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Wu W, Li W, Liu F, Chen S. Evidence of High Genetic Diversity and Differences in the Population Diversity of the Eucalyptus Leaf Blight Pathogen Calonectria pseudoreteaudii from Diseased Leaves and Soil in a Plantation in Guangxi, China. Microorganisms 2023; 11:2785. [PMID: 38004796 PMCID: PMC10673236 DOI: 10.3390/microorganisms11112785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Calonectria pseudoreteaudii is an important causal agent of Eucalyptus leaf blight in southern China. This pathogen causes Eucalyptus tree disease across numerous regions in southern China. In addition to diseased leaves, C. pseudoreteaudii has occasionally been isolated from soil in Eucalyptus plantations. The aim of this study was to clarify whether C. pseudoreteaudii causing Eucalyptus leaf blight in China is mainly clonally reproduced and to determine the potential spreading mechanism of C. pseudoreteaudii between diseased leaves and soil. To this end, 10 polymorphic microsatellite markers were analyzed to detect the genetic diversity of 97 C. pseudoreteaudii isolates from diseased leaves and soil in a Eucalyptus plantation in Guangxi Zhuang Autonomous Region, southern China. The analysis showed that the genetic diversity of the isolates from both the diseased leaves and soil was high. However, the gene and genotype diversity of the C. pseudoreteaudii isolates from diseased leaves were higher than those of the isolates from the soil. Moreover, all genotypes detected in the isolates from the soil were also found in the isolates from the diseased leaves. Structural analyses did not show clear population structures related to the population substrates of the diseased leaves or soil, and molecular variance analyses indicated that no significant genetic differentiation existed between the diseased leaf and soil populations. These results suggest that C. pseudoreteaudii in soil spreads from diseased leaves, and that an asexual cycle is the primary reproductive mode in both diseased leaf and soil populations. This is the first study on the genetic diversity and population structure of C. pseudoreteaudii. The high genetic diversity and spread pathways of this pathogen may pose challenges in controlling the disease. C. pseudoreteaudii from both diseased leaves and soils in Eucalyptus plantations needs to be carefully monitored for disease control and management.
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Affiliation(s)
- Wenxia Wu
- Research Institute of Fast-Growing Trees (RIFT), Chinese Academy of Forestry (CAF), Zhanjiang 524022, China; (W.W.); (W.L.); (F.L.)
- College of Forestry, Nanjing Forestry University (NJFU), Nanjing 210037, China
| | - Wenwen Li
- Research Institute of Fast-Growing Trees (RIFT), Chinese Academy of Forestry (CAF), Zhanjiang 524022, China; (W.W.); (W.L.); (F.L.)
| | - Feifei Liu
- Research Institute of Fast-Growing Trees (RIFT), Chinese Academy of Forestry (CAF), Zhanjiang 524022, China; (W.W.); (W.L.); (F.L.)
| | - Shuaifei Chen
- Research Institute of Fast-Growing Trees (RIFT), Chinese Academy of Forestry (CAF), Zhanjiang 524022, China; (W.W.); (W.L.); (F.L.)
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Comparative genomic analysis reveals contraction of gene families with putative roles in pathogenesis in the fungal boxwood pathogens Calonectria henricotiae and C. pseudonaviculata. BMC Ecol Evol 2022; 22:79. [PMID: 35725368 PMCID: PMC9210730 DOI: 10.1186/s12862-022-02035-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/08/2022] [Indexed: 11/23/2022] Open
Abstract
Background Boxwood blight disease caused by Calonectria henricotiae and C. pseudonaviculata is of ecological and economic significance in cultivated and native ecosystems worldwide. Prior research has focused on understanding the population genetic and genomic diversity of C. henricotiae and C. pseudonaviculata, but gene family evolution in the context of host adaptation, plant pathogenesis, and trophic lifestyle is poorly understood. This study applied bioinformatic and phylogenetic methods to examine gene family evolution in C. henricotiae, C. pseudonaviculata and 22 related fungi in the Nectriaceae that vary in pathogenic and saprobic (apathogenic) lifestyles. Results A total of 19,750 gene families were identified in the 24 genomes, of which 422 were rapidly evolving. Among the six Calonectria species, C. henricotiae and C. pseudonaviculata were the only species to experience high levels of rapid contraction of pathogenesis-related gene families (89% and 78%, respectively). In contrast, saprobic species Calonectria multiphialidica and C. naviculata, two of the closest known relatives of C. henricotiae and C. pseudonaviculata, showed rapid expansion of pathogenesis-related gene families. Conclusions Our results provide novel insight into gene family evolution within C. henricotiae and C. pseudonaviculata and suggest gene family contraction may have contributed to limited host-range expansion of these pathogens within the plant family Buxaceae. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02035-4.
