1
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Tran-Kiem C, Paredes MI, Perofsky AC, Frisbie LA, Xie H, Kong K, Weixler A, Greninger AL, Roychoudhury P, Peterson JM, Delgado A, Halstead H, MacKellar D, Dykema P, Gamboa L, Frazar CD, Ryke E, Stone J, Reinhart D, Starita L, Thibodeau A, Yun C, Aragona F, Black A, Viboud C, Bedford T. Fine-scale spatial and social patterns of SARS-CoV-2 transmission from identical pathogen sequences. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.24.24307811. [PMID: 38826243 PMCID: PMC11142302 DOI: 10.1101/2024.05.24.24307811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Pathogen genomics can provide insights into disease transmission patterns, but new methods are needed to handle modern large-scale pathogen genome datasets. Genetically proximal viruses indicate epidemiological linkage and are informative about transmission events. Here, we leverage pairs of identical sequences using 114,298 SARS-CoV-2 genomes collected via sentinel surveillance from March 2021 to December 2022 in Washington State, USA, with linked age and residence information to characterize fine-scale transmission. The location of pairs of identical sequences is highly consistent with expectations from mobility and social contact data. Outliers in the relationship between genetic and mobility data can be explained by SARS-CoV-2 transmission between postal codes with male prisons, consistent with transmission between prison facilities. Transmission patterns between age groups vary across spatial scales. Finally, we use the timing of sequence collection to understand the age groups driving transmission. This work improves our ability to characterize transmission from large pathogen genome datasets.
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Affiliation(s)
- Cécile Tran-Kiem
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Miguel I. Paredes
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Amanda C. Perofsky
- Brotman Baty Institute, University of Washington, Seattle, WA, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Kevin Kong
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Amelia Weixler
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alexander L. Greninger
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Andrew Delgado
- Washington State Department of Health, Shoreline, WA, USA
| | - Holly Halstead
- Washington State Department of Health, Shoreline, WA, USA
| | - Drew MacKellar
- Washington State Department of Health, Shoreline, WA, USA
| | - Philip Dykema
- Washington State Department of Health, Shoreline, WA, USA
| | - Luis Gamboa
- Brotman Baty Institute, University of Washington, Seattle, WA, USA
| | - Chris D. Frazar
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Erica Ryke
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jeremy Stone
- Brotman Baty Institute, University of Washington, Seattle, WA, USA
| | - David Reinhart
- Brotman Baty Institute, University of Washington, Seattle, WA, USA
| | - Lea Starita
- Brotman Baty Institute, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Cory Yun
- Washington State Department of Health, Shoreline, WA, USA
| | - Frank Aragona
- Washington State Department of Health, Shoreline, WA, USA
| | - Allison Black
- Washington State Department of Health, Shoreline, WA, USA
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Trevor Bedford
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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2
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Shen B, Pade LR, Nemes P. The 15-min (Sub)Cellular Proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580399. [PMID: 38405838 PMCID: PMC10888744 DOI: 10.1101/2024.02.15.580399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Single-cell mass spectrometry (MS) opens a proteomic window onto the inner workings of cells. Here, we report the discovery characterization of the subcellular proteome of single, identified embryonic cells in record speed and molecular coverage. We integrated subcellular capillary microsampling, fast capillary electrophoresis (CE), high-efficiency nano-flow electrospray ionization, and orbitrap tandem MS. In proof-of-principle tests, we found shorter separation times to hinder proteome detection using DDA, but not DIA. Within a 15-min effective separation window, CE data-independent acquisition (DIA) was able to identify 1,161 proteins from single HeLa-cell-equivalent (∼200 pg) proteome digests vs. 401 proteins by the reference data-dependent acquisition (DDA) on the same platform. The approach measured 1,242 proteins from subcellular niches in an identified cell in the live Xenopus laevis (frog) embryo, including many canonical components of organelles. CE-MS with DIA enables fast, sensitive, and deep profiling of the (sub)cellular proteome, expanding the bioanalytical toolbox of cell biology. Authorship Contributions P.N. and B.S. designed the study. L.R.P. collected the X. laevis cell aspirates. B.S. prepared and measured the samples. B.S. and P.N. analyzed the data and interpreted the results. P.N. and B.S. wrote the manuscript. All the authors commented on the manuscript.
