Modeling Epidemics Spreading on Social Contact Networks

The use of networks in spatial and temporal computational models for outbreak spread in epidemiology: A systematic review

OBJECTIVES

To examine recent literature in order to present a comprehensive overview of the current trends as regards the computational models used to represent the propagation of an infectious outbreak in a population, paying particular attention to those that represent network-based transmission.

METHODS

a systematic review was conducted following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. Papers published in English between 2010 and September 2021 were sought in the ACM Digital Library, IEEE Xplore, PubMed and Scopus databases.

RESULTS

Upon considering their titles and abstracts, 832 papers were obtained, of which 192 were selected for a full content-body check. Of these, 112 studies were eventually deemed suitable for quantitative and qualitative analysis. Emphasis was placed on the spatial and temporal scales studied, the use of networks or graphs, and the granularity of the data used to evaluate the models. The models principally used to represent the spreading of outbreaks have been stochastic (55.36%), while the type of networks most frequently used are relationship networks (32.14%). The most common spatial dimension used is a region (19.64%) and the most used unit of time is a day (28.57%). Synthetic data as opposed to an external source were used in 51.79% of the papers. With regard to the granularity of the data sources, aggregated data such as censuses or transportation surveys are the most common.

CONCLUSION

We identified a growing interest in the use of networks to represent disease transmission. We detected that research is focused on only certain combinations of the computational model, type of network (in both the expressive and the structural sense) and spatial scale, while the search for other interesting combinations has been left for the future.

The coevolution of the spread of a disease and competing opinions in multiplex networks

The COVID-19 pandemic has resulted in a proliferation of conflicting opinions on physical distancing across various media platforms, which has had a significant impact on human behavior and the transmission dynamics of the disease. Inspired by this social phenomenon, we present a novel UAP-SIS model to study the interaction between conflicting opinions and epidemic spreading in multiplex networks, in which individual behavior is based on diverse opinions. We distinguish susceptibility and infectivity among individuals who are unaware, pro-physical distancing and anti-physical distancing, and we incorporate three kinds of mechanisms for generating individual awareness. The coupled dynamics are analyzed in terms of a microscopic Markov chain approach that encompasses the aforementioned elements. With this model, we derive the epidemic threshold which is related to the diffusion of competing opinions and their coupling configuration. Our findings demonstrate that the transmission of the disease is shaped in a significant manner by conflicting opinions, due to the complex interaction between such opinions and the disease itself. Furthermore, the implementation of awareness-generating mechanisms can help to mitigate the overall prevalence of the epidemic, and global awareness and self-awareness can be interchangeable in certain instances. To effectively curb the spread of epidemics, policymakers should take steps to regulate social media and promote physical distancing as the mainstream opinion.

Modeling the Influence of Fake Accounts on User Behavior and Information Diffusion in Online Social Networks

The mechanisms of information diffusion in Online Social Networks (OSNs) have been studied extensively from various perspectives with some focus on identifying and modeling the role of heterogeneous nodes. However, none of these studies have considered the influence of fake accounts on human accounts and how this will affect the rumor diffusion process. This paper aims to present a new information diffusion model that characterizes the role of bots in the rumor diffusion process in OSNs. The proposed SIhIbR model extends the classical SIR model by introducing two types of infected users with different infection rates: the users who are infected by human (Ih) accounts with a normal infection rate and the users who are infected by bot accounts (Ib) with a different diffusion rate that reflects the intent and steadiness of this type of account to spread the rumors. The influence of fake accounts on human accounts diffusion rate has been measured using the social impact theory, as it better reflects the deliberate behavior of bot accounts to spread a rumor to a large portion of the network by considering both the strength and the bias of the source node. The experiment results show that the accuracy of the SIhIbR model outperforms the SIR model when simulating the rumor diffusion process in the existence of fake accounts. It has been concluded that fake accounts accelerate the rumor diffusion process as they impact many people in a short time.

