scholarly journals INFEKTA: A General Agent-based Model for Transmission of Infectious Diseases: Studying the COVID-19 Propagation in Bogotá - Colombia

Author(s):  
Jonatan Gomez ◽  
Jeisson Prieto ◽  
Elizabeth Leon ◽  
Arles Rodríguez

AbstractThe transmission dynamics of the coronavirus - COVID-19-have challenged humankind at almost every level. Currently, research groups around the globe are trying to figure out such transmission dynamics using different scientific and technological approaches. One of those is by using mathematical and computational models like the compartmental model or the agent-based models. In this paper, a general agent-based model, called INFEKTA, that combines the transmission dynamics of an infectious disease with agents (individuals) that can move on a complex network of accessible places defined over a Euclidean space representing a real town or city is proposed. The applicability of INFEKTA is shown by modeling the transmission dynamics of the COVID-19 in Bogotá city, the capital of Colombia.

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0245787
Author(s):  
Jonatan Gomez ◽  
Jeisson Prieto ◽  
Elizabeth Leon ◽  
Arles Rodríguez

The transmission dynamics of the coronavirus—COVID-19—have challenged humankind at almost every level. Currently, research groups around the globe are trying to figure out such transmission dynamics under special conditions such as separation policies enforced by governments. Mathematical and computational models, like the compartmental model or the agent-based model, are being used for this purpose. This paper proposes an agent-based model, called INFEKTA, for simulating the transmission of infectious diseases, not only the COVID-19, under social distancing policies. INFEKTA combines the transmission dynamic of a specific disease, (according to parameters found in the literature) with demographic information (population density, age, and genre of individuals) of geopolitical regions of the real town or city under study. Agents (virtual persons) can move, according to its mobility routines and the enforced social distancing policy, on a complex network of accessible places defined over an Euclidean space representing the town or city. The transmission dynamics of the COVID-19 under different social distancing policies in Bogotá city, the capital of Colombia, is simulated using INFEKTA with one million virtual persons. A sensitivity analysis of the impact of social distancing policies indicates that it is possible to establish a ‘medium’ (i.e., close 40% of the places) social distancing policy to achieve a significant reduction in the disease transmission.


2018 ◽  
Vol 10 (1) ◽  
Author(s):  
Sultanah Alshammari ◽  
Armin Mikler

ObjectiveTo develop a computational model to assess the risk of epidemics in global mass gatherings and evaluate the impact of various measures of prevention and control of infectious diseases.IntroductionGlobal Mass gatherings (MGs) such as Olympic Games, FIFA World Cup, and Hajj (Muslim pilgrimage to Makkah), attract millions of people from different countries. The gathering of a large population in a proximity facilitates transmission of infectious diseases [1]. Attendees arrive from different geographical areas with diverse disease history and immune responses. The associated travel patterns with global events can contribute to a further disease spread affecting a large number of people within a short period and lead to a potential pandemic. Global MGs pose serious health threats and challenges to the hosting countries and home countries of the participants [2]. Advanced planning and disease surveillance systems are required to control health risks in these events. The success of computational models in different areas of public health and epidemiology motivates using these models in MGs to study transmission of infectious diseases and assess the risk of epidemics. Computational models enable simulation and analysis of different disease transmission scenarios in global MGs. Epidemic models can be used to evaluate the impact of various measures of prevention and control of infectious diseases.MethodsThe annual event of the Hajj is selected to illustrate the main aspects of the proposed model and to address the associated challenges. Every year, more than two million pilgrims from over 186 countries arrive in Makkah to perform Hajj with the majority arriving by air. Foreign pilgrims can stay at one of the holy cities of Makkah and Madinah up to 30-35 days prior the starting date of the Hajj. The long duration of the arrival phase of the Hajj allows a potential epidemic to proceed in the population of international pilgrims. Stochastic SEIR (Susceptible−Exposed−Infected−Recovered) agent-based model is developed to simulate the disease transmission among pilgrims. The agent-based model is used to simulate pilgrims and their interactions during the various phases of the Hajj. Each agent represents a pilgrim and maintains a record of demographic data (gender, country of origin, age), health data (infectivity, susceptibility, number of days being exposed or infected), event related data (location, arrival date and time), and precautionary or health-related behaviors.Each pilgrim can be either healthy but susceptible to a disease, exposed who are infected but cannot transmit the infection, or infectious (asymptomatic or symptomatic) who are infected and can transmit the disease to other susceptibles. Exposed individuals transfer to the infectious compartment after 1/α days, and infectious individuals will recover and gain immunity to that disease after 1/γ days. Where α is the latent period and γ is the infectious period. Moving susceptible individuals to exposed compartment depends on a successful disease transmission given a contact with an infectious individual. The disease transmission rate is determined by the contact rate and thetransmission probability per contact. Contact rate and mixing patterns are defined by probabilistic weights based on the features of infectious pilgrims and the duration and setting of the stage where contacts are taking place. The initial infections are seeded in the population using two scenarios (Figure 1) to measure the effects of changing, the timing for introducing a disease into the population and the likelihood that a particular flight will arrive with one or more infected individuals.ResultsThe results showed that the number of initial infections is influenced by increasing the value of λ and selecting starting date within peak arrival days. When starting from the first day, the average size of the initial infectious ranges from 0.05% to 1% of the total arriving pilgrims. Using the SEIR agent-based model, a simulation of the H1N1 Influenza epidemic was completed for the 35-days arrival stage of the Hajj. The epidemic is initiated with one infectious pilgrim per flight resulting in infected 0.5% of the total arriving pilgrims. As pilgrims spend few hours at the airport, the results obtained from running the epidemic model showed only new cases of susceptible individuals entering the exposed state in a range of 0.20% to 0.35% of total susceptibles. The number of new cases is reduced by almost the same rate of the number of infectious individuals following precautionary behaviors.ConclusionsA data-driven stochastic SEIR agent-based model is developed to simulate disease spread at global mass gatherings. The proposed model can provide initial indicators of infectious disease epidemic at these events and evaluate the possible effects of intervention measures and health-related behaviors. The proposed model can be generalized to model the spread of various diseases in different mass gatherings, as it allows different factors to vary and entered as parameters.References1. Memish ZA, Stephens GM, Steffen R, Ahmed QA. Emergence of medicine for mass gatherings: lessons from the Hajj. The Lancet infectious diseases. 2012 Jan 31;12(1):56-65.2. Chowell G, Nishiura H, Viboud C. Modeling rapidly disseminating infectious disease during mass gatherings. BMC medicine. 2012 Dec 7;10(1):159.