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Weiland JE, Ohkura M, Scagel CF, Davis EA, Beck BR. Cool Temperatures Favor Growth of Oregon Isolates of Calonectria pseudonaviculata and Increase Severity of Boxwood Blight on Two Buxus Cultivars. PLANT DISEASE 2022; 106:3100-3108. [PMID: 35581912 DOI: 10.1094/pdis-04-22-0769-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Controlled environment experiments were conducted to evaluate the effects of temperature on Calonectria pseudonaviculata mycelial growth and the effects of temperature and infection period on boxwood blight severity. In experiment 1, 15 Oregon isolates (representing five genotypes) were grown on potato dextrose agar (PDA) and malt extract agar (MEA) at six temperatures from 5 to 30°C. Growth (culture diameter) was measured after 2 weeks. Optimal growth occurred at 25°C on PDA and 20°C on MEA. Isolates of genotype G1 also grew faster than genotype G2, but only on MEA at 25°C. In experiment 2, Buxus cultivars Green Velvet (GV, more susceptible) and Winter Gem (WG, more resistant) were inoculated and incubated in moist chambers for 9 or 24 h at 22°C (infection period), then moved into growth chambers at 15 or 25°C. After 4 weeks, chamber temperatures were switched, and plants were incubated for 4 more weeks. Disease severity was evaluated weekly. During the first 4 weeks, disease was generally more severe on GV than WG, on plants with a 24-h versus a 9-h infection period, and on plants incubated at 15°C versus 25°C. However, disease was just as severe on WG as GV when the 24-h infection period was followed by incubation at 15°C. After the temperatures were switched, disease increased only on WG that were cooled from 25 to 15°C. Results show that Oregon isolates of C. pseudonaviculata are capable of growing faster and causing more severe disease at temperatures cooler than those reported previously.
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Affiliation(s)
- Jerry E Weiland
- U.S. Department of Agriculture, Agricultural Research Service, Horticultural Crops Research Laboratory, 3420 NW Orchard Avenue, Corvallis, OR 97330
| | - Mana Ohkura
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Carolyn F Scagel
- U.S. Department of Agriculture, Agricultural Research Service, Horticultural Crops Research Laboratory, 3420 NW Orchard Avenue, Corvallis, OR 97330
| | - E Anne Davis
- U.S. Department of Agriculture, Agricultural Research Service, Horticultural Crops Research Laboratory, 3420 NW Orchard Avenue, Corvallis, OR 97330
| | - Bryan R Beck
- U.S. Department of Agriculture, Agricultural Research Service, Horticultural Crops Research Laboratory, 3420 NW Orchard Avenue, Corvallis, OR 97330
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Hong C, Daughtrey M, Howle M, Schirmer S, Kosta K, Kong P, Likins M, Suslow K. Rapid Decline of Calonectria pseudonaviculata Soil Population in Selected Gardens Across the United States. PLANT DISEASE 2022; 106:2831-2838. [PMID: 35486597 DOI: 10.1094/pdis-02-22-0443-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Calonectria pseudonaviculata (Cps) poses a serious threat to boxwood, an iconic landscape plant in American and European gardens. Under the mild climatic conditions of the United Kingdom, Cps remained recoverable in infected leaf debris after being left on the soil surface or buried for 5 years. The primary objective of this study was to determine how this fungus may be affected by the warmer summers and colder winters in the United States by sampling and baiting soil with boxwood cuttings and by on-site testing with sentinel plants. Soil sampling started in a Virginia garden in January 2016 and was extended to California, Illinois, New York, and South Carolina in early summer of 2017 through late fall of 2018. The Cps soil population as measured by the percentage of infected bait leaves declined sharply within the first year of blighted boxwood removal and fell to an almost undetectable level at the end of this study. To validate these baiting results, the Virginia garden was tested on site four times with container-grown boxwood plants while the South Carolina garden and three New York gardens were tested once. Each test began with sentinel plants set out for field exposure, followed by evaluation on site and then in the laboratory after plants were retrieved from these gardens and incubated under conducive environments for 2 weeks. Cps was not observed on any sentinel boxwood plant on site or in the laboratory with one exception. These observations indicate that Cps did not survive in the United States garden soil over time as well as it did in the United Kingdom. These results have important practical implications while challenging the notion that fungi producing microsclerotia will always survive in the soil for many years.
