Susceptible-exposed-infectious-recovered Research Articles

Contributing to health system resilience during pandemics via purchasing and supply strategies: an exploratory system dynamics approach

BackgroundHealth systems worldwide struggled to obtain sufficient personal protective equipment (PPE) and ventilators during the COVID-19 pandemic due to global supply chain disruptions. Our study’s aim was to create a proof-of-concept model that would simulate the effects of supply strategies under various scenarios, to ultimately help decision-makers decide on alternative supply strategies for future similar health system related crises.MethodsWe developed a system dynamics model that linked a disease transmission model structure (susceptible, exposed, infectious, recovered (SEIR)) with a model for the availability of critical supplies in hospitals; thereby connecting care demand (patients’ critical care in hospitals), with care supply (available critical equipment and supplies). To inform the model structure, we used data on critical decisions and events taking place surrounding purchase, supply, and availability of PPE and ventilators during the first phase of the COVID-19 pandemic within the English national health system. We used exploratory modelling and analysis to assess the effects of uncertainties on different supply strategies in the English health system under different scenarios. Strategies analysed were: (i) purchasing from the world market or (ii) through direct tender, (iii) stockpiling, (iv) domestic production, (v) supporting innovative supply strategies, or (vi) loaning ventilators from the private sector.ResultsWe found through our exploratory analysis that a long-lasting shortage in PPE and ventilators is likely to be apparent in various scenarios. When considering the worst-case scenario, our proof-of-concept model shows that purchasing PPE and ventilators from the world market or through direct tender have the greatest influence on reducing supply shortages, compared to producing domestically or through supporting innovative supply strategies. However, these supply strategies are affected most by delays in their shipment time or set-up.ConclusionWe demonstrated that using a system dynamics and exploratory modelling approach can be helpful in identifying the purchasing and supply chain strategies that contribute to the preparedness and responsiveness of health systems during crises. Our results suggest that to improve health systems’ resilience during pandemics or similar resource-constrained situations, purchasing and supply chain decision-makers can develop crisis frameworks that propose a plan of action and consequently accelerate and improve procurement processes and other governance processes during health-related crises; implement diverse supplier frameworks; and (re)consider stockpiling. This proof-of-concept model demonstrates the importance of including critical supply chain strategies as part of the preparedness and response activities to contribute to health system resilience.

Impact of policy incentives on technological innovation and diffusion within the new-energy vehicle industry: an ecosystem approach

ABSTRACT In the context of developing emerging industries in China, this study examines the specific effects of policy incentives on new energy vehicle (NEV) technological innovation and constructs a susceptible-exposed-infected-recovered (SEIR) infection model to simulate the diffusion of the NEV technological innovation process. The results highlight four main findings. First, an inverted U-shaped relationship exists between government-supported policies and technological innovation in NEVs. Second, regulatory policies can significantly incentivize the innovative behaviour of NEV enterprises. Third, the effects of policy incentives are more evident in the technological innovation of non-state-owned enterprises than in state-owned enterprises. Fourth, the SEIR infection model shows that policy incentives significantly accelerate the process of utilising, optimising, and replacing technologies in the technology innovation ecosystem, significantly shortening the iterative process of the entire system.

The Predicted Potential Impact of COVID-19 Pandemic on Tuberculosis Epidemic in Tamil Nadu, South India.

