1
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Yin S, Xu C, Zhang Y, de Boer WF, Mundkur T, Artois J, Velkers FC, Takekawa JY, Si Y, Tian H, Han GZ, Chen Y, Chai H, Cui L, Huang ZYX. Strong and consistent effects of waterbird composition on HPAI H5 occurrences across Europe. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2024; 34:e3010. [PMID: 38978282 DOI: 10.1002/eap.3010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 03/01/2024] [Accepted: 04/22/2024] [Indexed: 07/10/2024]
Abstract
Since 2014, highly pathogenic avian influenza (HPAI) H5 viruses of clade 2.3.4.4 have been dominating the outbreaks across Europe, causing massive deaths among poultry and wild birds. However, the factors shaping these broad-scale outbreak patterns, especially those related to waterbird community composition, remain unclear. In particular, we do not know whether these risk factors differ from those of other H5 clades. Addressing this knowledge gap is important for predicting and preventing future HPAI outbreaks. Using extensive waterbird survey datasets from about 6883 sites, we here explored the effect of waterbird community composition on HPAI H5Nx (clade 2.3.4.4) spatial patterns in the 2016/2017 and 2020/2021 epidemics in Europe, and compared it with the 2005/2006 HPAI H5N1 (clade 2.2) epidemic. We showed that HPAI H5 occurrences in wild birds in the three epidemics were strongly associated with very similar waterbird community attributes, which suggested that, in nature, similar interspecific transmission processes operate between the HPAI H5 subtypes or clades. Importantly, community phylogenetic diversity consistently showed a negative association with H5 occurrence in all three epidemics, suggesting a dilution effect of phylogenetic diversity. In contrast, waterbird community variables showed much weaker associations with HPAI H5Nx occurrence in poultry. Our results demonstrate that models based on previous epidemics can predict future HPAI H5 patterns in wild birds, implying that it is important to include waterbird community factors in future HPAI studies to predict outbreaks and improve surveillance activities.
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Affiliation(s)
- Shenglai Yin
- Department of Zoology, School of Life Sciences, Nanjing Forestry University, Nanjing, China
- Department of Ecology, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chi Xu
- Department of Ecology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yong Zhang
- Department of Zoology, School of Life Sciences, Nanjing Forestry University, Nanjing, China
| | - Willem F de Boer
- Wildlife Ecology and Conservation Group, Wageningen University, Wageningen, The Netherlands
| | | | - Jean Artois
- Spatial Epidemiology Lab, Université Libre de Bruxelles, Brussels, Belgium
| | - Francisca C Velkers
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | - Yali Si
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, Beijing Normal University, Beijing, China
| | - Guan-Zhu Han
- Department of Ecology, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yuyang Chen
- State Key Laboratory of Remote Sensing Science, Beijing Normal University, Beijing, China
| | - Hongliang Chai
- Department of Wildlife Conservation and Management, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Lijuan Cui
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Zheng Y X Huang
- Department of Ecology, School of Life Sciences, Nanjing Normal University, Nanjing, China
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2
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Suh DC, Lance SL, Park AW. Abiotic and biotic factors jointly influence the contact and environmental transmission of a generalist pathogen. Ecol Evol 2024; 14:e70167. [PMID: 39157664 PMCID: PMC11329300 DOI: 10.1002/ece3.70167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024] Open
Abstract
The joint influence of abiotic and biotic factors is important for understanding the transmission of generalist pathogens. Abiotic factors such as temperature can directly influence pathogen persistence in the environment and will also affect biotic factors, such as host community composition and abundance. At intermediate spatial scales, the effects of temperature, community composition, and host abundance are expected to contribute to generalist pathogen transmission. We use a simple transmission model to explain and predict how host community composition, host abundance, and environmental pathogen persistence times can independently and jointly influence transmission. Our transmission model clarifies how abiotic and biotic factors can synergistically support the transmission of a pathogen. The empirical data show that high community competence, high abundance, and low temperatures correlate with high levels of transmission of ranavirus in larval amphibian communities. Discrete wetlands inhabited by larval amphibians in the presence of ranavirus provide a compelling case study comprising distinct host communities at a spatial scale anticipated to demonstrate abiotic and biotic influence on transmission. We use these host communities to observe phenomena demonstrated in our theoretical model. These findings emphasize the importance of considering both abiotic and biotic factors, and concomitant direct and indirect mechanisms, in the study of pathogen transmission and should extend to other generalist pathogens with the capacity for environmental transmission.
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Affiliation(s)
- Daniel C. Suh
- Odum School of EcologyUniversity of GeorgiaAthensGeorgiaUSA
- Center for the Ecology of Infectious DiseasesUniversity of GeorgiaAthensGeorgiaUSA
| | - Stacey L. Lance
- Center for the Ecology of Infectious DiseasesUniversity of GeorgiaAthensGeorgiaUSA
- Savannah River Ecology LaboratoryUniversity of GeorgiaAikenSouth CarolinaUSA
| | - Andrew W. Park
- Odum School of EcologyUniversity of GeorgiaAthensGeorgiaUSA
- Center for the Ecology of Infectious DiseasesUniversity of GeorgiaAthensGeorgiaUSA
- Department of Infectious Diseases, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA
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3
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Morris R, Wang S. Building a pathway to One Health surveillance and response in Asian countries. SCIENCE IN ONE HEALTH 2024; 3:100067. [PMID: 39077383 PMCID: PMC11262298 DOI: 10.1016/j.soh.2024.100067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/27/2024] [Indexed: 07/31/2024]
Abstract
To detect and respond to emerging diseases more effectively, an integrated surveillance strategy needs to be applied to both human and animal health. Current programs in Asian countries operate separately for the two sectors and are principally concerned with detection of events that represent a short-term disease threat. It is not realistic to either invest only in efforts to detect emerging diseases, or to rely solely on event-based surveillance. A comprehensive strategy is needed, concurrently investigating and managing endemic zoonoses, studying evolving diseases which change their character and importance due to influences such as demographic and climatic change, and enhancing understanding of factors which are likely to influence the emergence of new pathogens. This requires utilisation of additional investigation tools that have become available in recent years but are not yet being used to full effect. As yet there is no fully formed blueprint that can be applied in Asian countries. Hence a three-step pathway is proposed to move towards the goal of comprehensive One Health disease surveillance and response.
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Affiliation(s)
- Roger Morris
- Massey University EpiCentre and EpiSoft International Ltd, 76/100 Titoki Street, Masterton 5810, New Zealand
| | - Shiyong Wang
- Health, Nutrition and Population, World Bank Group, Washington, DC, USA
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4
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Brian JI, Aldridge DC. Host and parasite identity interact in scale-dependent fashion to determine parasite community structure. Oecologia 2024; 204:199-211. [PMID: 38206416 PMCID: PMC10830602 DOI: 10.1007/s00442-023-05499-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 12/10/2023] [Indexed: 01/12/2024]
Abstract
Understanding the ecological assembly of parasite communities is critical to characterise how changing host and environmental landscapes will alter infection dynamics and outcomes. However, studies frequently assume that (a) closely related parasite species or those with identical life-history strategies are functionally equivalent, and (b) the same factors will drive infection dynamics for a single parasite across multiple host species, oversimplifying community assembly patterns. Here, we challenge these two assumptions using a naturally occurring host-parasite system, with the mussel Anodonta anatina infected by the digenean trematode Echinoparyphium recurvatum, and the snail Viviparus viviparus infected by both E. recurvatum and Echinostoma sp. By analysing the impact of temporal parasite dispersal, host species and size, and the impact of coinfection (moving from broader environmental factors to within-host dynamics), we show that neither assumption holds true, but at different ecological scales. The assumption that closely related parasites can be functionally grouped is challenged when considering dispersal to the host (i.e. larger scales), while the assumption that the same factors will drive infection dynamics for a single parasite across multiple host species is challenged when considering within-host interspecific competition (i.e. smaller scales). Our results demonstrate that host identity, parasite identity and ecological scale require simultaneous consideration in studies of parasite community composition and transmission.
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Affiliation(s)
- Joshua I Brian
- Aquatic Ecology Group, Department of Zoology, University of Cambridge, The David Attenborough Building, Cambridge, CB2 3QZ, UK.
- Department of Geography, Bush House North East, King's College London, London, WC2B 4BG, UK.
| | - David C Aldridge
- Aquatic Ecology Group, Department of Zoology, University of Cambridge, The David Attenborough Building, Cambridge, CB2 3QZ, UK
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5
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Huang ZYX, Halliday FW, Becker DJ. Host functional traits as the nexus for multilevel infection patterns. Trends Ecol Evol 2023; 38:1125-1128. [PMID: 37684132 DOI: 10.1016/j.tree.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/27/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023]
Abstract
Understanding pathogen transmission and infection patterns at multiple biological scales is a central issue in disease ecology and evolution. Here, we suggest that functional traits of host species readily affect infection patterns of species, communities, and landscapes, and thus serve as a linkage for multilevel studies of infectious disease.
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Affiliation(s)
- Zheng Y X Huang
- School of Life Sciences, Nanjing Normal University, 210023 Nanjing, Jiangsu, China.
| | - Fletcher W Halliday
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland; Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, OK 73019, USA.
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6
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Hu B, Han S, He H. Effect of epidemic diseases on wild animal conservation. Integr Zool 2023; 18:963-980. [PMID: 37202360 DOI: 10.1111/1749-4877.12720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Under the background of global species extinction, the impact of epidemic diseases on wild animal protection is increasingly prominent. Here, we review and synthesize the literature on this topic, and discuss the relationship between diseases and biodiversity. Diseases usually reduce species diversity by decreasing or extinction of species populations, but also accelerate species evolution and promote species diversity. At the same time, species diversity can regulate disease outbreaks through dilution or amplification effects. The synergistic effect of human activities and global change is emphasized, which further aggravates the complex relationship between biodiversity and diseases. Finally, we emphasize the importance of active surveillance of wild animal diseases, which can protect wild animals from potential diseases, maintain population size and genetic variation, and reduce the damage of diseases to the balance of the whole ecosystem and human health. Therefore, we suggest that a background survey of wild animal populations and their pathogens should be carried out to assess the impact of potential outbreaks on the population or species level. The mechanism of dilution and amplification effect between species diversity and diseases of wild animals should be further studied to provide a theoretical basis and technical support for human intervention measures to change biodiversity. Most importantly, we should closely combine the protection of wild animals with the establishment of an active surveillance, prevention, and control system for wild animal epidemics, in an effort to achieve a win-win situation between wild animal protection and disease control.
