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

Gilbertson, Marie L. J.; Fountain-Jones, Nicholas M.; Craft, Meggan E.

doi:10.1163/1568539x-00003471

Cited by 19 publications

(16 citation statements)

References 108 publications

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“…Such approaches have already incorporated landscape and other environmental features. In addition, the potential for inferring host contacts in network models using pathogen genetic markers (see below) has been acknowledged in recent reviews (Craft, ; Gilbertson, Fountain‐Jones, & Craft, ; White, Forester, & Craft, ), and some studies have directly compared host contact network parameters to parasite genotypes (Bull, Godfrey, & Gordon, ). Despite this, to our knowledge, no published studies have used network models to investigate pathogen movement within a landscape genetic framework.…”

Section: Common Methodological Approaches In Landscape Genetics and Tmentioning

confidence: 99%

Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics

Kozakiewicz

Burridge

Funk

et al. 2018

Evolutionary Applications

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Landscape genetics has provided many insights into how heterogeneous landscape features drive processes influencing spatial genetic variation in free‐living organisms. This rapidly developing field has focused heavily on vertebrates, and expansion of this scope to the study of infectious diseases holds great potential for landscape geneticists and disease ecologists alike. The potential application of landscape genetics to infectious agents has garnered attention at formative stages in the development of landscape genetics, but systematic examination is lacking. We comprehensively review how landscape genetics is being used to better understand pathogen dynamics. We characterize the field and evaluate the types of questions addressed, approaches used and systems studied. We also review the now established landscape genetic methods and their realized and potential applications to disease ecology. Lastly, we identify emerging frontiers in the landscape genetic study of infectious agents, including recent phylogeographic approaches and frameworks for studying complex multihost and host‐vector systems. Our review emphasizes the expanding utility of landscape genetic methods available for elucidating key pathogen dynamics (particularly transmission and spread) and also how landscape genetic studies of pathogens can provide insight into host population dynamics. Through this review, we convey how increasing awareness of the complementarity of landscape genetics and disease ecology among practitioners of each field promises to drive important cross‐disciplinary advances.

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Section: Common Methodological Approaches In Landscape Genetics and Tmentioning

confidence: 99%

Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics

Kozakiewicz

Burridge

Funk

et al. 2018

Evolutionary Applications

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“…The emerging field of phylodynamics coupled with parasite genomic data shows great potential for building upon and refining our understanding of parasite transmission in wildlife populations (see earlier section on ‘Spatial structure’). Additionally, incorporating social or contact data with parasite genomic data in a network analysis framework is an exciting open avenue for investigating disease dynamics (White et al 2017 ; Gilbertson et al 2018 ). For example, in a well-characterized European badger and cattle population, Crispell et al ( 2019 ) compared Mycobacterium bovis (causative agent for bovine tuberculosis) genomes from cattle and badgers to examine cross-species transmission and obtain fine-scale resolution of contact networks for bovine tuberculosis transmission.…”

Section: Fine Scale Transmission Dynamics: Contact Networkmentioning

confidence: 99%

Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservation†

Gupta

Robin

Dharmarajan

2020

J Genet

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Parasites, and the diseases they cause, are important from an ecological and evolutionary perspective because they can negatively affect host fitness and can regulate host populations. Consequently, conservation biology has long recognized the vital role that parasites can play in the process of species endangerment and recovery. However, we are only beginning to understand how deeply parasites are embedded in ecological systems, and there is a growing recognition of the important ways in which parasites affect ecosystem structure and function. Thus, there is an urgent need to revisit how parasites are viewed from a conservation perspective and broaden the role that disease ecology plays in conservation-related research and outcomes. This review broadly focusses on the role that disease ecology can play in biological conservation. Our review specifically emphasizes on how the integration of tools and analytical approaches associated with both disease and molecular ecology can be leveraged to aid conservation biology. Our review first concentrates on diseasemediated extinctions and wildlife epidemics. We then focus on elucidating how host-parasite interactions has improved our understanding of the eco-evolutionary dynamics affecting hosts at the individual, population, community and ecosystem scales. We believe that the role of parasites as drivers and indicators of ecosystem health is especially an exciting area of research that has the potential to fundamentally alter our view of parasites and their role in biological conservation. The review concludes with a broad overview of the current and potential applications of modern genomic tools in disease ecology to aid biological conservation.

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“…Such apathogenic agents should have rapid mutation rates to facilitate discernment of transmission relationships between individuals over time (31,32). Furthermore, these agents should be relatively common and well-sampled in a target population, have a well-characterized mode of transmission, and feature high strain alpha-diversity (local diversity) and high strain turnover (32,33). RNA viruses align well with these characteristics (34,35) such that apathogenic RNA viruses could act as "proxies" of specific modes of transmission (i.e., direct transmission) and indicate which drivers underlie transmission processes (36).…”

Section: Introductionmentioning

confidence: 99%

Transmission of one predicts another: Apathogenic proxies for transmission dynamics of a fatal virus

Gilbertson

Fountain-Jones

Malmberg

et al. 2021

Preprint

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Identifying drivers of transmission prior to an epidemic—especially of an emerging pathogen—is a formidable challenge for proactive disease management efforts. To overcome this gap, we tested a novel approach hypothesizing that an apathogenic virus could elucidate drivers of transmission processes, and thereby predict transmission dynamics of an analogously transmitted virulent pathogen. We evaluated this hypothesis in a model system, the Florida panther (Puma concolor coryi), using apathogenic feline immunodeficiency virus (FIV) to predict transmission dynamics for another retrovirus, pathogenic feline leukemia virus (FeLV). We derived a transmission network using FIV whole genome sequences, and used exponential random graph models to determine drivers structuring this network. We used the identified drivers to predict transmission pathways among panthers; simulated FeLV transmission using these pathways and three alternate modeling approaches; and compared predictions against empirical data collected during a historical FeLV outbreak in panthers. FIV transmission was primarily driven by panther age class and distances between panther home range centroids. Prospective FIV-based predictions of FeLV transmission dynamics performed at least as well as simpler, often retrospective approaches, with evidence that FIV-based predictions could capture the spatial structuring of the observed FeLV outbreak. Our finding that an apathogenic agent can predict transmission of an analogously transmitted pathogen is an innovative approach that warrants testing in other host-pathogen systems to determine generalizability. Use of such apathogenic agents holds promise for improving predictions of pathogen transmission in novel host populations, and can thereby revolutionize proactive pathogen management in human and animal systems.Significance StatementPredicting infectious disease transmission dynamics is fraught with assumptions which limit our ability to proactively develop targeted control strategies. We show that transmission of non-disease causing (apathogenic) agents provides invaluable insight into drivers of transmission prior to outbreaks of more serious diseases. Integrating genomic and network approaches, we tested an apathogenic virus as a proxy for predicting transmission dynamics of a deadly virus in the Florida panther. We found that apathogenic virus-based predictions of pathogen transmission dynamics performed at least as well as simpler transmission models, and offered the advantage of prospectively identifying the underlying management-relevant drivers of transmission. Our innovative approach offers an opportunity to proactively design disease control strategies in at-risk animal and human populations.

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

Cited by 19 publications

References 108 publications

Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics

Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics

Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservation†

Transmission of one predicts another: Apathogenic proxies for transmission dynamics of a fatal virus

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