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Ma Y, Liu P, Li Z, Yue Y, Zhao Y, He J, Zhao J, Song X, Wang J, Liu Q, Lu L. High genetic diversity of the himalayan marmot relative to plague outbreaks in the Qinghai-Tibet Plateau, China. BMC Genomics 2024; 25:262. [PMID: 38459433 PMCID: PMC10921737 DOI: 10.1186/s12864-024-10171-y] [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: 09/17/2023] [Accepted: 02/28/2024] [Indexed: 03/10/2024] Open
Abstract
Plague, as an ancient zoonotic disease caused by Yersinia pestis, has brought great disasters. The natural plague focus of Marmota himalayana in the Qinghai-Tibet Plateau is the largest, which has been constantly active and the leading source of human plague in China for decades. Understanding the population genetics of M. himalayana and relating that information to the biogeographic distribution of Yersinia pestis and plague outbreaks are greatly beneficial for the knowledge of plague spillover and arecrucial for pandemic prevention. In the present research, we assessed the population genetics of M. himalayana. We carried out a comparative study of plague outbreaks and the population genetics of M. himalayana on the Qinghai-Tibet Plateau. We found that M. himalayana populations are divided into two main clusters located in the south and north of the Qinghai-Tibet Plateau. Fourteen DFR genomovars of Y. pestis were found and exhibited a significant region-specific distribution. Additionally, the increased genetic diversity of plague hosts is positively associated with human plague outbreaks. This insight gained can improve our understanding of biodiversity for pathogen spillover and provide municipally directed targets for One Health surveillance development, which will be an informative next step toward increased monitoring of M. himalayana dynamics.
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Affiliation(s)
- Ying Ma
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, 811602, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Pengbo Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Ziyan Li
- College of Life Sciences, WuHan University, Wuhan, 430072, China
| | - Yujuan Yue
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Yanmei Zhao
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, 811602, China
| | - Jian He
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, 811602, China
| | - Jiaxin Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
- Center for Disease Control and Prevention of Chaoyang District, Beijing, 100021, China
| | - Xiuping Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Jun Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Qiyong Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Liang Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China.
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2
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Talbot B, Alanazi TJ, Albert V, Bordeleau É, Bouchard É, Leighton PA, Marshall HD, Rondeau-Geoffrion D, Simon A, Massé A. Low levels of genetic differentiation and structure in red fox populations in Eastern Canada and implications for Arctic fox rabies propagation potential. PLoS One 2023; 18:e0286784. [PMID: 37279210 DOI: 10.1371/journal.pone.0286784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 05/23/2023] [Indexed: 06/08/2023] Open
Abstract
Rabies is a lethal zoonosis present in most parts of the world which can be transmitted to humans through the bite from an infected mammalian reservoir host. The Arctic rabies virus variant (ARVV) persists mainly in populations of Arctic foxes (Vulpes lagopus), and to a lesser extent in red fox populations (Vulpes vulpes). Red foxes are thought to be responsible for sporadic southward movement waves of the ARVV outside the enzootic area of northern Canada. In this study, we wanted to investigate whether red foxes displayed notable levels of genetic structure across the Quebec-Labrador Peninsula, which includes portions of the provinces of Quebec and Newfoundland-Labrador in Canada, and is a region with a history of southward ARVV movement waves. We combined two datasets that were collected and genotyped using different protocols, totalling 675 red fox individuals across the whole region and genotyped across 13 microsatellite markers. We found two genetic clusters across the region, reflecting a latitudinal gradient, and characterized by low genetic differentiation. We also observed weak but significant isolation by distance, which seems to be marginally more important for females than for males. These findings suggest a general lack of resistance to movement in red fox populations across the Quebec-Labrador Peninsula, regardless of sex. Implications of these findings include additional support for the hypothesis of long-distance southward ARVV propagation through its red fox reservoir host.