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Affiliation(s)
- Bin Hu
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuyi Han
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hongxuan He
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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7
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Yin S, Li N, Xu W, Becker DJ, de Boer WF, Xu C, Mundkur T, Fountain-Jones NM, Li C, Han GZ, Wu Q, Prosser DJ, Cui L, Huang ZYX. Functional traits explain waterbirds' host status, subtype richness, and community-level infection risk for avian influenza. Ecol Lett 2023; 26:1780-1791. [PMID: 37586885 DOI: 10.1111/ele.14294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/17/2023] [Indexed: 08/18/2023]
Abstract
Species functional traits can influence pathogen transmission processes, and consequently affect species' host status, pathogen diversity, and community-level infection risk. We here investigated, for 143 European waterbird species, effects of functional traits on host status and pathogen diversity (subtype richness) for avian influenza virus at species level. We then explored the association between functional diversity and HPAI H5Nx occurrence at the community level for 2016/17 and 2021/22 epidemics in Europe. We found that both host status and subtype richness were shaped by several traits, such as diet guild and dispersal ability, and that the community-weighted means of these traits were also correlated with community-level risk of H5Nx occurrence. Moreover, functional divergence was negatively associated with H5Nx occurrence, indicating that functional diversity can reduce infection risk. Our findings highlight the value of integrating trait-based ecology into the framework of diversity-disease relationship, and provide new insights for HPAI prediction and prevention.
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Affiliation(s)
- Shenglai Yin
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ning Li
- Institute of Applied Ecology, Nanjing Xiaozhuang University, Nanjing, China
| | - Wenjie Xu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Willem F de Boer
- Wildlife Ecology and Conservation Group, Wageningen University, Wageningen, The Netherlands
| | - Chi Xu
- School of Life Sciences, Nanjing University, Nanjing, China
| | - Taej Mundkur
- Wetlands International, Ede, The Netherlands
- Good Earth Environmental, Arnhem, The Netherlands
| | | | - Chunlin Li
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
| | - Guan-Zhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qiang Wu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Diann J Prosser
- Eastern Ecological Science Center, United States Geological Survey, Laurel, Maryland, USA
| | - Lijuan Cui
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Zheng Y X Huang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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8
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Hamede R, Fountain‐Jones NM, Arce F, Jones M, Storfer A, Hohenlohe PA, McCallum H, Roche B, Ujvari B, Thomas F. The tumour is in the detail: Local phylogenetic, population and epidemiological dynamics of a transmissible cancer in Tasmanian devils. Evol Appl 2023; 16:1316-1327. [PMID: 37492149 PMCID: PMC10363845 DOI: 10.1111/eva.13569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 06/01/2023] [Accepted: 06/01/2023] [Indexed: 07/27/2023] Open
Abstract
Infectious diseases are a major threat for biodiversity conservation and can exert strong influence on wildlife population dynamics. Understanding the mechanisms driving infection rates and epidemic outcomes requires empirical data on the evolutionary trajectory of pathogens and host selective processes. Phylodynamics is a robust framework to understand the interaction of pathogen evolutionary processes with epidemiological dynamics, providing a powerful tool to evaluate disease control strategies. Tasmanian devils have been threatened by a fatal transmissible cancer, devil facial tumour disease (DFTD), for more than two decades. Here we employ a phylodynamic approach using tumour mitochondrial genomes to assess the role of tumour genetic diversity in epidemiological and population dynamics in a devil population subject to 12 years of intensive monitoring, since the beginning of the epidemic outbreak. DFTD molecular clock estimates of disease introduction mirrored observed estimates in the field, and DFTD genetic diversity was positively correlated with estimates of devil population size. However, prevalence and force of infection were the lowest when devil population size and tumour genetic diversity was the highest. This could be due to either differential virulence or transmissibility in tumour lineages or the development of host defence strategies against infection. Our results support the view that evolutionary processes and epidemiological trade-offs can drive host-pathogen coexistence, even when disease-induced mortality is extremely high. We highlight the importance of integrating pathogen and population evolutionary interactions to better understand long-term epidemic dynamics and evaluating disease control strategies.
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Affiliation(s)
- Rodrigo Hamede
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
| | | | - Fernando Arce
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Menna Jones
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Andrew Storfer
- School of Biological SciencesWashington State UniversityPullmanWashingtonUSA
| | - Paul A. Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdahoUSA
| | - Hamish McCallum
- Centre for Planetary Health and Food SecurityGriffith University, Nathan CampusNathanQueenslandAustralia
| | - Benjamin Roche
- CREEC, MIVEGEC (CREES)University of Montpellier, CNRS, IRDMontpelierFrance
| | - Beata Ujvari
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityWaurn PondsVictoriaAustralia
| | - Frédéric Thomas
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
- CREEC, MIVEGEC (CREES)University of Montpellier, CNRS, IRDMontpelierFrance
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9
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Webber QMR, Albery GF, Farine DR, Pinter-Wollman N, Sharma N, Spiegel O, Vander Wal E, Manlove K. Behavioural ecology at the spatial-social interface. Biol Rev Camb Philos Soc 2023; 98:868-886. [PMID: 36691262 DOI: 10.1111/brv.12934] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/25/2023]
Abstract
Spatial and social behaviour are fundamental aspects of an animal's biology, and their social and spatial environments are indelibly linked through mutual causes and shared consequences. We define the 'spatial-social interface' as intersection of social and spatial aspects of individuals' phenotypes and environments. Behavioural variation at the spatial-social interface has implications for ecological and evolutionary processes including pathogen transmission, population dynamics, and the evolution of social systems. We link spatial and social processes through a foundation of shared theory, vocabulary, and methods. We provide examples and future directions for the integration of spatial and social behaviour and environments. We introduce key concepts and approaches that either implicitly or explicitly integrate social and spatial processes, for example, graph theory, density-dependent habitat selection, and niche specialization. Finally, we discuss how movement ecology helps link the spatial-social interface. Our review integrates social and spatial behavioural ecology and identifies testable hypotheses at the spatial-social interface.
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Affiliation(s)
- Quinn M R Webber
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Gregory F Albery
- Department of Biology, Georgetown University, 37th and O Streets, Washington, DC, 20007, USA.,Wissenschaftskolleg zu Berlin, Wallotstraße 19, 14193, Berlin, Germany.,Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany
| | - Damien R Farine
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Department of Collective Behavior, Max Planck Institute of Animal Behavior, Universitatsstraße 10, 78464, Constance, Germany.,Division of Ecology and Evolution, Research School of Biology, Australian National University, 46 Sullivans Creek Road, Canberra, ACT, 2600, Australia
| | - Noa Pinter-Wollman
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Nitika Sharma
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Orr Spiegel
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Eric Vander Wal
- Department of Biology, Memorial University, St. John's, NL, A1C 5S7, Canada
| | - Kezia Manlove
- Department of Wildland Resources and Ecology Center, Utah State University, 5200 Old Main Hill, Logan, UT, 84322, USA
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10
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Wang YXG, Matson KD, Prins HHT, Xu Y, Huang ZYX, de Boer WF. Risk factors for Lyme disease: A scale-dependent effect of host species diversity and a consistent negative effect of host phylogenetic diversity. Ticks Tick Borne Dis 2023; 14:102073. [PMID: 36345067 DOI: 10.1016/j.ttbdis.2022.102073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 10/13/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
Abstract
Biodiversity can influence disease risk. One example of a diversity-disease relationship is the dilution effect, which suggests higher host species diversity (often indexed by species richness) reduces disease risk. While numerous studies support the dilution effect, its generality remains controversial. Most studies of diversity-disease relationships have overlooked the potential importance of phylogenetic diversity. Furthermore, most studies have tested diversity-disease relationships at one spatial scale, even though such relationships are likely scale dependent. Using Lyme disease as a model system, we investigated the effects of host species richness and phylogenetic relatedness on the number of reported Lyme disease cases in humans in the U.S.A. at two spatial scales (the county level and the state level) using piecewise structural equation modelling. We also accounted for relevant climatic and habitat-related factors and tested their correlations with the number of Lyme disease cases. We found that species assemblages with more related species (i.e., host species in the order Rodentia) were associated with more Lyme disease cases in humans. Host species richness correlated negatively with the number of Lyme disease cases at the state level (i.e., a dilution effect), a pattern that might be explained by the higher number of reservoir-incompetent species at high levels of species richness at this larger spatial scale. In contrast, a positive correlation was found between species richness and the number of Lyme disease cases at the county level, where a higher proportion of rodent species was associated with higher levels of species richness, potentially amplifying the disease risk. Our results highlight that analyse at a single spatial scale can miss some impacts of biodiversity on human health. Thus, multi-scale analyses with consideration of host phylogenetic diversity are critical for improving our understanding of diversity-disease relationships.
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Affiliation(s)
- Yingying X G Wang
- Wildlife Ecology and Conservation Group, Wageningen University & Research, 6708 PB Wageningen, Netherlands; Department of Biological and Environmental Science, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Kevin D Matson
- Wildlife Ecology and Conservation Group, Wageningen University & Research, 6708 PB Wageningen, Netherlands
| | - Herbert H T Prins
- Department of Animal Sciences, Wageningen University & Research, 6708 WD Wageningen, Netherlands
| | - Yanjie Xu
- Wildlife Ecology and Conservation Group, Wageningen University & Research, 6708 PB Wageningen, Netherlands; Finnish Museum of Natural History, University of Helsinki, 17, 00014, Finland
| | - Zheng Y X Huang
- College of Life Sciences, Nanjing Normal University, 210046 Nanjing, China.
| | - Willem F de Boer
- Wildlife Ecology and Conservation Group, Wageningen University & Research, 6708 PB Wageningen, Netherlands
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11
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Kozakiewicz CP, Burridge CP, Lee JS, Kraberger SJ, Fountain-Jones NM, Fisher RN, Lyren LM, Jennings MK, Riley SPD, Serieys LEK, Craft ME, Funk WC, Crooks KR, VandeWoude S, Carver S. Habitat connectivity and host relatedness influence virus spread across an urbanising landscape in a fragmentation-sensitive carnivore. Virus Evol 2022; 9:veac122. [PMID: 36694819 PMCID: PMC9865512 DOI: 10.1093/ve/veac122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/22/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Spatially heterogeneous landscape factors such as urbanisation can have substantial effects on the severity and spread of wildlife diseases. However, research linking patterns of pathogen transmission to landscape features remains rare. Using a combination of phylogeographic and machine learning approaches, we tested the influence of landscape and host factors on feline immunodeficiency virus (FIVLru) genetic variation and spread among bobcats (Lynx rufus) sampled from coastal southern California. We found evidence for increased rates of FIVLru lineage spread through areas of higher vegetation density. Furthermore, single-nucleotide polymorphism (SNP) variation among FIVLru sequences was associated with host genetic distances and geographic location, with FIVLru genetic discontinuities precisely correlating with known urban barriers to host dispersal. An effect of forest land cover on FIVLru SNP variation was likely attributable to host population structure and differences in forest land cover between different populations. Taken together, these results suggest that the spread of FIVLru is constrained by large-scale urban barriers to host movement. Although urbanisation at fine spatial scales did not appear to directly influence virus transmission or spread, we found evidence that viruses transmit and spread more quickly through areas containing higher proportions of natural habitat. These multiple lines of evidence demonstrate how urbanisation can change patterns of contact-dependent pathogen transmission and provide insights into how continued urban development may influence the incidence and management of wildlife disease.
