Whole Genome Sequencing for Rapid Characterization of Rabies Virus Using Nanopore Technology.

Area of Science:

• Genomics
• Epidemiology
• Public Health

Background:

• Genomic surveillance is crucial for tracking infectious diseases, but sequencing capacity is limited in many low- and middle-income countries (LMICs).
• Rabies, transmitted by dogs and wildlife like vampire bats, presents significant public health and economic challenges in LMICs.
• Existing genomic surveillance methods may be too costly or complex for widespread implementation in resource-limited settings.

Purpose of the Study:

• To develop and validate a rapid, affordable, and accessible sample-to-sequence-to-interpretation workflow for rabies virus genomic surveillance.
• To enable LMICs to establish local genomic surveillance capacity for rabies.
• To support global efforts to eliminate human rabies deaths and monitor wildlife rabies.

Main Methods:

• Utilized nanopore technology for whole genome sequencing of rabies virus.
• Optimized multiplex polymerase chain reaction (PCR) with novel primer design.
• Developed a low-cost library preparation method and employed live/offline base calling.
• Integrated publicly available genomic tools (GLUE, MADDOG) for data analysis and phylogenetic placement.

Main Results:

• The workflow provides results within 2-3 days.
• Costs range from $25 to $80 per sample, depending on the scale of the run.
• Demonstrated successful implementation, highlighting critical steps for local deployment.
• The workflow enables genetic lineage designation and phylogenetic analysis for tracking disease transmission.

Conclusions:

• Establishing rabies virus genomic surveillance in LMICs is feasible with this workflow.
• The technology supports progress towards the global goal of zero human rabies deaths by 2030.
• The adaptable platform enhances epidemic and pandemic preparedness by building versatile genomic capacity for other pathogens.