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Carnegie L, Raghwani J, Fournié G, Hill SC. Phylodynamic approaches to studying avian influenza virus. Avian Pathol 2023; 52:289-308. [PMID: 37565466 DOI: 10.1080/03079457.2023.2236568] [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: 02/02/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023]
Abstract
Avian influenza viruses can cause severe disease in domestic and wild birds and are a pandemic threat. Phylodynamics is the study of how epidemiological, evolutionary, and immunological processes can interact to shape viral phylogenies. This review summarizes how phylodynamic methods have and could contribute to the study of avian influenza viruses. Specifically, we assess how phylodynamics can be used to examine viral spread within and between wild or domestic bird populations at various geographical scales, identify factors associated with virus dispersal, and determine the order and timing of virus lineage movement between geographic regions or poultry production systems. We discuss factors that can complicate the interpretation of phylodynamic results and identify how future methodological developments could contribute to improved control of the virus.
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Affiliation(s)
- L Carnegie
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - J Raghwani
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - G Fournié
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint Genes Champanelle, France
| | - S C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
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Teitelbaum CS, Casazza ML, McDuie F, De La Cruz SEW, Overton CT, Hall LA, Matchett EL, Ackerman JT, Sullivan JD, Ramey AM, Prosser DJ. Waterfowl recently infected with low pathogenic avian influenza exhibit reduced local movement and delayed migration. Ecosphere 2023. [DOI: 10.1002/ecs2.4432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Affiliation(s)
- Claire S. Teitelbaum
- Akima Systems Engineering Herndon Virginia USA
- Contractor to U.S. Geological Survey Eastern Ecological Science Center Laurel Maryland USA
| | - Michael L. Casazza
- U.S. Geological Survey Western Ecological Research Center, Dixon Field Station Dixon California USA
| | - Fiona McDuie
- U.S. Geological Survey Western Ecological Research Center, Dixon Field Station Dixon California USA
- San Jose State University Research Foundation Moss Landing Marine Laboratories Moss Landing California USA
| | - Susan E. W. De La Cruz
- U.S. Geological Survey Western Ecological Research Center San Francisco Bay Estuary Field Station Moffett Field California USA
| | - Cory T. Overton
- U.S. Geological Survey Western Ecological Research Center, Dixon Field Station Dixon California USA
| | - Laurie A. Hall
- U.S. Geological Survey Western Ecological Research Center San Francisco Bay Estuary Field Station Moffett Field California USA
| | - Elliott L. Matchett
- U.S. Geological Survey Western Ecological Research Center, Dixon Field Station Dixon California USA
| | - Joshua T. Ackerman
- U.S. Geological Survey Western Ecological Research Center, Dixon Field Station Dixon California USA
| | - Jeffery D. Sullivan
- U.S. Geological Survey Eastern Ecological Science Center Laurel Maryland USA
| | - Andrew M. Ramey
- U.S. Geological Survey Alaska Science Center Anchorage Alaska USA
| | - Diann J. Prosser
- U.S. Geological Survey Eastern Ecological Science Center Laurel Maryland USA
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3
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Teitelbaum CS, Ackerman JT, Hill MA, Satter JM, Casazza ML, De La Cruz SEW, Boyce WM, Buck EJ, Eadie JM, Herzog MP, Matchett EL, Overton CT, Peterson SH, Plancarte M, Ramey AM, Sullivan JD, Prosser DJ. Avian influenza antibody prevalence increases with mercury contamination in wild waterfowl. Proc Biol Sci 2022; 289:20221312. [PMID: 36069010 PMCID: PMC9449466 DOI: 10.1098/rspb.2022.1312] [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: 07/06/2022] [Accepted: 08/15/2022] [Indexed: 11/12/2022] Open
Abstract
Environmental contamination is widespread and can negatively impact wildlife health. Some contaminants, including heavy metals, have immunosuppressive effects, but prior studies have rarely measured contamination and disease simultaneously, which limits our understanding of how contaminants and pathogens interact to influence wildlife health. Here, we measured mercury concentrations, influenza infection, influenza antibodies and body condition in 749 individuals from 11 species of wild ducks overwintering in California. We found that the odds of prior influenza infection increased more than fivefold across the observed range of blood mercury concentrations, while accounting for species, age, sex and date. Influenza infection prevalence was also higher in species with higher average mercury concentrations. We detected no relationship between influenza infection and body fat content. This positive relationship between influenza prevalence and mercury concentrations in migratory waterfowl suggests that immunotoxic effects of mercury contamination could promote the spread of avian influenza along migratory flyways, especially if influenza has minimal effects on bird health and mobility. More generally, these results show that the effects of environmental contamination could extend beyond the geographical area of contamination itself by altering the prevalence of infectious diseases in highly mobile hosts.
