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Cintron R, Whitmer SLM, Moscoso E, Campbell EM, Kelly R, Talundzic E, Mobley M, Chiu KW, Shedroff E, Shankar A, Montgomery JM, Klena JD, Switzer WM. HantaNet: A New MicrobeTrace Application for Hantavirus Classification, Genomic Surveillance, Epidemiology and Outbreak Investigations. Viruses 2023; 15:2208. [PMID: 38005885 PMCID: PMC10675615 DOI: 10.3390/v15112208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Hantaviruses zoonotically infect humans worldwide with pathogenic consequences and are mainly spread by rodents that shed aerosolized virus particles in urine and feces. Bioinformatics methods for hantavirus diagnostics, genomic surveillance and epidemiology are currently lacking a comprehensive approach for data sharing, integration, visualization, analytics and reporting. With the possibility of hantavirus cases going undetected and spreading over international borders, a significant reporting delay can miss linked transmission events and impedes timely, targeted public health interventions. To overcome these challenges, we built HantaNet, a standalone visualization engine for hantavirus genomes that facilitates viral surveillance and classification for early outbreak detection and response. HantaNet is powered by MicrobeTrace, a browser-based multitool originally developed at the Centers for Disease Control and Prevention (CDC) to visualize HIV clusters and transmission networks. HantaNet integrates coding gene sequences and standardized metadata from hantavirus reference genomes into three separate gene modules for dashboard visualization of phylogenetic trees, viral strain clusters for classification, epidemiological networks and spatiotemporal analysis. We used 85 hantavirus reference datasets from GenBank to validate HantaNet as a classification and enhanced visualization tool, and as a public repository to download standardized sequence data and metadata for building analytic datasets. HantaNet is a model on how to deploy MicrobeTrace-specific tools to advance pathogen surveillance, epidemiology and public health globally.
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Affiliation(s)
- Roxana Cintron
- Laboratory Branch, Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (A.S.); (W.M.S.)
| | - Shannon L. M. Whitmer
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (M.M.); (E.S.); (J.D.K.)
| | - Evan Moscoso
- General Dynamics Information Technology, Atlanta, GA 30329, USA; (E.M.); (R.K.)
| | - Ellsworth M. Campbell
- Laboratory Branch, Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (A.S.); (W.M.S.)
| | - Reagan Kelly
- General Dynamics Information Technology, Atlanta, GA 30329, USA; (E.M.); (R.K.)
| | - Emir Talundzic
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (M.M.); (E.S.); (J.D.K.)
| | - Melissa Mobley
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (M.M.); (E.S.); (J.D.K.)
| | - Kuo Wei Chiu
- General Dynamics Information Technology, Atlanta, GA 30329, USA; (E.M.); (R.K.)
| | - Elizabeth Shedroff
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (M.M.); (E.S.); (J.D.K.)
| | - Anupama Shankar
- Laboratory Branch, Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (A.S.); (W.M.S.)
| | - Joel M. Montgomery
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (M.M.); (E.S.); (J.D.K.)
| | - John D. Klena
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (M.M.); (E.S.); (J.D.K.)
| | - William M. Switzer
- Laboratory Branch, Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA (A.S.); (W.M.S.)
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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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Campos PE, Pruvost O, Boyer K, Chiroleu F, Cao TT, Gaudeul M, Baider C, Utteridge TMA, Becker N, Rieux A, Gagnevin L. Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history. Nat Commun 2023; 14:4306. [PMID: 37474518 PMCID: PMC10359311 DOI: 10.1038/s41467-023-39950-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).
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Affiliation(s)
- Paola E Campos
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
| | | | - Karine Boyer
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
| | | | - Thuy Trang Cao
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
| | - Myriam Gaudeul
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
- Herbier national, Muséum national d'Histoire naturelle, CP39, 57 rue Cuvier, 75005, Paris, France
| | - Cláudia Baider
- The Mauritius Herbarium, Agricultural Services, Ministry of Agro-Industry and Food Security, R.E. Vaughan Building (MSIRI Compound), Reduit, 80835, Mauritius
| | | | - Nathalie Becker
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
| | - Adrien Rieux
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France.
| | - Lionel Gagnevin
- PHIM Plant Health Institute, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.
- CIRAD, UMR PHIM, Montpellier, France.
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Dellicour S, Lemey P, Suchard MA, Gilbert M, Baele G. Accommodating sampling location uncertainty in continuous phylogeography. Virus Evol 2022; 8:veac041. [PMID: 35795297 PMCID: PMC9248920 DOI: 10.1093/ve/veac041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/22/2022] [Accepted: 05/18/2022] [Indexed: 02/01/2023] Open
Abstract
Phylogeographic inference of the dispersal history of viral lineages offers key opportunities to tackle epidemiological questions about the spread of fast-evolving pathogens across human, animal and plant populations. In continuous space, i.e. when locations are specified by longitude and latitude, these reconstructions are however often limited by the availability or accessibility of precise sampling locations required for such spatially explicit analyses. We here review the different approaches that can be considered when genomic sequences are associated with a geographic area of sampling instead of precise coordinates. In particular, we describe and compare the approaches to define homogeneous and heterogeneous prior ranges of sampling coordinates.
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Affiliation(s)
| | | | | | - Marius Gilbert
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 av. FD Roosevelt, Bruxelles 1050, Belgium
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Stam R, Gladieux P, Vinatzer BA, Goss EM, Potnis N, Candresse T, Brewer MT. Population Genomic- and Phylogenomic-Enabled Advances to Increase Insight Into Pathogen Biology and Epidemiology. PHYTOPATHOLOGY 2021; 111:8-11. [PMID: 33513042 DOI: 10.1094/phyto-11-20-0528-fi] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Population genetics has been a key discipline in phytopathology for many years. The recent rise in cost-effective, high-throughput DNA sequencing technologies, allows sequencing of dozens, if not hundreds of specimens, turning population genetics into population genomics and opening up new, exciting opportunities as described in this Focus Issue. Without the limitations of genetic markers and the availability of whole or near whole-genome data, population genomics can give new insights into the biology, evolution and adaptation, and dissemination patterns of plant-associated microbes.
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Affiliation(s)
- Remco Stam
- Phytopathology, Technical University Munich, 85354 Freising, Germany
| | - Pierre Gladieux
- UMR BGPI, University of Montpellier, INRA, CIRAD, Montpellier SupAgro, 34398 Montpellier, France
| | - Boris A Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, U.S.A
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Rouse Life Science Building, Auburn University, Auburn, AL 36849, U.S.A
| | | | - Marin Talbot Brewer
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, U.S.A
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