2020 ◽  
Author(s):  
Christian Alvin H. Buhat ◽  
Destiny SM. Lutero ◽  
Yancee H. Olave ◽  
Monica C. Torres ◽  
Jomar F. Rabajante

AbstractWe formulate an agent-based model and a compartmental model (SEIR) that simulate the spread of a respiratory infectious disease between two neighboring cities. We consider preventive measures such as implementation of social distancing and lockdown in a city, as well as the effect of protective gears or practices. The chance of travelling to another city and within the city during lockdown, and initial percentage of exposed and infected individuals on both cities influence the increase in the number of newly-infected individuals on both models. Our simulations show that (i) increase in exposed individuals results in increase in number of new infections, hence the need for increased testing-isolation efforts; (ii) protection level of 75-100% effectiveness impedes disease transmission; (iii) travelling within city or to other city can be an option given that strict preventive measures (e.g., non-pharmaceutical interventions) are observed; and (iv) the ideal set-up for neighboring cities is to implement lockdown when there is high risk of disease local transmission while individuals observe social distancing, maximizing protective measures, and isolating those that are exposed. The results of the agent-based and compartmental models show similar qualitative dynamics; the differences are due to different spatio-temporal heterogeneity and stochasticity. These models can aid decision makers in designing infectious disease-related policies to protect individuals while continuing population movement.


Symmetry ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 90
Author(s):  
Nicolò Cogno ◽  
Roman Bauer ◽  
Marco Durante

Understanding the pathophysiology of lung fibrosis is of paramount importance to elaborate targeted and effective therapies. As it onsets, the randomly accumulating extracellular matrix (ECM) breaks the symmetry of the branching lung structure. Interestingly, similar pathways have been reported for both idiopathic pulmonary fibrosis and radiation-induced lung fibrosis (RILF). Individuals suffering from the disease, the worldwide incidence of which is growing, have poor prognosis and a short mean survival time. In this context, mathematical and computational models have the potential to shed light on key underlying pathological mechanisms, shorten the time needed for clinical trials, parallelize hypotheses testing, and improve personalized drug development. Agent-based modeling (ABM) has proven to be a reliable and versatile simulation tool, whose features make it a good candidate for recapitulating emergent behaviors in heterogeneous systems, such as those found at multiple scales in the human body. In this paper, we detail the implementation of a 3D agent-based model of lung fibrosis using a novel simulation platform, namely, BioDynaMo, and prove that it can qualitatively and quantitatively reproduce published results. Furthermore, we provide additional insights on late-fibrosis patterns through ECM density distribution histograms. The model recapitulates key intercellular mechanisms, while cell numbers and types are embodied by alveolar segments that act as agents and are spatially arranged by a custom algorithm. Finally, our model may hold potential for future applications in the context of lung disorders, ranging from RILF (by implementing radiation-induced cell damage mechanisms) to COVID-19 and inflammatory diseases (such as asthma or chronic obstructive pulmonary disease).