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Affiliation(s)
- Claire S. Teitelbaum
- Akima Systems Engineering, Herndon, VA, USA
- Contractor to U.S. Geological Survey Eastern Ecological Science Center, Laurel, MD, USA
| | - Joshua T. Ackerman
- U.S. Geological Survey Western Ecological Research Center, Dixon Field Station, Dixon, CA, USA
| | - Mason A. Hill
- U.S. Geological Survey Western Ecological Research Center, San Francisco Bay Estuary Field Station, Moffett Field, CA, USA
| | - Jacqueline M. Satter
- UC Davis College of Agricultural and Environmental Sciences, Department of Wildlife, Fish, and Conservation Biology, Davis, CA, USA
| | - Michael L. Casazza
- U.S. Geological Survey Western Ecological Research Center, Dixon Field Station, Dixon, CA, USA
| | - Susan E. W. De La Cruz
- U.S. Geological Survey Western Ecological Research Center, San Francisco Bay Estuary Field Station, Moffett Field, CA, USA
| | | | - Evan J. Buck
- U.S. Geological Survey Eastern Ecological Science Center, Laurel, MD, USA
| | - John M. Eadie
- UC Davis College of Agricultural and Environmental Sciences, Department of Wildlife, Fish, and Conservation Biology, Davis, CA, USA
| | - Mark P. Herzog
- U.S. Geological Survey Western Ecological Research Center, Dixon Field Station, Dixon, CA, USA
| | - Elliott L. Matchett
- U.S. Geological Survey Western Ecological Research Center, Dixon Field Station, Dixon, CA, USA
| | - Cory T. Overton
- U.S. Geological Survey Western Ecological Research Center, Dixon Field Station, Dixon, CA, USA
| | - Sarah H. Peterson
- U.S. Geological Survey Western Ecological Research Center, Dixon Field Station, Dixon, CA, USA
| | | | - Andrew M. Ramey
- U.S. Geological Survey Alaska Science Center, Anchorage, AK, USA
| | | | - Diann J. Prosser
- U.S. Geological Survey Eastern Ecological Science Center, Laurel, MD, USA
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Ramey AM, Hill NJ, DeLiberto TJ, Gibbs SEJ, Camille Hopkins M, Lang AS, Poulson RL, Prosser DJ, Sleeman JM, Stallknecht DE, Wan X. Highly pathogenic avian influenza is an emerging disease threat to wild birds in North America. J Wildl Manage 2022. [DOI: 10.1002/jwmg.22171] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Andrew M. Ramey
- U.S. Geological Survey Alaska Science Center 4210 University Drive Anchorage AK 99508 USA
| | - Nichola J. Hill
- Department of Infectious Disease & Global Health, Cummings School of Veterinary Medicine Tufts University 200 Westboro Road North Grafton MA 01536 USA
| | - Thomas J. DeLiberto
- National Wildlife Disease Program, Wildlife Services, Animal and Plant Health Inspection Service U.S. Department of Agriculture 4101 LaPorte Avenue Fort Collins CO 80521 USA
| | - Samantha E. J. Gibbs
- Wildlife Health Office Natural Resource Program Center, National Wildlife Refuge System, U.S. Fish and Wildlife Service 16450 NW 31st Place Chiefland FL 32626 USA
| | - M. Camille Hopkins
- U.S. Geological Survey Ecosystems Mission Area 12201 Sunrise Valley Drive, MS 300 (Room 4A100F) Reston VA 20192 USA
| | - Andrew S. Lang
- Department of Biology Memorial University of Newfoundland 232 Elizabeth Avenue St. John's Newfoundland A1B 3X9 Canada
| | - Rebecca L. Poulson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia 589 D.W. Brooks Drive Athens GA 30602 USA
| | - Diann J. Prosser
- U.S. Geological Survey Eastern Ecological Science Center at the Patuxent Research Refuge 12100 Beech Forest Road Laurel MD 20708 USA
| | - Jonathan M. Sleeman
- U.S. Geological Survey National Wildlife Health Center 6006 Schroeder Road Madison WI 53711 USA
| | - David E. Stallknecht
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia 589 D.W. Brooks Drive Athens GA 30602 USA
| | - Xiu‐Feng Wan
- Center for Influenza and Emerging Infectious Diseases (CIEID), Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, Department of Electronic Engineering and Computer Science University of Missouri Columbia MO 65211 USA
