Brunker, K. et al. (2020) Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes. Wellcome Open Research, 5, 3. (doi: 10.12688/wellcomeopenres.15518.2) (PMID:32090172) (PMCID:PMC7001756)
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Abstract
Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.
| Item Type: | Articles |
|---|---|
| Additional Information: | Version 2; peer review: 3 approved |
| Status: | Published |
| Refereed: | Yes |
| Glasgow Author(s) Enlighten ID: | Gifford, Dr Robert and Czupryna, Dr Anna and Manalo, Dr Daria and Steenson, Miss Rachel and Kamat, Maya and Singer, Dr Josh and Miranda, Dr Mary Elizabeth and Biek, Professor Roman and Brunker, Dr Kirstyn and Zhu, Wenlong and Lugelo, Dr Ahmed and Lushasi, Mr Kennedy and Hampson, Professor Katie and Rysava, Ms Kristyna |
| Creator Roles: | Brunker, K.Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Validation, Visualization, Writing – original draft, Writing – review and editing Lushasi, K.Investigation Lugelo, A.Investigation Czupryna, A. M.Investigation, Project administration Steenson, R.Visualization Manalo, D. L.Resources Miranda, M. E.Resources Kamat, M.Investigation Rysava, K.Resources Zhu, W.Investigation Gifford, R. J.Data curation, Methodology, Resources, Software Singer, J. B.Data curation, Resources, Software, Writing – review and editing Biek, R.Writing – review and editing Hampson, K.Conceptualization, Data curation, Funding acquisition, Project administration, Resources, Supervision, Visualization, Writing – original draft, Writing – review and editing |
| Authors: | Brunker, K., Jaswant, G., Thumbi, S.M., Lushasi, K., Lugelo, A., Czupryna, A. M., Ade, F., Wambura, G., Chuchu, V., Steenson, R., Ngeleja, C., Bautista, C., Manalo, D. L., Gomez, M. R. R., Chu, M. Y. J. V., Miranda, M. E., Kamat, M., Rysava, K., Espineda, J., Silo, E. A. V., Aringo, A. M., Bernales, R. P., Adonay, F. F., Tildesley, M. J., Marston, D. A., Jennings, D. L., Fooks, A. R., Zhu, W., Meredith, L. W., Hill, S. C., Poplawski, R., Gifford, R. J., Singer, J. B., Maturi, M., Mwatondo, A., Biek, R., and Hampson, K. |
| College/School: | College of Medical Veterinary and Life Sciences > School of Infection & Immunity College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine |
| Journal Name: | Wellcome Open Research |
| Publisher: | F1000Research |
| ISSN: | 2398-502X |
| ISSN (Online): | 2398-502X |
| Copyright Holders: | Copyright © 2020 Brunker K et al. |
| First Published: | First published in Wellcome Open Research 5: 3 |
| Publisher Policy: | Reproduced under a Creative Commons License |
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