To estimate the prevalence and incidence of TB before and during the COVID-19 pandemic in Tamil Nadu, south India. In the present study, the effect of COVID-19 epidemiology on the TB epidemic was assessed by the SEIR (Susceptible-Exposed-Infected-Recovered), a compartmental epidemiological model. The model input parameters on compartments of TB and incidence of COVID-19 were collected from the published literature. Based on the data collected, point prevalence and incidence of TB per 100,000 population is calculated with and without COVID-19. A prediction was conducted up to 2025, trend analysis was performed, and a trend chi-square test and chi-square test of independence were used to test the difference between the prevalence with and without COVID-19. R software 2000 (R 4.0.0) was used for analysis. The TB prevalence without and with COVID-19 decreases from 289 in 2020 to 271 in 2025 and from 289 in 2020 to 269 in 2025, respectively. Similarly, the incidence of TB was decreasing from 144 in 2020 to 135 in 2025 without COVID-19 and 143 in 2020 to 134 in 2025 with COVID-19. Though the TB burden is decreasing over the years, the trend was not statistically significant (p > 0.05). With respect to the district level, the prevalence and incidence of TB with and without COVID-19 is also found to be decreasing over the years. It was also found that the difference in the prevalence and incidence of TB with and without COVID-19 was not statically significant. The results of our study shows that there was an annual decline of around 2% from 2020 to 2025 in the trend of the prevalence and incidence of TB with and without COVID-19. Overall, there is a reduction, but it was not significant, and there is no significant effect of COVID-19 on TB in Tamil Nadu.

Comparative analysis of practical identifiability methods for an SEIR model

<p>Identifiability of a mathematical model plays a crucial role in the parameterization of the model. In this study, we established the structural identifiability of a susceptible-exposed-infected-recovered (SEIR) model given different combinations of input data and investigated practical identifiability with respect to different observable data, data frequency, and noise distributions. The practical identifiability was explored by both Monte Carlo simulations and a correlation matrix approach. Our results showed that practical identifiability benefits from higher data frequency and data from the peak of an outbreak. The incidence data gave the best practical identifiability results compared to prevalence and cumulative data. In addition, we compared and distinguished the practical identifiability by Monte Carlo simulations and a correlation matrix approach, providing insights into when to use which method for other applications.</p>

Using hybrid automata to model mitigation of global disease spread via travel restriction

<abstract><p>Inspired by the COVID-19 pandemic, we build a large-scale epidemiological model that accounts for coordination between regions, each using travel restrictions in order to attempt to mitigate the spread of disease. There is currently a need for simulations of countries cooperating since travel restriction policies are typically taken without global considerations. It is possible, for instance, that a strategy which appears unfavorable to a region at some point during a pandemic might be best for containing the global spread, or that only by coordinating policies among several regions can a restriction strategy be truly effective. We use the formalism of hybrid automata to model the global disease spread among the coordinating regions. We model a connected network of coupled Susceptible-Exposed-Infected-Recovered (SEIR) models by considering a weighted directed graph with each node corresponding to a single region's disease model. The SEIR dynamics for each region admit terms for inter-regional travel determined by the graph's Laplacian that additionally accounts for travel restrictions between regions. The existence of an edge may change according to so-called guard conditions, which are triggered when the proportion of symptomatic infected individuals in a region reaches a critical value. Lastly, we run simulations in MATLAB of a global disease spreading among regions using automated travel restrictions and analyze the results.</p></abstract>

Analysis of a COVID-19 model with media coverage and limited resources.

The novel coronavirus disease (COVID-19) pandemic has profoundly impacted the global economy and human health. The paper mainly proposed an improved susceptible-exposed-infected-recovered (SEIR) epidemic model with media coverage and limited medical resources to investigate the spread of COVID-19. We proved the positivity and boundedness of the solution. The existence and local asymptotically stability of equilibria were studied and a sufficient criterion was established for backward bifurcation. Further, we applied the proposed model to study the trend of COVID-19 in Shanghai, China, from March to April 2022. The results showed sensitivity analysis, bifurcation, and the effects of critical parameters in the COVID-19 model.

Assessment of tuberculosis transmission probability in three Thai prisons based on five dynamic models.