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Bianchini EA, Bogiatto RJ, Donatello RA, Casazza ML, Ackerman JT, De La Cruz SEW, Cline TD. Host Correlates of Avian Influenza Virus Infection in Wild Waterfowl of the Sacramento Valley, California. Avian Dis 2021; 66:20-28. [DOI: 10.1637/aviandiseases-d-21-00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/15/2021] [Indexed: 11/05/2022]
Affiliation(s)
| | - Raymond J. Bogiatto
- Department of Biological Sciences, California State University, Chico, Chico, CA 95929
| | - Robin A. Donatello
- Department of Mathematics and Statistics, California State University, Chico, Chico, CA 95929
| | - Michael L. Casazza
- United States Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, CA 95620
| | - Joshua T. Ackerman
- United States Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, CA 95620
| | - Susan E. W. De La Cruz
- United States Geological Survey, Western Ecological Research Center, San Francisco Bay Estuary Field Station, Vallejo, CA 94592
| | - Troy D. Cline
- Department of Biological Sciences, California State University, Chico, Chico, CA 95929
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Acosta S, Kelman T, Feirer S, Matchett E, Smolinsky J, Pitesky M, Buler J. Using the California Waterfowl Tracker to Assess Proximity of Waterfowl to Commercial Poultry in the Central Valley of California. Avian Dis 2021; 65:483-492. [PMID: 34699147 DOI: 10.1637/aviandiseases-d-20-00137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 07/02/2021] [Indexed: 11/05/2022]
Abstract
Migratory waterfowl are the primary reservoir of avian influenza viruses (AIV), which can be spread to commercial poultry. Surveillance efforts that track the location and abundance of wild waterfowl and link those data to inform assessments of risk and sampling for AIV currently do not exist. To assist surveillance and minimize poultry exposure to AIV, here we explored the utility of Remotely Sensed Moderate Resolution Imaging Spectroradiometer (MODIS) satellite imagery in combination with land-based climate measurements (e.g., temperature and precipitation) to predict waterfowl location and abundance in near real-time in the California Central Valley (CCV), where both wild waterfowl and domestic poultry are densely located. Specifically, remotely collected MODIS and climate data were integrated into a previously developed boosted regression tree (BRT) model to predict and visualize waterfowl distributions across the CCV. Daily model-based predictions are publicly available during the winter as part of the dynamic California Waterfowl Tracker (CWT) web app hosted on the University of California's Cooperative Extension webpage. In this study, we analyzed 52 days of model predictions and produced daily spatiotemporal maps of waterfowl concentrations near the 605 commercial poultry farms in the CCV during January and February of 2019. Exposure of each poultry farm to waterfowl during each day was classified as high, medium, low, or none, depending on the density of waterfowl within 4 km of a farm. Results indicated that farms were at substantially greater risk of exposure in January, when CCV waterfowl populations peak, than in February. For example, during January, 33% (199/605) of the farms were exposed for ≥1 day to high waterfowl density vs. 19% (115/605) of the farms in February. In addition to demonstrating the overall variability of waterfowl location and density, these data demonstrate how remote sensing can be used to better triage AIV surveillance and biosecurity efforts via the utilization of a functional web app-based tool. The ability to leverage remote sensing is an integral advancement toward improving AIV surveillance in waterfowl in close proximity to commercial poultry. Expansion of these types of remote sensing methods, linked to a user-friendly web tool, could be further developed across the continental United States. The BRT model incorporated into the CWT reflects a first attempt to give an accurate representation of waterfowl distribution and density relative to commercial poultry.