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Affiliation(s)
- Benoit Talbot
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON, Canada
- Research Group on Epidemiology of Zoonoses and Public Health (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Thaneah J Alanazi
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Vicky Albert
- Ministère des Forêts, de la Faune et des Parcs, Québec, QC, Canada
| | - Émilie Bordeleau
- Ministère des Forêts, de la Faune et des Parcs, Québec, QC, Canada
| | - Émilie Bouchard
- Research Group on Epidemiology of Zoonoses and Public Health (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Department of Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Patrick A Leighton
- Research Group on Epidemiology of Zoonoses and Public Health (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - H Dawn Marshall
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | | | - Audrey Simon
- Research Group on Epidemiology of Zoonoses and Public Health (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Ariane Massé
- Ministère des Forêts, de la Faune et des Parcs, Québec, QC, Canada
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Baecklund TM, Donaldson ME, Hueffer K, Kyle CJ. Genetic structure of immunologically associated candidate genes suggests arctic rabies variants exert differential selection in arctic fox populations. PLoS One 2021; 16:e0258975. [PMID: 34714859 PMCID: PMC8555846 DOI: 10.1371/journal.pone.0258975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/10/2021] [Indexed: 11/24/2022] Open
Abstract
Patterns of local adaptation can emerge in response to the selective pressures diseases exert on host populations as reflected in increased frequencies of respective, advantageous genotypes. Elucidating patterns of local adaptation enhance our understanding of mechanisms of disease spread and the capacity for species to adapt in context of rapidly changing environments such as the Arctic. Arctic rabies is a lethal disease that largely persists in northern climates and overlaps with the distribution of its natural host, arctic fox. Arctic fox populations display little neutral genetic structure across their North American range, whereas phylogenetically unique arctic rabies variants are restricted in their geographic distributions. It remains unknown if arctic rabies variants impose differential selection upon host populations, nor what role different rabies variants play in the maintenance and spread of this disease. Using a targeted, genotyping-by-sequencing assay, we assessed correlations of arctic fox immunogenetic variation with arctic rabies variants to gain further insight into the epidemiology of this disease. Corroborating past research, we found no neutral genetic structure between sampled regions, but did find moderate immunogenetic structuring between foxes predominated by different arctic rabies variants. FST outliers associated with host immunogenetic structure included SNPs within interleukin and Toll-like receptor coding regions (IL12B, IL5, TLR3 and NFKB1); genes known to mediate host responses to rabies. While these data do not necessarily reflect causation, nor a direct link to arctic rabies, the contrasting genetic structure of immunologically associated candidate genes with neutral loci is suggestive of differential selection and patterns of local adaptation in this system. These data are somewhat unexpected given the long-lived nature and dispersal capacities of arctic fox; traits expected to undermine local adaptation. Overall, these data contribute to our understanding of the co-evolutionary relationships between arctic rabies and their primary host and provide data relevant to the management of this disease.
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Affiliation(s)
- Tristan M. Baecklund
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
- * E-mail:
| | - Michael E. Donaldson
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | - Karsten Hueffer
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK, United States of America
| | - Christopher J. Kyle
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
- Forensic Science Department, Trent University, Peterborough, ON, Canada
- Natural Resources DNA Profiling & Forensic Centre, Trent University, Peterborough, ON, Canada
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Huettmann F, Hueffer K. The ecological niche of reported rabies cases in Canada is similar to Alaska. Zoonoses Public Health 2021; 68:677-683. [PMID: 33955689 PMCID: PMC8453923 DOI: 10.1111/zph.12835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 03/03/2021] [Accepted: 04/03/2021] [Indexed: 12/03/2022]
Abstract
The ecology of rabies in the circumpolar North is still not well understood. We use machine learning, a geographic information system and data explicit in time and space obtained for reported rabies cases and predictors in Canada to develop an ecological niche model for the distribution of reported rabies cases in the American north (Alaska and Canada). The ecological niche model based on reported rabies cases in Canada predicted reported rabies cases in Alaska, suggesting a rather robust inference and even similar drivers on a continental scale. As found in Alaska, proximity to human infrastructure—specifically along the coast—was a strong predictor in the detection of rabies cases in Canada. Also, this finding highlights the need for a more systematic landscape sampling for rabies infection model predictions to better understand and tackle the ecology of this important zoonotic disease on a landscape scale at some distance from human infrastructure in wilderness areas.
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Affiliation(s)
- Falk Huettmann
- EWHALE lab- Inst of Arctic Biology, Department of Biology & Wildlife, University of Alaska, Fairbanks, AK, USA
| | - Karsten Hueffer
- Department of Veterinary Medicine, University of Alaska, Fairbanks, AK, USA
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5
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Baecklund TM, Morrison J, Donaldson ME, Hueffer K, Kyle CJ. The role of a mechanistic host in maintaining arctic rabies variant distributions: Assessment of functional genetic diversity in Alaskan red fox (Vulpes vulpes). PLoS One 2021; 16:e0249176. [PMID: 33831031 PMCID: PMC8031376 DOI: 10.1371/journal.pone.0249176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 03/12/2021] [Indexed: 11/18/2022] Open
Abstract
Populations are exposed to different types and strains of pathogens across heterogeneous landscapes, where local interactions between host and pathogen may present reciprocal selective forces leading to correlated patterns of spatial genetic structure. Understanding these coevolutionary patterns provides insight into mechanisms of disease spread and maintenance. Arctic rabies (AR) is a lethal disease with viral variants that occupy distinct geographic distributions across North America and Europe. Red fox (Vulpes vulpes) are a highly susceptible AR host, whose range overlaps both geographically distinct AR strains and regions where AR is absent. It is unclear if genetic structure exists among red fox populations relative to the presence/absence of AR or the spatial distribution of AR variants. Acquiring these data may enhance our understanding of the role of red fox in AR maintenance/spread and inform disease control strategies. Using a genotyping-by-sequencing assay targeting 116 genomic regions of immunogenetic relevance, we screened for sequence variation among red fox populations from Alaska and an outgroup from Ontario, including areas with different AR variants, and regions where the disease was absent. Presumed neutral SNP data from the assay found negligible levels of neutral genetic structure among Alaskan populations. The immunogenetically-associated data identified 30 outlier SNPs supporting weak to moderate genetic structure between regions with and without AR in Alaska. The outliers included SNPs with the potential to cause missense mutations within several toll-like receptor genes that have been associated with AR outcome. In contrast, there was a lack of genetic structure between regions with different AR variants. Combined, we interpret these data to suggest red fox populations respond differently to the presence of AR, but not AR variants. This research increases our understanding of AR dynamics in the Arctic, where host/disease patterns are undergoing flux in a rapidly changing Arctic landscape, including the continued northward expansion of red fox into regions previously predominated by the arctic fox (Vulpes lagopus).
