scholarly journals Inferring high-resolution human mixing patterns for disease modeling

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dina Mistry ◽  
Maria Litvinova ◽  
Ana Pastore y Piontti ◽  
Matteo Chinazzi ◽  
Laura Fumanelli ◽  
...  

AbstractMathematical and computational modeling approaches are increasingly used as quantitative tools in the analysis and forecasting of infectious disease epidemics. The growing need for realism in addressing complex public health questions is, however, calling for accurate models of the human contact patterns that govern the disease transmission processes. Here we present a data-driven approach to generate effective population-level contact matrices by using highly detailed macro (census) and micro (survey) data on key socio-demographic features. We produce age-stratified contact matrices for 35 countries, including 277 sub-national administratvie regions of 8 of those countries, covering approximately 3.5 billion people and reflecting the high degree of cultural and societal diversity of the focus countries. We use the derived contact matrices to model the spread of airborne infectious diseases and show that sub-national heterogeneities in human mixing patterns have a marked impact on epidemic indicators such as the reproduction number and overall attack rate of epidemics of the same etiology. The contact patterns derived here are made publicly available as a modeling tool to study the impact of socio-economic differences and demographic heterogeneities across populations on the epidemiology of infectious diseases.

2018 ◽  
Author(s):  
Sergio Arregui ◽  
Alberto Aleta ◽  
Joaquín Sanz ◽  
Yamir Moreno

AbstractThe modeling of large-scale communicable epidemics has greatly benefited in the last years from the increasing availability of highly detailed data. Particularly, in order to achieve quantitative descriptions of the evolution of epidemics, contact networks and mixing patterns are key. These heterogeneous patterns depend on several factors such as location, socioeconomic conditions, time, and age. This last factor has been shown to encapsulate a large fraction of the observed inter-individual variation in contact patterns, an observation validated by different measurements of age-dependent contact matrices. Recently, several works have studied how to project those matrices to areas where empiric data is not available. However, the dependence of contact matrices on demographic structures and their time evolution has been largely neglected. In this work, we tackle the problem of how to transform an empirical contact matrix that has been obtained for a given demographic structure into a different contact matrix that is compatible with a different demography. The methodology discussed here allows extrapolating a contact structure measured in a particular area to any other whose demographic structure is known, as well as to obtain the time evolution of contact matrices as a function of the demographic dynamics of the populations they refer to. To quantify the effect of considering time-dynamics of contact patterns on disease modeling, we implemented a Susceptible-Exposed-Infected-Recovered (SEIR) model on 16 different countries and evaluated the impact of neglecting the temporal evolution of mixing patterns. Our results show that simulated disease incidence rates, both at the aggregated and age-specific levels, are significantly dependent on contact structures variation driven by demographic evolution. The present work opens the path to eliminate technical biases from model-based impact evaluations of future epidemic threats and warns against the use of contact matrices to model diseases without correcting for demographic evolution or geographic variations.Author summaryLarge scale epidemic outbreaks represent an ever increasing threat to humankind. In order to anticipate eventual pandemics, mathematical modeling should not only have the capacity to model in real time an ongoing disease, but also to predict the evolution of potential outbreaks in different locations and times. To this end, computational frameworks need to incorporate, among other ingredients, realistic contact patterns into the models. This not only implies anticipating the demographic structure of the populations under study, but also understanding how demographic evolution reshapes social mixing patterns along time. Here we present a mathematical framework to solve this problem and test our modeling approach on 16 different empirical contact matrices. We also evaluate the impact of an eventual future outbreak by simulating a SEIR scenario in the countries analyzed. Our results show that using outdated or imported contact matrices that do not take into account demographic structure or its evolution can lead to largely misleading conclusions.


2021 ◽  
Author(s):  
Jesse Knight ◽  
Huiting Ma ◽  
Amir Ghasemi ◽  
Mackenzie Hamilton ◽  
Kevin Brown ◽  
...  

