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dc.contributor.authorBrunker, Kirstyn
dc.contributor.authorJaswant, Gurdeep
dc.contributor.authorThumbi, S M
dc.contributor.authorLushasi, Kennedy
dc.contributor.authorLugelo, Ahmed
dc.contributor.authorCzupryna, Anna M
dc.contributor.authorAde, Fred
dc.contributor.authorWambura, Gati
dc.contributor.authorChuchu, Veronicah
dc.contributor.authorSteenson, Rachel
dc.contributor.authorNgeleja, Chanasa
dc.contributor.authorBautista, Criselda
dc.contributor.authorManalo, Daria L
dc.contributor.authorGomez, Ma Ricci R
dc.contributor.authorChu, Maria Yna Joyce V
dc.contributor.authorMiranda, Mary Elizabeth
dc.contributor.authorKamat, Maya
dc.contributor.authorRysava, Kristyna
dc.contributor.authorEspineda, Jason
dc.contributor.authorSilo, Eva Angelica V
dc.contributor.authorAringo, Ariane Mae
dc.contributor.authorBernales, Rona P
dc.contributor.authorAdonay, Florencio F
dc.contributor.authorTildesley, Michael J
dc.contributor.authorMarston, Denise A
dc.contributor.authorJennings, Daisy L
dc.contributor.authorFooks, Anthony R
dc.contributor.authorZhu, Wenlong
dc.contributor.authorMeredith, Luke W
dc.contributor.authorHill, Sarah C
dc.contributor.authorPoplawski, Radoslaw
dc.contributor.authorGifford, Robert J
dc.contributor.authorSinger, Joshua B
dc.contributor.authorMaturi, Mathew
dc.contributor.authorMwatondo, Athman
dc.contributor.authorBiek, Roman
dc.contributor.authorHampson, Katie
dc.date.accessioned2020-03-27T01:51:28Z
dc.date.available2020-03-27T01:51:28Z
dc.date.issued2020-01-07
dc.identifier.issn2398-502X
dc.identifier.otherPMC7001756
dc.identifier.other32090172
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/303807
dc.description.abstractGenomic 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.
dc.languageeng
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.sourceessn: 2398-502X
dc.sourcenlmid: 101696457
dc.subjectRabies virus
dc.subjectSurveillance
dc.subjectPhylogenetic
dc.subjectZoonoses
dc.subjectNanopore
dc.subjectLyssavirus
dc.subjectNeglected Tropical Diseases
dc.subjectWhole Genome Sequencing
dc.subjectMinion
dc.subjectDog-mediated Rabies
dc.subjectField Sequencing
dc.titleRapid in-country sequencing of whole virus genomes to inform rabies elimination programmes.
dc.typeArticle
dc.date.updated2020-03-27T01:51:28Z
prism.publicationNameWellcome open research
prism.volume5
dc.identifier.doi10.17863/CAM.50887
rioxxterms.versionofrecord10.12688/wellcomeopenres.15518.1
rioxxterms.versionVoR
rioxxterms.licenseref.urihttps://creativecommons.org/licenses/by/4.0/
dc.contributor.orcidBrunker, Kirstyn [0000-0001-9990-6299]
dc.contributor.orcidThumbi, S M [0000-0002-5754-0556]
dc.contributor.orcidLushasi, Kennedy [0000-0002-2060-4202]
dc.contributor.orcidWambura, Gati [0000-0002-3137-2355]
dc.contributor.orcidSteenson, Rachel [0000-0002-1579-6596]
dc.contributor.orcidManalo, Daria L [0000-0001-9290-5146]
dc.contributor.orcidChu, Maria Yna Joyce V [0000-0001-6709-2534]
dc.contributor.orcidKamat, Maya [0000-0002-7792-2084]
dc.contributor.orcidRysava, Kristyna [0000-0002-3475-931X]
dc.contributor.orcidTildesley, Michael J [0000-0002-6875-7232]
dc.contributor.orcidMeredith, Luke W [0000-0002-3802-8290]
dc.contributor.orcidGifford, Robert J [0000-0003-4028-9884]
dc.contributor.orcidSinger, Joshua B [0000-0001-6989-475X]
dc.contributor.orcidBiek, Roman [0000-0003-3471-5357]
pubs.funder-project-idMedical Research Council (MC_UU_12014/12)
pubs.funder-project-idWellcome Trust (110330, 204820, 207569, 107753)


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Attribution 4.0 International
Except where otherwise noted, this item's licence is described as Attribution 4.0 International