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Affiliation(s)
- Sarai Acosta
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616
| | - Todd Kelman
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616
| | - Shane Feirer
- Hopland Research and Extension Center, UC-Agriculture and Natural Resources, Hopland, CA 95449
| | - Elliott Matchett
- Dixon Field Station, Western Ecological Research Center, U.S. Geological Survey, Dixon, CA 95620
| | - Jaclyn Smolinsky
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE 19716
| | - Maurice Pitesky
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616,
| | - Jeffrey Buler
- Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE 19716,
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Respiratory Tract Explant Infection Dynamics of Influenza A Virus in California Sea Lions, Northern Elephant Seals, and Rhesus Macaques. J Virol 2021; 95:e0040321. [PMID: 34037419 PMCID: PMC8312873 DOI: 10.1128/jvi.00403-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
To understand susceptibility of wild California sea lions and Northern elephant seals to influenza A virus (IAV), we developed an ex vivo respiratory explant model and used it to compare infection kinetics for multiple IAV subtypes. We first established the approach using explants from colonized rhesus macaques, a model for human IAV. Trachea, bronchi, and lungs from 11 California sea lions, 2 Northern elephant seals, and 10 rhesus macaques were inoculated within 24 h postmortem with 6 strains representing 4 IAV subtypes. Explants from the 3 species showed similar IAV infection kinetics, with peak viral titers 48 to 72 h post-inoculation that increased by 2 to 4 log10 PFU/explant relative to the inoculum. Immunohistochemistry localized IAV infection to apical epithelial cells. These results demonstrate that respiratory tissue explants from wild marine mammals support IAV infection. In the absence of the ability to perform experimental infections of marine mammals, this ex vivo culture of respiratory tissues mirrors the in vivo environment and serves as a tool to study IAV susceptibility, host range, and tissue tropism. IMPORTANCE Although influenza A virus can infect marine mammals, a dearth of marine mammal cell lines and ethical and logistical challenges prohibiting experimental infections of living marine mammals mean that little is known about IAV infection kinetics in these species. We circumvented these limitations by adapting a respiratory tract explant model first to establish the approach with rhesus macaques and then for use with explants from wild marine mammals euthanized for nonrespiratory medical conditions. We observed that multiple strains representing 4 IAV subtypes infected trachea, bronchi, and lungs of macaques and marine mammals with variable peak titers and kinetics. This ex vivo model can define infection dynamics for IAV in marine mammals. Further, use of explants from animals euthanized for other reasons reduces use of animals in research.
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TARGETED RESEQUENCING OF WETLAND SEDIMENT AS A TOOL FOR AVIAN INFLUENZA VIRUS SURVEILLANCE. J Wildl Dis 2020. [DOI: 10.7589/2019-05-135] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Humphreys JM, Ramey AM, Douglas DC, Mullinax JM, Soos C, Link P, Walther P, Prosser DJ. Waterfowl occurrence and residence time as indicators of H5 and H7 avian influenza in North American Poultry. Sci Rep 2020; 10:2592. [PMID: 32054908 PMCID: PMC7018751 DOI: 10.1038/s41598-020-59077-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 01/15/2020] [Indexed: 01/25/2023] Open
Abstract
Avian influenza (AI) affects wild aquatic birds and poses hazards to human health, food security, and wildlife conservation globally. Accordingly, there is a recognized need for new methods and tools to help quantify the dynamic interaction between wild bird hosts and commercial poultry. Using satellite-marked waterfowl, we applied Bayesian joint hierarchical modeling to concurrently model species distributions, residency times, migration timing, and disease occurrence probability under an integrated animal movement and disease distribution modeling framework. Our results indicate that migratory waterfowl are positively related to AI occurrence over North America such that as waterfowl occurrence probability or residence time increase at a given location, so too does the chance of a commercial poultry AI outbreak. Analyses also suggest that AI occurrence probability is greatest during our observed waterfowl northward migration, and less during the southward migration. Methodologically, we found that when modeling disparate facets of disease systems at the wildlife-agriculture interface, it is essential that multiscale spatial patterns be addressed to avoid mistakenly inferring a disease process or disease-environment relationship from a pattern evaluated at the improper spatial scale. The study offers important insights into migratory waterfowl ecology and AI disease dynamics that aid in better preparing for future outbreaks.
