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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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Alonso D, Iglesias A, Coelho R, Periolo N, Bruno A, Córdoba M, Filomarino N, Quipildor M, Biondo E, Fortunato E, Bellomo C, Martínez V. Epidemiological description, case‐fatality rate, and trends of Hantavirus Pulmonary Syndrome: 9 years of surveillance in Argentina. J Med Virol 2019; 91:1173-1181. [DOI: 10.1002/jmv.25446] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/23/2019] [Accepted: 02/26/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Daniel Oscar Alonso
- Laboratorio Nacional de Referencia para HantavirusInstituto Nacional de Enfermedades Infecciosas (INEI) Administración Nacional de Laboratorio e Institutos de Salud (ANLIS) “Dr. C. G. Malbrán”Ciudad Autónoma de Buenos Aires Argentina
| | - Ayelen Iglesias
- Laboratorio Nacional de Referencia para HantavirusInstituto Nacional de Enfermedades Infecciosas (INEI) Administración Nacional de Laboratorio e Institutos de Salud (ANLIS) “Dr. C. G. Malbrán”Ciudad Autónoma de Buenos Aires Argentina
| | - Rocio Coelho
- Laboratorio Nacional de Referencia para HantavirusInstituto Nacional de Enfermedades Infecciosas (INEI) Administración Nacional de Laboratorio e Institutos de Salud (ANLIS) “Dr. C. G. Malbrán”Ciudad Autónoma de Buenos Aires Argentina
| | - Natalia Periolo
- Laboratorio Nacional de Referencia para HantavirusInstituto Nacional de Enfermedades Infecciosas (INEI) Administración Nacional de Laboratorio e Institutos de Salud (ANLIS) “Dr. C. G. Malbrán”Ciudad Autónoma de Buenos Aires Argentina
| | - Agostina Bruno
- Laboratorio de Enfermedades TropicalesHospital San Vicente de Paúl, OránSalta Oran Argentina
| | - Maria Teresa Córdoba
- Laboratorio de Enfermedades TropicalesHospital San Vicente de Paúl, OránSalta Oran Argentina
| | - Noemi Filomarino
- Laboratorio Provincial de HantavirusHospital Señor Del MilagroSalta Argentina
| | - Marcelo Quipildor
- Laboratorio de Enfermedades TropicalesHospital San Vicente de Paúl, OránSalta Oran Argentina
| | - Emiliano Biondo
- Area Programatica EsquelMinisterio de Salud de la Provincia de ChubutEsquel Chubut Argentina
| | - Eduardo Fortunato
- Region Sanitaria XIMinisterio de Salud de la Provincia de Buenos AiresBuenos Aires Argentina
| | - Carla Bellomo
- Laboratorio Nacional de Referencia para HantavirusInstituto Nacional de Enfermedades Infecciosas (INEI) Administración Nacional de Laboratorio e Institutos de Salud (ANLIS) “Dr. C. G. Malbrán”Ciudad Autónoma de Buenos Aires Argentina
| | - Valeria Paula Martínez
- Laboratorio Nacional de Referencia para HantavirusInstituto Nacional de Enfermedades Infecciosas (INEI) Administración Nacional de Laboratorio e Institutos de Salud (ANLIS) “Dr. C. G. Malbrán”Ciudad Autónoma de Buenos Aires Argentina
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