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Affiliation(s)
- Tristan M. Baecklund
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- * E-mail:
| | - Jaycee Morrison
- Forensic Science Undergraduate Program, Trent University, Peterborough, Ontario, Canada
| | - Michael E. Donaldson
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Karsten Hueffer
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Christopher J. Kyle
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Forensic Science Department, Trent University, Peterborough, Ontario, Canada
- Natural Resources DNA Profiling & Forensic Centre, Trent University, Peterborough, Ontario, Canada
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6
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Nadin-Davis SA, Falardeau E, Flynn A, Whitney H, Marshall HD. Relationships between fox populations and rabies virus spread in northern Canada. PLoS One 2021; 16:e0246508. [PMID: 33592018 PMCID: PMC7886166 DOI: 10.1371/journal.pone.0246508] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 01/20/2021] [Indexed: 01/02/2023] Open
Abstract
Rabies spreads in both Arctic (Vulpes lagopus) and red foxes (Vulpes vulpes) throughout the Canadian Arctic but limited wildlife disease surveillance, due to the extensive landmass of the Canadian north and its small widely scattered human population, undermines our knowledge of disease transmission patterns. This study has explored genetic population structure in both the rabies virus and its fox hosts to better understand factors that impact rabies spread. Phylogenetic analysis of 278 samples of the Arctic lineage of rabies virus recovered over 40 years identified four sub-lineages, A1 to A4. The A1 lineage has been restricted to southern regions of the Canadian province of Ontario. The A2 lineage, which predominates in Siberia, has also spread to northern Alaska while the A4 lineage was recovered from southern Alaska only. The A3 sub-lineage, which was also found in northern Alaska, has been responsible for virtually all cases across northern Canada and Greenland, where it further differentiated into 18 groups which have systematically evolved from a common predecessor since 1975. In areas of Arctic and red fox sympatry, viral groups appear to circulate in both hosts, but both mitochondrial DNA control region sequences and 9-locus microsatellite genotypes revealed contrasting phylogeographic patterns for the two fox species. Among 157 Arctic foxes, 33 mitochondrial control region haplotypes were identified but little genetic structure differentiating localities was detected. Among 162 red foxes, 18 control region haplotypes delineated three groups which discriminated among the Churchill region of Manitoba, northern Quebec and Labrador populations, and the coastal Labrador locality of Cartwright. Microsatellite analyses demonstrated some genetic heterogeneity among sampling localities of Arctic foxes but no obvious pattern, while two or three clusters of red foxes suggested some admixture between the Churchill and Quebec-Labrador regions but uniqueness of the Cartwright group. The limited population structure of Arctic foxes is consistent with the rapid spread of rabies virus subtypes throughout the north, while red fox population substructure suggests that disease spread in this host moves most readily down certain independent corridors such as the northeastern coast of Canada and the central interior. Interestingly the evidence suggests that these red fox populations have limited capacity to maintain the virus over the long term, but they may contribute to viral persistence in areas of red and Arctic fox sympatry.
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Affiliation(s)
- Susan A. Nadin-Davis
- National Reference Centre for Rabies, Canadian Food Inspection Agency, Ottawa Laboratory Fallowfield, Ottawa, Ontario, Canada
| | - Emilie Falardeau
- National Reference Centre for Rabies, Canadian Food Inspection Agency, Ottawa Laboratory Fallowfield, Ottawa, Ontario, Canada
| | - Alex Flynn
- Biology Department, Memorial University of Newfoundland, St. John’s, Newfoundland & Labrador, Canada
| | - Hugh Whitney
- Biology Department, Memorial University of Newfoundland, St. John’s, Newfoundland & Labrador, Canada
| | - H. Dawn Marshall
- Biology Department, Memorial University of Newfoundland, St. John’s, Newfoundland & Labrador, Canada
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Sacks BN, Lounsberry ZT, Rando HM, Kluepfel K, Fain SR, Brown SK, Kukekova AV. Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography. Genes (Basel) 2021; 12:genes12010097. [PMID: 33466657 PMCID: PMC7828831 DOI: 10.3390/genes12010097] [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: 12/09/2020] [Revised: 01/01/2021] [Accepted: 01/11/2021] [Indexed: 11/28/2022] Open
Abstract
The red fox (Vulpes vulpes) has a wide global distribution with many ecotypes and has been bred in captivity for various traits, making it a useful evolutionary model system. The Y chromosome represents one of the most informative markers of phylogeography, yet it has not been well-studied in the red fox due to a lack of the necessary genomic resources. We used a target capture approach to sequence a portion of the red fox Y chromosome in a geographically diverse red fox sample, along with other canid species, to develop single nucleotide polymorphism (SNP) markers, 13 of which we validated for use in subsequent studies. Phylogenetic analyses of the Y chromosome sequences, including calibration to outgroups, confirmed previous estimates of the timing of two intercontinental exchanges of red foxes, the initial colonization of North America from Eurasia approximately half a million years ago and a subsequent continental exchange before the last Pleistocene glaciation (~100,000 years ago). However, in contrast to mtDNA, which showed unidirectional transfer from Eurasia to North America prior to the last glaciation, the Y chromosome appears to have been transferred from North America to Eurasia during this period. Additional sampling is needed to confirm this pattern and to further clarify red fox Y chromosome phylogeography.
