34, and 2.94; 1.62, 0.62, 0.38, and 2.62, and 1.55, 0.61, 0.39, and 2.55, respectively. The average COVID-19 related case fatality rate for 8 African countries in this study was estimated to be 2.86%. Contact and removal rates among an affected African population were positively and significantly associated with COVID-19 related deaths (p-value < 0.003). The larger than one estimates of the basic reproductive number in the studies of African countries indicate that COVID-19 was still being transmitted exponentially by the 31 December 2021, though at different rates. The spread was even higher for the three countries with substantial COVID-19 outbreaks. The lower removal rates in the USA, Brazil, and India could be indicative of lower death rates (a proxy for good health systems). Our findings of variation in the estimate of COVID-19 contagiousness parameters imply that countries in the region may implement differential COVID-19 containment measures.

Set-Valued Control to COVID-19 Spread with Treatment and Limitation of Vaccination Resources

In this paper, we consider an SEIR model that describes the dynamics of the COVID-19 pandemic. Subject to this model with vaccination and treatment as controls, we formulate a control problem that aims to reduce the number of infectious individuals to zero. The novelty of this work consists of considering a more realistic control problem by adding mixed constraints to take into account the limited vaccines supply. Furthermore, to solve this problem, we use a set-valued approach combining a Lyapunov function defined in the sense of viability theory with some results from the set-valued analysis. The expressions of the control variables are given via continuous selection of an adequately designed feedback map. The main result of our study shows that even though there are limits of vaccination resources, the combination of treatment and vaccination strategies can significantly reduce the number of exposed and infectious individuals. Some numerical simulations are proposed to show the efficiency of our set-valued approach and to validate our theoretical results.

How Seasonality and Control Measures Jointly Determine the Multistage Waves of the COVID-19 Epidemic: A Modelling Study and Implications

The current novel Coronavirus Disease 2019 (COVID-19) is a multistage epidemic consisting of multiple rounds of alternating outbreak and containment periods that cannot be modeled with a conventional single-stage Suspected-Exposed-Infectious-Removed (SEIR) model. Seasonality and control measures could be the two most important driving factors of the multistage epidemic. Our goal is to formulate and incorporate the influences of seasonality and control measures into an epidemic model and interpret how these two factors interact to shape the multistage epidemic curves. New confirmed cases will be collected daily from seven Northern Hemisphere countries and five Southern Hemisphere countries from March 2020 to March 2021 to fit and validate the modified model. Results show that COVID-19 is a seasonal epidemic and that epidemic curves can be clearly distinguished in the two hemispheres. Different levels of control measures between different countries during different seasonal periods have different influences on epidemic transmission. Seasonality alone cannot cause the baseline reproduction number R0 to fall below one and control measures must be taken. A superposition of a high level of seasonality and a low level of control measures can lead to a dramatically rapid increase in reported cases.

Explainability of the COVID-19 epidemiological model with nonnegative tensor factorization

The world is witnessing the devastating effects of the COVID-19 pandemic. Each country responded to contain the spread of the virus in the early stages through diverse response measures. Interpreting these responses and their patterns globally is essential to inform future responses to COVID-19 variants and future pandemics. A stochastic epidemiological model (SEM) is a well-established mathematical tool that helps to analyse the spread of infectious diseases through communities and the effects of various response measures. However, interpreting the outcome of these models is complex and often requires manual effort. In this paper, we propose a novel method to provide the explainability of an epidemiological model. We represent the output of SEM as a tensor model. We then apply nonnegative tensor factorization (NTF) to identify patterns of global response behaviours of countries and cluster the countries based on these patterns. We interpret the patterns and clusters to understand the global response behaviour of countries in the early stages of the pandemic. Our experimental results demonstrate the advantage of clustering using NTF and provide useful insights into the characteristics of country clusters.