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Affiliation(s)
- John M Humphreys
- Michigan State University, East Lansing, Michigan, USA.
- U.S. Geological Survey, Patuxent Wildlife Research Center, Laurel, Maryland, USA.
| | - Andrew M Ramey
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, USA
| | - David C Douglas
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, USA
| | | | - Catherine Soos
- Environment and Climate Change Canada, Ecotoxicology and Wildlife Health Division, Saskatchewan, Canada
| | - Paul Link
- Louisiana Department of Wildlife and Fisheries, Baton Rouge, Louisiana, USA
| | - Patrick Walther
- U.S. Fish and Wildlife Service, Texas Chenier Plain Refuge Complex, Anahuac, Texas, USA
| | - Diann J Prosser
- U.S. Geological Survey, Patuxent Wildlife Research Center, Laurel, Maryland, USA
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LIMITED DETECTION OF ANTIBODIES TO CLADE 2.3.4.4 A/GOOSE/GUANGDONG/1/1996 LINEAGE HIGHLY PATHOGENIC H5 AVIAN INFLUENZA VIRUS IN NORTH AMERICAN WATERFOWL. J Wildl Dis 2019. [PMID: 31556839 DOI: 10.7589/2019-01-003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
During 2014, highly pathogenic (HP) influenza A viruses (IAVs) of the A/Goose/Guangdong/1/1996 lineage (GsGD-HP-H5), originating from Asia, were detected in domestic poultry and wild birds in Canada and the US. These clade 2.3.4.4 GsGD-HP-H5 viruses included reassortants possessing North American lineage gene segments; were detected in wild birds in the Pacific, Central, and Mississippi flyways; and caused the largest HP IAV outbreak in poultry in US history. To determine if an antibody response indicative of previous infection with clade 2.3.4.4 GsGD-HP-H5 IAV could be detected in North American wild waterfowl sampled before, during, and after the 2014-15 outbreak, sera from 2,793 geese and 3,715 ducks were tested by blocking enzyme-linked immunosorbent assay and hemagglutination inhibition (HI) tests using both clade 2.3.4.4 GsGD-HPH5 and North American lineage low pathogenic (LP) H5 IAV antigens. We detected an antibody response meeting a comparative titer-based criteria (HI titer observed with 2.3.4.4 GsGD-HP-H5 antigens exceeded the titer observed for LP H5 antigen by two or more dilutions) for previous infection with clade 2.3.4.4 GsGD-HP-H5 IAV in only five birds, one Blue-winged Teal (Spatula discors) sampled during the outbreak and three Mallards (Anas platyrhynchos) and one Canada Goose (Branta canadensis) sampled during the post-outbreak period. These serologic results are consistent with the spatiotemporal extent of the outbreak in wild birds in North America during 2014 and 2015 and limited exposure of waterfowl to GsGD-HP-H5 IAV, particularly in the central and eastern US.
