A multi-scale agent-based model of infectious disease transmission to assess the impact of vaccination and non-pharmaceutical interventions: The COVID-19 case

Predictive models for health outcomes due to SARS-CoV-2, including the effect of vaccination: a systematic review

BACKGROUND

The interaction between modelers and policymakers is becoming more common due to the increase in computing speed seen in recent decades. The recent pandemic caused by the SARS-CoV-2 virus was no exception. Thus, this study aims to identify and assess epidemiological mathematical models of SARS-CoV-2 applied to real-world data, including immunization for coronavirus 2019 (COVID-19).

METHODOLOGY

PubMed, JSTOR, medRxiv, LILACS, EconLit, and other databases were searched for studies employing epidemiological mathematical models of SARS-CoV-2 applied to real-world data. We summarized the information qualitatively, and each article included was assessed for bias risk using the Joanna Briggs Institute (JBI) and PROBAST checklist tool. The PROSPERO registration number is CRD42022344542.

FINDINGS

In total, 5646 articles were retrieved, of which 411 were included. Most of the information was published in 2021. The countries with the highest number of studies were the United States, Canada, China, and the United Kingdom; no studies were found in low-income countries. The SEIR model (susceptible, exposed, infectious, and recovered) was the most frequently used approach, followed by agent-based modeling. Moreover, the most commonly used software were R, Matlab, and Python, with the most recurring health outcomes being death and recovery. According to the JBI assessment, 61.4% of articles were considered to have a low risk of bias.

INTERPRETATION

The utilization of mathematical models increased following the onset of the SARS-CoV-2 pandemic. Stakeholders have begun to incorporate these analytical tools more extensively into public policy, enabling the construction of various scenarios for public health. This contribution adds value to informed decision-making. Therefore, understanding their advancements, strengths, and limitations is essential.

Study of optimal vaccination strategies for early COVID-19 pandemic using an age-structured mathematical model: A case study of the USA

In this paper we study different vaccination strategies that could have been implemented for the early COVID-19 pandemic. We use a demographic epidemiological mathematical model based on differential equations in order to investigate the efficacy of a variety of vaccination strategies under limited vaccine supply. We use the number of deaths as the metric to measure the efficacy of each of these strategies. Finding the optimal strategy for the vaccination programs is a complex problem due to the large number of variables that affect the outcomes. The constructed mathematical model takes into account demographic risk factors such as age, comorbidity status and social contacts of the population. We perform simulations to assess the performance of more than three million vaccination strategies which vary depending on the vaccine priority of each group. This study focuses on the scenario corresponding to the early vaccination period in the USA, but can be extended to other countries. The results of this study show the importance of designing an optimal vaccination strategy in order to save human lives. The problem is extremely complex due to the large amount of factors, high dimensionality and nonlinearities. We found that for low/moderate transmission rates the optimal strategy prioritizes high transmission groups, but for high transmission rates, the optimal strategy focuses on groups with high CFRs. The results provide valuable information for the design of optimal vaccination programs. Moreover, the results help to design scientific vaccination guidelines for future pandemics.

Using a real-world network to model the trade-off between stay-at-home restriction, vaccination, social distancing and working hours on COVID-19 dynamics

Background

Human behaviour, economic activity, vaccination, and social distancing are inseparably entangled in epidemic management. This study aims to investigate the effects of various parameters such as stay-at-home restrictions, work hours, vaccination, and social distance on the containment of pandemics such as COVID-19.

Methods

To achieve this, we have developed an agent based model based on a time-dynamic graph with stochastic transmission events. The graph is constructed from a real-world social network. The edges of graph have been categorized into three categories: home, workplaces, and social environment. The conditions needed to mitigate the spread of wild-type COVID-19 and the delta variant have been analyzed. Our purposeful agent based model has carefully executed tens of thousands of individual-based simulations. We propose simple relationships for the trade-offs between effective reproduction number (R _e), transmission rate, working hours, vaccination, and stay-at-home restrictions.