This study aimed to assess and compare the probability of tuberculosis (TB) transmission based on five dynamic models: the Wells-Riley equation, two Rudnick & Milton-proposed models based on air changes per hour (ACH) and liters per second per person (L/s/p), the model proposed by Issarow et al, and the Applied Susceptible-Exposed-Infected-Recovered (SEIR) TB transmission model. This study also aimed to determine the impact of model parameters on such probabilities in three Thai prisons. A cross-sectional study was conducted using data from 985 prison cells. The TB transmission probability for each cell was calculated using parameters relevant to the specific model formula, and the magnitude of the model agreement was examined by Spearman's rank correlation and Bland-Altman plot. Subsequently, a multiple linear regression analysis was conducted to investigate the influence of each model parameter on the estimated probability. Results revealed that the median (Quartiles 1 and 3) of TB transmission probability among these cells was 0.052 (0.017, 0.180). Compared with the pioneered Wells-Riley's model, the remaining models projected discrepant TB transmission probability from less to more commensurate to the degree of model modification from the pioneered model as follows: Rudnick & Milton (ACH), Issarow et al., and Rudnick & Milton (L/s/p), and the applied SEIR models. The ventilation rate and number of infectious TB patients in each cell or zone had the greatest impact on the estimated TB transmission probability in most models. Additionally, the number of inmates in each cell, the area per person in square meters, and the inmate turnover rate were identified as high-impact parameters in the applied SEIR model. All stakeholders must urgently address these influential parameters to reduce TB transmission in prisons. Moreover, further studies are required to determine their relative validity in accurately predicting TB incidence in prison settings.

Exploring of Homotopy Perturbation Method (HPM) for Solving Spread of COVID-19

This article discusses the solution to the non-linear differential equation system for the spread of COVID19 with SEIR (Susceptible, Exposed, Infected, Recovered) model using the Homotopy Perturbation Method. Specifically, this article examines the impact of moving the recovered subpopulation back to the susceptible subpopulation on the spread of COVID-19 in the city of Medan. The data used is real data for the city of Medan in 2021. The results of constructing a model for the spread of COVID-19 were analyzed to obtain a disease-free critical point. By using the Next Generation Matrix method, the Basic Reproduction number R0 = 4.61 is obtained, this indicates that COVID-19 is still possible to spread in Medan City. Simulations using the Homotopy Perturbation Method numerical approach and the results compared with the Runge Kutte Order 4 method show results that accurately describe the dynamics of the spread of COVID-19 in Medan City. The very small error indicates that the Homotopy Perturbation Method is very suitable for use in solving non-linear differential equation systems, especially in the SEIRS model of the spread of COVID-19. The simulation results show that the impact of the movement of recovered sub-populations to susceptible sub-populations results in accelerated transmission of COVID-19. The greater the number of movements higher the rate of spread of COVID-19.

Selection of models and parameter estimation for monitoring the COVID-19 epidemic in Brazil via Bayesian inference

In 2019, a new strain of coronavirus led to an outbreak of disease cases named COVID-19, evolving rapidly into a pandemic. In Brazil, delayed decision making and lack of knowledge have resulted in an alarming increase in daily transmission and deaths. In this context, researchers used mathematical models to assist in determining the parameters that act in the spread of diseases, revealing containment measures. However, numerous mathematical models exist in the literature, each with specific parameters to be specified, leading to an important question about which model best represents the pandemic behavior. In this regard, this work aims to apply the Approximate Bayesian Computation method to select the best model and simultaneously estimate the parameters to resolve the abovementioned issue. The models adopted were susceptible-infected-recovered (SIR), susceptible-exposed-infected-recovered (SEIR), susceptible-infected-recovered-susceptible (SIRS), and susceptible-exposed-infected-recovered-susceptible (SEIRS). Approximate Bayesian Computation Monte Carlo Sequencing (ABC-SMC) was used to select among four competing models to represent the number of infected individuals and to estimate the model parameters based on three periods of Brazil COVID-19 data. A forecasting test was performed to test the ABC-SMC algorithm and the selected models for two months. The result was compared with the actual number of infected that were reported. Among the teste models, it was found that the ABC-SMC algorithm had a promising performance, since the data were noisy and the models could not predict all parameters.

The Potential Benefits of Delaying Seasonal Influenza Vaccine Selections for the Northern Hemisphere: A Retrospective Modeling Study in the United States.

