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Updated: May 31, 2026

Whole Genome Sequencing for Rapid Characterization of Rabies Virus Using Nanopore Technology
Published on: August 18, 2023
Biosurveillance and early outbreak detection of rabies in settings with limited laboratory capacity using
Ravikiran Keshavamurthy1, Jesse Blanton2, Lillian Orciari2
1Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Atlanta, GA, 30329-4027, USA. mfl3@cdc.gov.
Abstract:
Rabies is an important but often neglected zoonotic disease with significant public health, veterinary, and economic impacts. Inadequate surveillance and diagnostic resources in low- and middle-income countries impede its effective public health responses. This study demonstrates the use of an extreme gradient boosting (XGB) technique for animal rabies risk assessment in endemic areas of Haiti with limited diagnostic resources. We employed spatiotemporal clustering and trend analysis techniques to assess rabies status across large geographic areas. The XGB model achieved high specificity (0.99, 95% CI: 0.98-0.99), sensitivity (0.78, 95% CI: 0.61-0.95), negative predictive value (1.0, 95% CI: 0.99-1.00), and accuracy (0.98, 95% CI: 0.98-0.99) in predicting animal rabies cases. The framework identified 20 high-risk rabies clusters, representing a 40% increase in detected transmission zones compared to laboratory-confirmed data alone. This included 8 clusters in underserved communities where no diagnostic infrastructure was previously available, enabling real-time monitoring of disease and surveillance trends in previously unmonitored regions. Trend analysis facilitated real-time monitoring of high-risk clusters with significantly changing disease and surveillance statuses. This study showcases a data-driven, evidence-based framework for neglected and emerging zoonotic disease surveillance in economically constrained regions.
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