Parameter estimation and uncertainty quantification using information geometry

In this work, we: (i) review likelihood-based inference for parameter estimation and the construction of confidence regions; and (ii) explore the use of techniques from information geometry, including geodesic curves and Riemann scalar curvature, to supplement typical techniques for uncertainty quantification, such as Bayesian methods, profile likelihood, asymptotic analysis and bootstrapping. These techniques from information geometry provide data-independent insights into uncertainty and identifiability, and can be used to inform data collection decisions. All code used in this work to implement the inference and information geometry techniques is available on GitHub.

A Non-Uniform Continuous Cellular Automata for Analyzing and Predicting the Spreading Patterns of COVID-19

During the COVID-19 outbreak, modeling the spread of infectious diseases became a challenging research topic due to its rapid spread and high mortality rate. The main objective of a standard epidemiological model is to estimate the number of infected, suspected, and recovered from the illness by mathematical modeling. This model does not capture how the disease transmits between neighboring regions through interaction. A more general framework such as Cellular Automata (CA) is required to accommodate a more complex spatial interaction within the epidemiological model. The critical issue of modeling in the spread of diseases is how to reduce the prediction error. This research aims to formulate the influence of the interaction of a neighborhood on the spreading pattern of COVID-19 using a neighborhood frame model in a Cellular-Automata (CA) approach and obtain a predictive model for the COVID-19 spread with the error reduction to improve the model. We propose a non-uniform continuous CA (N-CCA) as our contribution to demonstrate the influence of interactions on the spread of COVID-19. The model has succeeded in demonstrating the influence of the interaction between regions on the COVID-19 spread, as represented by the coefficients obtained. These coefficients result from multiple regression models. The coefficient obtained represents the population’s behavior interacting with its neighborhood in a cell and influences the number of cases that occur the next day. The evaluation of the N-CCA model is conducted by root mean square error (RMSE) for the difference in the number of cases between prediction and real cases per cell in each region. This study demonstrates that this approach improves the prediction of accuracy for 14 days in the future using data points from the past 42 days, compared to a baseline model.

The Assessment of COVID-19 Vulnerability Risk for Crisis Management

The subject of this article is to determine COVID-19 vulnerability risk and its change over time in association with the state health care system, turnover, and transport to support the crisis management decision-making process. The aim was to determine the COVID-19 Vulnerability Index (CVI) based on the selected criteria. The risk assessment was carried out with methodology that includes the application of multicriteria analysis and spatiotemporal aspect of available data. Particularly the Spatial Multicriteria Analysis (SMCA) compliant with the Analytical Hierarchy Process (AHP), which incorporated selected population and environmental criteria were used to analyse the ongoing pandemic situation. The influence of combining several factors in the pandemic situation analysis was illustrated. Furthermore, the static and dynamic factors to COVID-19 vulnerability risk were determined to prevent and control the spread of COVID-19 at the early stage of the pandemic situation. As a result, areas with a certain level of risk in different periods of time were determined. Furthermore, the number of people exposed to COVID-19 vulnerability risk in time was presented. These results can support the decision-making process by showing the area where preventive actions should be considered.

Using the SARIMA Model to Forecast the Fourth Global Wave of Cumulative Deaths from COVID-19: Evidence from 12 Hard-Hit Big Countries

