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HantaNet: A New MicrobeTrace Application for Hantavirus Classification, Genomic Surveillance, Epidemiology and Outbreak Investigations

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 app...

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Autores principales: Cintron, Roxana, Whitmer, Shannon L. M., Moscoso, Evan, Campbell, Ellsworth M., Kelly, Reagan, Talundzic, Emir, Mobley, Melissa, Chiu, Kuo Wei, Shedroff, Elizabeth, Shankar, Anupama, Montgomery, Joel M., Klena, John D., Switzer, William M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10675615/
https://www.ncbi.nlm.nih.gov/pubmed/38005885
http://dx.doi.org/10.3390/v15112208
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author Cintron, Roxana
Whitmer, Shannon L. M.
Moscoso, Evan
Campbell, Ellsworth M.
Kelly, Reagan
Talundzic, Emir
Mobley, Melissa
Chiu, Kuo Wei
Shedroff, Elizabeth
Shankar, Anupama
Montgomery, Joel M.
Klena, John D.
Switzer, William M.
author_facet Cintron, Roxana
Whitmer, Shannon L. M.
Moscoso, Evan
Campbell, Ellsworth M.
Kelly, Reagan
Talundzic, Emir
Mobley, Melissa
Chiu, Kuo Wei
Shedroff, Elizabeth
Shankar, Anupama
Montgomery, Joel M.
Klena, John D.
Switzer, William M.
author_sort Cintron, Roxana
collection PubMed
description 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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spelling pubmed-106756152023-11-02 HantaNet: A New MicrobeTrace Application for Hantavirus Classification, Genomic Surveillance, Epidemiology and Outbreak Investigations Cintron, Roxana Whitmer, Shannon L. M. Moscoso, Evan Campbell, Ellsworth M. Kelly, Reagan Talundzic, Emir Mobley, Melissa Chiu, Kuo Wei Shedroff, Elizabeth Shankar, Anupama Montgomery, Joel M. Klena, John D. Switzer, William M. Viruses Article 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. MDPI 2023-11-02 /pmc/articles/PMC10675615/ /pubmed/38005885 http://dx.doi.org/10.3390/v15112208 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Cintron, Roxana
Whitmer, Shannon L. M.
Moscoso, Evan
Campbell, Ellsworth M.
Kelly, Reagan
Talundzic, Emir
Mobley, Melissa
Chiu, Kuo Wei
Shedroff, Elizabeth
Shankar, Anupama
Montgomery, Joel M.
Klena, John D.
Switzer, William M.
HantaNet: A New MicrobeTrace Application for Hantavirus Classification, Genomic Surveillance, Epidemiology and Outbreak Investigations
title HantaNet: A New MicrobeTrace Application for Hantavirus Classification, Genomic Surveillance, Epidemiology and Outbreak Investigations
title_full HantaNet: A New MicrobeTrace Application for Hantavirus Classification, Genomic Surveillance, Epidemiology and Outbreak Investigations
title_fullStr HantaNet: A New MicrobeTrace Application for Hantavirus Classification, Genomic Surveillance, Epidemiology and Outbreak Investigations
title_full_unstemmed HantaNet: A New MicrobeTrace Application for Hantavirus Classification, Genomic Surveillance, Epidemiology and Outbreak Investigations
title_short HantaNet: A New MicrobeTrace Application for Hantavirus Classification, Genomic Surveillance, Epidemiology and Outbreak Investigations
title_sort hantanet: a new microbetrace application for hantavirus classification, genomic surveillance, epidemiology and outbreak investigations
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10675615/
https://www.ncbi.nlm.nih.gov/pubmed/38005885
http://dx.doi.org/10.3390/v15112208
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