Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes
| Autor: | Florencio F Adonay, Rachel Steenson, Kennedy Lushasi, Criselda Bautista, Anthony R. Fooks, Michael J. Tildesley, Kirstyn Brunker, Wenlong Zhu, Jason Espineda, Roman Biek, Ma Ricci R Gomez, Fred Ade, Maya Kamat, Eva Angelica V Silo, Daria L. Manalo, Ahmed Lugelo, Robert J. Gifford, Denise A. Marston, Luke W. Meredith, Mathew Maturi, Ariane Mae Aringo, Rona P Bernales, Joshua B Singer, Athman Mwatondo, Kristyna Rysava, Katie Hampson, Daisy Jennings, Maria Yna Joyce V Chu, Veronicah Chuchu, Mary Elizabeth Miranda, Samuel M. Thumbi, Gurdeep Jaswant, Chanasa Ngeleja, Anna Czupryna, Sarah C. Hill, Gati Wambura, Radoslaw Poplawski |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
030231 tropical medicine MinION Medicine (miscellaneous) field sequencing medicine.disease_cause Genome General Biochemistry Genetics and Molecular Biology 03 medical and health sciences 0302 clinical medicine medicine rabies virus nanopore dog mediated rabies neglected tropical diseases Environmental planning Lyssavirus Whole genome sequencing whole genome sequencing biology Rabies virus lyssavirus medicine.disease biology.organism_classification zoonoses 3. Good health 030104 developmental biology Workflow Metagenomics surveillance Neglected tropical diseases Rabies phylogenetic Business |
| Zdroj: | 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, Poplawski, R, Singer, J B, Maturi, M, Mwatondo, A, Biek, R & Hampson, K 2020, ' Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes ', Wellcome Open Research, vol. 5, no. 3 . https://doi.org/10.12688/wellcomeopenres.15518.2 |
| ISSN: | 2398-502X |
| DOI: | 10.12688/wellcomeopenres.15518.2 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|