Optimal vaccine roll-out strategies including social distancing for pandemics

Non-pharmacological interventions (NPIs), principally social distancing, in combination with effective vaccines, aspire to develop a protective immunity shield against pandemics and particularly against the COVID-19 pandemic. In this study, an agent-based network model with small-world topology is employed to find optimal policies against pandemics, including social distancing and vaccination strategies. The agents' states are characterized by a variation of the SEIR model (susceptible, exposed, infected, recovered). To explore optimal policies, an equation-free method is proposed to solve the inverse problem of calibrating an agent's infection rate with respect to the vaccination efficacy. The results show that prioritizing the first vaccine dose in combination with mild social restrictions, is sufficient to control the pandemic, with respect to the number of deaths. Moreover, for the same mild number of social contacts, we find an optimal vaccination ratio of 0.85 between older people of ages > 65 compared to younger ones.

Optimizing Living Material Delivery During the COVID-19 Outbreak

The coronavirus disease 2019 (COVID-19) epidemic has spread worldwide, posing a great threat to human beings. The stay-home quarantine is an effective way to reduce physical contacts and the associated COVID-19 transmission risk, which requires the support of efficient living materials (such as meats, vegetables, grain, and oil) delivery. Notably, the presence of potential infected individuals increases the COVID-19 transmission risk during the delivery. The deliveryman may be the medium through which the virus spreads among urban residents. However, traditional delivery route optimization methods don't take the virus transmission risk into account. Here, we propose a novel living material delivery route approach considering the possible COVID-19 transmission during the delivery. A complex network-based virus transmission model is developed to simulate the possible COVID-19 infection between urban residents and the deliverymen. A bi-objective model considering the COVID-19 transmission risk and the total route length is proposed and solved by the hybrid meta-heuristics integrating the adaptive large neighborhood search and simulated annealing. The experiment was conducted in Wuhan, China to assess the performance of the proposed approach. The results demonstrate that 935 vehicles will totally travel 56,424.55 km to deliver necessary living materials to 3,154 neighborhoods, with total risk [Formula: see text]. The presented approach reduces the risk of COVID-19 transmission by 67.55% compared to traditional distance-based optimization methods. The presented approach can facilitate a well response to the COVID-19 in the transportation sector.

Neighborhood Characteristics and Racial Disparities in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Seropositivity in Pregnancy

OBJECTIVE

To quantify the extent to which neighborhood characteristics contribute to racial and ethnic disparities in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seropositivity in pregnancy.

METHODS

This cohort study included pregnant patients who presented for childbirth at two hospitals in Philadelphia, Pennsylvania from April 13 to December 31, 2020. Seropositivity for SARS-CoV-2 was determined by measuring immunoglobulin G and immunoglobulin M antibodies by enzyme-linked immunosorbent assay in discarded maternal serum samples obtained for clinical purposes. Race and ethnicity were self-reported and abstracted from medical records. Patients' residential addresses were geocoded to obtain three Census tract variables: community deprivation, racial segregation (Index of Concentration at the Extremes), and crowding. Multivariable mixed effects logistic regression models and causal mediation analyses were used to quantify the extent to which neighborhood variables may explain racial and ethnic disparities in seropositivity.

RESULTS

Among 5,991 pregnant patients, 562 (9.4%) were seropositive for SARS-CoV-2. Higher seropositivity rates were observed among Hispanic (19.3%, 104/538) and Black (14.0%, 373/2,658) patients, compared with Asian (3.2%, 13/406) patients, White (2.7%, 57/2,133) patients, and patients of another race or ethnicity (5.9%, 15/256) (P<.001). In adjusted models, per SD increase, deprivation (adjusted odds ratio [aOR] 1.16, 95% CI 1.02-1.32) and crowding (aOR 1.15, 95% CI 1.05-1.26) were associated with seropositivity, but segregation was not (aOR 0.90, 95% CI 0.78-1.04). Mediation analyses revealed that crowded housing may explain 6.7% (95% CI 2.0-14.7%) of the Hispanic-White disparity and that neighborhood deprivation may explain 10.2% (95% CI 0.5-21.1%) of the Black-White disparity.

CONCLUSION

Neighborhood deprivation and crowding were associated with SARS-CoV-2 seropositivity in pregnancy in the prevaccination era and may partially explain high rates of SARS-CoV-2 seropositivity among Black and Hispanic patients. Investing in structural neighborhood improvements may reduce inequities in viral transmission.