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Affiliation(s)
- Benjamin N. Sacks
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, CA 95616, USA; (Z.T.L.); (K.K.); (S.K.B.)
- Department of Population Health and Reproduction, University of California, Davis, CA 95616, USA
- Correspondence:
| | - Zachary T. Lounsberry
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, CA 95616, USA; (Z.T.L.); (K.K.); (S.K.B.)
| | - Halie M. Rando
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (H.M.R.); (A.V.K.)
| | - Kristopher Kluepfel
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, CA 95616, USA; (Z.T.L.); (K.K.); (S.K.B.)
| | - Steven R. Fain
- U. S. Fish & Wildlife Service, National Forensics Laboratory, Ashland, OR 97520, USA;
| | - Sarah K. Brown
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, CA 95616, USA; (Z.T.L.); (K.K.); (S.K.B.)
| | - Anna V. Kukekova
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (H.M.R.); (A.V.K.)
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Kuo YH, Vanderzwan SL, Kasprowicz AE, Sacks BN. Using Ancestry-Informative SNPs to Quantify Introgression of European Alleles into North American Red Foxes. J Hered 2020; 110:782-792. [PMID: 31562767 DOI: 10.1093/jhered/esz053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/18/2019] [Indexed: 11/13/2022] Open
Abstract
A recent study demonstrated that British red foxes introduced to the mid-Atlantic coastal plain (ACP) of the eastern United States during the late 18th century successfully interbred with indigenous American red foxes despite half a million year's divergence. However, a large disparity in frequency of European mitochondria (27%) versus Y chromosomes (1%) left unclear the magnitude of genetic exchange. We sought to quantify genomic introgression using 35 autosomal and 5 X-chromosome ancestry-informative markers (AIMs) in conjunction with diagnostic Y chromosome single nucleotide polymorphism (Y-SNP) markers to characterize the modern state of red foxes in the eastern United States and to gain insight into the potential role of reproductive barriers. European admixture was highest in the ACP and apparently restricted to the central eastern United States. We estimated only slightly (and nonsignificantly) European ancestry in autosomal than X-chromosome markers. European ancestry from autosomal and X-chromosome markers (36.4%) was higher than the corresponding mitochondrial (mt) DNA estimate (26.4%) in the ACP. Only 1 of 124 males (<1%) in the ACP had European Y chromosomes, which was similar to the neighboring regions, in which 2 of 99 (2%) males carried a European Y chromosome (the same haplotype). Although we could not rule out drift as the cause of low European Y-chromosome frequency, results were also consistent with F1 male infertility. In the future, more extensive genomic sequencing will enable a more thorough investigation of possible barrier genes on the X chromosome as well as throughout the genome.
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Affiliation(s)
- Yi Hung Kuo
- Forensic Sciences Graduate Program, University of California, Davis, Davis, CA.,The Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA
| | - Stevi L Vanderzwan
- The Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA
| | | | - Benjamin N Sacks
- The Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA
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Olival KJ, Latinne A, Islam A, Epstein JH, Hersch R, Engstrand RC, Gurley ES, Amato G, Luby SP, Daszak P. Population genetics of fruit bat reservoir informs the dynamics, distribution and diversity of Nipah virus. Mol Ecol 2019; 29:970-985. [PMID: 31652377 DOI: 10.1111/mec.15288] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/21/2019] [Accepted: 10/21/2019] [Indexed: 12/26/2022]
Abstract
The structure and connectivity of wildlife host populations may influence zoonotic disease dynamics, evolution and therefore spillover risk to people. Fruit bats in the genus Pteropus, or flying foxes, are the primary natural reservoir for henipaviruses-a group of emerging paramyxoviruses that threaten livestock and public health. In Bangladesh, Pteropus medius is the reservoir for Nipah virus-and viral spillover has led to human fatalities nearly every year since 2001. Here, we use mitochondrial DNA and nuclear microsatellite markers to measure the population structure, demographic history and phylogeography of P. medius in Bangladesh. We combine this with a phylogeographic analysis of all known Nipah virus sequences and strains currently available to better inform the dynamics, distribution and evolutionary history of Nipah virus. We show that P. medius is primarily panmictic, but combined analysis of microsatellite and morphological data shows evidence for differentiation of two populations in eastern Bangladesh, corresponding to a divergent strain of Nipah virus also found in bats from eastern Bangladesh. Our demographic analyses indicate that a large, expanding population of flying foxes has existed in Bangladesh since the Late Pleistocene, coinciding with human population expansion in South Asia, suggesting repeated historical spillover of Nipah virus likely occurred. We present the first evidence of mitochondrial introgression, or hybridization, between P. medius and flying fox species found in South-East Asia (P. vampyrus and P. hypomelanus), which may help to explain the distribution of Nipah virus strains across the region.