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Affiliation(s)
- Chuanxue Hong
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA 23455
| | - Margery Daughtrey
- Long Island Horticultural Research and Extension Center, Cornell University, Riverhead, NY 11901
| | - Matthew Howle
- Department of Plant Industry, Clemson University, Florence, SC 29506
| | - Scott Schirmer
- Bureau of Environmental Programs, Illinois Department of Agriculture, DeKalb, IL 60115
| | - Kathleen Kosta
- California Department of Food and Agriculture, Sacramento, CA 95814
| | - Ping Kong
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA 23455
| | - Michael Likins
- Chesterfield Cooperative Extension, Chesterfield Co., VA 23832
| | - Karen Suslow
- National Ornamental Research Site at Dominican University of California, San Rafael, CA 94901
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Sotiropoulos AG, Arango-Isaza E, Ban T, Barbieri C, Bourras S, Cowger C, Czembor PC, Ben-David R, Dinoor A, Ellwood SR, Graf J, Hatta K, Helguera M, Sánchez-Martín J, McDonald BA, Morgounov AI, Müller MC, Shamanin V, Shimizu KK, Yoshihira T, Zbinden H, Keller B, Wicker T. Global genomic analyses of wheat powdery mildew reveal association of pathogen spread with historical human migration and trade. Nat Commun 2022; 13:4315. [PMID: 35882860 PMCID: PMC9315327 DOI: 10.1038/s41467-022-31975-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 07/13/2022] [Indexed: 12/25/2022] Open
Abstract
The fungus Blumeria graminis f. sp. tritici causes wheat powdery mildew disease. Here, we study its spread and evolution by analyzing a global sample of 172 mildew genomes. Our analyses show that B.g. tritici emerged in the Fertile Crescent during wheat domestication. After it spread throughout Eurasia, colonization brought it to America, where it hybridized with unknown grass mildew species. Recent trade brought USA strains to Japan, and European strains to China. In both places, they hybridized with local ancestral strains. Thus, although mildew spreads by wind regionally, our results indicate that humans drove its global spread throughout history and that mildew rapidly evolved through hybridization.
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Affiliation(s)
| | - Epifanía Arango-Isaza
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Tomohiro Ban
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Chiara Barbieri
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Salim Bourras
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christina Cowger
- USDA-ARS Department of Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Paweł C Czembor
- Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, 05-870 Błonie, Poland
| | - Roi Ben-David
- Department of Vegetables and Field crops, Institute of Plant Sciences, ARO-Volcani Center, Rishon LeZion, 7528809, Israel
| | - Amos Dinoor
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Simon R Ellwood
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Johannes Graf
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Koichi Hatta
- Hokkaido Agricultural Research Center Field Crop Research and Development, National Agricultural Research Organization, Sapporo, Hokkaido, Japan
| | - Marcelo Helguera
- Centro de Investigaciones Agropecuarias (CIAP), INTA, Córdoba, Argentina
| | - Javier Sánchez-Martín
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Alexey I Morgounov
- Food and Agriculture Organization of the United Nations, Riyadh, Saudi Arabia
| | - Marion C Müller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | | | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Taiki Yoshihira
- Department of Sustainable Agriculture, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
| | - Helen Zbinden
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
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Aiello D, Guarnaccia V, Vitale A, LeBlanc N, Shishkoff N, Polizzi G. Impact of Calonectria Diseases on Ornamental Horticulture: Diagnosis and Control Strategies. PLANT DISEASE 2022; 106:1773-1787. [PMID: 35084942 DOI: 10.1094/pdis-11-21-2610-fe] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Diseases caused by fungi in the genus Calonectria pose a significant threat to the ornamental horticulture industries in Europe and the United States. Calonectria spp. are particularly challenging pathogens to manage in ornamental production systems and the urban landscape for multiple reasons. A high level of species diversity and poorly resolved taxonomy in the genus makes proper pathogen identification and disease diagnosis a challenge, though recent molecular phylogenetic studies have made significant advances in species delimitation. From a disease management perspective, Calonectria spp. produce long-lived survival structures (microsclerotia) that contaminate nursery production systems and can survive multiple years in the absence of a susceptible plant host. Latent infection of plant material is poorly understood but likely contributes to long-distance dissemination of these fungal pathogens, including the clonal Calonectria spp. responsible for the global emergence of boxwood blight. Breeding for disease resistance represents a sustainable strategy for managing Calonectria diseases but is challenging due to the perennial nature of many ornamental plants and high levels of susceptibility in commercial cultivars. Ultimately, long-term sustainable management of Calonectria diseases will require an improved understanding of pathogen biology as well as integration of multiple disease management strategies.