Analysis and prediction of COVID-19 epidemic in South Africa

The coronavirus disease-2019 (COVID-19) has been spreading rapidly in South Africa (SA) since its first case on 5 March 2020. In total, 674,339 confirmed cases and 16,734 mortality cases were reported by 30 September 2020, and this pandemic has made severe impacts on economy and life. In this paper, analysis and long-term prediction of the epidemic dynamics of SA are made, which could assist the government and public in assessing the past Infection Prevention and Control Measures and designing the future ones to contain the epidemic more effectively. A Susceptible-Infectious-Recovered model is adopted to analyse epidemic dynamics. The model parameters are estimated over different phases with the SA data. They indicate variations in the transmissibility of COVID-19 under different phases and thus reveal weakness of the past Infection Prevention and Control Measures in SA. The model also shows that transient behaviours of the daily growth rate and the cumulative removal rate exhibit periodic oscillations. Such dynamics indicates that the underlying signals are not stationary and conventional linear and nonlinear models would fail for long-term prediction. Therefore, a large class of mappings with rich functions and operations is chosen as the model class and the evolutionary algorithm is utilized to obtain the optimal model for long term prediction. The resulting models on the daily growth rate, the cumulative removal rate and the cumulative mortality rate predict that the peak and inflection point will occur on November 4, 2020 and October 15, 2020, respectively; the virus shall cease spreading on April 28, 2021; and the ultimate numbers of the COVID-19 cases and mortality cases will be 785,529 and 17,072, respectively. The approach is also benchmarked against other methods and shows better accuracy of long-term prediction.

Epidemic-like Calcium Signaling in Mobile Molecular Communication Networks

Molecular Communication is an emerging technology enabling communications in nano-networks. Ca2+ signal is one promising option of MC due to the important role in biometabolisms and the available characteristics in communication engineering. So far, scientists analyze Ca2+ signaling via bioexperiments and simulations. Current researches lack a mathematical model for quantitative analysis of Ca2+ signal propagation on the network scale. In this work, we investigate the propagation patterns of Ca2+ signals in bio-cellular network. Firstly, we propose an improved Ca2+ dynamics model to describe Ca2+ signals considering movements of cells and attenuation of Ca2+ concentration. Then, we perform multi-modal analysis through the waveform characteristics, and classify cells according to their states. Moreover, a mathematical model is put forward to analyze the propagation of calcium signals based on typical epidemic model. The proposed model fully considers the similarity between: 1) epidemic disease propagates among mobile individuals; 2) Ca2+ signal propagates among mobile cells. The proposed model is amended to fit the case considering unique characters of Ca2+ signal. Finally, simulation results show that the proposed Ca2+ propagation model is coincident with Monte Carlo simulation results, indicating that the model is helpful for understanding how far and how fast Ca2+ signal can propagate.

Analysis, Modeling, and Representation of COVID-19 Spread: A Case Study on India

Coronavirus outbreak is one of the challenging pandemics for the entire human population on Earth. Techniques, such as the isolation of infected people and maintaining social distancing, are the only preventive measures against the pandemic. The actual estimation of the number of infected peoples with limited data is an indeterminate problem faced by data scientists. There are several techniques in the existing literature, including reproduction number and case fatality rate, for predicting the duration of a pandemic and infectious population. This article presents a case study of different techniques for analyzing, modeling, and representing the data associated with a pandemic such as COVID-19. We further propose an algorithm for estimating infection transmission states in a particular area. This work also presents an algorithm for estimating end time of a pandemic from the susceptible infectious and recovered model. Finally, this article presents the empirical and data analysis to study the impact of transmission probability, rate of contact, infectious, and susceptible population on the pandemic spread.

