Journal
VIRUSES-BASEL
Volume 12, Issue 11, Pages -Publisher
MDPI
DOI: 10.3390/v12111255
Keywords
rabies; lyssavirus; canine rabies elimination; portable sequencing; nanopore; MinION
Categories
Funding
- CDC Poxvirus and Rabies Branch
- Mission Rabies
- University of Edinburgh
- Vietnam Department of Animal Health
- Vietnam National Center for Veterinary Diseases, Kenya Medical Research Institute
- University of Nairobi
- Guatemala Ministry of Agriculture, Livestock, and Fisheries
- Guatemala National Health Laboratory
- University del Valle
- Goa Directorate of Animal Health and Veterinary Services
- Office of Advanced Molecular Detection and Global Health Security (United States CDC)
- MRC [MR/R025649/1] Funding Source: UKRI
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As countries with endemic canine rabies progress towards elimination by 2030, it will become necessary to employ techniques to help plan, monitor, and confirm canine rabies elimination. Sequencing can provide critical information to inform control and vaccination strategies by identifying genetically distinct virus variants that may have different host reservoir species or geographic distributions. However, many rabies testing laboratories lack the resources or expertise for sequencing, especially in remote or rural areas where human rabies deaths are highest. We developed a low-cost, high throughput rabies virus sequencing method using the Oxford Nanopore MinION portable sequencer. A total of 259 sequences were generated from diverse rabies virus isolates in public health laboratories lacking rabies virus sequencing capacity in Guatemala, India, Kenya, and Vietnam. Phylogenetic analysis provided valuable insight into rabies virus diversity and distribution in these countries and identified a new rabies virus lineage in Kenya, the first published canine rabies virus sequence from Guatemala, evidence of rabies spread across an international border in Vietnam, and importation of a rabid dog into a state working to become rabies-free in India. Taken together, our evaluation highlights the MinION's potential for low-cost, high volume sequencing of pathogens in locations with limited resources.
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