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3
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Zhao M, Plough LV, Behringer DC, Bojko J, Kough AS, Alper NW, Xu L, Schott EJ. Cross-Hemispheric Genetic Diversity and Spatial Genetic Structure of Callinectes sapidus Reovirus 1 (CsRV1). Viruses 2023; 15:v15020563. [PMID: 36851777 PMCID: PMC9962310 DOI: 10.3390/v15020563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The movement of viruses in aquatic systems is rarely studied over large geographic scales. Oceanic currents, host migration, latitude-based variation in climate, and resulting changes in host life history are all potential drivers of virus connectivity, adaptation, and genetic structure. To expand our understanding of the genetic diversity of Callinectes sapidus reovirus 1 (CsRV1) across a broad spatial and host life history range of its blue crab host (Callinectes sapidus), we obtained 22 complete and 96 partial genomic sequences for CsRV1 strains from the US Atlantic coast, Gulf of Mexico, Caribbean Sea, and the Atlantic coast of South America. Phylogenetic analyses of CsRV1 genomes revealed that virus genotypes were divided into four major genogroups consistent with their host geographic origins. However, some CsRV1 sequences from the US mid-Atlantic shared high genetic similarity with the Gulf of Mexico genotypes, suggesting potential human-mediated movement of CsRV1 between the US mid-Atlantic and Gulf coasts. This study advances our understanding of how climate, coastal geography, host life history, and human activity drive patterns of genetic structure and diversity of viruses in marine animals and contributes to the capacity to infer broadscale host population connectivity in marine ecosystems from virus population genetic data.
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Affiliation(s)
- Mingli Zhao
- Institute of Marine and Environmental Technology, University of Maryland Baltimore County, Baltimore, MD 21202, USA
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London AL9 7TA, UK
| | - Louis V. Plough
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD 21613, USA
| | - Donald C. Behringer
- Fisheries and Aquatic Sciences, University of Florida, Gainesville, FL 32653, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32608, USA
| | - Jamie Bojko
- School of Health and Life Sciences, Teesside University, Middlesbrough TS1 3BA, UK
| | - Andrew S. Kough
- John G. Shedd Aquarium, Haerther Center for Conservation Research, Chicago, IL 60605, USA
| | - Nathaniel W. Alper
- Baltimore Polytechnic Institute, Columbia University, New York, NY 20027, USA
| | - Lan Xu
- Department of Marine Biotechnology and Institute of Marine and Environmental Technology, University of Maryland, Baltimore County, Baltimore, MD 21202, USA
| | - Eric J. Schott
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
- Correspondence:
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4
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Gunasekara U, Bertram MR, Van Long N, Minh PQ, Chuong VD, Perez A, Arzt J, VanderWaal K. Phylogeography as a Proxy for Population Connectivity for Spatial Modeling of Foot-and-Mouth Disease Outbreaks in Vietnam. Viruses 2023; 15:v15020388. [PMID: 36851602 PMCID: PMC9958845 DOI: 10.3390/v15020388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/31/2023] Open
Abstract
Bayesian space-time regression models are helpful tools to describe and predict the distribution of infectious disease outbreaks and to delineate high-risk areas for disease control. In these models, structured and unstructured spatial and temporal effects account for various forms of non-independence amongst case counts across spatial units. Structured spatial effects capture correlations in case counts amongst neighboring provinces arising from shared risk factors or population connectivity. For highly mobile populations, spatial adjacency is an imperfect measure of connectivity due to long-distance movement, but we often lack data on host movements. Phylogeographic models inferring routes of viral dissemination across a region could serve as a proxy for patterns of population connectivity. The objective of this study was to investigate whether the effects of population connectivity in space-time regressions of case counts were better captured by spatial adjacency or by inferences from phylogeographic analyses. To compare these two approaches, we used foot-and-mouth disease virus (FMDV) outbreak data from across Vietnam as an example. We identified that accounting for virus movement through phylogeographic analysis serves as a better proxy for population connectivity than spatial adjacency in spatial-temporal risk models. This approach may contribute to design surveillance activities in countries lacking movement data.
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Affiliation(s)
- Umanga Gunasekara
- Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Miranda R. Bertram
- Foreign Animal Disease Research Unit, USDA-ARS, Plum Island Animal Disease Center, Southold, NY 11957, USA
| | - Nguyen Van Long
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - Phan Quang Minh
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - Vo Dinh Chuong
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - Andres Perez
- Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Jonathan Arzt
- Foreign Animal Disease Research Unit, USDA-ARS, Plum Island Animal Disease Center, Southold, NY 11957, USA
- Correspondence: (J.A.); (K.V.)
| | - Kimberly VanderWaal
- Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108, USA
- Correspondence: (J.A.); (K.V.)
