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

• Published in: Viruses Vol. 15; no. 11; p. 2208
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 01.11.2023
• Subjects: Animals; Applications software; Automatic classification; Bioinformatics; Communicable Diseases - epidemiology; Contact tracing; Datasets; Disease Outbreaks; Disease transmission; Distribution; Epidemics; Epidemiology; Fourier transforms; Genetic aspects; Genomes; Genomics; Hantavirus; Hantavirus Infections - epidemiology; Hantaviruses; HIV; Human immunodeficiency virus; Humans; Identification and classification; Laboratories; Metadata; Methods; MicrobeTrace; networks; Orthohantavirus - genetics; outbreak; Outbreaks; Phylogenetics; Phylogeny; Public health; RNA polymerase; Rodentia; Surveillance; United States; viral classification; Virus research; Viruses; Visualization; Web browsers; Zoonoses; United States; South America; Asia; United States > US; Europe; MicrobeTrace; epidemiology; visualization; viral classification; hantavirus; bioinformatics; outbreak; surveillance; networks
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v15112208

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.