Antigenic similarity between vaccine viruses and circulating viruses is crucial for achieving high vaccine effectiveness against seasonal influenza. New non-egg-based vaccine production technologies could revise current vaccine formulation schedules. We aim to assess the potential benefit of delaying seasonal influenza vaccine virus selection decisions. We identified seasons where season-dominant viruses presented increasing prevalence after vaccine formulation had been decided in February for the Northern Hemisphere, contributing to their antigenic discrepancy with vaccine viruses. Using a SEIR (susceptible-exposed-infectious-recovered) model of seasonal influenza in the United States, we evaluated the impact of updating vaccine decisions with more antigenically similar vaccine viruses on the influenza burden in the United States. In 2014-2015 and 2019-2020, the season-dominant A(H3N2) subclade and B/Victoria clade, respectively, presented increasing prevalence after vaccine decisions were already made for the Northern Hemisphere. Our model showed that the updated A(H3N2) vaccine could have averted 5000-65 000 influenza hospitalizations in the United States in 2014-2015, whereas updating the B/Victoria vaccine component did not substantially change influenza burden in the 2019-2020 season. With rapid vaccine production, revising current timelines for vaccine selection could result in substantial epidemiological benefits, particularly when additional data could help improve the antigenic match between vaccine and circulating viruses.

Deep reinforcement learning based medical supplies dispatching model for major infectious diseases: Case study of COVID-19

Stockpiling and scheduling plans for medical supplies represent essential preventive and control measures in major public health events. In the face of major infectious diseases, such as the novel coronavirus disease (COVID-19), the outbreak trend and variability of disease strains are often unpredictable. Hence, it is necessary to optimally adjust the prevention and control dispatching strategy according to the circumstances and outbreak locations to maintain economic development while ensuring the human health survival, however, many models in this scenario seldom consider the dynamic material prediction and the measurement of multiple costs at the same time. Taking the COVID-19 scenario as a case study, we establish a deep reinforcement learning (DRL)-based medical supplies dispatching (MSD) model for major infectious diseases, considering the volatility of the COVID-19 situation and the discrepancy between medical material demand and supply due to the high infectiousness of the Omicron series strains. The present model has three main components: 1) First, for the dynamic medical material prediction problem in complex infectious disease scenarios, taking the lifted COVID-19 lockdown scenario as an example, the modified susceptible-exposed-infected-recovered (SEIR) model was utilized to analyze the spread of the COVID-19, understand its characteristics, and map out the related medical supplies demand; 2) Second, to break away from the previous premise of only considering supply-demand, this study adds scheduling rules and cost function that weighs health and economic costs. An epidemic dispatching optimization model (Epi_DispatchOptim) was established using the OpenAI Gym toolkit to form an environment structure with virus transmission space, and emergency MSD while considering both human health and economic costs. This architecture interprets the balance between the supply-demand of medical supplies and reflects the importance of MSD in the balanced development of health and economy under the spread of infectious diseases; 3) Finally, the MSD strategy under the balance of health and economic cost is explored in Epi_DispatchOptim using reinforcement learning (RL) and the evolutionary algorithm (EA). Experiments conducted on two datasets indicate that the RL and EA reduce economic as well as health costs compared to the original environmental strategies. The above study illustrates how to use epidemiological models to predict the demand for healthcare supplies as the premise of scheduling models, and use Epi_DispatchOptim to explore the dynamic MSD decisions under mortality and economic equilibrium. In Shanghai, China, the economic cost of the exploration strategy is reduced by 27.36–27.07B compared to static scheduling, and deaths are reduced by 126–150 in 150 day compared to the no-intervention scenario. By integrating knowledge of epidemiology, optimal decision making, and economics, Epi_DispatchOptim further constructs epidemiological models, cost functions, state-action spaces, and other modules to assist public health decision makers in adopting appropriate MSD strategies for major public health event.

