CTCmodeler: An Agent-Based Framework to Simulate Pathogen Transmission Along an Inter-individual Contact Network in a Hospital

Pathogens inflict a wide variety of disease manifestations on their hosts, yet the impacts of disease on the behaviour of infected hosts are rarely studied empirically and are seldom accounted for in mathematical models of transmission dynamics. We explored the potential impacts of one of the most common disease manifestations, fever, on a key determinant of pathogen transmission, host mobility, in residents of the Amazonian city of Iquitos, Peru. We did so by comparing two groups of febrile individuals (dengue-positive and dengue-negative) with an afebrile control group. A retrospective, semi-structured interview allowed us to quantify multiple aspects of mobility during the two-week period preceding each interview. We fitted nested models of each aspect of mobility to data from interviews and compared models using likelihood ratio tests to determine whether there were statistically distinguishable differences in mobility attributable to fever or its aetiology. Compared with afebrile individuals, febrile study participants spent more time at home, visited fewer locations, and, in some cases, visited locations closer to home and spent less time at certain types of locations. These multifaceted impacts are consistent with the possibility that disease-mediated changes in host mobility generate dynamic and complex changes in host contact network structure.

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Incorporating genomic methods into contact networks to reveal new insights into animal behaviour and infectious disease dynamics

Behaviour ◽

10.1163/1568539x-00003471 ◽

2018 ◽

Vol 155 (7-9) ◽

pp. 759-791 ◽

Cited By ~ 5

Author(s):

Marie L.J. Gilbertson ◽

Nicholas M. Fountain-Jones ◽

Meggan E. Craft

Keyword(s):

Infectious Disease ◽

Disease Ecology ◽

Pathogen Transmission ◽

Contact Network ◽

Contact Networks ◽

Host Behaviour ◽

Infectious Disease Dynamics ◽

Insight Into ◽

Dynamic Interplay ◽

Broad Overview

Abstract Utilization of contact networks has provided opportunities for assessing the dynamic interplay between pathogen transmission and host behaviour. Genomic techniques have, in their own right, provided new insight into complex questions in disease ecology, and the increasing accessibility of genomic approaches means more researchers may seek out these tools. The integration of network and genomic approaches provides opportunities to examine the interaction between behaviour and pathogen transmission in new ways and with greater resolution. While a number of studies have begun to incorporate both contact network and genomic approaches, a great deal of work has yet to be done to better integrate these techniques. In this review, we give a broad overview of how network and genomic approaches have each been used to address questions regarding the interaction of social behaviour and infectious disease, and then discuss current work and future horizons for the merging of these techniques.

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Data on face-to-face contacts in an office building suggest a low-cost vaccination strategy based on community linkers

Network Science ◽

10.1017/nws.2015.10 ◽

2015 ◽

Vol 3 (3) ◽

pp. 326-347 ◽

Cited By ~ 71

Author(s):

MATHIEU GÉNOIS ◽

CHRISTIAN L. VESTERGAARD ◽

JULIE FOURNET ◽

ANDRÉ PANISSON ◽

ISABELLE BONMARIN ◽

...

Keyword(s):

Low Cost ◽

A Priori ◽

Vaccination Strategy ◽

Social Contexts ◽

Office Building ◽

Disease Spread ◽

Contact Network ◽

Time Resolved ◽

Agent Based ◽

Face To Face

AbstractEmpirical data on contacts between individuals in social contexts play an important role in providing information for models describing human behavior and how epidemics spread in populations. Here, we analyze data on face-to-face contacts collected in an office building. The statistical properties of contacts are similar to other social situations, but important differences are observed in the contact network structure. In particular, the contact network is strongly shaped by the organization of the offices in departments, which has consequences in the design of accurate agent-based models of epidemic spread. We consider the contact network as a potential substrate for infectious disease spread and show that its sparsity tends to prevent outbreaks of rapidly spreading epidemics. Moreover, we define three typical behaviors according to the fraction f of links each individual shares outside its own department: residents, wanderers, and linkers. Linkers (f ~ 50%) act as bridges in the network and have large betweenness centralities. Thus, a vaccination strategy targeting linkers efficiently prevents large outbreaks. As such a behavior may be spotted a priori in the offices' organization or from surveys, without the full knowledge of the time-resolved contact network, this result may help the design of efficient, low-cost vaccination or social-distancing strategies.