Results

We have found that the effect of a 13.6% increase in vaccination for wild-type (WT) COVID-19 is equivalent to reducing four hours of work or a one-day stay-at-home restriction. For the delta, 20.2% vaccination has the same effect. Also, since we can keep track of household and non-household infections, we observed that the change in household transmission rate does not significantly alter the R _e. Household infections are not limited by transmission rate due to the high frequency of connections. For the specifications of COVID-19, the R _e depends on the non-household transmissions rate.

Conclusions

Our findings highlight that decreasing working hours is the least effective among the non-pharmaceutical interventions. Our results suggest that policymakers decrease work-related activities as a last resort and should probably not do so when the effects are minimal, as shown. Furthermore, the enforcement of stay-at-home restrictions is moderately effective and can be used in conjunction with other measures if absolutely necessary.

Evaluation of vaccination strategies for the metropolitan area of Madrid via agent-based simulation

OBJECTIVE

We analyse the impact of different vaccination strategies on the propagation of COVID-19 within the Madrid metropolitan area, starting on 27 December 2020 and ending in Summer of 2021.

MATERIALS AND METHODS

The predictions are based on simulation using EpiGraph, an agent-based COVID-19 simulator. We first summarise the different models implemented in the simulator, then provide a comprehensive description of the vaccination model and define different vaccination strategies. The simulator-including the vaccination model-is validated by comparing its results with real data from the metropolitan area of Madrid during the third COVID-19 wave. This work considers different COVID-19 propagation scenarios for a simulated population of about 5 million.

RESULTS

The main result shows that the best strategy is to vaccinate first the elderly with the two doses spaced 56 days apart; this approach reduces the final infection rate by an additional 6% and the number of deaths by an additional 3% with respect to vaccinating first the elderly at the interval recommended by the vaccine producer. The reason is the increase in the number of vaccinated individuals at any time during the simulation.

CONCLUSION

The existing level of detail and maturity of EpiGraph allowed us to evaluate complex scenarios and thus use it successfully to help guide the strategy for the COVID-19 vaccination campaign of the Spanish health authorities.

Stability Analysis of an Extended SEIR COVID-19 Fractional Model with Vaccination Efficiency

This work is aimed at presenting a new numerical scheme for COVID-19 epidemic model based on Atangana-Baleanu fractional order derivative in Caputo sense (ABC) to investigate the vaccine efficiency. Our construction of the model is based on the classical SEIR, four compartmental models with an additional compartment V of vaccinated people extending it SEIRV model, for the transmission as well as an effort to cure this infectious disease. The point of disease-free equilibrium is calculated, and the stability analysis of the equilibrium point using the reproduction number is performed. The endemic equilibrium's existence and uniqueness are investigated. For the solution of the nonlinear system presented in the model at different fractional orders, a new numerical scheme based on modified Simpson's 1/3 method is developed. Convergence and stability of the numerical scheme are thoroughly analyzed. We attempted to develop an epidemiological model presenting the COVID-19 dynamics in Italy. The proposed model's dynamics are graphically interpreted to observe the effect of vaccination by altering the vaccination rate.

Optimizing global COVID-19 vaccine allocation: An agent-based computational model of 148 countries

BACKGROUND

Based on the principles of equity and effectiveness, the World Health Organization and COVAX formulate vaccine allocation as a mathematical optimization problem. This study aims to solve the optimization problem using agent-based simulations.

METHODS

We built open-sourced agent-based models to simulate virus transition among a demographically representative sample of 198 million people in 148 countries using advanced computational services. All countries continuing their current vaccine progress is defined as the baseline scenario. Comparison scenarios include achieving minimum vaccination rates and allocating vaccines based on pandemic levels.

FINDINGS

The simulations are fitted using the pandemic data from 148 countries from January 2020 to June 2021. Under the baseline scenario, the world will add 24.36 million cases and 468,945 deaths during the projection period of three months. Inoculating at least 10%, 20%, and 26% of populations in all countries requires 1.12, 3.31, and 5.00 million additional vaccine doses every day, respectively. Achieving these benchmarks reduces new cases by 0.56, 2.74, and 3.32 million, respectively. If allocated by the current global distribution, 5.00 million additional vaccine doses will only avert 1.45 million new cases. If those 5.00 million vaccines are allocated based on projected cases in each country, the averted cases will increase more than six-fold to 9.20 million. Similar differences between allocation methods are observed in averted deaths.