Envisioning urban environments resilient to vector-borne diseases: a protocol to study dengue in Vietnam

Transmitted primarily by Aedes aegypti (Ae. aegypti) and Aedes albopictus (Ae. albopictus), arboviral diseases pose a major global public health threat. Dengue, chikungunya, and Zika are increasingly prevalent in Southeast Asia. Among other arboviruses, dengue and Zika are becoming more common in Central and South America. Given human encroachment into previously uninhabited, often deforested areas, to provide new housing in regions of population expansion, conceptualizing built urban environments in a novel way is urgently needed to safeguard against the growing climate change-driven threat of vector-borne diseases. By understanding the spread from a One Health perspective, enhanced control and prevention can be achieved. This is particularly important considering that climate change is likely to significantly impact the persistence of ponded water where mosquitoes breed due to increasing temperature and shifting rainfall patterns with regard to magnitude, duration, frequency, and season. Models can incorporate aquatic mosquito stages and adult spatial dynamics when habitats are heterogeneously available, thereby including dispersal and susceptible-exposed-infected-recovered (SEIR) epidemiology. Coupled with human population distribution (density, locations), atmospheric conditions (air temperature, precipitation), and hydrological conditions (soil moisture distribution, ponding persistence in topographic depressions), modeling has improved predictive ability for infection rates. However, it has not informed interventional approaches from an urban environment perspective which considers the role of ponds/lakes that support green spaces, the density of population that enables rapid spread of disease, and varying micro-habitats for various mosquito stages under climate change. Here, for an example of dengue in Vietnam, a preventive and predictive approach to design resilient urban environments is proposed, which uses data from rapidly expanding metropolitan communities to learn continually. This protocol deploys computational approaches including simulation and machine learning/artificial intelligence, underpinned by surveillance and medical data for validation and adaptive learning. Its application may best inform urban planning in low-middle income countries in tropical zones where arboviral pathogens are prevalent.

A Multi-Objective Simulated Annealing Local Search Algorithm in Memetic CENSGA: Application to Vaccination Allocation for Influenza

Flu vaccine allocation is of great importance for safeguarding public health and mitigating the impact of influenza outbreaks. In this regard, decision-makers face multifaceted challenges, including limited vaccine supply, targeting vulnerable people, adapting to regional variations, ensuring fairness in distribution, and promoting public trust. The objective of this work is to address the vaccination allocation problem by introducing a novel optimization scheme with the simulated annealing (SA) algorithm. A dual-objective model is developed to both manage infection rates and minimize the unit cost of the vaccination campaign. The proposed approach is designed to promote convergence toward the best Pareto front in multi-objective optimization, wherein SA attempts to embed diversity and uniformity within a memetic version of the controlled elitism nondominated sorting genetic algorithm (CENSGA). To model the underlying vaccination allocation problem, the dynamics of the disease are described using the susceptible–exposed–infectious–recovered (SEIR) epidemiological model to better express hidden flu characteristics. This model specifically analyzes the effects of pulsive vaccination allocation in two phases aiming to minimize the number of infected individuals to an acceptable level in a finite amount of time, which can help in stabilizing the model against sudden flu endemics over the long run. The computational experiments show that the proposed algorithm effectively explores the extensive search space of the vaccination allocation problem. The results of the suggested framework indicate that the obtained Pareto front best represents complete vaccination campaigns. The findings of this research can help in evidence-based decision making that can optimize flu vaccine distribution, contribute to the prevention of illness and reduction in hospitalizations, and potentially save countless lives.

Topic and Trend Analysis of Weibo Discussions About COVID-19 Medications Before and After China's Exit from the Zero-COVID Policy: Retrospective Infoveillance Study.