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Affiliation(s)
| | | | | | | | - Rebecca Hersch
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Rachel C Engstrand
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | | | - George Amato
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
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10
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Sacks BN, Lounsberry ZT, Statham MJ. Nuclear Genetic Analysis of the Red Fox Across its Trans-Pacific Range. J Hered 2019; 109:573-584. [PMID: 29889225 DOI: 10.1093/jhered/esy028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 06/05/2018] [Indexed: 11/14/2022] Open
Abstract
The red fox (Vulpes vulpes) occurs on multiple continents in diverse habitats, making it an informative system for evolutionary genomic research. However, its phylogeography remains unclear. Previously, mitochondrial DNA and small numbers of nuclear loci provided discordant views. Both markers indicated deep divergence (~ 0.5 million years [MY]) between Eurasian and southern North American populations but differed in the apparent continental affinity of Alaskan red foxes, implying some degree of gene exchange during secondary contact (~0.1 MY). We assayed >173000 nuclear genomic sites in 52 red foxes, along with 2 Rueppell's foxes (Vulpes rueppellii) and a gray wolf (Canis lupus) using the Illumina CanineHD BeadChip. We obtained 5107 single nucleotide polymorphisms (SNPs) in the foxes. Consistent with the Afro-Eurasian origins of red foxes, genetic diversity was higher in Eurasian than North American samples. Phylogenetic trees indicated that Alaskan and southern North American red foxes formed a monophyletic group nested within the Eurasian clade. However, admixture models suggested Alaskan red foxes contained up to 40% Eurasian ancestry. We hypothesize that North American red foxes either hybridized with Eurasian foxes in Beringia at the start of the last glaciation or merged with a Beringian population after the last glaciation. Future work is needed to test between these scenarios and assess speciation.
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Affiliation(s)
- Benjamin N Sacks
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, Davis, CA.,Department of Population Health and Reproduction, University of California, Davis, Davis, CA
| | - Zachary T Lounsberry
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, Davis, CA
| | - Mark J Statham
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, Davis, CA.,Department of Population Health and Reproduction, University of California, Davis, Davis, CA
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11
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Zecchin B, De Nardi M, Nouvellet P, Vernesi C, Babbucci M, Crestanello B, Bagó Z, Bedeković T, Hostnik P, Milani A, Donnelly CA, Bargelloni L, Lorenzetto M, Citterio C, Obber F, De Benedictis P, Cattoli G. Genetic and spatial characterization of the red fox (Vulpes vulpes) population in the area stretching between the Eastern and Dinaric Alps and its relationship with rabies and canine distemper dynamics. PLoS One 2019; 14:e0213515. [PMID: 30861028 PMCID: PMC6413928 DOI: 10.1371/journal.pone.0213515] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/24/2019] [Indexed: 01/02/2023] Open
Abstract
Information on the population dynamics of a reservoir species have been increasingly adopted to understand and eventually predict the dispersal patterns of infectious diseases throughout an area. Although potentially relevant, to date there are no studies which have investigated the genetic structure of the red fox population in relation to infectious disease dynamics. Therefore, we genetically and spatially characterised the red fox population in the area stretching between the Eastern and Dinaric Alps, which has been affected by both distemper and rabies at different time intervals. Red foxes collected from north-eastern Italy, Austria, Slovenia and Croatia between 2006–2012, were studied using a set of 21 microsatellite markers. We confirmed a weak genetic differentiation within the fox population using Bayesian clustering analyses, and we were able to differentiate the fox population into geographically segregated groups. Our finding might be due to the presence of geographical barriers that have likely influenced the distribution of the fox population, limiting in turn gene flow and spread of infectious diseases. Focusing on the Italian red fox population, we observed interesting variations in the prevalence of both diseases among distinct fox clusters, with the previously identified Italy 1 and Italy 2 rabies as well as distemper viruses preferentially affecting different sub-groups identified in the study. Knowledge of the regional-scale population structure can improve understanding of the epidemiology and spread of diseases. Our study paves the way for an integrated approach for disease control coupling pathogen, host and environmental data to inform targeted control programs in the future.