PLoS ONE ◽  
2018 ◽  
Vol 13 (12) ◽  
pp. e0208775 ◽  
Author(s):  
Elizabeth Hunter ◽  
Brian Mac Namee ◽  
John Kelleher

2012 ◽  
Vol 54 (1-2) ◽  
pp. 37-49 ◽  
Author(s):  
BENJAMIN J. BINDER ◽  
JOSHUA V. ROSS ◽  
MATTHEW J. SIMPSON

AbstractWe consider a hybrid model, created by coupling a continuum and an agent-based model of infectious disease. The framework of the hybrid model provides a mechanism to study the spread of infection at both the individual and population levels. This approach captures the stochastic spatial heterogeneity at the individual level, which is directly related to deterministic population level properties. This facilitates the study of spatial aspects of the epidemic process. A spatial analysis, involving counting the number of infectious agents in equally sized bins, reveals when the spatial domain is nonhomogeneous.


2021 ◽  
Author(s):  
Kian Boon Law ◽  
Kalaiarasu M. Peariasamy ◽  
Hishamshah Mohd. Ibrahim ◽  
Noor Hisham Abdullah

Abstract Background The conventional susceptible-infectious-recovered (SIR) model tends to overestimate the transmission dynamics of infectious diseases and ends up with total infections and total immunized population exceeding the threshold required for control and eradication of infectious diseases. The study aims to overcome the limitation by allowing the transmission rate of infectious disease to decline along with the reducing risk of contact infection. Methods Two new SIR models were developed to mimic the declining transmission rate of infectious diseases at different stages of transmission. Model A mimicked the declining transmission rate along with the reducing risk of transmission following infection, while Model B mimicked the declining transmission rate following recovery. Then, the conventional SIR model, Model A and Model B were used to simulate an infectious disease with a basic reproduction number (r0) of 3.0 and a herd immunity threshold (HIT) of 0.667 with and without vaccination. The infectious disease was expected to be controlled or eradicated when the total immunized population either through infection or vaccination reached the level predicted by the HIT. Outcomes of simulations were assessed at the time when the total immunized population reached the level predicted by the HIT, and at the end of simulations. Findings All three models performed likewise at the beginning of the transmission when sizes of infectious and recovered were relatively small as compared with the population size. The infectious disease modelled using the conventional SIR model appeared completely out of control even when the HIT was achieved in all scenarios with and without vaccination. The infectious disease modelled using Model A appeared to be controlled at the level predicted by the HIT in all scenarios with and without vaccination. Model B projected the infectious disease to be controlled at the level predicted by the HIT only at high vaccination rates. At lower vaccination rates or without vaccination, the level at which the infectious disease was controlled cannot be accurately predicted by the HIT. Conclusion Transmission dynamics of infectious diseases with herd immunity can accurately be modelled by allowing the transmission rate of infectious disease to decline along with the combined risk of contact infection. Model B provides a more credible framework for modelling infectious diseases with herd immunity in a randomly mixed population.


2021 ◽  
Author(s):  
Augusto Cabrera-Becerril ◽  
Pedro Miramontes ◽  
Raúl Peralta

AbstractWe introduce an agent-based model to simulate the epidemiological dynamics of COVID-19. Most computational models proposed to study this epidemic do no take into account human mobility. We present a direct simulation model where mobility plays a key role and propose as well four quarantine strategies. The results show that the no-quarantine strategy does lead to a high peak of contagions with no rebound. Quarantined strategies, for their part, show a re-emergence of the epidemic with smaller and softer peaks.


Author(s):  
Yunhwan Kim ◽  
Hohyung Ryu ◽  
Sunmi Lee

Super-spreading events have been observed in the transmission dynamics of many infectious diseases. The 2015 MERS-CoV outbreak in the Republic of Korea has also shown super-spreading events with a significantly high level of heterogeneity in generating secondary cases. It becomes critical to understand the mechanism for this high level of heterogeneity to develop effective intervention strategies and preventive plans for future emerging infectious diseases. In this regard, agent-based modeling is a useful tool for incorporating individual heterogeneity into the epidemic model. In the present work, a stochastic agent-based framework is developed in order to understand the underlying mechanism of heterogeneity. Clinical (i.e., an infectivity level) and social or environmental (i.e., a contact level) heterogeneity are modeled. These factors are incorporated in the transmission rate functions under assumptions that super-spreaders have stronger transmission and/or higher links. Our agent-based model has employed real MERS-CoV epidemic features based on the 2015 MERS-CoV epidemiological data. Monte Carlo simulations are carried out under various epidemic scenarios. Our findings highlight the roles of super-spreaders in a high level of heterogeneity, underscoring that the number of contacts combined with a higher level of infectivity are the most critical factors for substantial heterogeneity in generating secondary cases of the 2015 MERS-CoV transmission.


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