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Affiliation(s)
| | | | - Justin S Lee
- Genomic Sequencing Laboratory, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | | | | | - Robert N Fisher
- Western Ecological Research Center, U.S. Geological Survey, San Diego, CA 92101, USA
| | - Lisa M Lyren
- Western Ecological Research Center, U.S. Geological Survey, San Diego, CA 92101, USA
| | - Megan K Jennings
- Biology Department, San Diego State University, San Diego, CA 92182, USA
| | - Seth P D Riley
- National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, CA 91360, USA
| | | | - Meggan E Craft
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN 55108, USA
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kevin R Crooks
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA,Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
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12
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Combs MA, Kache PA, VanAcker MC, Gregory N, Plimpton LD, Tufts DM, Fernandez MP, Diuk-Wasser MA. Socio-ecological drivers of multiple zoonotic hazards in highly urbanized cities. GLOBAL CHANGE BIOLOGY 2022; 28:1705-1724. [PMID: 34889003 DOI: 10.1111/gcb.16033] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/14/2021] [Accepted: 12/04/2021] [Indexed: 06/13/2023]
Abstract
The ongoing COVID-19 pandemic is a stark reminder of the devastating consequences of pathogen spillover from wildlife to human hosts, particularly in densely populated urban centers. Prevention of future zoonotic disease is contingent on informed surveillance for known and novel threats across diverse human-wildlife interfaces. Cities are a key venue for potential spillover events because of the presence of zoonotic pathogens transmitted by hosts and vectors living in close proximity to dense human settlements. Effectively identifying and managing zoonotic hazards requires understanding the socio-ecological processes driving hazard distribution and pathogen prevalence in dynamic and heterogeneous urban landscapes. Despite increasing awareness of the human health impacts of zoonotic hazards, the integration of an eco-epidemiological perspective into public health management plans remains limited. Here we discuss how landscape patterns, abiotic conditions, and biotic interactions influence zoonotic hazards across highly urbanized cities (HUCs) in temperate climates to promote their efficient and effective management by a multi-sectoral coalition of public health stakeholders. We describe how to interpret both direct and indirect ecological processes, incorporate spatial scale, and evaluate networks of connectivity specific to different zoonotic hazards to promote biologically-informed and targeted decision-making. Using New York City, USA as a case study, we identify major zoonotic threats, apply knowledge of relevant ecological factors, and highlight opportunities and challenges for research and intervention. We aim to broaden the toolbox of urban public health stakeholders by providing ecologically-informed, practical guidance for the evaluation and management of zoonotic hazards.
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Affiliation(s)
- Matthew A Combs
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York, USA
| | - Pallavi A Kache
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York, USA
| | - Meredith C VanAcker
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York, USA
| | - Nichar Gregory
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York, USA
| | - Laura D Plimpton
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York, USA
| | - Danielle M Tufts
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York, USA
- Infectious Diseases and Microbiology Department, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Maria P Fernandez
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York, USA
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, Washington, USA
| | - Maria A Diuk-Wasser
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York, USA
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13
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Filion A, Doherty JF, Poulin R, Godfrey SS. Building a comprehensive phylogenetic framework in disease ecology. Trends Parasitol 2022; 38:424-427. [DOI: 10.1016/j.pt.2022.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 10/19/2022]
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14
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Gagne RB, Crooks KR, Craft ME, Chiu ES, Fountain-Jones NM, Malmberg JL, Carver S, Funk WC, VandeWoude S. Parasites as conservation tools. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13719. [PMID: 33586245 DOI: 10.1111/cobi.13719] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Parasite success typically depends on a close relationship with one or more hosts; therefore, attributes of parasitic infection have the potential to provide indirect details of host natural history and are biologically relevant to animal conservation. Characterization of parasite infections has been useful in delineating host populations and has served as a proxy for assessment of environmental quality. In other cases, the utility of parasites is just being explored, for example, as indicators of host connectivity. Innovative studies of parasite biology can provide information to manage major conservation threats by using parasite assemblage, prevalence, or genetic data to provide insights into the host. Overexploitation, habitat loss and fragmentation, invasive species, and climate change are major threats to animal conservation, and all of these can be informed by parasites.
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Affiliation(s)
- Roderick B Gagne
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Kevin R Crooks
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Meggan E Craft
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, Minnesota, USA
| | - Elliott S Chiu
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | | | - Jennifer L Malmberg
- Department of Veterinary Sciences, Wyoming State Veterinary Laboratory, University of Wyoming, Laramie, Wyoming, USA
| | - Scott Carver
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - W Chris Funk
- Graduate Degree Program in Ecology, Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
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15
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Hunting alters viral transmission and evolution in a large carnivore. Nat Ecol Evol 2022; 6:174-182. [PMID: 35087217 PMCID: PMC10111630 DOI: 10.1038/s41559-021-01635-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022]
Abstract
Hunting can fundamentally alter wildlife population dynamics but the consequences of hunting on pathogen transmission and evolution remain poorly understood. Here, we present a study that leverages a unique landscape-scale quasi-experiment coupled with pathogen-transmission tracing, network simulation and phylodynamics to provide insights into how hunting shapes feline immunodeficiency virus (FIV) dynamics in puma (Puma concolor). We show that removing hunting pressure enhances the role of males in transmission, increases the viral population growth rate and increases the role of evolutionary forces on the pathogen compared to when hunting was reinstated. Changes in transmission observed with the removal of hunting could be linked to short-term social changes while the male puma population increased. These findings are supported through comparison with a region with stable hunting management over the same time period. This study shows that routine wildlife management can have impacts on pathogen transmission and evolution not previously considered.
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16
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Euclydes L, De La Torre GM, Dudczak AC, Melo FTDV, Campião KM. Ecological specificity explains infection parameters of anuran parasites at different scales. Parasitology 2022:1-8. [PMID: 35195062 DOI: 10.1017/s0031182022000087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Understanding the determinants of parasite infection in different hosts is one of the main goals of disease ecology. Evaluating the relationship between parasite–host specificity and infection parameters within host communities and populations may contribute to this understanding. Here we propose two measures of specificity that encompasses phylogenetic and ecological relatedness among hosts and investigated how such metrics explain parasite infection prevalence and mean infection intensity (MII). We analysed the parasites associated with an anuran community in an area of Atlantic Forest and used the number of infected hosts and the net relatedness index to calculate the phylogenetic and ecological specificities of the parasites. These specificity measures were related to infection metrics (prevalence and MII) with generalized linear mixed models at community (all hosts) and population (infected host species) scales. Parasite prevalence was correlated with the number of infected hosts and, when considering only multi-host parasites, was positively related to parasite ecological specificity at community and population scales. Thus, parasite species have similar prevalences in ecologically closer hosts. No relationship was found for parasite MII. Incorporating ecological characteristics of hosts in parasite specificity analyses improves the detection of patterns of specificity across scales.
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Affiliation(s)
- Lorena Euclydes
- Department of Zoology, Faculty of Biological Sciences, Federal University of Paraná, Curitiba, Paraná81531-980, Brazil
| | - Gabriel M De La Torre
- Department of Zoology, Faculty of Biological Sciences, Federal University of Paraná, Curitiba, Paraná81531-980, Brazil
| | - Amanda Caroline Dudczak
- Department of Zoology, Faculty of Biological Sciences, Federal University of Paraná, Curitiba, Paraná81531-980, Brazil
| | - Francisco Tiago de Vasconcelos Melo
- Laboratory of Cell Biology and Helminthology 'Prof. Dr. Reinalda Marisa Lanfredi', Institute of Biological Sciences, Federal University of Pará, Belém, Pará66075-110, Brazil
| | - Karla Magalhães Campião
- Department of Zoology, Faculty of Biological Sciences, Federal University of Paraná, Curitiba, Paraná81531-980, Brazil
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17
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Fountain-Jones NM, Smith ML, Austerlitz F. Machine learning in molecular ecology. Mol Ecol Resour 2021; 21:2589-2597. [PMID: 34738721 DOI: 10.1111/1755-0998.13532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/26/2022]
Affiliation(s)
| | - Megan L Smith
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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18
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Doherty JF, Chai X, Cope LE, de Angeli Dutra D, Milotic M, Ni S, Park E, Filion A. The rise of big data in disease ecology. Trends Parasitol 2021; 37:1034-1037. [PMID: 34602364 DOI: 10.1016/j.pt.2021.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Big data have become readily available to explore patterns in large-scale disease ecology. However, the rate at which these public databases are exploited remains unknown. We highlight trends in big data usage in disease ecology during the past decade and encourage researchers to integrate big data into their study framework.
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Affiliation(s)
| | - Xuhong Chai
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Laurie E Cope
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | | | - Marin Milotic
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Steven Ni
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Eunji Park
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Antoine Filion
- Department of Zoology, University of Otago, Dunedin, New Zealand.
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19
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Millán J, Becker DJ. Patterns of Exposure and Infection with Microparasites in Iberian Wild Carnivores: A Review and Meta-Analysis. Animals (Basel) 2021; 11:2708. [PMID: 34573674 PMCID: PMC8469010 DOI: 10.3390/ani11092708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 11/28/2022] Open
Abstract
We use a suite of meta-analytic and comparative methods to derive fundamental insights into how sampling effort, pathogen richness, infection prevalence, and seroprevalence vary across Carnivora taxa and Iberian geography. The red fox was the most studied species, the wolf and Iberian lynx were disproportionally studied, and the Arctoidea were understudied. Sampling effort was higher in Mediterranean areas, but central Spain showed the higher pathogen richness. Excluding studies analyzing fecal samples, 53 different pathogens have been detected in Iberian carnivores, including 16 viruses, 27 bacteria, and 10 protozoa but no fungi. Sampling effort and pathogen diversity were generally more similar among closely related carnivore species. Seropositivity to viruses was lower and higher in the Mustelinae and the Canidae, respectively, and seropositivity to protozoa was higher in both taxa. Canine distemper virus exposure was greatest in canids and mustelids. Carnivore protoparvovirus-1 exposure was greatest in the Atlantic regions, and the Felidae and the Musteloidea had lower infection prevalence. A subclade of the Mustelidae had a greater prevalence of Leishmania infection. We observed no relationships between host phylogenetic distance and pathogen sharing among species. Lastly, we identify important research pitfalls and future directions to improve the study of infectious disease in Iberian wild carnivore communities.