After 3 years of its zero-COVID policy, China lifted its stringent pandemic control measures with the announcement of the 10 new measures on December 7, 2022. Existing estimates suggest 90%-97% of the total population was infected during December. This change created a massive demand for COVID-19 medications and treatments, either modern medicines or traditional Chinese medicine (TCM). This study aimed to explore (1) how China's exit from the zero-COVID policy impacted media and the public's attention to COVID-19 medications; (2) how social COVID-19 medication discussions were related to existing model estimates of daily cases during that period; (3) what the diversified themes and topics were and how they changed and developed from November 1 to December 31, 2022; and (4) which topics about COVID-19 medications were focused on by mainstream and self-media accounts during the exit. The answers to these questions could help us better understand the consequences of exit strategies and explore the utilities of Sina Weibo data for future infoveillance studies. Using a scrapper for data retrieval and the structural topic modeling (STM) algorithm for analysis, this study built 3 topic models (all data, before a policy change, and after a policy change) of relevant discussions on the Chinese social media platform Weibo. We compared topic distributions against existing estimates of daily cases and between models before and after the change. We also compared proportions of weibos published by mainstream versus self-media accounts over time on different topics. We found that Weibo discussions shifted sharply from concerns of social risks (case tracking, governmental regulations, etc) to those of personal risks (symptoms, purchases, etc) surrounding COVID-19 infection after the exit from the zero-COVID policy. Weibo topics of "symptom sharing" and "purchase and shortage" of modern medicines correlated more strongly with existing susceptible-exposed-infected-recovered (SEIR) model estimates compared to "TCM formulae" and other topics. During the exit, mainstream accounts showed efforts to specifically engage in topics related to worldwide pandemic control policy comparison and regulations about import and reimbursement of medications. The exit from the zero-COVID policy in China was accompanied by a sudden increase in social media discussions about COVID-19 medications, the demand for which substantially increased after the exit. A large proportion of Weibo discussions were emotional and expressed increased risk concerns over medication shortage, unavailability, and delay in delivery. Topic keywords showed that self-medication was sometimes practiced alone or with unprofessional help from others, while mainstream accounts also tried to provide certain medication instructions. Of the 16 topics identified in all 3 STM models, only "symptom sharing" and "purchase and shortage" showed a considerable correlation with SEIR model estimates of daily cases. Future studies could consider topic exploration before conducting predictive infoveillance analysis, even with narrowly defined search criteria with Weibo data.

To Evaluate The Impact Of Expansionary Fiscal Policy In Curbing The Impact Of Unemployment In The Singaporean Economy During The Covid-19 Pandemic

With the COVID-19 pandemic becoming increasingly prominent in early 2020 in Singapore, the amount of cases were on the rise. As shown in the Susceptible-Exposed-Infected-Recovered (SEIR) distribution chart, the number of people infected follows a hump-like pattern, indicating that it increased first and then fell subsequently. Given that this happened in a very short time frame, it is intriguing how the first wave of the COVID-19 pandemic and its subsequent economic consequences were dealt with incredibly well, only possible through economic policy-making, fiscal policy being primarily significant. Expansionary fiscal policy comprises policies of reduction in tax rate and increase in public expenditure undertaken by the government to increase the Aggregate Demand (AD) in the economy.

A COVID-19 vaccine effectiveness model using the susceptible-exposed-infectious-recovered model

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) caused the start of the COVID-19 outbreak in the world, including Malaysia and Thailand. This study identifies the trend of the COVID-19 outbreak before and after the vaccination campaign by using the Susceptible-Exposed-Infectious-Recovered (SEIR) and Susceptible-Exposed-Infectious-Recovered-Vaccinated (SEIRV) models. Moreover, we predict the daily reported death and recovery cases using the SEIR model and Holt's linear trend method and then evaluate their performance. The data used in this study is real data from Malaysia and Thailand. The SEIRV model provides a comprehensive view of the efficacy of COVID-19 vaccinations in curbing the COVID-19 outbreak. This research reveals that the SEIR model outperforms Holt's linear trend method in predicting daily reported cases.

Optimal logistics scheduling with dynamic information in emergency response: Case studies for humanitarian objectives

The mathematical model of infectious disease is a typical problem in mathematical modeling, and the common infectious disease models include the susceptible-infected (SI) model, the susceptible-infected-recovered model (SIR), the susceptible-infected-recovered-susceptible model (SIRS) and the susceptible-exposed-infected-recovered (SEIR) model. These models can be used to predict the impact of regional return to work after the epidemic. In this paper, we use the SEIR model to solve the dynamic medicine demand information in humanitarian relief phase. A multistage mixed integer programming model for the humanitarian logistics and transport resource is proposed. The objective functions of the model include delay cost and minimum running time in the time-space network. The model describes that how to distribute and deliver medicine resources from supply locations to demand locations with an efficient and lower-cost way through a transportation network. The linear programming problem is solved by the proposed Benders decomposition algorithm. Finally, we use two cases to calculate model and algorithm. The results of the case prove the validity of the model and algorithm.

