Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes.
Creators: name: Brunker, Kirstyn
name: Jaswant, Gurdeep
name: Thumbi, S M
name: Lushasi, Kennedy
name: Lugelo, Ahmed
name: Czupryna, Anna M
name: Ade, Fred
name: Wambura, Gati
name: Chuchu, Veronicah
name: Steenson, Rachel
name: Ngeleja, Chanasa
name: Bautista, Criselda
name: Manalo, Daria L
name: Gomez, Ma Ricci R
name: Chu, Maria Yna Joyce V
name: Miranda, Mary Elizabeth
name: Kamat, Maya
name: Rysava, Kristyna
name: Espineda, Jason
name: Silo, Eva Angelica V
name: Aringo, Ariane Mae
name: Bernales, Rona P
name: Adonay, Florencio F
name: Tildesley, Michael J
name: Marston, Denise A
name: Jennings, Daisy L
name: Fooks, Anthony R
name: Zhu, Wenlong
name: Meredith, Luke W
name: Hill, Sarah C
name: Poplawski, Radoslaw
name: Gifford, Robert J
name: Singer, Joshua B
name: Maturi, Mathew
name: Mwatondo, Athman
name: Biek, Roman
name: Hampson, Katie
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Rabies virus
Surveillance
Phylogenetic
Zoonoses
Nanopore
Lyssavirus
Neglected Tropical Diseases
Whole Genome Sequencing
Minion
Dog-mediated Rabies
Field Sequencing

description: 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.