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Affiliation(s)
- Javier Millán
- Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza-CITA, 50013 Zaragoza, Spain
- Fundación ARAID, Avda. Ranillas 1, 50018 Zaragoza, Spain
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8320000, Chile
| | - Daniel J. Becker
- Department of Biology, University of Oklahoma, Norman, OK 73019, USA;
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20
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Humphreys JM, Pelzel-McCluskey AM, Cohnstaedt LW, McGregor BL, Hanley KA, Hudson AR, Young KI, Peck D, Rodriguez LL, Peters DPC. Integrating Spatiotemporal Epidemiology, Eco-Phylogenetics, and Distributional Ecology to Assess West Nile Disease Risk in Horses. Viruses 2021; 13:v13091811. [PMID: 34578392 PMCID: PMC8473291 DOI: 10.3390/v13091811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/13/2022] Open
Abstract
Mosquito-borne West Nile virus (WNV) is the causative agent of West Nile disease in humans, horses, and some bird species. Since the initial introduction of WNV to the United States (US), approximately 30,000 horses have been impacted by West Nile neurologic disease and hundreds of additional horses are infected each year. Research describing the drivers of West Nile disease in horses is greatly needed to better anticipate the spatial and temporal extent of disease risk, improve disease surveillance, and alleviate future economic impacts to the equine industry and private horse owners. To help meet this need, we integrated techniques from spatiotemporal epidemiology, eco-phylogenetics, and distributional ecology to assess West Nile disease risk in horses throughout the contiguous US. Our integrated approach considered horse abundance and virus exposure, vector and host distributions, and a variety of extrinsic climatic, socio-economic, and environmental risk factors. Birds are WNV reservoir hosts, and therefore we quantified avian host community dynamics across the continental US to show intra-annual variability in host phylogenetic structure and demonstrate host phylodiversity as a mechanism for virus amplification in time and virus dilution in space. We identified drought as a potential amplifier of virus transmission and demonstrated the importance of accounting for spatial non-stationarity when quantifying interaction between disease risk and meteorological influences such as temperature and precipitation. Our results delineated the timing and location of several areas at high risk of West Nile disease and can be used to prioritize vaccination programs and optimize virus surveillance and monitoring.
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Affiliation(s)
- John M. Humphreys
- Pest Management Research Unit, Agricultural Research Service, US Department of Agriculture, Sidney, MT 59270, USA
- Correspondence:
| | - Angela M. Pelzel-McCluskey
- Veterinary Services, Animal and Plant Health Inspection Service (APHIS), US Department of Agriculture, Fort Collins, CO 80526, USA;
| | - Lee W. Cohnstaedt
- Arthropod-Borne Animal Disease Research Unit, Agricultural Research Service, US Department of Agriculture, Manhattan, KS 66502, USA; (L.W.C.); (B.L.M.)
| | - Bethany L. McGregor
- Arthropod-Borne Animal Disease Research Unit, Agricultural Research Service, US Department of Agriculture, Manhattan, KS 66502, USA; (L.W.C.); (B.L.M.)
| | - Kathryn A. Hanley
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA; (K.A.H.); (K.I.Y.)
| | - Amy R. Hudson
- Big Data Initiative and SCINet Program for Scientific Computing, Agricultural Research Service, US Department of Agriculture, Beltsville, MD 20704, USA; (A.R.H.); (D.P.C.P.)
| | - Katherine I. Young
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA; (K.A.H.); (K.I.Y.)
| | - Dannele Peck
- Northern Plains Climate Hub, US Department of Agriculture, Fort Collins, CO 80526, USA;
| | - Luis L. Rodriguez
- Plum Island Animal Disease Center, US Department of Agriculture, Orient Point, NY 11957, USA;
| | - Debra P. C. Peters
- Big Data Initiative and SCINet Program for Scientific Computing, Agricultural Research Service, US Department of Agriculture, Beltsville, MD 20704, USA; (A.R.H.); (D.P.C.P.)
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21
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Fountain-Jones NM, Kozakiewicz CP, Forester BR, Landguth EL, Carver S, Charleston M, Gagne RB, Greenwell B, Kraberger S, Trumbo DR, Mayer M, Clark NJ, Machado G. MrIML: Multi-response interpretable machine learning to model genomic landscapes. Mol Ecol Resour 2021; 21:2766-2781. [PMID: 34448358 DOI: 10.1111/1755-0998.13495] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 08/01/2021] [Accepted: 08/23/2021] [Indexed: 12/29/2022]
Abstract
We introduce a new R package "MrIML" ("Mister iml"; Multi-response Interpretable Machine Learning). MrIML provides a powerful and interpretable framework that enables users to harness recent advances in machine learning to quantify multilocus genomic relationships, to identify loci of interest for future landscape genetics studies, and to gain new insights into adaptation across environmental gradients. Relationships between genetic variation and environment are often nonlinear and interactive; these characteristics have been challenging to address using traditional landscape genetic approaches. Our package helps capture this complexity and offers functions that fit and interpret a wide range of highly flexible models that are routinely used for single-locus landscape genetics studies but are rarely extended to estimate response functions for multiple loci. To demonstrate the package's broad functionality, we test its ability to recover landscape relationships from simulated genomic data. We also apply the package to two empirical case studies. In the first, we model genetic variation of North American balsam poplar (Populus balsamifera, Salicaceae) populations across environmental gradients. In the second case study, we recover the landscape and host drivers of feline immunodeficiency virus genetic variation in bobcats (Lynx rufus). The ability to model thousands of loci collectively and compare models from linear regression to extreme gradient boosting, within the same analytical framework, has the potential to be transformative. The MrIML framework is also extendable and not limited to modelling genetic variation; for example, it can quantify the environmental drivers of microbiomes and coinfection dynamics.
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Affiliation(s)
| | | | - Brenna R Forester
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Erin L Landguth
- School of Public and Community Health Sciences, University of Montana, Missoula, Montana, USA
| | - Scott Carver
- School of Natural Sciences, University of Tasmania, Hobart, Tas., Australia
| | - Michael Charleston
- School of Natural Sciences, University of Tasmania, Hobart, Tas., Australia
| | - Roderick B Gagne
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, USA
| | - Brandon Greenwell
- Department of Operations, Business Analytics, and Information Systems, University of Cincinnati, Cincinnati, Ohio, USA
| | - Simona Kraberger
- Biodesign Center for Fundamental & Applied Microbiomics, Arizona State University, Tempe, Arizona, USA
| | - Daryl R Trumbo
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Michael Mayer
- Actuarial Department, La Mobilière, Bern, Switzerland
| | - Nicholas J Clark
- UQ Spatial Epidemiology Laboratory, School of Veterinary Science, The University of Queensland, Gatton, Qld., Australia
| | - Gustavo Machado
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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22
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Nunn CL, Vining AQ, Chakraborty D, Reiskind MH, Young HS. Effects of host extinction and vector preferences on vector-borne disease risk in phylogenetically structured host-hector communities. PLoS One 2021; 16:e0256456. [PMID: 34424937 PMCID: PMC8382198 DOI: 10.1371/journal.pone.0256456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/08/2021] [Indexed: 11/26/2022] Open
Abstract
Anthropogenic disturbance impacts the phylogenetic composition and diversity of ecological communities. While changes in diversity are known to dramatically change species interactions and alter disease dynamics, the effects of phylogenetic changes in host and vector communities on disease have been relatively poorly studied. Using a theoretical model, we investigated how phylogeny and extinction influence network structural characteristics relevant to disease transmission in disturbed environments. We modelled a multi-host, multi-vector community as a bipartite ecological network, where nodes represent host and vector species and edges represent connections among them through vector feeding, and we simulated vector preferences and threat status on host and parasite phylogenies. We then simulated loss of hosts, including phylogenetically clustered losses, to investigate how extinction influences network structure. We compared effects of phylogeny and extinction to those of host specificity, which we predicted to strongly increase network modularity and reduce disease prevalence. The simulations revealed that extinction often increased modularity, with higher modularity as species loss increased, although not as much as increasing host specificity did. These results suggest that extinction itself, all else being equal, may reduce disease prevalence in disturbed communities. However, in real communities, systematic patterns in species loss (e.g. favoring high competence species) or changes in abundance may counteract these effects. Unexpectedly, we found that effects of phylogenetic signal in host and vector traits were relatively weak, and only important when phylogenetic signal of host and vector traits were similar, or when these traits both varied.
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Affiliation(s)
- Charles L. Nunn
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
- Duke Global Health Institute, Durham, North Carolina, United States of America
| | - Alexander Q. Vining
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
- Graduate Program in Animal Behavior, UC Davis, Davis, California, United States of America
| | - Debapriyo Chakraborty
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
- INRAE ENVT IHAP, National Veterinary School of Toulouse, Toulouse, France
| | - Michael H. Reiskind
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Hillary S. Young
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, United States of America
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23
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Comparison of Antimicrobial-Resistant Escherichia coli Isolates from Urban Raccoons and Domestic Dogs. Appl Environ Microbiol 2021; 87:e0048421. [PMID: 33990315 DOI: 10.1128/aem.00484-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Wildlife can be exposed to antimicrobial-resistant bacteria (ARB) via multiple pathways. Spatial overlap with domestic animals is a prominent exposure pathway. However, most studies of wildlife-domestic animal interfaces have focused on livestock and little is known about the wildlife-companion animal interface. Here, we investigated the prevalence and phylogenetic relatedness of extended-spectrum cephalosporin-resistant (ESC-R) Escherichia coli from raccoons (Procyon lotor) and domestic dogs (Canis lupus familiaris) in the metropolitan area of Chicago, IL, USA. To assess the potential importance of spatial overlap with dogs, we explored whether raccoons sampled at public parks (i.e., parks where people and dogs could enter) differed in prevalence and phylogenetic relatedness of ESC-R E. coli to raccoons sampled at private parks (i.e., parks where people and dogs could not enter). Raccoons had a significantly higher prevalence of ESC-R E. coli (56.9%) than dogs (16.5%). However, the richness of ESC-R E. coli did not vary by host species. Further, core single-nucleotide polymorphism (SNP)-based phylogenetic analyses revealed that isolates did not cluster by host species, and in some cases displayed a high degree of similarity (i.e., differed by less than 20 core SNPs). Spatial overlap analyses revealed that ESC-R E. coli were more likely to be isolated from raccoons at public parks than raccoons at private parks, but only for parks located in suburban areas of Chicago, not urban areas. That said, ESC-R E. coli isolated from raccoons did not genetically cluster by park of origin. Our findings suggest that domestic dogs and urban/suburban raccoons can have a diverse range of ARB, some of which display a high degree of genetic relatedness (i.e., differ by less than 20 core SNPs). Given the differences in prevalence, domestic dogs are unlikely to be an important source of exposure for mesocarnivores in urbanized areas. IMPORTANCE Antimicrobial-resistant bacteria (ARB) have been detected in numerous wildlife species across the globe, which may have important implications for human and animal health. Wildlife can be exposed to ARB via numerous pathways, including via spatial overlap with domestic animals. However, the interface with domestic animals has mostly been explored for livestock and little is known about the interface between wild animals and companion animals. Our work suggests that urban and suburban wildlife can have similar ARB to local domestic dogs, but local dogs are unlikely to be a direct source of exposure for urban-adapted wildlife. This finding is important because it underscores the need to incorporate wildlife into antimicrobial resistance surveillance efforts, and to investigate whether certain urban wildlife species could act as additional epidemiological pathways of exposure for companion animals, and indirectly for humans.