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5
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Gilbertson MLJ, Fountain-Jones NM, Malmberg JL, Gagne RB, Lee JS, Kraberger S, Kechejian S, Petch R, Chiu ES, Onorato D, Cunningham MW, Crooks KR, Funk WC, Carver S, VandeWoude S, VanderWaal K, Craft ME. Apathogenic proxies for transmission dynamics of a fatal virus. Front Vet Sci 2022; 9:940007. [PMID: 36157183 PMCID: PMC9493079 DOI: 10.3389/fvets.2022.940007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Identifying drivers of transmission-especially of emerging pathogens-is a formidable challenge for proactive disease management efforts. While close social interactions can be associated with microbial sharing between individuals, and thereby imply dynamics important for transmission, such associations can be obscured by the influences of factors such as shared diets or environments. Directly-transmitted viral agents, specifically those that are rapidly evolving such as many RNA viruses, can allow for high-resolution inference of transmission, and therefore hold promise for elucidating not only which individuals transmit to each other, but also drivers of those transmission events. Here, we tested a novel approach in the Florida panther, which is affected by several directly-transmitted feline retroviruses. We first inferred the transmission network for an apathogenic, directly-transmitted retrovirus, feline immunodeficiency virus (FIV), and then used exponential random graph models to determine drivers structuring this network. We then evaluated the utility of these drivers in predicting transmission of the analogously transmitted, pathogenic agent, feline leukemia virus (FeLV), and compared FIV-based predictions of outbreak dynamics against empirical FeLV outbreak data. FIV transmission was primarily driven by panther age class and distances between panther home range centroids. FIV-based modeling predicted FeLV dynamics similarly to common modeling approaches, but with evidence that FIV-based predictions captured the spatial structuring of the observed FeLV outbreak. While FIV-based predictions of FeLV transmission performed only marginally better than standard approaches, our results highlight the value of proactively identifying drivers of transmission-even based on analogously-transmitted, apathogenic agents-in order to predict transmission of emerging infectious agents. The identification of underlying drivers of transmission, such as through our workflow here, therefore holds promise for improving predictions of pathogen transmission in novel host populations, and could provide new strategies for proactive pathogen management in human and animal systems.
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Affiliation(s)
- Marie L. J. Gilbertson
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States
| | | | - Jennifer L. Malmberg
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
- Department of Veterinary Sciences, University of Wyoming, Laramie, WY, United States
| | - Roderick B. Gagne
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
- Wildlife Futures Program, Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Kennett Square, PA, United States
| | - Justin S. Lee
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
| | - Sarah Kechejian
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Raegan Petch
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Elliott S. Chiu
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Dave Onorato
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL, United States
| | - Mark W. Cunningham
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Gainesville, FL, United States
| | - Kevin R. Crooks
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, United States
| | - W. Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
| | - Scott Carver
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Kimberly VanderWaal
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Meggan E. Craft
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, United States
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6
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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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7
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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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8
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Hunting shapes wildlife disease transmission. Nat Ecol Evol 2022; 6:136-137. [PMID: 35087216 DOI: 10.1038/s41559-021-01633-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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9
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Liu E, Ma L, Huang S, You D, Guo L, Li X, Xu H, Liu D, Chai H, Wang Y. The first feline immunodeficiency virus from Siberian tigers (Panthera tigris altaica) in northeastern China. Arch Virol 2022; 167:545-551. [DOI: 10.1007/s00705-022-05370-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 12/13/2021] [Indexed: 12/21/2022]
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10
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The ecology of zoonotic parasites in the Carnivora. Trends Parasitol 2021; 37:1096-1110. [PMID: 34544647 DOI: 10.1016/j.pt.2021.08.006] [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: 03/29/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 01/08/2023]
Abstract
The order Carnivora includes over 300 species that vary many orders of magnitude in size and inhabit all major biomes, from tropical rainforests to polar seas. The high diversity of carnivore parasites represents a source of potential emerging diseases of humans. Zoonotic risk from this group may be driven in part by exceptionally high functional diversity of host species in behavioral, physiological, and ecological traits. We review global macroecological patterns of zoonotic parasites within carnivores, and explore the traits of species that serve as hosts of zoonotic parasites. We synthesize theoretical and empirical research and suggest future work on the roles of carnivores as biotic multipliers, regulators, and sentinels of zoonotic disease as timely research frontiers.