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Reopen Schools Safely: Simulating COVID-19 Transmission on Campus With a Contact Network Agent-based Model

10.21203/rs.3.rs-627505/v1 ◽

2021 ◽

Author(s):

Chuyao Liao ◽

Xiang Chen ◽

Li Zhuo ◽

Yuan Liu ◽

Haiyan Tao

Keyword(s):

Disease Transmission ◽

Local Governments ◽

Vaccination Rate ◽

Contact Network ◽

Agent Based Model ◽

School Officials ◽

Agent Based ◽

Epidemic Curve ◽

Prime Concern ◽

Peak Value

Abstract Background: As phases of COVID-19 vaccination are quickly rolling out, how to evaluate the vaccination effects and then make safe reopening plans has become a prime concern for local governments and school officials.Methods: We develop a contact network agent-based model (CN-ABM) to simulate on-campus disease transmission scenarios at the micro-scale. The CN-ABM establishes a contact network for each agent based on their daily activity pattern, evaluates the agent's health status change in different activity environments, and then simulates the epidemic curve on campus. Based on the developed model, we identify how different community risk levels, teaching modalities, and vaccination rates would shape the epidemic curve. Results: The results show that in scenarios where vaccination is not available, restricting on-campus students to under 50% can largely flatten the epi curve (peak value < 2%); and the best result (peak value < 1%) can be achieved by limiting on-campus students to less than 25%. In scenarios where vaccination is available, it is suggested to maintain a maximum of 75% on-campus students and a vaccination rate of at least 45% to suppress the curve (peak value < 2%); and the best result (peak value < 1%) can be achieved at a vaccination rate of 65%. The study also derives the transmission chain of infectious agents, which can be used to identify high-risk activity environments. Conclusions: The developed CN-ABM model can be employed to evaluate the health outcome of COVID-19 outbreaks on campus based on different disease transmission scenarios. It can assist local government and school officials with developing proactive intervention strategies to safely reopen schools.

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Seasonality and pathogen transmission in pastoral cattle contact networks

Royal Society Open Science ◽

10.1098/rsos.170808 ◽

2017 ◽

Vol 4 (12) ◽

pp. 170808 ◽

Cited By ~ 19

Author(s):

Kimberly VanderWaal ◽

Marie Gilbertson ◽

Sharon Okanga ◽

Brian F. Allan ◽

Meggan E. Craft

Keyword(s):

Water Resources ◽

Disease Outbreaks ◽

Dry Season ◽

Pathogen Transmission ◽

Contact Network ◽

Wet Season ◽

Contact Networks ◽

Contact Rates ◽

Animal Populations ◽

The Impact

Capturing heterogeneity in contact patterns in animal populations is essential for understanding the spread of infectious diseases. In contrast to other regions of the world in which livestock movement networks are integral to pathogen prevention and control policies, contact networks are understudied in pastoral regions of Africa due to the challenge of measuring contact among mobile herds of cattle whose movements are driven by access to resources. Furthermore, the extent to which seasonal changes in the distribution of water and resources impacts the structure of contact networks in cattle is uncertain. Contact networks may be more conducive to pathogen spread in the dry season due to congregation at limited water sources. Alternatively, less abundant forage may result in decreased pathogen transmission due to competitive avoidance among herds, as measured by reduced contact rates. Here, we use GPS technology to concurrently track 49 free-roaming cattle herds within a semi-arid region of Kenya, and use these data to characterize seasonal contact networks and model the spread of a highly infectious pathogen. This work provides the first empirical data on the local contact network structure of mobile herds based on quantifiable contact events. The contact network demonstrated high levels of interconnectivity. An increase in contacts near to water resources in the dry season resulted in networks with both higher contact rates and higher potential for pathogen spread than in the wet season. Simulated disease outbreaks were also larger in the dry season. Results support the hypothesis that limited water resources enhance connectivity and transmission within contact networks, as opposed to reducing connectivity as a result of competitive avoidance. These results cast light on the impact of seasonal heterogeneity in resource availability on predicting pathogen transmission dynamics, which has implications for other free-ranging wild and domestic populations.

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Brown spider monkeys ( Ateles hybridus ): a model for differentiating the role of social networks and physical contact on parasite transmission dynamics

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2014.0110 ◽

2015 ◽

Vol 370 (1669) ◽

pp. 20140110 ◽

Cited By ~ 46

Author(s):

Rebecca Rimbach ◽

Donal Bisanzio ◽

Nelson Galvis ◽

Andrés Link ◽

Anthony Di Fiore ◽

...