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24
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Turner WC, Kamath PL, van Heerden H, Huang YH, Barandongo ZR, Bruce SA, Kausrud K. The roles of environmental variation and parasite survival in virulence-transmission relationships. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210088. [PMID: 34109041 PMCID: PMC8170194 DOI: 10.1098/rsos.210088] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Disease outbreaks are a consequence of interactions among the three components of a host-parasite system: the infectious agent, the host and the environment. While virulence and transmission are widely investigated, most studies of parasite life-history trade-offs are conducted with theoretical models or tractable experimental systems where transmission is standardized and the environment controlled. Yet, biotic and abiotic environmental factors can strongly affect disease dynamics, and ultimately, host-parasite coevolution. Here, we review research on how environmental context alters virulence-transmission relationships, focusing on the off-host portion of the parasite life cycle, and how variation in parasite survival affects the evolution of virulence and transmission. We review three inter-related 'approaches' that have dominated the study of the evolution of virulence and transmission for different host-parasite systems: (i) evolutionary trade-off theory, (ii) parasite local adaptation and (iii) parasite phylodynamics. These approaches consider the role of the environment in virulence and transmission evolution from different angles, which entail different advantages and potential biases. We suggest improvements to how to investigate virulence-transmission relationships, through conceptual and methodological developments and taking environmental context into consideration. By combining developments in life-history evolution, phylogenetics, adaptive dynamics and comparative genomics, we can improve our understanding of virulence-transmission relationships across a diversity of host-parasite systems that have eluded experimental study of parasite life history.
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Affiliation(s)
- Wendy C. Turner
- US Geological Survey, Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Pauline L. Kamath
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Henriette van Heerden
- Faculty of Veterinary Science, Department of Veterinary Tropical Diseases, University of Pretoria, Onderstepoort, South Africa
| | - Yen-Hua Huang
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zoe R. Barandongo
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Spencer A. Bruce
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Kyrre Kausrud
- Section for Epidemiology, Norwegian Veterinary Institute, Ullevålsveien 68, 0454 Oslo, Norway
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25
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Lynch SC, Eskalen A, Gilbert GS. Host evolutionary relationships explain tree mortality caused by a generalist pest-pathogen complex. Evol Appl 2021; 14:1083-1094. [PMID: 33897822 PMCID: PMC8061262 DOI: 10.1111/eva.13182] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 11/30/2022] Open
Abstract
The phylogenetic signal of transmissibility (competence) and attack severity among hosts of generalist pests is poorly understood. In this study, we examined the phylogenetic effects on hosts differentially affected by an emergent generalist beetle-pathogen complex in California and South Africa. Host types (non-competent, competent and killed-competent) are based on nested types of outcomes of interactions between host plants, the beetles and the fungal pathogens. Phylogenetic dispersion analysis of each host type revealed that the phylogenetic preferences of beetle attack and fungal growth were a nonrandom subset of all available tree and shrub species. Competent hosts were phylogenetically narrower by 62 Myr than the set of all potential hosts, and those with devastating impacts were the most constrained by 107 Myr. Our results show a strong phylogenetic signal in the relative effects of a generalist pest-pathogen complex on host species, demonstrating that the strength of multi-host pest impacts in plants can be predicted by host evolutionary relationships. This study presents a unifying theoretical approach to identifying likely disease outcomes across multiple host-pest combinations.
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Affiliation(s)
- Shannon Colleen Lynch
- Department of Environmental StudiesUniversity of California Santa CruzSanta CruzCaliforniaUSA
- Department of Plant PathologyUniversity of California DavisDavisCaliforniaUSA
| | - Akif Eskalen
- Department of Plant PathologyUniversity of California DavisDavisCaliforniaUSA
| | - Gregory S. Gilbert
- Department of Environmental StudiesUniversity of California Santa CruzSanta CruzCaliforniaUSA
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26
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Malmberg JL, White LA, VandeWoude S. Bioaccumulation of Pathogen Exposure in Top Predators. Trends Ecol Evol 2021; 36:411-420. [PMID: 33549372 DOI: 10.1016/j.tree.2021.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/10/2021] [Accepted: 01/14/2021] [Indexed: 12/13/2022]
Abstract
Predator-prey interactions present heightened opportunities for pathogen spillover, as predators are at risk of exposure to infectious agents harbored by prey. Epizootics with high morbidity and mortality have been recorded following prey-to-predator spillover events, which have had significant conservation implications for sensitive species. Using felids as a detailed case study, we have documented both virulent and clinically silent infections in apex predators following transfer of microbes from prey. We draw on these examples and others to examine the mechanisms that determine frequency and outcome of predator exposure to prey-based pathogens. We propose that predator-prey dynamics should be more thoroughly considered in empirical research and disease dynamic modeling approaches in order to reveal answers to outstanding questions relating to pathogen bioaccumulation.
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Affiliation(s)
- Jennifer L Malmberg
- Department of Veterinary Sciences, University of Wyoming, Wyoming State Veterinary Laboratory, Laramie, WY82070, USA.
| | - Lauren A White
- National Socio-Environmental Synthesis Center, University of Maryland, Annapolis, MD 21401, USA.
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, 80523-1619, USA.
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27
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Host relatedness and landscape connectivity shape pathogen spread in the puma, a large secretive carnivore. Commun Biol 2021; 4:12. [PMID: 33398025 PMCID: PMC7782801 DOI: 10.1038/s42003-020-01548-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 11/25/2020] [Indexed: 01/29/2023] Open
Abstract
Urban expansion can fundamentally alter wildlife movement and gene flow, but how urbanization alters pathogen spread is poorly understood. Here, we combine high resolution host and viral genomic data with landscape variables to examine the context of viral spread in puma (Puma concolor) from two contrasting regions: one bounded by the wildland urban interface (WUI) and one unbounded with minimal anthropogenic development (UB). We found landscape variables and host gene flow explained significant amounts of variation of feline immunodeficiency virus (FIV) spread in the WUI, but not in the unbounded region. The most important predictors of viral spread also differed; host spatial proximity, host relatedness, and mountain ranges played a role in FIV spread in the WUI, whereas roads might have facilitated viral spread in the unbounded region. Our research demonstrates how anthropogenic landscapes can alter pathogen spread, providing a more nuanced understanding of host-pathogen relationships to inform disease ecology in free-ranging species.
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28
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Fountain-Jones NM, Appaw RC, Carver S, Didelot X, Volz E, Charleston M. Emerging phylogenetic structure of the SARS-CoV-2 pandemic. Virus Evol 2020; 6:veaa082. [PMID: 33335743 PMCID: PMC7717445 DOI: 10.1093/ve/veaa082] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Since spilling over into humans, SARS-CoV-2 has rapidly spread across the globe, accumulating significant genetic diversity. The structure of this genetic diversity and whether it reveals epidemiological insights are fundamental questions for understanding the evolutionary trajectory of this virus. Here, we use a recently developed phylodynamic approach to uncover phylogenetic structures underlying the SARS-CoV-2 pandemic. We find support for three SARS-CoV-2 lineages co-circulating, each with significantly different demographic dynamics concordant with known epidemiological factors. For example, Lineage C emerged in Europe with a high growth rate in late February, just prior to the exponential increase in cases in several European countries. Non-synonymous mutations that characterize Lineage C occur in functionally important gene regions responsible for viral replication and cell entry. Even though Lineages A and B had distinct demographic patterns, they were much more difficult to distinguish. Continuous application of phylogenetic approaches to track the evolutionary epidemiology of SARS-CoV-2 lineages will be increasingly important to validate the efficacy of control efforts and monitor significant evolutionary events in the future.
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Affiliation(s)
| | - Raima Carol Appaw
- School of Natural Sciences, University of Tasmania, Hobart, 7001, Australia
| | - Scott Carver
- School of Natural Sciences, University of Tasmania, Hobart, 7001, Australia
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry CV47AL, UK
| | - Erik Volz
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, Imperial College London, London W2 1PG, UK
| | - Michael Charleston
- School of Natural Sciences, University of Tasmania, Hobart, 7001, Australia
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29
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Omondi GP, Gakuya F, Arzt J, Sangula A, Hartwig E, Pauszek S, Smoliga G, Brito B, Perez A, Obanda V, VanderWaal K. The role of African buffalo in the epidemiology of foot-and-mouth disease in sympatric cattle and buffalo populations in Kenya. Transbound Emerg Dis 2020; 67:2206-2221. [PMID: 32303117 DOI: 10.1111/tbed.13573] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/12/2020] [Accepted: 03/04/2020] [Indexed: 02/06/2023]
Abstract
Quantitative knowledge on the contribution of African buffalo to the epidemiology of foot-and-mouth disease virus (FMDV) in East Africa is lacking, and this information is essential for the design of control programs in the region. The objective of this study was to investigate the epidemiology of FMDV in buffalo, including the role of buffalo in the circulation of FMDV in livestock populations. We collected blood and oropharyngeal fluids from 92 wild buffalo and 98 sympatric cattle in central Kenya and sequenced the virus' VP1 coding region. We show that FMDV has a high seroprevalence in buffalo (~77%) and targeted cattle (~93%). In addition, we recovered 80 FMDV sequences from buffalo, all of which were serotype SAT1 and SAT2, and four serotype O and A sequences from sympatric cattle. Notably, six individual buffalo were co-infected with both SAT1 and SAT2. Amongst sympatric buffalo and cattle, the fact that no SAT1 or 2 sequences were found in cattle suggests that transmission of FMDV from buffalo to sympatric cattle is rare. Similarly, there was no evidence that serotype O and A sequences found in cattle were transmitted to buffalo. However, viruses from FMDV outbreaks in cattle elsewhere in Kenya were closely related to SAT1 and SAT2 viruses found in buffalo in this study, suggesting that FMDV in cattle and buffalo do not constitute independently evolving populations. We also show that fine-scale geographic features, such as rivers, influence the circulation of FMDV in buffalo and that social segregation amongst sympatric herds may limit between-herd transmission. These results significantly advance our understanding of the ecology and molecular epidemiology of FMDV at wildlife-livestock interfaces in East Africa and will help to inform the design of control and surveillance strategies for this disease in the region.