The COVID-19 pandemic is a serious threat to all of us. It has caused an unprecedented shock to the world’s economy, and it has interrupted the lives and livelihood of millions of people. In the last two years, a large body of literature has attempted to forecast the main dimensions of the COVID-19 outbreak using a wide set of models. In this paper, I forecast the short- to mid-term cumulative deaths from COVID-19 in 12 hard-hit big countries around the world as of 20 August 2021. The data used in the analysis were extracted from the Our World in Data COVID-19 dataset. Both non-seasonal and seasonal autoregressive integrated moving averages (ARIMA and SARIMA) were estimated. The analysis showed that: (i) ARIMA/SARIMA forecasts were sufficiently accurate in both the training and test set by always outperforming the simple alternative forecasting techniques chosen as benchmarks (Mean, Naïve, and Seasonal Naïve); (ii) SARIMA models outperformed ARIMA models in 47 out 48 metrics (in forecasting future values), i.e., on 97.9% of all the considered forecast accuracy measures (mean absolute error [MAE], mean absolute percentage error [MAPE], mean absolute scaled error [MASE], and the root mean squared error [RMSE]), suggesting a clear seasonal pattern in the data; and (iii) the forecasted values from SARIMA models fitted very well the observed (real-time) data for the period 21 August 2021–19 September 2021 for almost all the countries analyzed. This article shows that SARIMA can be safely used for both the short- and medium-term predictions of COVID-19 deaths. Thus, this approach can help government authorities to monitor and manage the huge pressure that COVID-19 is exerting on national healthcare systems.

Estimating surge in COVID-19 cases, hospital resources and PPE demand with the interactive and locally-informed COVID-19 Health System Capacity Planning Tool

Introduction

The COVID-19 pandemic revealed an urgent need for analytic tools to help health system leaders plan for surges in hospital capacity. Our objective was to develop a practical and locally informed Tool to help explore the effects of public health interventions on SARS-CoV-2 transmission and create scenarios to project potential surges in hospital admissions and resource demand.

Methods

Our Excel-based Tool uses a modified S(usceptible)-E(xposed)-I(nfected)-R(emoved) model with vaccination to simulate the potential spread of COVID-19 cases in the community and subsequent demand for hospitalizations, intensive care unit beds, ventilators, health care workers, and personal protective equipment. With over 40+ customizable parameters, planners can adapt the Tool to their jurisdiction and changes in the pandemic.

Results

We showcase the Tool using data for Ontario, Canada. Using healthcare utilization data to fit hospitalizations and ICU cases, we illustrate how public health interventions influenced the COVID-19 reproduction number and case counts. We also demonstrate the Tool's ability to project a potential epidemic trajectory and subsequent demand for hospital resources. Using local data, we built three planning scenarios for Ontario for a 3-month period. Our worst-case scenario accurately projected the surge in critical care demand that overwhelmed hospital capacity in Ontario during Spring 2021.

Conclusions

Our Tool can help different levels of health authorities plan their response to the pandemic. The main differentiators between this Tool and other existing tools include its ease of use, ability to build scenarios, and that it provides immediate outcomes that are ready to share with executive decision makers. The Tool is used by provincial health ministries, public health departments, and hospitals to make operational decisions and communicate possible scenarios to the public. The Tool provides educational value for the healthcare community and can be adapted for existing and emerging diseases.

You are only as safe as your riskiest contact: Effective COVID-19 vaccine distribution using local network information

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Using simulation to evaluate nomination of most popular contacts for vaccination.

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Simulating spread of COVID-19 across two contact networks among high-schoolers.

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Targeting in this way can reduce spread to the susceptible population by 20% or more.

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Results are robust in a synthetic network replicating spread in a small town.

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Results are robust across a wide range of infectiousness, and mistaken nomination.

When vaccines are limited, prior research has suggested it is most protective to distribute vaccines to the most central individuals – those who are most likely to spread the disease. But surveying the population’s social network is a costly and time-consuming endeavour, often not completed before vaccination must begin. This paper validates a local targeting method for distributing vaccines. That is, ask randomly chosen individuals to nominate for vaccination the person they are in contact with who has the most disease-spreading contacts. Even better, ask that person to nominate the next person for vaccination, and so on. To validate this approach, we simulate the spread of COVID-19 along empirical contact networks collected in two high schools, in the United States and France, pre-COVID. These weighted networks are built by recording whenever students are in close spatial proximity and facing one another. We show here that nomination of most popular contacts performs significantly better than random vaccination, and on par with strategies which assume a full survey of the population. These results are robust over a range of realistic disease-spread parameters, as well as a larger synthetic contact network of 3000 individuals.