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11
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Gagne RB, Kraberger S, McMinn R, Trumbo DR, Anderson CR, Logan KA, Alldredge MW, Griffin K, Vandewoude S. Viral Sequences Recovered From Puma Tooth DNA Reconstruct Statewide Viral Phylogenies. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.734462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Monitoring pathogens in wildlife populations is imperative for effective management, and for identifying locations for pathogen spillover among wildlife, domestic species and humans. Wildlife pathogen surveillance is challenging, however, as sampling often requires the capture of a significant proportion of the population to understand host pathogen dynamics. To address this challenge, we assessed the ability to use hunter-collected teeth from puma across Colorado to recover genetic data of two feline retroviruses, feline foamy virus (FFV) and feline immunodeficiency virus (FIVpco) and show they can be utilized for this purpose. Comparative phylogenetic analyses of FIVpco and FFV from tooth and blood samples to previous analyses conducted with blood samples collected over a nine-year period from two distinct areas was undertaken highlighting the value of tooth derived samples. We found less FIVpco phylogeographic structuring than observed from sampling only two regions and that FFV data confirmed previous findings of endemic infection, minimal geographic structuring, and supported frequent cross-species transmission from domestic cats to pumas. Viral analysis conducted using intentionally collected blood samples required extensive financial, capture and sampling efforts. This analysis illustrates that viral genomic data can be cost effectively obtained using tooth samples incidentally-collected from hunter harvested pumas, taking advantage of samples collected for morphological age identification. This technique should be considered as an opportunistic method to provide broad geographic sampling to define viral dynamics more accurately in wildlife.
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12
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Epps CW, Weldy MJ, Crowhurst RS, Spaan RS. Estimating the distribution and habitat suitability for aardvarks (
Orycteropus afer
) in Kruger National Park, South Africa. Afr J Ecol 2021. [DOI: 10.1111/aje.12916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Clinton W. Epps
- Department of Fisheries Wildlife and Conservation Sciences Oregon State University Corvallis OR USA
| | - Matthew J. Weldy
- Department of Fisheries Wildlife and Conservation Sciences Oregon State University Corvallis OR USA
| | - Rachel S. Crowhurst
- Department of Fisheries Wildlife and Conservation Sciences Oregon State University Corvallis OR USA
| | - Robert S. Spaan
- Department of Fisheries Wildlife and Conservation Sciences Oregon State University Corvallis OR USA
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13
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Chafin TK, Zbinden ZD, Douglas MR, Martin BT, Middaugh CR, Gray MC, Ballard JR, Douglas ME. Spatial population genetics in heavily managed species: Separating patterns of historical translocation from contemporary gene flow in white-tailed deer. Evol Appl 2021; 14:1673-1689. [PMID: 34178112 PMCID: PMC8210790 DOI: 10.1111/eva.13233] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 03/10/2021] [Indexed: 01/16/2023] Open
Abstract
Approximately 100 years ago, unregulated harvest nearly eliminated white-tailed deer (Odocoileus virginianus) from eastern North America, which subsequently served to catalyze wildlife management as a national priority. An extensive stock-replenishment effort soon followed, with deer broadly translocated among states as a means of re-establishment. However, an unintended consequence was that natural patterns of gene flow became obscured and pretranslocation signatures of population structure were replaced. We applied cutting-edge molecular and biogeographic tools to disentangle genetic signatures of historical management from those reflecting spatially heterogeneous dispersal by evaluating 35,099 single nucleotide polymorphisms (SNPs) derived via reduced-representation genomic sequencing from 1143 deer sampled statewide in Arkansas. We then employed Simpson's diversity index to summarize ancestry assignments and visualize spatial genetic transitions. Using sub-sampled transects across these transitions, we tested clinal patterns across loci against theoretical expectations of their response under scenarios of re-colonization and restricted dispersal. Two salient results emerged: (A) Genetic signatures from historic translocations are demonstrably apparent; and (B) Geographic filters (major rivers; urban centers; highways) now act as inflection points for the distribution of this contemporary ancestry. These results yielded a statewide assessment of contemporary population structure in deer as driven by historic translocations as well as ongoing processes. In addition, the analytical framework employed herein to effectively decipher extant/historic drivers of deer distribution in Arkansas is also applicable for other biodiversity elements with similarly complex demographic histories.
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Affiliation(s)
- Tyler K. Chafin
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
- Present address:
Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderCOUSA
| | - Zachery D. Zbinden
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Marlis R. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Bradley T. Martin
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | | | - M. Cory Gray
- Research DivisionArkansas Game and Fish CommissionLittle RockARUSA
| | | | - Michael E. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
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