Spread of Epidemic Disease on Edge-Weighted Graphs from a Database: A Case Study of COVID-19

The understanding of infectious diseases is a priority in the field of public health. This has generated the inclusion of several disciplines and tools that allow for analyzing the dissemination of infectious diseases. The aim of this manuscript is to model the spreading of a disease in a population that is registered in a database. From this database, we obtain an edge-weighted graph. The spreading was modeled with the classic SIR model. The model proposed with edge-weighted graph allows for identifying the most important variables in the dissemination of epidemics. Moreover, a deterministic approximation is provided. With database COVID-19 from a city in Chile, we analyzed our model with relationship variables between people. We obtained a graph with 3866 vertices and 6,841,470 edges. We fitted the curve of the real data and we have done some simulations on the obtained graph. Our model is adjusted to the spread of the disease. The model proposed with edge-weighted graph allows for identifying the most important variables in the dissemination of epidemics, in this case with real data of COVID-19. This valuable information allows us to also include/understand the networks of dissemination of epidemics diseases as well as the implementation of preventive measures of public health. These findings are important in COVID-19's pandemic context.

Real-Time Spatiotemporal Analysis of Microepidemics of Influenza and COVID-19 Based on Hospital Network Data: Colocalization of Neighborhood-Level Hotspots

Objectives. To identify spatiotemporal patterns of epidemic spread at the community level.Methods. We extracted influenza cases reported between 2016 and 2019 and COVID-19 cases reported in March and April 2020 from a hospital network in Rhode Island. We performed a spatiotemporal hotspot analysis to simulate a real-time surveillance scenario.Results. We analyzed 6527 laboratory-confirmed influenza cases and identified microepidemics in more than 1100 neighborhoods, and more than half of the neighborhoods that had hotspots in a season became hotspots in the next season. We used data from 731 COVID-19 cases, and we found that a neighborhood was 1.90 times more likely to become a COVID-19 hotspot if it had been an influenza hotspot in 2018 to 2019.Conclusions. The use of readily available hospital data allows the real-time identification of spatiotemporal trends and hotspots of microepidemics.Public Health Implications. As local governments move to reopen the economy and ease physical distancing, the use of historic influenza hotspots could guide early prevention interventions, while the real-time identification of hotspots would enable the implementation of interventions that focus on small-area containment and mitigation.

Motifs enable communication efficiency and fault-tolerance in transcriptional networks

Analysis of the topology of transcriptional regulatory networks (TRNs) is an effective way to study the regulatory interactions between the transcription factors (TFs) and the target genes. TRNs are characterized by the abundance of motifs such as feed forward loops (FFLs), which contribute to their structural and functional properties. In this paper, we focus on the role of motifs (specifically, FFLs) in signal propagation in TRNs and the organization of the TRN topology with FFLs as building blocks. To this end, we classify nodes participating in FFLs (termed motif central nodes) into three distinct roles (namely, roles A, B and C), and contrast them with TRN nodes having high connectivity on the basis of their potential for information dissemination, using metrics such as network efficiency, path enumeration, epidemic models and standard graph centrality measures. We also present the notion of a three tier architecture and how it can help study the structural properties of TRN based on connectivity and clustering tendency of motif central nodes. Finally, we motivate the potential implication of the structural properties of motif centrality in design of efficient protocols of information routing in communication networks as well as their functional properties in global regulation and stress response to study specific disease conditions and identification of drug targets.

Graph-theoretic node importance mining in world city networks: methods and applications

Purpose

This study aims to review the literature on graph-theoretic mining methods for node importance in both static and dynamic world city networks, which is correspondingly categorised by graph-theoretic node importance mining on network topologies and transmission mechanisms.

Design/methodology/approach

The authors overview the graph-theoretic indicators of node importance: centrality and power. Then, the methods of graph-theoretic node importance mining on network topologies are assessed with node relevance, centrality- and power-based measurements, heterogeneous fusion and other miscellaneous approaches. The latest progress in transmission mechanisms is also reviewed in this study involving network evolution, node immunisation and robustness in dynamics. Finally, the findings are analysed and future directions in this field are suggested.

Findings

The method development of node importance mining is driven by complex application-based problems within a transmission mechanism. Fusion measurements, based on centrality and power, are extended by other graph mining techniques in which power has a significant role. In conclusion, the trends of node importance mining focus on power-embedded fusion measurements in the transmission mechanism-based complex applications.

Originality/value

This is the first systematic literature review of node importance from the view of graph-theoretic mining.