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Affiliation(s)
- George P Omondi
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
- Ahadi Veterinary Resource Center, Nairobi, Kenya
| | - Francis Gakuya
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, Kenya
| | - Jonathan Arzt
- Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, ARS, USDA, NY, USA
| | | | - Ethan Hartwig
- Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, ARS, USDA, NY, USA
| | - Steven Pauszek
- Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, ARS, USDA, NY, USA
| | - George Smoliga
- Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, ARS, USDA, NY, USA
| | - Barbara Brito
- Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, ARS, USDA, NY, USA
| | - Andres Perez
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Vincent Obanda
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, Kenya
| | - Kimberly VanderWaal
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
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30
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Latinne A, Hu B, Olival KJ, Zhu G, Zhang L, Li H, Chmura AA, Field HE, Zambrana-Torrelio C, Epstein JH, Li B, Zhang W, Wang LF, Shi ZL, Daszak P. Origin and cross-species transmission of bat coronaviruses in China. Nat Commun 2020; 11:4235. [PMID: 32843626 PMCID: PMC7447761 DOI: 10.1038/s41467-020-17687-3] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 07/06/2020] [Indexed: 12/31/2022] Open
Abstract
Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. Here we use a Bayesian statistical framework and a large sequence data set from bat-CoVs (including 630 novel CoV sequences) in China to study their macroevolution, cross-species transmission and dispersal. We find that host-switching occurs more frequently and across more distantly related host taxa in alpha- than beta-CoVs, and is more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus. Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.
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Affiliation(s)
- Alice Latinne
- EcoHealth Alliance, New York, USA
- Wildlife Conservation Society, Viet Nam Country Program, Ha Noi, Viet Nam; Wildlife Conservation Society, Health Program, Bronx, NY, USA
| | - Ben Hu
- Key Laboratory of Special Pathogens And Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | | | | | - Libiao Zhang
- Guangdong Institute of Applied Biological Resources, Guangdong Academy of Sciences, Guangzhou, China
| | | | | | - Hume E Field
- EcoHealth Alliance, New York, USA
- School of Veterinary Science, The University of Queensland, Brisbane, QLD, Australia
| | | | | | - Bei Li
- Key Laboratory of Special Pathogens And Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Wei Zhang
- Key Laboratory of Special Pathogens And Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Zheng-Li Shi
- Key Laboratory of Special Pathogens And Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
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31
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Jara M, Rasmussen DA, Corzo CA, Machado G. Porcine reproductive and respiratory syndrome virus dissemination across pig production systems in the United States. Transbound Emerg Dis 2020; 68:667-683. [PMID: 32657491 DOI: 10.1111/tbed.13728] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/25/2020] [Accepted: 07/08/2020] [Indexed: 12/16/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) remains widespread in the North American pig population. Despite improvements in virus characterization, it is unclear whether PRRSV infections are a product of viral circulation within production systems (local) or across production systems (external). Here, we examined the local and external dissemination dynamics of PRRSV and the processes facilitating its spread in three production systems. Overall, PRRSV genetic diversity has declined since 2018, while phylodynamic results support frequent external transmission. We found that PRRSV dissemination predominantly occurred mostly through transmission between farms of different production companies for several months, especially from November until May, a timeframe already established as PRRSV season. Although local PRRSV dissemination occurred mainly through regular pig flow (from sow to nursery and then to finisher farms), an important flux of PRRSV dissemination also occurred in the opposite direction, from finisher to sow and nursery farms, highlighting the importance of downstream farms as sources of the virus. Our results also showed that farms with pig densities of 500 to 1,000 pig/km2 and farms located at a range within 0.5 km and 0.7 km from major roads were more likely to be infected by PRRSV, whereas farms at an elevation of 41 to 61 meters and surrounded by denser vegetation were less likely to be infected, indicating their role as dissemination barriers. In conclusion, our results demonstrate that external dissemination was intense, and reinforce the importance of farm proximity on PRRSV spread. Thus, consideration of farm location, geographic characteristics and animal densities across production systems may help to forecast PRRSV collateral dissemination.
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Affiliation(s)
- Manuel Jara
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - David A Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Cesar A Corzo
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St Paul, MN, USA
| | - Gustavo Machado
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
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32
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Affiliation(s)
- Andrew S Flies
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, TAS 7000, Australia.
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33
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Jara M, Frias-De-Diego A, Machado G. Phylogeography of Equine Infectious Anemia Virus. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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34
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Becker DJ, Speer KA, Brown AM, Fenton MB, Washburne AD, Altizer S, Streicker DG, Plowright RK, Chizhikov VE, Simmons NB, Volokhov DV. Ecological and evolutionary drivers of haemoplasma infection and bacterial genotype sharing in a Neotropical bat community. Mol Ecol 2020; 29:1534-1549. [PMID: 32243630 PMCID: PMC8299350 DOI: 10.1111/mec.15422] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/16/2020] [Accepted: 03/23/2020] [Indexed: 12/21/2022]
Abstract
Most emerging pathogens can infect multiple species, underlining the importance of understanding the ecological and evolutionary factors that allow some hosts to harbour greater infection prevalence and share pathogens with other species. However, our understanding of pathogen jumps is based primarily around viruses, despite bacteria accounting for the greatest proportion of zoonoses. Because bacterial pathogens in bats (order Chiroptera) can have conservation and human health consequences, studies that examine the ecological and evolutionary drivers of bacterial prevalence and barriers to pathogen sharing are crucially needed. Here were studied haemotropic Mycoplasma spp. (i.e., haemoplasmas) across a species-rich bat community in Belize over two years. Across 469 bats spanning 33 species, half of individuals and two-thirds of species were haemoplasma positive. Infection prevalence was higher for males and for species with larger body mass and colony sizes. Haemoplasmas displayed high genetic diversity (21 novel genotypes) and strong host specificity. Evolutionary patterns supported codivergence of bats and bacterial genotypes alongside phylogenetically constrained host shifts. Bat species centrality to the network of shared haemoplasma genotypes was phylogenetically clustered and unrelated to prevalence, further suggesting rare-but detectable-bacterial sharing between species. Our study highlights the importance of using fine phylogenetic scales when assessing host specificity and suggests phylogenetic similarity may play a key role in host shifts not only for viruses but also for bacteria. Such work more broadly contributes to increasing efforts to understand cross-species transmission and the epidemiological consequences of bacterial pathogens.
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Affiliation(s)
- Daniel J. Becker
- Department of BiologyIndiana UniversityBloomingtonINUSA
- Center for the Ecology of Infectious DiseaseUniversity of GeorgiaAthensGAUSA
| | - Kelly A. Speer
- Richard Gilder Graduate SchoolAmerican Museum of Natural HistoryNew YorkNYUSA
- Department of Invertebrate ZoologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDCUSA
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Alexis M. Brown
- Department of Ecology and EvolutionStony Brook UniversityStony BrookNYUSA
| | | | - Alex D. Washburne
- Department of Microbiology and ImmunologyMontana State UniversityBozemanMTUSA
| | - Sonia Altizer
- Center for the Ecology of Infectious DiseaseUniversity of GeorgiaAthensGAUSA
- Odum School of EcologyUniversity of GeorgiaAthensGAUSA
| | - Daniel G. Streicker
- Odum School of EcologyUniversity of GeorgiaAthensGAUSA
- MRC–University of Glasgow Centre for Virus ResearchGlasgowUK
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
| | - Raina K. Plowright
- Department of Microbiology and ImmunologyMontana State UniversityBozemanMTUSA
| | - Vladimir E. Chizhikov
- Center for Biologics Evaluation and Research, Food and Drug AdministrationSilver SpringMDUSA
| | - Nancy B. Simmons
- Richard Gilder Graduate SchoolAmerican Museum of Natural HistoryNew YorkNYUSA
- Department of MammalogyDivision of Vertebrate ZoologyAmerican Museum of Natural HistoryNew YorkNYUSA
| | - Dmitriy V. Volokhov
- Center for Biologics Evaluation and Research, Food and Drug AdministrationSilver SpringMDUSA
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35
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Carver S, Lunn T. When are pathogen dynamics likely to reflect host population genetic structure? Mol Ecol 2020; 29:859-861. [PMID: 32045058 DOI: 10.1111/mec.15379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/21/2020] [Accepted: 02/07/2020] [Indexed: 12/16/2022]
Abstract
Does the structure and connectivity of host populations influence the dynamics and evolution of their pathogens? This topical question is the essence of research investigating the ecology of a Pteropus fruit bat and its zoonotic Nipah virus (NiV) published by Olival et al. in this issue of Molecular Ecology. Questioned less overtly, but nonetheless implicit to the study, is "what are the mechanisms underpinning intraspecific host-pathogen congruence (IHPC) of genetic structure?". Olival et al. investigated the phylogeographical structure of Pteropus medius and NiV isolates across Bangladesh, from areas inside and outside of the Nipah belt-an area where most human spillover events occur. A high degree of host panmixia was discovered, with some population differentiation east of the Nipah belt. NiV genetic structure was congruent with the host. The authors attributed the panmixia and structuring, respectively, to (a) the highly vagile nature of P. medius, and (b) possible differences between bioregions within and outside the Nipah belt. Other potential explanatory mechanisms were acknowledged, including hybridization and transmission mode. This study makes a valuable contribution to a growing body of literature examining IHPC. This has implications not only for pathogen spillover to humans and domestic animals, but more generally for thinking about the mechanisms that underlie patterns of host and pathogen genetic associations.
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Affiliation(s)
- Scott Carver
- Department of Biological Sciences, University of Tasmania, Hobart, Tas., Australia
| | - Tamika Lunn
- Environmental Futures Research Institute, Griffith University, Nathan, Qld, Australia
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36
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Kraberger S, Fountain-Jones NM, Gagne RB, Malmberg J, Dannemiller NG, Logan K, Alldredge M, Varsani A, Crooks KR, Craft M, Carver S, VandeWoude S. Frequent cross-species transmissions of foamy virus between domestic and wild felids. Virus Evol 2020; 6:vez058. [PMID: 31942245 PMCID: PMC6955097 DOI: 10.1093/ve/vez058] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Emerging viral outbreaks resulting from host switching is an area of continued scientific interest. Such events can result in disease epidemics or in some cases, clinically silent outcomes. These occurrences are likely relatively common and can serve as tools to better understand disease dynamics, and may result in changes in behavior, fecundity, and, ultimately survival of the host. Feline foamy virus (FFV) is a common retrovirus infecting domestic cats globally, which has also been documented in the North American puma (Puma concolor). The prevalent nature of FFV in domestic cats and its ability to infect wild felids, including puma, provides an ideal system to study cross-species transmission across trophic levels (positions in the food chain), and evolution of pathogens transmitted between individuals following direct contact. Here we present findings from an extensive molecular analysis of FFV in pumas, focused on two locations in Colorado, and in relation to FFV recovered from domestic cats in this and previous studies. Prevalence of FFV in puma was high across the two regions, ∼77 per cent (urban interface site) and ∼48 per cent (rural site). Comparison of FFV from pumas living across three states; Colorado, Florida, and California, indicates FFV is widely distributed across North America. FFV isolated from domestic cats and pumas was not distinguishable at the host level, with FFV sequences sharing >93 per cent nucleotide similarity. Phylogenetic, Bayesian, and recombination analyses of FFV across the two species supports frequent cross-species spillover from domestic cat to puma during the last century, as well as frequent puma-to-puma intraspecific transmission in Colorado, USA. Two FFV variants, distinguished by significant difference in the surface unit of the envelope protein, were commonly found in both hosts. This trait is also shared by simian foamy virus and may represent variation in cell tropism or a unique immune evasion mechanism. This study elucidates evolutionary and cross-species transmission dynamics of a highly prevalent multi-host adapted virus, a system which can further be applied to model spillover and transmission of pathogenic viruses resulting in widespread infection in the new host.