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Titcomb GC, Jerde CL, Young HS. High-Throughput Sequencing for Understanding the Ecology of Emerging Infectious Diseases at the Wildlife-Human Interface. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00126] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Franklin AB, Bevins SN, Ellis JW, Miller RS, Shriner S, Root JJ, Walsh DP, Deliberto TJ. Predicting the initial spread of novel Asian origin influenza A viruses in the continental USA by wild waterfowl. Transbound Emerg Dis 2018; 66:705-714. [DOI: 10.1111/tbed.13070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 10/05/2018] [Accepted: 11/01/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Alan. B. Franklin
- U. S. Department of Agriculture APHIS‐WS National Wildlife Research Center Fort Collins Colorado
| | - Sarah N. Bevins
- U. S. Department of Agriculture APHIS‐WS National Wildlife Research Center Fort Collins Colorado
| | - Jeremy W. Ellis
- U. S. Department of Agriculture APHIS‐WS National Wildlife Research Center Fort Collins Colorado
| | - Ryan S. Miller
- U. S. Department of Agriculture APHIS‐VS Center for Epidemiology and Animal Health Fort Collins Colorado
| | - Susan A. Shriner
- U. S. Department of Agriculture APHIS‐WS National Wildlife Research Center Fort Collins Colorado
| | - J. Jeffrey Root
- U. S. Department of Agriculture APHIS‐WS National Wildlife Research Center Fort Collins Colorado
| | - Daniel P. Walsh
- U. S. Geological Survey National Wildlife Health Center Madison Wisconsin
| | - Thomas J. Deliberto
- U. S. Department of Agriculture APHIS‐WS National Wildlife Research Center Fort Collins Colorado
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Genomic sequence and phylogenetic analyses of two novel orthoreovirus strains isolated from Pekin ducks in 2014 in Germany. Virus Res 2018; 257:57-62. [DOI: 10.1016/j.virusres.2018.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/31/2018] [Accepted: 09/03/2018] [Indexed: 11/15/2022]
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14
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Belkhiria J, Hijmans RJ, Boyce W, Crossley BM, Martínez-López B. Identification of high risk areas for avian influenza outbreaks in California using disease distribution models. PLoS One 2018; 13:e0190824. [PMID: 29385158 PMCID: PMC5791985 DOI: 10.1371/journal.pone.0190824] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 12/20/2017] [Indexed: 11/18/2022] Open
Abstract
The coexistence of different types of poultry operations such as free range and backyard flocks, large commercial indoor farms and live bird markets, as well as the presence of many areas where wild and domestic birds co-exist, make California susceptible to avian influenza outbreaks. The 2014-2015 highly pathogenic Avian Influenza (HPAI) outbreaks affecting California and other states in the United States have underscored the need for solutions to protect the US poultry industry against this devastating disease. We applied disease distribution models to predict where Avian influenza is likely to occur and the risk for HPAI outbreaks is highest. We used observations on the presence of Low Pathogenic Avian influenza virus (LPAI) in waterfowl or water samples at 355 locations throughout the state and environmental variables relevant to the disease epidemiology. We used two algorithms, Random Forest and MaxEnt, and two data-sets Presence-Background and Presence-Absence data. The models performed well (AUCc > 0.7 for testing data), particularly those using Presence-Background data (AUCc > 0.85). Spatial predictions were similar between algorithms, but there were large differences between the predictions with Presence-Absence and Presence-Background data. Overall, predictors that contributed most to the models included land cover, distance to coast, and broiler farm density. Models successfully identified several counties as high-to-intermediate risk out of the 8 counties with observed outbreaks during the 2014-2015 HPAI epizootics. This study provides further insights into the spatial epidemiology of AI in California, and the high spatial resolution maps may be useful to guide risk-based surveillance and outreach efforts.
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Affiliation(s)
- Jaber Belkhiria
- Center for Animal Disease Modeling and Surveillance, Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, California, United States of America
- * E-mail:
| | - Robert J. Hijmans
- Department of Environmental Science & Policy, University of California, Davis, California, United States of America
| | - Walter Boyce
- Department of Pathology, Microbiology & Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Beate M. Crossley
- California Animal Health and Food Safety Lab, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Beatriz Martínez-López
- Center for Animal Disease Modeling and Surveillance, Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, California, United States of America
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