AbstractInfectious disease transmission models often stratify populations by age and geographic patches. Contact patterns between age groups and patches are key parameters in such models. Arenas et al. (2020) develop an approach to simulate contact patterns associated with recurrent mobility between patches, such as due to work, school, and other regular travel. Using their approach, mixing between patches is greater than mobility data alone would suggest, because individuals from patches A and B can form a contact if they meet in patch C. We build upon their approach to address three potential gaps that remain. First, our approach includes a distribution of contacts by age that is responsive to underlying age distribution of the mixing pool. Second, different age distributions by contact type are also maintained in our approach, such that changes to the numbers of different types of contacts are appropriately reflected in changes to the overall age mixing patterns. Finally, we introduce and distinguish between two mixing pools associated with each patch, with possible implications for the overall connectivity of the population: the home pool, in which contacts can only be formed with other individuals residing in the same patch; and the travel pool, in which contacts can be formed with some residents of, and any other visitors to the patch. We describe in detail the steps required to implement our approach, and present results of an example application.Graphical Abstract


Vaccines ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1180
Author(s):  
Tinevimbo Shiri ◽  
Marc Evans ◽  
Carla A. Talarico ◽  
Angharad R. Morgan ◽  
Maaz Mussad ◽  
...  

Debate persists around the risk–benefit balance of vaccinating adolescents and children against COVID-19. Central to this debate is quantifying the contribution of adolescents and children to the transmission of SARS-CoV-2, and the potential impact of vaccinating these age groups. In this study, we present a novel SEIR mathematical disease transmission model that quantifies the impact of different vaccination strategies on population-level SARS-CoV-2 infections and clinical outcomes. The model employs both age- and time-dependent social mixing patterns to capture the impact of changes in restrictions. The model was used to assess the impact of vaccinating adolescents and children on the natural history of the COVID-19 pandemic across all age groups, using the UK as an example. The base case model demonstrates significant increases in COVID-19 disease burden in the UK following a relaxation of restrictions, if vaccines are limited to those ≥18 years and vulnerable adolescents (≥12 years). Including adolescents and children in the vaccination program could reduce overall COVID-related mortality by 57%, and reduce cases of long COVID by 75%. This study demonstrates that vaccinating adolescents and children has the potential to play a vital role in reducing SARS-CoV-2 infections, and subsequent COVID-19 morbidity and mortality, across all ages. Our results have major global public health implications and provide valuable information to inform a potential pandemic exit strategy.


Author(s):  
Katharina Hauck

Economics can make immensely valuable contributions to our understanding of infectious disease transmission and the design of effective policy responses. The one unique characteristic of infectious diseases makes it also particularly complicated to analyze: the fact that it is transmitted from person to person. It explains why individuals’ behavior and externalities are a central topic for the economics of infectious diseases. Many public health interventions are built on the assumption that individuals are altruistic and consider the benefits and costs of their actions to others. This would imply that even infected individuals demand prevention, which stands in conflict with the economic theory of rational behavior. Empirical evidence is conflicting for infected individuals. For healthy individuals, evidence suggests that the demand for prevention is affected by real or perceived risk of infection. However, studies are plagued by underreporting of preventive behavior and non-random selection into testing. Some empirical studies have shown that the impact of prevention interventions could be far greater than one case prevented, resulting in significant externalities. Therefore, economic evaluations need to build on dynamic transmission models in order to correctly estimate these externalities. Future research needs are significant. Economic research needs to improve our understanding of the role of human behavior in disease transmission; support the better integration of economic and epidemiological modeling, evaluation of large-scale public health interventions with quasi-experimental methods, design of optimal subsidies for tackling the global threat of antimicrobial resistance, refocusing the research agenda toward underresearched diseases; and most importantly to assure that progress translates into saved lives on the ground by advising on effective health system strengthening.


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.


Author(s):  
Fatima Khadadah ◽  
Abdullah A. Al-Shammari ◽  
Ahmad Alhashemi ◽  
Dari Alhuwail ◽  
Bader Al-Saif ◽  
...  