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Affiliation(s)
- Bianca Zecchin
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
- * E-mail:
| | - Marco De Nardi
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Pierre Nouvellet
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - Barbara Crestanello
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Zoltán Bagó
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control, Mödling, Austria
| | | | - Peter Hostnik
- Virology Unit, Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Adelaide Milani
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Christl Ann Donnelly
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- National Institute for Health Research Health Protection Research Unit in Modelling Methodology, Imperial College London, London, United Kingdom
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - Monica Lorenzetto
- Department of Veterinary Epidemiology, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Carlo Citterio
- SCT2 Belluno, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Belluno, Italy
| | - Federica Obber
- SCT2 Belluno, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Belluno, Italy
| | - Paola De Benedictis
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Giovanni Cattoli
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
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12
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Hueffer K, Murphy M. Rabies in Alaska, from the past to an uncertain future. Int J Circumpolar Health 2018; 77:1475185. [PMID: 29764319 PMCID: PMC7011961 DOI: 10.1080/22423982.2018.1475185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/03/2018] [Indexed: 12/19/2022] Open
Abstract
Rabies is a serious zoonotic disease with significant public health consequences in the circumpolar North. Recent studies have advanced our understanding of the disease ecology in Alaska. In this paper, we review historical records of rabies in Alaska ranging from the late nineteenth century to the present, analyse the public health impact in the state and review studies on disease ecology before assessing challenges and anticipated altered disease dynamics in the face of a rapidly changing North. Rabies is a disease that has been present in Alaska continuously for over 100 years. It is maintained in bats and foxes with the arctic fox likely playing a bigger role in maintaining the virus, although a multi-host system with both red and arctic foxes cannot be excluded. Some modelling evidence suggest a possible decrease in rabies due to a changing climate, although uncertainty is high around these predictions for rabies distribution in Alaska into the future.
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Affiliation(s)
- Karsten Hueffer
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Molly Murphy
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, Alaska, USA
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13
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Rodríguez-Nevado C, Lam TTY, Holmes EC, Pagán I. The impact of host genetic diversity on virus evolution and emergence. Ecol Lett 2017; 21:253-263. [PMID: 29207441 DOI: 10.1111/ele.12890] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/23/2017] [Accepted: 11/02/2017] [Indexed: 01/16/2023]
Abstract
Accumulating evidence indicates that biodiversity has an important impact on parasite evolution and emergence. The vast majority of studies in this area have only considered the diversity of species within an environment as an overall measure of biodiversity, overlooking the role of genetic diversity within a particular host species. Although theoretical models propose that host genetic diversity in part shapes that of the infecting parasite population, and hence modulates the risk of parasite emergence, this effect has seldom been tested empirically. Using Rabies virus (RABV) as a model parasite, we provide evidence that greater host genetic diversity increases both parasite genetic diversity and the likelihood of a host being a donor in RABV cross-species transmission events. We conclude that host genetic diversity may be an important determinant of parasite evolution and emergence.
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Affiliation(s)
- Cristina Rodríguez-Nevado
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Madrid, 28223, Spain
| | - Tommy T-Y Lam
- State Key Laboratory of Emerging Infectious Diseases, Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Madrid, 28223, Spain
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14
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Donaldson ME, Rico Y, Hueffer K, Rando HM, Kukekova AV, Kyle CJ. Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure. Ecol Evol 2017; 8:572-583. [PMID: 29321894 PMCID: PMC5756825 DOI: 10.1002/ece3.3583] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/28/2017] [Accepted: 10/02/2017] [Indexed: 12/30/2022] Open
Abstract
Pathogens are recognized as major drivers of local adaptation in wildlife systems. By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High‐throughput sequencing (HTS) technologies, such as genotype‐by‐sequencing (GBS), facilitate expanded explorations of genomic variation among populations. Hybridization‐based GBS techniques can be leveraged in systems not well characterized for specific variants associated with disease outcome to “capture” specific genes and regulatory regions known to influence expression and disease outcome. We developed a multiplexed, sequence capture assay for red foxes to simultaneously assess ~300‐kbp of genomic sequence from 116 adaptive, intrinsic, and innate immunity genes of predicted adaptive significance and their putative upstream regulatory regions along with 23 neutral microsatellite regions to control for demographic effects. The assay was applied to 45 fox DNA samples from Alaska, where three arctic rabies strains are geographically restricted and endemic to coastal tundra regions, yet absent from the boreal interior. The assay provided 61.5% on‐target enrichment with relatively even sequence coverage across all targeted loci and samples (mean = 50×), which allowed us to elucidate genetic variation across introns, exons, and potential regulatory regions (4,819 SNPs). Challenges remained in accurately describing microsatellite variation using this technique; however, longer‐read HTS technologies should overcome these issues. We used these data to conduct preliminary analyses and detected genetic structure in a subset of red fox immune‐related genes between regions with and without endemic arctic rabies. This assay provides a template to assess immunogenetic variation in wildlife disease systems.
