Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes

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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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
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
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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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
301620The Science of Rabies EliminationKatie HampsonWellcome Trust (WELLCOTR)207569/Z/17/ZInstitute of Biodiversity, Animal Health and Comparative Medicine
173707Institutional Strategic Support Fund (2016)Anna DominiczakWellcome Trust (WELLCOTR)204820/Z/16/ZInstitute of Cardiovascular & Medical Sciences
300909Moving from laboratory-based to real-time genomic surveillance of canine rabies virus in the field.Kirstyn BrunkerRoyal Society of Tropical Medicine and Hygiene (RSTMH)GR000892Institute of Biodiversity, Animal Health and Comparative Medicine
306188EPSRC-GCRF Global Impact Accelerator Account 2018 UofGJonathan CooperEngineering and Physical Sciences Research Council (EPSRC)EP/S51584X/1Research and Innovation Services
173142African Science Partnership for Intervention Research Excellence (Afrique One-ASPIRE)Daniel HaydonWellcome Trust (WELLCOTR)107753/B/15/ZInstitute of Biodiversity, Animal Health and Comparative Medicine