Background: Aggressive non-pharmaceutical interventions (NPIs) may reduce transmission of SARS-CoV2. The extent to which these interventions are successful in stopping the spread have not been characterized in countries with distinct socioeconomic groups. We compared the effects of a partial lockdown on disease transmission among Kuwaitis (P1) and non-Kuwaitis (P2) living in Kuwait. Methods: We fit a metapopulation Susceptible-Exposed-Infectious-Recovered (SEIR) model to reported cases stratified by two groups to estimate the impact of a lockdown on the effective reproduction number (Re). We estimated the basic reproduction number (R0) for the transmission in each group and simulated the potential trajectories of an outbreak from the first recorded case of community transmission until 12 days after the lockdown. We estimated R­e values of both groups before and after the lockdown, simulated the effect of these values on epidemic curves and explored a range of cross-transmission scenarios. Results: We estimate R0 at 1·06 (95% CI: 1·05-1·28) for P1 and 1·83 (1·58-2·33) for P2. On March 22nd, Re for P1 and P2 are estimated at 1·13 (1·07-1·17) and 1·38 (1·25-1·63) respectively. After the curfew had taken effect, Re for P1 dropped modestly to 1·04 (1·02-1·06) but almost doubled for P2 to 2·47 (1·98-3·45). Our simulated epidemic trajectories show that the partial curfew measure modestly reduced and delayed the height of the peak in P1, yet significantly elevated and hastened the peak in P2. Modest cross-transmission from P2 to P1 elevated the height of the peak in P1 and brought it forward in time closer to the peak of P2.    Conclusion: Our results demonstrate that a lockdown can reduce SARS-CoV2 transmission in one subpopulation but accelerate it in another. At the population level, the consequences of lockdowns may vary across the socioeconomic spectrum. Any public health intervention needs to be sensitive to disparities within populations.


2021 ◽  
Vol 17 (2) ◽  
pp. e1008713 ◽  
Author(s):  
Joshua Havumaki ◽  
Ted Cohen ◽  
Chengwei Zhai ◽  
Joel C. Miller ◽  
Seth D. Guikema ◽  
...  

There is an emerging consensus that achieving global tuberculosis control targets will require more proactive case finding approaches than are currently used in high-incidence settings. Household contact tracing (HHCT), for which households of newly diagnosed cases are actively screened for additional infected individuals is a potentially efficient approach to finding new cases of tuberculosis, however randomized trials assessing the population-level effects of such interventions in settings with sustained community transmission have shown mixed results. One potential explanation for this is that household transmission is responsible for a variable proportion of population-level tuberculosis burden between settings. For example, transmission is more likely to occur in households in settings with a lower tuberculosis burden and where individuals mix preferentially in local areas, compared with settings with higher disease burden and more dispersed mixing. To better understand the relationship between endemic incidence levels, social mixing, and the impact of HHCT, we developed a spatially explicit model of coupled household and community transmission. We found that the impact of HHCT was robust across settings of varied incidence and community contact patterns. In contrast, we found that the effects of community contact tracing interventions were sensitive to community contact patterns. Our results suggest that the protective benefits of HHCT are robust and the benefits of this intervention are likely to be maintained across epidemiological settings.


2007 ◽  
Vol 4 (16) ◽  
pp. 879-891 ◽  
Author(s):  
Shweta Bansal ◽  
Bryan T Grenfell ◽  
Lauren Ancel Meyers

Heterogeneity in host contact patterns profoundly shapes population-level disease dynamics. Many epidemiological models make simplifying assumptions about the patterns of disease-causing interactions among hosts. In particular, homogeneous-mixing models assume that all hosts have identical rates of disease-causing contacts. In recent years, several network-based approaches have been developed to explicitly model heterogeneity in host contact patterns. Here, we use a network perspective to quantify the extent to which real populations depart from the homogeneous-mixing assumption, in terms of both the underlying network structure and the resulting epidemiological dynamics. We find that human contact patterns are indeed more heterogeneous than assumed by homogeneous-mixing models, but are not as variable as some have speculated. We then evaluate a variety of methodologies for incorporating contact heterogeneity, including network-based models and several modifications to the simple SIR compartmental model. We conclude that the homogeneous-mixing compartmental model is appropriate when host populations are nearly homogeneous, and can be modified effectively for a few classes of non-homogeneous networks. In general, however, network models are more intuitive and accurate for predicting disease spread through heterogeneous host populations.


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