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Affiliation(s)
- Simona Kraberger
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USA
| | - Nicholas M Fountain-Jones
- Department of Veterinary Population Medicine, University of Minnesota, 1365 Gortner Ave, Falcon Heights, St Paul, MN 55108, USA
| | - Roderick B Gagne
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Jennifer Malmberg
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Nicholas G Dannemiller
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Ken Logan
- Colorado Parks and Wildlife, 317 W Prospect Rd, Fort Collins, CO 80526, USA
| | - Mat Alldredge
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, 1474 Campus Delivery Fort Collins, CO 80523, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa
| | - Kevin R Crooks
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, 1474 Campus Delivery Fort Collins, CO 80523, USA
| | - Meggan Craft
- Department of Veterinary Population Medicine, University of Minnesota, 1365 Gortner Ave, Falcon Heights, St Paul, MN 55108, USA
| | - Scott Carver
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Sue VandeWoude
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
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37
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Forest Connectivity, Host Assemblage Characteristics of Local and Neighboring Counties, and Temperature Jointly Shape the Spatial Expansion of Lyme Disease in United States. REMOTE SENSING 2019. [DOI: 10.3390/rs11202354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Understanding risk factors for the spread of infectious diseases over time and across the landscape is critical for managing disease risk. While habitat connectivity and characteristics of local and neighboring animal (i.e., host) assemblages are known to influence the spread of diseases, the interactions among these factors remain poorly understood. In this study, we conducted a county-level analysis to test the effects of forest connectivity, together with the suitability of local assemblage (measured by the similarity of local host assemblage with neighboring assemblages) and the infection intensity of neighboring counties on the spatial expansion of Lyme disease in the United States. Our results suggested that both the similarity of local host assemblage and the infection intensity of neighboring counties were positively correlated with the probability of disease spread. Moreover, we found that increasing forest connectivity could facilitate the positive effect of neighbor infection intensity. In contrast, the effect size of the host assemblage similarity decreased with increasing connectivity, suggesting that host assemblage similarity was less effective in well-connected habitats. Our results thus indicate that habitat connectivity can indirectly influence disease spread by mediating the effects of other risk factors.
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38
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Galen SC, Speer KA, Perkins SL. Evolutionary lability of host associations promotes phylogenetic overdispersion of co‐infecting blood parasites. J Anim Ecol 2019; 88:1936-1949. [DOI: 10.1111/1365-2656.13089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/12/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Spencer C. Galen
- Sackler Institute for Comparative Genomics, American Museum of Natural History New York NY USA
- Richard Gilder Graduate School American Museum of Natural History New York NY USA
| | - Kelly A. Speer
- Sackler Institute for Comparative Genomics, American Museum of Natural History New York NY USA
- Richard Gilder Graduate School American Museum of Natural History New York NY USA
| | - Susan L. Perkins
- Sackler Institute for Comparative Genomics, American Museum of Natural History New York NY USA
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39
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Jara M, Escobar LE, Rodriges RO, Frias-De-Diego A, Sanhueza J, Machado G. Spatial distribution and spread potential of sixteen Leptospira serovars in a subtropical region of Brazil. Transbound Emerg Dis 2019; 66:2482-2495. [PMID: 31342664 DOI: 10.1111/tbed.13306] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 07/11/2019] [Accepted: 07/17/2019] [Indexed: 12/14/2022]
Abstract
Leptospirosis is a bacterial disease that represents a major problem in animal and public health due to its high prevalence and widespread distribution. This zoonotic disease is most prevalent in tropical environments where conditions favour pathogen survival. The ecological preferences of Leptospira serovars are poorly understood, limiting our knowledge of where and when outbreaks can occur, which may result in misinformed prevention and control plans. While the disease can occur consistently in time and space in tropical regions, research on the ecology of leptospirosis remains limited in subtropical regions. This research gap regarding Leptospira ecology brings public and veterinary health problems, impacting local economies. To fill this gap of knowledge, we suggest to assess geographic and ecological features among Leptospira serovars in a subtropical area of Brazil where leptospirosis is endemic to (a) highlight environmental conditions that facilitate or limit Leptospira spread and survival and (b) reconstruct its geographic distribution. An ecological niche modelling framework was used to characterize and compare Leptospira serovars in both geographic and environmental space. Our results show that despite the geographic overlap exhibited by the different serovars assessed, we found ecological divergence among their occupied ecological niches. Ecological divergences were expressed as ranges of potential distributions and environmental conditions found suitably by serovar, Sejroe being the most asymmetric (<0.15). Most important predictors for the potential distribution of most serovars were soil pH (31.7%) and landscape temperature (24.2%). Identification of environmental preferences will allow epidemiologists to better infer the presence of a serovar based on the environmental characteristics of regions rather than inferences based solely on historical epidemiological records. Including geographic and ecological ranges of serovars also may help to forecast transmission potential of Leptospira in public health and the food animal practice.
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Affiliation(s)
- Manuel Jara
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, North Carolina, USA
| | - Luis E Escobar
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, USA
| | - Rogério O Rodriges
- Desidério Finamor Veterinary Research Institute, Diagnostic and Agricultural Research Department of Agriculture, Livestock and Irrigation (DDPA/SEAPI), Porto Alegre, Brazil
| | - Alba Frias-De-Diego
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, North Carolina, USA
| | - Juan Sanhueza
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St Paul, Minnesota, USA
| | - Gustavo Machado
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, North Carolina, USA
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Huang ZYX, Xu C, van Langevelde F, Ma Y, Langendoen T, Mundkur T, Si Y, Tian H, Kraus RHS, Gilbert M, Han G, Ji X, Prins HHT, de Boer WF. Contrasting effects of host species and phylogenetic diversity on the occurrence of HPAI H5N1 in European wild birds. J Anim Ecol 2019; 88:1044-1053. [DOI: 10.1111/1365-2656.12997] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 03/15/2019] [Indexed: 01/13/2023]
Affiliation(s)
- Zheng Y. X. Huang
- College of Life Sciences Nanjing Normal University Nanjing China
- Resource Ecology Group Wageningen University Wageningen The Netherlands
| | - Chi Xu
- School of Life Sciences Nanjing University Nanjing China
| | - Frank van Langevelde
- Resource Ecology Group Wageningen University Wageningen The Netherlands
- School of Life Sciences Westville Campus, University of KwaZulu‐Natal Durban South Africa
| | - Yuying Ma
- College of Life Sciences Nanjing Normal University Nanjing China
| | | | | | - Yali Si
- Resource Ecology Group Wageningen University Wageningen The Netherlands
- Department of Earth System Science, Ministry of Education Key Laboratory for Earth System Modeling Tsinghua University Beijing China
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science Beijing Normal University Beijing China
| | - Robert H. S. Kraus
- Department of Migration and Immuno‐Ecology Max Planck Institute for Ornithology Radolfzell Germany
- Department of Biology University of Konstanz Konstanz Germany
| | - Marius Gilbert
- Spatial Epidemiology Lab. (SpELL) Université Libre de Bruxelles Brussels Belgium
- Fonds National de la Recherche Scientifique Brussels Belgium
| | - Guan‐Zhu Han
- College of Life Sciences Nanjing Normal University Nanjing China
| | - Xiang Ji
- College of Life Sciences Nanjing Normal University Nanjing China
| | | | - Willem F. de Boer
- Resource Ecology Group Wageningen University Wageningen The Netherlands
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41
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Johnson EE, Escobar LE, Zambrana-Torrelio C. An Ecological Framework for Modeling the Geography of Disease Transmission. Trends Ecol Evol 2019; 34:655-668. [PMID: 31078330 PMCID: PMC7114676 DOI: 10.1016/j.tree.2019.03.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 03/01/2019] [Accepted: 03/18/2019] [Indexed: 01/10/2023]
Abstract
Ecological niche modeling (ENM) is widely employed in ecology to predict species’ potential geographic distributions in relation to their environmental constraints and is rapidly becoming the gold-standard method for disease risk mapping. However, given the biological complexity of disease systems, the traditional ENM framework requires reevaluation. We provide an overview of the application of ENM to disease systems and propose a theoretical framework based on the biological properties of both hosts and parasites to produce reliable outputs resembling disease system distributions. Additionally, we discuss the differences between biological considerations when implementing ENM for distributional ecology and epidemiology. This new framework will help the field of disease ecology and applications of biogeography in the epidemiology of infectious diseases. Infectious diseases greatly impact human health, biodiversity, and global economies, highlighting the need to understand and predict their distributions. Ecological niche modeling (ENM) was not originally designed to explicitly reconstruct complex biological phenomena such as diseases or parasitism, requiring a reevaluation of the traditional framework. We provide an integrative ENM framework for disease systems that considers suitable host availability, parasite ecologies, and different scales of modeling. Disease transmission is driven by factors related to parasite availability and host exposure and susceptibility, which can be incorporated in ENM frameworks.