CONCLUSION

The global distribution of COVID-19 vaccines can be optimized to achieve better outcomes in terms of both equity and effectiveness. Alternative vaccine allocation methods may avert several times more cases and deaths than the current global distribution. With reasonable requirements on additional vaccines, COVAX could adopt alternative allocation strategies that reduce cross-country inequity and save more lives.

An agent-based model to assess large-scale COVID-19 vaccination campaigns for the Italian territory: The case study of Lombardy region

BACKGROUND

In Italy, the administration of COVID-19 vaccines began in late 2020. In the early stages, the number of available doses was limited. To maximize the effectiveness of the vaccine campaign, the national health agency assigned priority access to at-risk individuals, such as health care workers and the elderly. Current vaccination campaign strategies do not take full advantage of the latest mathematical models, which capture many subtle nuances, allowing different territorial situations to be analyzed aiming to make context-specific decisions.

OBJECTIVES

The main objective is the definition of an agent-based model using open data and scientific literature to assess and optimize the impact of vaccine campaigns for an Italian region. Specifically, the aim is twofold: (i) estimate the reduction in the number of infections and deaths attributable to vaccines, and (ii) assess the performances of alternative vaccine allocation strategies.

METHODS

The COVID-19 Agent-based simulator Covasim has been employed to build an agent-based model by considering the Lombardy region as case study. The model has been tailored by leveraging open data and knowledge from the scientific literature. Dynamic mobility restrictions and the presence of Variant of Concern have been explicitly represented. Free parameters have been calibrated using the grid search methodology.

RESULTS

The model mimics the COVID-19 wave that hit Lombardy from September 2020 to April 2021. It suggests that 168,492 cumulative infections 2,990 cumulative deaths have been avoided due to the vaccination campaign in Lombardy from January 1 to April 30, 2021. Without vaccines, the number of deaths would have been 66% greater in the 80-89 age group and 114% greater for those over 90. The best vaccine allocation strategy depends on the goal. To minimize infections, the best policy is related to dose availability. If at least 1/3 of the population can be covered in 4 months, targeting at-risk individuals and the elderly first is recommended; otherwise, the youngest people should be vaccinated first. To minimize overall deaths, priority is best given to at-risk groups and the elderly in all scenarios.

CONCLUSIONS

This work proposes a methodological approach that leverages open data and scientific literature to build a model of COVID-19 capable of assessing and optimizing the impact of vaccine campaigns. This methodology can help national institutions to design regional mathematical models that can support pandemic-related decision-making processes.

Modeling COVID-19 Outbreaks in Long-Term Care Facilities Using an Agent-Based Modeling and Simulation Approach

The elderly, especially those individuals with pre-existing health problems, have been disproportionally at a higher risk during the COVID-19 pandemic. Residents of long-term care facilities have been gravely affected by the pandemic and resident death numbers have been far above those of the general population. To better understand how infectious diseases such as COVID-19 can spread through long-term care facilities, we developed an agent-based simulation tool that uses a contact matrix adapted from previous infection control research in these types of facilities. This matrix accounts for the average distinct daily contacts between seven different agent types that represent the roles of individuals in long-term care facilities. The simulation results were compared to actual COVID-19 outbreaks in some of the long-term care facilities in Ontario, Canada. Our analysis shows that this simulation tool is capable of predicting the number of resident deaths after 50 days with a less than 0.1 variation in death rate. We modeled and predicted the effectiveness of infection control measures by utilizing this simulation tool. We found that to reduce the number of resident deaths, the effectiveness of personal protective equipment must be above 50%. We also found that daily random COVID-19 tests for as low as less than 10% of a long-term care facility’s population will reduce the number of resident deaths by over 75%. The results further show that combining several infection control measures will lead to more effective outcomes.