Brunker, Kirstyn 
ORCID: 0000-0001-9990-6299, Jaswant, Gurdeep, Thumbi, SM ORCID: 0000-0002-5754-0556, Lushasi, Kennedy ORCID: 0000-0002-2060-4202, Lugelo, Ahmed, Czupryna, Anna M, Ade, Fred, Wambura, Gati ORCID: 0000-0002-3137-2355, Chuchu, Veronicah, Steenson, Rachel ORCID: 0000-0002-1579-6596 et al (show 27 more authors)
(2020)
Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes.
Wellcome open research, 5.
3-.
|
PDF
Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes.pdf - Open Access published version Download (4MB) | Preview |
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: | Article |
|---|---|
| Uncontrolled Keywords: | MinION, dog-mediated rabies, field sequencing, lyssavirus, nanopore, neglected tropical diseases, phylogenetic, rabies virus, surveillance, whole genome sequencing, zoonoses |
| Divisions: | Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 18 Mar 2024 10:06 |
| Last Modified: | 18 Mar 2024 10:06 |
| DOI: | 10.12688/wellcomeopenres.15518.2 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3179572 |
Dimensions
Dimensions