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Affiliation(s)
- Erica E Johnson
- EcoHealth Alliance, 460 W. 34th Street, New York, NY, USA; Current Address: Department of Biology, City College of the City University of New York, New York, NY 10031, USA; Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Luis E Escobar
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA, USA
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42
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Ecology, not distance, explains community composition in parasites of sky-island Audubon’s Warblers. Int J Parasitol 2019; 49:437-448. [DOI: 10.1016/j.ijpara.2018.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 11/13/2018] [Accepted: 11/19/2018] [Indexed: 12/31/2022]
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Kechejian SR, Dannemiller N, Kraberger S, Ledesma-Feliciano C, Malmberg J, Roelke Parker M, Cunningham M, McBride R, Riley SPD, Vickers WT, Logan K, Alldredge M, Crooks K, Löchelt M, Carver S, VandeWoude S. Feline Foamy Virus is Highly Prevalent in Free-Ranging Puma concolor from Colorado, Florida and Southern California. Viruses 2019; 11:E359. [PMID: 31010173 PMCID: PMC6521117 DOI: 10.3390/v11040359] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/15/2019] [Accepted: 04/17/2019] [Indexed: 12/21/2022] Open
Abstract
Feline foamy virus (FFV) is a retrovirus that has been detected in multiple feline species, including domestic cats (Felis catus) and pumas (Puma concolor). FFV results in persistent infection but is generally thought to be apathogenic. Sero-prevalence in domestic cat populations has been documented in several countries, but the extent of viral infections in nondomestic felids has not been reported. In this study, we screened sera from 348 individual pumas from Colorado, Southern California and Florida for FFV exposure by assessing sero-reactivity using an FFV anti-Gag ELISA. We documented a sero-prevalence of 78.6% across all sampled subpopulations, representing 69.1% in Southern California, 77.3% in Colorado, and 83.5% in Florida. Age was a significant risk factor for FFV infection when analyzing the combined populations. This high prevalence in geographically distinct populations reveals widespread exposure of puma to FFV and suggests efficient shedding and transmission in wild populations.
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Affiliation(s)
- Sarah R Kechejian
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| | - Nick Dannemiller
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| | - Simona Kraberger
- Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA.
| | - Carmen Ledesma-Feliciano
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, 12700 E 19th Ave, Aurora, CO 80045, USA.
| | - Jennifer Malmberg
- Wyoming State Vet Lab, University of Wyoming, 1174 Snowy Range Road, Laramie, WY 82072, USA.
| | - Melody Roelke Parker
- Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA.
| | - Mark Cunningham
- Florida Fish and Wildlife Conservation Commission, 1105 SW Williston Road, Gainesville, FL 32601, USA.
| | - Roy McBride
- Rancher's Supply Inc., Alpine, TX 79830, USA.
| | - Seth P D Riley
- National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, CA 90265, USA.
| | - Winston T Vickers
- Karen C. Drayer Wildlife Health Center, University of California, Davis, CA 95616, USA.
| | - Ken Logan
- Wildlife Researcher Colorado Parks and Wildlife, 2300 S. Townsend Avenue, Montrose, CO 80203, USA.
| | - Mat Alldredge
- Colorado Division of Wildlife Office, Mammals Research, 317 W. Prospect Rd, For Collins, CO 80526, USA.
| | - Kevin Crooks
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University 115 Wagar, Fort Collins, CO 80523, USA.
| | - Martin Löchelt
- Department of Molecular Diagnostics of Oncogenic Infections, Research Program Infection, Inflammation and Cancer, German Cancer Research Center, (Deutsches Krebsforschungszentrum Heidelberg, DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany.
| | - Scott Carver
- School of Biological Sciences, University of Tasmania, Sandy Bay, Tasmania 7005, Australia.
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
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Wang YXG, Matson KD, Prins HHT, Gort G, Awada L, Huang ZYX, Boer WF. Phylogenetic structure of wildlife assemblages shapes patterns of infectious livestock diseases in Africa. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13311] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Yingying X. G. Wang
- College of Life Sciences Nanjing Normal University Nanjing China
- Resource Ecology Group Wageningen University Wageningen The Netherlands
| | - Kevin D. Matson
- Resource Ecology Group Wageningen University Wageningen The Netherlands
| | | | - Gerrit Gort
- Biometris, Plant Sciences Group Wageningen University Wageningen The Netherlands
| | - Lina Awada
- Animal Health Information Department World Organisation for Animal Health Paris France
| | - Zheng Y. X. Huang
- College of Life Sciences Nanjing Normal University Nanjing China
- Resource Ecology Group Wageningen University Wageningen The Netherlands
| | - Willem F. Boer
- Resource Ecology Group Wageningen University Wageningen The Netherlands
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45
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Kozakiewicz CP, Burridge CP, Funk WC, VandeWoude S, Craft ME, Crooks KR, Ernest HB, Fountain‐Jones NM, Carver S. Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics. Evol Appl 2018; 11:1763-1778. [PMID: 30459828 PMCID: PMC6231466 DOI: 10.1111/eva.12678] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/24/2018] [Accepted: 06/28/2018] [Indexed: 12/30/2022] Open
Abstract
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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Affiliation(s)
| | | | - W. Chris Funk
- Department of BiologyGraduate Degree Program in EcologyColorado State UniversityFort CollinsColorado
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsColorado
| | - Meggan E. Craft
- Department of Veterinary Population MedicineUniversity of MinnesotaSt. PaulMinnesota
| | - Kevin R. Crooks
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsColorado
| | - Holly B. Ernest
- Wildlife Genomics and Disease Ecology LaboratoryDepartment of Veterinary SciencesUniversity of WyomingLaramieWyoming
| | | | - Scott Carver
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
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46
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Beard R, Wentz E, Scotch M. A systematic review of spatial decision support systems in public health informatics supporting the identification of high risk areas for zoonotic disease outbreaks. Int J Health Geogr 2018; 17:38. [PMID: 30376842 PMCID: PMC6208014 DOI: 10.1186/s12942-018-0157-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/19/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Zoonotic diseases account for a substantial portion of infectious disease outbreaks and burden on public health programs to maintain surveillance and preventative measures. Taking advantage of new modeling approaches and data sources have become necessary in an interconnected global community. To facilitate data collection, analysis, and decision-making, the number of spatial decision support systems reported in the last 10 years has increased. This systematic review aims to describe characteristics of spatial decision support systems developed to assist public health officials in the management of zoonotic disease outbreaks. METHODS A systematic search of the Google Scholar database was undertaken for published articles written between 2008 and 2018, with no language restriction. A manual search of titles and abstracts using Boolean logic and keyword search terms was undertaken using predefined inclusion and exclusion criteria. Data extraction included items such as spatial database management, visualizations, and report generation. RESULTS For this review we screened 34 full text articles. Design and reporting quality were assessed, resulting in a final set of 12 articles which were evaluated on proposed interventions and identifying characteristics were described. Multisource data integration, and user centered design were inconsistently applied, though indicated diverse utilization of modeling techniques. CONCLUSIONS The characteristics, data sources, development and modeling techniques implemented in the design of recent SDSS that target zoonotic disease outbreak were described. There are still many challenges to address during the design process to effectively utilize the value of emerging data sources and modeling methods. In the future, development should adhere to comparable standards for functionality and system development such as user input for system requirements, and flexible interfaces to visualize data that exist on different scales. PROSPERO registration number: CRD42018110466.
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Affiliation(s)
- Rachel Beard
- College of Health Solutions, Arizona State University, Phoenix, AZ USA
- Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Elizabeth Wentz
- School of Geographical Sciences and Urban Planning, Arizona State University, Tempe, AZ USA
| | - Matthew Scotch
- College of Health Solutions, Arizona State University, Phoenix, AZ USA
- Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ USA
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Maintenance of Trypanosoma cruzi, T. evansi and Leishmania spp. by domestic dogs and wild mammals in a rural settlement in Brazil-Bolivian border. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2018; 7:398-404. [PMID: 30370220 PMCID: PMC6199764 DOI: 10.1016/j.ijppaw.2018.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/30/2018] [Accepted: 10/13/2018] [Indexed: 11/05/2022]
Abstract
Domestic dogs are considered reservoirs hosts for several vector-borne parasites. This study aimed to evaluate the role of domestic dogs as hosts for Trypanosoma cruzi, Trypanosoma evansi and Leishmania spp. in single and co-infections in the Urucum settlement, near the Brazil-Bolivian border. Additionally, we evaluated the involvement of wild mammals’ in the maintenance of these parasites in the study area. Blood samples of dogs (n = 62) and six species of wild mammals (n = 36) were collected in July and August of 2015. The infections were assessed using parasitological, serological and molecular tests. Clinical examination of dogs was performed and their feeding habits were noted. Overall, 87% (54/62) of sampled dogs were positive for at least one trypanosomatid species, in single (n = 9) and co-infections (n = 45). We found that 76% of dogs were positive for T. cruzi, four of them displayed high parasitemias demonstrated by hemoculture, including one strain types TcI, two TcIII and one TcIII/TcV. Around 73% (45/62) of dogs were positive to T. evansi, three with high parasitemias as seen by positive microhematocrit centrifuge technique. Of dogs sampled, 50% (31/62) were positive for Leishmania spp. by PCR or serology. We found a positive influence of (i) T. evansi on mucous pallor, (ii) co-infection by T. cruzi and Leishmania with onychogryphosis, and (iii) all parasites to skin lesions of sampled dogs. Finally, feeding on wild mammals had a positive influence in the Leishmania spp. infection in dogs. We found that 28% (5/18) coati Nasua nasua was co-infected for all three trypanosamatids, demonstrating that it might play a key role in maintenance of these parasites. Our results showed the importance of Urucum region as a hotspot for T. cruzi, T. evansi and Leishmania spp. and demonstrated that dogs can be considered as incidental hosts. Observation of high occurrence of dogs co-infected by trypanosomatids. Dogs infected by TcI, TcIII and TcIII/TcV. Nasua nasua is a key species in the sylvatic cycles of trypanosomatids. Direct effect of trypanosomatids' infection in clinical signs of dogs. Dogs as sentinels to human infection in the Brazil-Bolivian border.
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Dellicour S, Vrancken B, Trovão NS, Fargette D, Lemey P. On the importance of negative controls in viral landscape phylogeography. Virus Evol 2018; 4:vey023. [PMID: 30151241 PMCID: PMC6101606 DOI: 10.1093/ve/vey023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Phylogeographic reconstructions are becoming an established procedure to evaluate the factors that could impact virus spread. While a discrete phylogeographic approach can be used to test predictors of transition rates among discrete locations, alternative continuous phylogeographic reconstructions can also be exploited to investigate the impact of underlying environmental layers on the dispersal velocity of a virus. The two approaches are complementary tools for studying pathogens' spread, but in both cases, care must be taken to avoid misinterpretations. Here, we analyse rice yellow mottle virus (RYMV) sequence data from West and East Africa to illustrate how both approaches can be used to study the impact of environmental factors on the virus’ dispersal frequency and velocity. While it was previously reported that host connectivity was a major determinant of RYMV spread, we show that this was a false positive result due to the lack of appropriate negative controls. We also discuss and compare the phylodynamic tools currently available for investigating the impact of environmental factors on virus spread.
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Affiliation(s)
- Simon Dellicour
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium.,Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12 50, av. FD Roosevelt, 1050 Bruxelles, Belgium
| | - Bram Vrancken
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nídia S Trovão
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Denis Fargette
- Institut de Recherche pour le Développement (IRD), UMR IPME (IRD, CIRAD, Université de Montpellier), BP 64051 34394 Montpellier cedex 5, France
| | - Philippe Lemey
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
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