Keyword(s):

Social Interactions ◽

Disease Transmission ◽

Group Living ◽

Social Contact ◽

Pathogen Transmission ◽

Physical Contact ◽

Contact Network ◽

Spider Monkeys ◽

Parasite Transmission ◽

Brown Spider

Elevated risk of disease transmission is considered a major cost of sociality, although empirical evidence supporting this idea remains scant. Variation in spatial cohesion and the occurrence of social interactions may have profound implications for patterns of interindividual parasite transmission. We used a social network approach to shed light on the importance of different aspects of group-living (i.e. within-group associations versus physical contact) on patterns of parasitism in a neotropical primate, the brown spider monkey ( Ateles hybridus ), which exhibits a high degree of fission–fusion subgrouping. We used daily subgroup composition records to create a ‘proximity’ network, and built a separate ‘contact’ network using social interactions involving physical contact. In the proximity network, connectivity between individuals was homogeneous, whereas the contact network highlighted high between-individual variation in the extent to which animals had physical contact with others, which correlated with an individual's age and sex. The gastrointestinal parasite species richness of highly connected individuals was greater than that of less connected individuals in the contact network, but not in the proximity network. Our findings suggest that among brown spider monkeys, physical contact impacts the spread of several common parasites and supports the idea that pathogen transmission is one cost associated with social contact.

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Sex, synchrony, and skin contact: integrating multiple behaviors to assess pathogen transmission risk

Behavioral Ecology ◽

10.1093/beheco/araa002 ◽

2020 ◽

Vol 31 (3) ◽

pp. 651-660 ◽

Cited By ~ 6

Author(s):

Stephan T Leu ◽

Pratha Sah ◽

Ewa Krzyszczyk ◽

Ann-Marie Jacoby ◽

Janet Mann ◽

...

Keyword(s):

Disease Risk ◽

Bottlenose Dolphins ◽

Social Contact ◽

Social Behaviors ◽

Pathogen Transmission ◽

Transmission Risk ◽

Spatial Proximity ◽

Contact Network ◽

Skin Contact ◽

Animal Populations

Abstract Direct pathogen and parasite transmission is fundamentally driven by a population’s contact network structure and its demographic composition and is further modulated by pathogen life-history traits. Importantly, populations are most often concurrently exposed to a suite of pathogens, which is rarely investigated, because contact networks are typically inferred from spatial proximity only. Here, we use 5 years of detailed observations of Indo-Pacific bottlenose dolphins (Tursiops aduncus) that distinguish between four different types of social contact. We investigate how demography (sex and age) affects these different social behaviors. Three of the four social behaviors can be used as a proxy for understanding key routes of direct pathogen transmission (sexual contact, skin contact, and aerosol contact of respiratory vapor above the water surface). We quantify the demography-dependent network connectedness, representing the risk of exposure associated with the three pathogen transmission routes, and quantify coexposure risks and relate them to individual sociability. Our results suggest demography-driven disease risk in bottlenose dolphins, with males at greater risk than females, and transmission route-dependent implications for different age classes. We hypothesize that male alliance formation and the divergent reproductive strategies in males and females drive the demography-dependent connectedness and, hence, exposure risk to pathogens. Our study provides evidence for the risk of coexposure to pathogens transmitted along different transmission routes and that they relate to individual sociability. Hence, our results highlight the importance of a multibehavioral approach for a more complete understanding of the overall pathogen transmission risk in animal populations, as well as the cumulative costs of sociality.

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Advances from the nexus of animal behaviour and pathogen transmission: new directions and opportunities using contact networks

Behaviour ◽

10.1163/1568539x-00003507 ◽

2018 ◽

Vol 155 (7-9) ◽

pp. 567-583 ◽

Cited By ~ 1

Author(s):

Stephan T. Leu ◽

Stephanie S. Godfrey

Keyword(s):

High Resolution ◽

Disease Transmission ◽

Network Models ◽

Population Level ◽

Pathogen Transmission ◽

Molecular Techniques ◽

Gps Tracking ◽

Contact Network ◽

Computational Techniques ◽

Contact Networks

Abstract Contact network models have enabled significant advances in understanding the influence of behaviour on parasite and pathogen transmission. They are an important tool that links variation in individual behaviour, to epidemiological consequences at the population level. Here, in our introduction to this special issue, we highlight the importance of applying network approaches to disease ecological and epidemiological questions, and how this has provided a much deeper understanding of these research areas. Recent advances in tracking host behaviour (bio-logging: e.g., GPS tracking, barcoding) and tracking pathogens (high-resolution sequencing), as well as methodological advances (multi-layer networks, computational techniques) started producing exciting new insights into disease transmission through contact networks. We discuss some of the exciting directions that the field is taking, some of the challenges, and importantly the opportunities that lie ahead. For instance, we suggest to integrate multiple transmission pathways, multiple pathogens, and in some systems, multiple host species, into the next generation of network models. Corresponding opportunities exist in utilising molecular techniques, such as high-resolution sequencing, to establish causality in network connectivity and disease outcomes. Such novel developments and the continued integration of network tools offers a more complete understanding of pathogen transmission processes, their underlying mechanisms and their evolutionary consequences.

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