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Affiliation(s)
- Michael E Donaldson
- Environmental and Life Sciences Graduate Program Trent University Peterborough ON Canada
| | - Yessica Rico
- CONACYT Instituto de Ecología A.C.Centro Regional del Bajio Pátzcuaro Michoacán Mexico
| | - Karsten Hueffer
- Department of Veterinary Medicine University of Alaska Fairbanks Fairbanks AK USA
| | - Halie M Rando
- Department of Animal Sciences College of ACES University of Illinois at Urbana-Champaign Urbana IL USA
| | - Anna V Kukekova
- Department of Animal Sciences College of ACES University of Illinois at Urbana-Champaign Urbana IL USA
| | - Christopher J Kyle
- Environmental and Life Sciences Graduate Program Trent University Peterborough ON Canada.,Forensic Science Department Trent University Peterborough ON Canada
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15
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Lai S, Quiles A, Lambourdière J, Berteaux D, Lalis A. Fine-scale population genetic structure of arctic foxes (Vulpes lagopus) in the High Arctic. BMC Res Notes 2017; 10:663. [PMID: 29191239 PMCID: PMC5710073 DOI: 10.1186/s13104-017-3002-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/25/2017] [Indexed: 11/18/2022] Open
Abstract
Objective The arctic fox (Vulpes lagopus) is a circumpolar species inhabiting all accessible Arctic tundra habitats. The species forms a panmictic population over areas connected by sea ice, but recently, kin clustering and population differentiation were detected even in regions where sea ice was present. The purpose of this study was to examine the genetic structure of a population in the High Arctic using a robust panel of highly polymorphic microsatellites. Results We analyzed the genotypes of 210 individuals from Bylot Island, Nunavut, Canada, using 15 microsatellite loci. No pattern of isolation-by-distance was detected, but a spatial principal component analysis (sPCA) revealed the presence of genetic subdivisions. Overall, the sPCA revealed two spatially distinct genetic clusters corresponding to the northern and southern parts of the study area, plus another subdivision within each of these two clusters. The north–south genetic differentiation partly matched the distribution of a snow goose colony, which could reflect a preference for settling into familiar ecological environments. Secondary clusters may result from higher-order social structures (neighbourhoods) that use landscape features to delimit their borders. The cryptic genetic subdivisions found in our population may highlight ecological processes deserving further investigations in arctic foxes at larger, regional spatial scales. Electronic supplementary material The online version of this article (10.1186/s13104-017-3002-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sandra Lai
- Canada Research Chair on Northern Biodiversity, Centre for Northern Studies and Quebec Center for Biodiversity Science, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada.
| | - Adrien Quiles
- UMR7205 ISYEB CNRS-MNHN-EPHE-UPMC, Muséum National d'Histoire Naturelle, CP 51, 75231, Paris Cedex 05, France
| | - Josie Lambourdière
- UMS 2700 OMSI Service de Systématique Moléculaire, Muséum National d'Histoire Naturelle, CP 26, 75231, Paris Cedex 05, France
| | - Dominique Berteaux
- Canada Research Chair on Northern Biodiversity, Centre for Northern Studies and Quebec Center for Biodiversity Science, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada
| | - Aude Lalis
- UMR7205 ISYEB CNRS-MNHN-EPHE-UPMC, Muséum National d'Histoire Naturelle, CP 51, 75231, Paris Cedex 05, France
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16
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Huettmann F, Magnuson EE, Hueffer K. Ecological niche modeling of rabies in the changing Arctic of Alaska. Acta Vet Scand 2017; 59:18. [PMID: 28320440 PMCID: PMC5359834 DOI: 10.1186/s13028-017-0285-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 03/09/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rabies is a disease of global significance including in the circumpolar Arctic. In Alaska enzootic rabies persist in northern and western coastal areas. Only sporadic cases have occurred in areas outside of the regions considered enzootic for the virus, such as the interior of the state and urbanized regions. RESULTS Here we examine the distribution of diagnosed rabies cases in Alaska, explicit in space and time. We use a geographic information system (GIS), 20 environmental data layers and provide a quantitative non-parsimonious estimate of the predicted ecological niche, based on data mining, machine learning and open access data. We identify ecological correlates and possible drivers that determine the ecological niche of rabies virus in Alaska. More specifically, our models show that rabies cases are closely associated with human infrastructure, and reveal an ecological niche in remote northern wilderness areas. Furthermore a model utilizing climate modeling suggests a reduction of the current ecological niche for detection of rabies virus in Alaska, a state that is disproportionately affected by a changing climate. CONCLUSIONS Our results may help to better inform public health decisions in the future and guide further studies on individual drivers of rabies distribution in the Arctic.
