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Whitmer SL, Whitesell A, Mobley M, Talundzic E, Shedroff E, Cossaboom CM, Messenger S, Deldari M, Bhatnagar J, Estetter L, Zufan S, Cannon D, Chiang CF, Gibbons A, Krapiunaya I, Morales-Betoulle M, Choi M, Knust B, Amman B, Montgomery JM, Shoemaker T, Klena JD. Human Orthohantavirus disease prevalence and genotype distribution in the U.S., 2008-2020: a retrospective observational study. LANCET REGIONAL HEALTH. AMERICAS 2024; 37:100836. [PMID: 39100240 PMCID: PMC11296052 DOI: 10.1016/j.lana.2024.100836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 06/06/2024] [Accepted: 06/26/2024] [Indexed: 08/06/2024]
Abstract
Background In the United States (U.S.), hantavirus pulmonary syndrome (HPS) and non-HPS hantavirus infection are nationally notifiable diseases. Criteria for identifying human cases are based on clinical symptoms (HPS or non-HPS) and acute diagnostic results (IgM+, rising IgG+ titers, RT-PCR+, or immunohistochemistry (IHC)+). Here we provide an overview of diagnostic testing and summarize human Hantavirus disease occurrence and genotype distribution in the U.S. from 2008 to 2020. Methods Epidemiological data from the national hantavirus registry was merged with laboratory diagnostic testing results performed at the CDC. Residual hantavirus-positive specimens were sequenced, and the available epidemiological and genetic data sets were linked to conduct a genomic epidemiological study of hantavirus disease in the U.S. Findings From 1993 to 2020, 833 human hantavirus cases have been identified, and from 2008 to 2020, 335 human cases have occurred. Among New World (NW) hantavirus cases detected at the CDC diagnostic laboratory (representing 29.2% of total cases), most (85.0%) were detected during acute disease, however, some convalescent cases were detected in states not traditionally associated with hantavirus infections (Connecticut, Missouri, New Jersey, Pennsylvania, Tennessee, and Vermont). From 1993 to 2020, 94.9% (745/785) of U.S. hantaviruses cases were detected west of the Mississippi with 45.7% (359/785) in the Four Corners region of the U.S. From 2008 to 2020, 67.7% of NW hantavirus cases were detected between the months of March and August. Sequencing of RT-PCR-positive cases demonstrates a geographic separation of Orthohantavirus sinnombreense species [Sin Nombre virus (SNV), New York virus, and Monongahela virus]; however, there is a large gap in viral sequence data from the Northwestern and Central U.S. Finally, these data indicate that commercial IgM assays are not concordant with CDC-developed assays, and that "concordant positive" (i.e., commercial IgM+ and CDC IgM+ results) specimens exhibit clinical characteristics of hantavirus disease. Interpretation Hantaviral disease is broadly distributed in the contiguous U.S, viral variants are localised to specific geographic regions, and hantaviral disease infrequently detected in most Southeastern states. Discordant results between two diagnostic detection methods highlight the need for an improved standardised testing plan in the U.S. Hantavirus surveillance and detection will continue to improve with clearly defined, systematic reporting methods, as well as explicit guidelines for clinical characterization and diagnostic criteria. Funding This work was funded by core funds provided to the Viral Special Pathogens Branch at CDC.
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Affiliation(s)
- Shannon L.M. Whitmer
- Viral Special Pathogens Branch, U.S. Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd., NE Atlanta, GA, 30333, USA
| | - Amy Whitesell
- Viral Special Pathogens Branch, U.S. Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd., NE Atlanta, GA, 30333, USA
| | - Melissa Mobley
- Viral Special Pathogens Branch, U.S. Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd., NE Atlanta, GA, 30333, USA
| | - Emir Talundzic
- Viral Special Pathogens Branch, U.S. Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd., NE Atlanta, GA, 30333, USA
| | - Elizabeth Shedroff
- Viral Special Pathogens Branch, U.S. Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd., NE Atlanta, GA, 30333, USA
| | - Caitlin M. Cossaboom
- Viral Special Pathogens Branch, U.S. Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd., NE Atlanta, GA, 30333, USA
| | - Sharon Messenger
- Zoonotic and Vector-borne Diseases Section, Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, 94804, USA
| | - Mojgan Deldari
- Zoonotic and Vector-borne Diseases Section, Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, 94804, USA
| | - Julu Bhatnagar
- Infectious Diseases Pathology Branch, U.S. Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd., NE Atlanta, GA, 30333, USA
| | - Lindsey Estetter
- Infectious Diseases Pathology Branch, U.S. Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd., NE Atlanta, GA, 30333, USA
| | - Sara Zufan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, VIC, 3000, Australia
| | - Debi Cannon
- Viral Special Pathogens Branch, U.S. Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd., NE Atlanta, GA, 30333, USA
| | - Cheng-Feng Chiang
- Viral Special Pathogens Branch, U.S. Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd., NE Atlanta, GA, 30333, USA
| | - Ardith Gibbons
- Viral Special Pathogens Branch, U.S. Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd., NE Atlanta, GA, 30333, USA
| | - Inna Krapiunaya
- Viral Special Pathogens Branch, U.S. Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd., NE Atlanta, GA, 30333, USA
| | - Maria Morales-Betoulle
- Viral Special Pathogens Branch, U.S. Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd., NE Atlanta, GA, 30333, USA
| | - Mary Choi
- Viral Special Pathogens Branch, U.S. Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd., NE Atlanta, GA, 30333, USA
| | - Barbara Knust
- Immigrant, Refugee, and Migrant Health Branch, Division of Global Migration and Quarantine, Bangkok, Thailand
| | - Brian Amman
- Viral Special Pathogens Branch, U.S. Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd., NE Atlanta, GA, 30333, USA
| | - Joel M. Montgomery
- Viral Special Pathogens Branch, U.S. Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd., NE Atlanta, GA, 30333, USA
| | - Trevor Shoemaker
- Viral Special Pathogens Branch, U.S. Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd., NE Atlanta, GA, 30333, USA
| | - John D. Klena
- Viral Special Pathogens Branch, U.S. Centers for Disease Control and Prevention (CDC), 1600 Clifton Rd., NE Atlanta, GA, 30333, USA
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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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