An interactive agent-based modelling framework for assessing COVID-19 transmission risk on construction site

The outbreak of COVID-19 has impacted the world and society in its entirety. The labour-intensive construction industry is especially disrupted by COVID-19 and construction workers have a higher chance of exposure to COVID-19. Despite the extensiveness of qualitative and quantitative research around the impact of COVID-19 on the construction industry, it is observed that very limited proportion of such research actually investigated the COVID-19 dynamics within a specific construction site as well as the effectiveness of the corresponding safety control measures. Given this context, this study developed an interactive agent-based modelling framework embedded with a modified susceptible-exposed-infectious-recovered (SEIR) model for assessing COVID-19 transmission risk on construction sites, with the application of five safety control measures (i.e., SCM including face covering, vaccination, ventilation, social distance and isolation). This study afterwards set up 108 SCM scenarios based on the five SCM and sensitivity analyses were conducted in order to generate robust results. Based on the simulation results, the efficacy of the 5 SCM in preventing COVID-19 spread was assessed. Therefore, the results of the 108 scenarios are a useful scientific reference for stakeholders or policymakers when making decisions regarding mitigating the spread of COVID-19 and other infectious diseases within the construction sector.

REAL-TIME MECHANISTIC BAYESIAN FORECASTS OF COVID-19 MORTALITY.

The COVID-19 pandemic emerged in late December 2019. In the first six months of the global outbreak, the U.S. reported more cases and deaths than any other country in the world. Effective modeling of the course of the pandemic can help assist with public health resource planning, intervention efforts, and vaccine clinical trials. However, building applied forecasting models presents unique challenges during a pandemic. First, case data available to models in real time represent a nonstationary fraction of the true case incidence due to changes in available diagnostic tests and test-seeking behavior. Second, interventions varied across time and geography leading to large changes in transmissibility over the course of the pandemic. We propose a mechanistic Bayesian model that builds upon the classic compartmental susceptible-exposed-infected-recovered (SEIR) model to operationalize COVID-19 forecasting in real time. This framework includes nonparametric modeling of varying transmission rates, nonparametric modeling of case and death discrepancies due to testing and reporting issues, and a joint observation likelihood on new case counts and new deaths; it is implemented in a probabilistic programming language to automate the use of Bayesian reasoning for quantifying uncertainty in probabilistic forecasts. The model has been used to submit forecasts to the U.S. Centers for Disease Control through the COVID-19 Forecast Hub under the name MechBayes. We examine the performance relative to a baseline model as well as alternate models submitted to the forecast hub. Additionally, we include an ablation test of our extensions to the classic SEIR model. We demonstrate a significant gain in both point and probabilistic forecast scoring measures using MechBayes, when compared to a baseline model, and show that MechBayes ranks as one of the top two models out of nine which regularly submitted to the COVID-19 Forecast Hub for the duration of the pandemic, trailing only the COVID-19 Forecast Hub ensemble model of which which MechBayes is a part.

Delay-differential SEIR modeling for improved modelling of infection dynamics

SEIR (Susceptible–Exposed–Infected–Recovered) approach is a classic modeling method that is frequently used to study infectious diseases. However, in the vast majority of such models transitions from one population group to another are described using the mass-action law. That causes inability to reproduce observable dynamics of an infection such as the incubation period or progression of the disease's symptoms. In this paper, we propose a new approach to simulate the epidemic dynamics based on a system of differential equations with time delays and instant transitions to approximate durations of transition processes more correctly and make model parameters more clear. The suggested approach can be applied not only to Covid-19 but also to the study of other infectious diseases. We utilized it in the development of the delay-based model of the COVID-19 pandemic in Germany and France. The model takes into account testing of different population groups, symptoms progression from mild to critical, vaccination, duration of protective immunity and new virus strains. The stringency index was used as a generalized characteristic of the non-pharmaceutical government interventions in corresponding countries to contain the virus spread. The parameter identifiability analysis demonstrated that the presented modeling approach enables to significantly reduce the number of parameters and make them more identifiable. Both models are publicly available.