Bautista, C., Jaswant, G., French, H., Campbell, K., Durrant, R. , Gifford, R. , Kia, G. S.N., Ogoti, B., Hampson, K. and Brunker, K. (2023) Whole genome sequencing for rapid characterization of rabies virus using nanopore technology. Journal of Visualized Experiments(191), e65414. (doi: 10.3791/65414) (PMID:37677046)
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Abstract
Genomic data can be used to track the transmission and geographic spread of infectious diseases. However, the sequencing capacity required for genomic surveillance remains limited in many low- and middle-income countries (LMICs), where dog-mediated rabies and/or rabies transmitted by wildlife such as vampire bats pose major public health and economic concerns. We present here a rapid and affordable sample-to-sequence-to-interpretation workflow using nanopore technology. Protocols for sample collection and the diagnosis of rabies are briefly described, followed by details of the optimized whole genome sequencing workflow, including primer design and optimization for multiplex polymerase chain reaction (PCR), a modified, low-cost sequencing library preparation, sequencing with live and offline base calling, genetic lineage designation, and phylogenetic analysis. Implementation of the workflow is demonstrated, and critical steps are highlighted for local deployment, such as pipeline validation, primer optimization, inclusion of negative controls, and the use of publicly available data and genomic tools (GLUE, MADDOG) for classification and placement within regional and global phylogenies. The turnaround time for the workflow is 2-3 days, and the cost ranges from $25 per sample for a 96 sample run to $80 per sample for a 12 sample run. We conclude that setting up rabies virus genomic surveillance in LMICs is feasible and can support progress toward the global goal of zero dog-mediated human rabies deaths by 2030, as well as enhanced monitoring of wildlife rabies spread. Moreover, the platform can be adapted for other pathogens, helping to build a versatile genomic capacity that contributes to epidemic and pandemic preparedness.
| Item Type: | Articles |
|---|---|
| Status: | Published |
| Refereed: | Yes |
| Glasgow Author(s) Enlighten ID: | Gifford, Dr Robert and Kia, Grace Sabo Nok and French, Hollie and jaswant, gurdeep and Bautista, Criselda and Brunker, Dr Kirstyn and Durrant, Rowan and Campbell, Kathryn and Hampson, Professor Katie |
| Authors: | Bautista, C., Jaswant, G., French, H., Campbell, K., Durrant, R., Gifford, R., Kia, G. S.N., Ogoti, B., Hampson, K., and Brunker, K. |
| College/School: | College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research |
| Journal Name: | Journal of Visualized Experiments |
| Publisher: | JoVE |
| ISSN: | 1940-087X |
| ISSN (Online): | 1940-087X |
| Copyright Holders: | Copyright © 2023 JoVE |
| First Published: | First published in Journal of Visualized Experiments 191: e65414 |
| Publisher Policy: | Reproduced under a Creative Commons License |
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