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Affiliation(s)
- Dalia Aiello
- Dipartimento di Agricoltura, Alimentazione e Ambiente, sez. Patologia vegetale, University of Catania, Via S. Sofia 100, 95123 Catania, Italy
| | - Vladimiro Guarnaccia
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo Braccini 2, 10095 Grugliasco (TO), Italy
| | - Alessandro Vitale
- Dipartimento di Agricoltura, Alimentazione e Ambiente, sez. Patologia vegetale, University of Catania, Via S. Sofia 100, 95123 Catania, Italy
| | - Nicholas LeBlanc
- Crop Improvement and Protection Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Salinas, CA 93905, U.S.A
| | - Nina Shishkoff
- Foreign Disease-Weed Science Research Unit, USDA-ARS, Frederick, MD 21702, U.S.A
| | - Giancarlo Polizzi
- Dipartimento di Agricoltura, Alimentazione e Ambiente, sez. Patologia vegetale, University of Catania, Via S. Sofia 100, 95123 Catania, Italy
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Barker BS, Coop L, Hong C. Potential Distribution of Invasive Boxwood Blight Pathogen ( Calonectriapseudonaviculata) as Predicted by Process-Based and Correlative Models. BIOLOGY 2022; 11:849. [PMID: 35741370 PMCID: PMC9220671 DOI: 10.3390/biology11060849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/20/2022] [Accepted: 05/28/2022] [Indexed: 12/04/2022]
Abstract
Boxwood blight caused by Cps is an emerging disease that has had devastating impacts on Buxus spp. in the horticultural sector, landscapes, and native ecosystems. In this study, we produced a process-based climatic suitability model in the CLIMEX program and combined outputs of four different correlative modeling algorithms to generate an ensemble correlative model. All models were fit and validated using a presence record dataset comprised of Cps detections across its entire known invaded range. Evaluations of model performance provided validation of good model fit for all models. A consensus map of CLIMEX and ensemble correlative model predictions indicated that not-yet-invaded areas in eastern and southern Europe and in the southeastern, midwestern, and Pacific coast regions of North America are climatically suitable for Cps establishment. Most regions of the world where Buxus and its congeners are native are also at risk of establishment. These findings provide the first insights into Cps global invasion threat, suggesting that this invasive pathogen has the potential to significantly expand its range.
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Affiliation(s)
- Brittany S. Barker
- Oregon Integrated Pest Management Center, Oregon State University, 4575 Research Way, Corvallis, OR 97331, USA;
- Department of Horticulture, Oregon State University, 4017 Agriculture and Life Sciences Building, Corvallis, OR 97331, USA
| | - Leonard Coop
- Oregon Integrated Pest Management Center, Oregon State University, 4575 Research Way, Corvallis, OR 97331, USA;
- Department of Horticulture, Oregon State University, 4017 Agriculture and Life Sciences Building, Corvallis, OR 97331, USA
| | - Chuanxue Hong
- Hampton Roads Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University, 1444 Diamond Springs Road, Virginia Beach, VA 23455, USA;
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Yang S, Johnson MA, Hansen MA, Bush E, Li S, Vinatzer BA. Metagenomic sequencing for detection and identification of the boxwood blight pathogen Calonectria pseudonaviculata. Sci Rep 2022; 12:1399. [PMID: 35082361 PMCID: PMC8791934 DOI: 10.1038/s41598-022-05381-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 01/10/2022] [Indexed: 11/16/2022] Open
Abstract
Pathogen detection and identification are key elements in outbreak control of human, animal, and plant diseases. Since many fungal plant pathogens cause similar symptoms, are difficult to distinguish morphologically, and grow slowly in culture, culture-independent, sequence-based diagnostic methods are desirable. Whole genome metagenomic sequencing has emerged as a promising technique because it can potentially detect any pathogen without culturing and without the need for pathogen-specific probes. However, efficient DNA extraction protocols, computational tools, and sequence databases are required. Here we applied metagenomic sequencing with the Oxford Nanopore Technologies MinION to the detection of the fungus Calonectria pseudonaviculata, the causal agent of boxwood (Buxus spp.) blight disease. Two DNA extraction protocols, several DNA purification kits, and various computational tools were tested. All DNA extraction methods and purification kits provided sufficient quantity and quality of DNA. Several bioinformatics tools for taxonomic identification were found suitable to assign sequencing reads to the pathogen with an extremely low false positive rate. Over 9% of total reads were identified as C. pseudonaviculata in a severely diseased sample and identification at strain-level resolution was approached as the number of sequencing reads was increased. We discuss how metagenomic sequencing could be implemented in routine plant disease diagnostics.
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Affiliation(s)
- Shu Yang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Marcela A Johnson
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA.,Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, USA
| | - Mary Ann Hansen
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Elizabeth Bush
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Song Li
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Boris A Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA.
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