HantaNet: A New MicrobeTrace Application for Hantavirus Classification, Genomic Surveillance, Epidemiology and Outbreak Investigations
Roxana Cintron,
Shannon L. M. Whitmer,
Evan Moscoso,
Ellsworth M. Campbell,
Reagan Kelly,
Emir Talundzic,
Melissa Mobley,
Kuo Wei Chiu,
Elizabeth Shedroff,
Anupama Shankar,
Joel M. Montgomery,
John D. Klena,
William M. Switzer
Affiliations
Roxana Cintron
Laboratory Branch, Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
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
Evan Moscoso
General Dynamics Information Technology, Atlanta, GA 30329, USA
Ellsworth M. Campbell
Laboratory Branch, Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
Reagan Kelly
General Dynamics Information Technology, Atlanta, GA 30329, USA
Emir Talundzic
Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
Melissa Mobley
Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
Kuo Wei Chiu
General Dynamics Information Technology, Atlanta, GA 30329, USA
Elizabeth Shedroff
Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
Anupama Shankar
Laboratory Branch, Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
Joel M. Montgomery
Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
John D. Klena
Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
William M. Switzer
Laboratory Branch, Division of HIV Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
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.