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Affiliation(s)
- Falk Huettmann
- EWHALE Lab, Institute of Arctic Biology, Department of Wildlife Biology, University of Alaska Fairbanks, 902 N. Koyukuk Dr., P.O. Box 757000, Fairbanks, AK 99775 USA
| | - Emily Elizabeth Magnuson
- Department of Biology and Wildlife, University of Alaska Fairbanks, 982 N. Koyukuk Dr., PO Box 756100, Fairbanks, AK 99775 USA
| | - Karsten Hueffer
- Department of Veterinary Medicine, University of Alaska Fairbanks, 901 Koyukuk Drive, PO Box 757750, Fairbanks, AK 99775 USA
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17
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Hanke D, Freuling CM, Fischer S, Hueffer K, Hundertmark K, Nadin-Davis S, Marston D, Fooks AR, Bøtner A, Mettenleiter TC, Beer M, Rasmussen TB, Müller TF, Höper D. Spatio-temporal Analysis of the Genetic Diversity of Arctic Rabies Viruses and Their Reservoir Hosts in Greenland. PLoS Negl Trop Dis 2016; 10:e0004779. [PMID: 27459154 PMCID: PMC4961414 DOI: 10.1371/journal.pntd.0004779] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 05/24/2016] [Indexed: 12/05/2022] Open
Abstract
There has been limited knowledge on spatio-temporal epidemiology of zoonotic arctic fox rabies among countries bordering the Arctic, in particular Greenland. Previous molecular epidemiological studies have suggested the occurrence of one particular arctic rabies virus (RABV) lineage (arctic-3), but have been limited by a low number of available samples preventing in-depth high resolution phylogenetic analysis of RABVs at that time. However, an improved knowledge of the evolution, at a molecular level, of the circulating RABVs and a better understanding of the historical perspective of the disease in Greenland is necessary for better direct control measures on the island. These issues have been addressed by investigating the spatio-temporal genetic diversity of arctic RABVs and their reservoir host, the arctic fox, in Greenland using both full and partial genome sequences. Using a unique set of 79 arctic RABV full genome sequences from Greenland, Canada, USA (Alaska) and Russia obtained between 1977 and 2014, a description of the historic context in relation to the genetic diversity of currently circulating RABV in Greenland and neighboring Canadian Northern territories has been provided. The phylogenetic analysis confirmed delineation into four major arctic RABV lineages (arctic 1–4) with viruses from Greenland exclusively grouping into the circumpolar arctic-3 lineage. High resolution analysis enabled distinction of seven geographically distinct subclades (3.I – 3.VII) with two subclades containing viruses from both Greenland and Canada. By combining analysis of full length RABV genome sequences and host derived sequences encoding mitochondrial proteins obtained simultaneously from brain tissues of 49 arctic foxes, the interaction of viruses and their hosts was explored in detail. Such an approach can serve as a blueprint for analysis of infectious disease dynamics and virus-host interdependencies. The results showed a fine-scale spatial population structure in Greenland arctic foxes based on mitochondrial sequences, but provided no evidence for independent isolated evolutionary development of RABV in different arctic fox lineages. These data are invaluable to support future initiatives for arctic fox rabies control and elimination in Greenland. Next to dog-mediated rabies, wildlife rabies continues to pose a public health problem, particularly in the northern hemisphere. Control of this zoonosis at the animal source has been proven the most efficient route to reduction of human rabies burden. Successful elimination of red fox-mediated rabies in Western Europe and parts of North America has demonstrated the viability of wildlife rabies control strategies. In some regions, the epidemiology of wildlife rabies is well understood; this is not the case for arctic rabies, particularly in Greenland. Previous molecular epidemiological studies demonstrated the occurrence of one particular arctic rabies virus (RABV) lineage (arctic-3) but were limited by low sample numbers and limited sequence length so as to preclude generation of high resolution phylogenetic analysis. Here, a unique set comprised of 79 complete genome sequences of RABVs from Greenland, Canada, USA (Alaska) and Russia collected over the past four decades was analysed. The use of next generation sequencing (NGS) allowed simultaneous determination of host derived sequences encoding mitochondrial proteins from the same brain tissue of 49 arctic foxes. These sequence data combined with geographical and temporal information permit the study of the genetic diversity and evolution of circulating RABVs in Greenland against the background of reservoir host genetics. The results reveal the existence of a single arctic RABV lineage (arctic-3) in Greenland, which has evolved into multiple distinct variants. These analyses provide an improved knowledge of the evolution of the circulating viruses at the molecular level and a better understanding of the historical perspective of the disease in Greenland compared to other parts of the Arctic. This knowledge will support policy on rabies control in mammalian wildlife reservoirs.
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Affiliation(s)
- Dennis Hanke
- Friedrich-Loeffler-Institut (FLI), Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Conrad M. Freuling
- FLI, Institute of Molecular Virology and Cell Biology, Greifswald-Insel Riems, Germany
| | - Susanne Fischer
- FLI, Institute of Epidemiology, Greifswald-Insel Riems, Germany
| | - Karsten Hueffer
- Department of Veterinary Medicine, University of Alaska, Fairbanks, Alaska, United States of America
| | - Kris Hundertmark
- Institute of Arctic Biology, University of Alaska, Fairbanks, Alaska, United States of America
| | - Susan Nadin-Davis
- Animal Health Microbiology Research, Canadian Food Inspection Agency (CFIA), Centre of Expertise for Rabies, Ottawa Laboratory, Ottawa, Ontario, Canada
| | - Denise Marston
- Animal and Plant Health Agency (APHA), Wildlife Zoonoses and Vector-borne Diseases Research Group, Addlestone, Surrey, United Kingdom
| | - Anthony R. Fooks
- Animal and Plant Health Agency (APHA), Wildlife Zoonoses and Vector-borne Diseases Research Group, Addlestone, Surrey, United Kingdom
- University of Liverpool, Department of Clinical Infection, Microbiology and Immunology, Liverpool, United Kingdom
| | - Anette Bøtner
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave, Denmark
| | | | - Martin Beer
- Friedrich-Loeffler-Institut (FLI), Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Thomas B. Rasmussen
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave, Denmark
| | - Thomas F. Müller
- FLI, Institute of Molecular Virology and Cell Biology, Greifswald-Insel Riems, Germany
- * E-mail:
| | - Dirk Höper
- Friedrich-Loeffler-Institut (FLI), Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
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