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

Wellcome Open Research

article

Daria L. Manalo¹  Ma. Ricci R. Gomez¹  Maria Yna Joyce V. Chu¹  Mary Elizabeth Miranda¹  Maya Kamat³  Kristyna Rysava⁴  Jason Espineda⁵  Eva Angelica V. Silo⁵  Ariane Mae Aringo⁵  Rona P. Bernales⁵  Florencio F. Adonay⁶  Michael J. Tildesley⁴  Denise A. Marston⁷  Daisy L. Jennings⁷  Anthony R. Fooks⁷  Wenlong Zhu³  Luke W. Meredith⁹  Sarah C. Hill^1,10  Radoslaw Poplawski^1,11  Robert J. Gifford^1,13  Joshua B. Singer^1,13  Mathew Maturi^1,14  Athman Mwatondo^1,14  Roman Biek³  Katie Hampson³  Kirstyn Brunker³  Gurdeep Jaswant³  S.M. Thumbi^1,16  Kennedy Lushasi^1,19  Ahmed Lugelo^2,20  Anna M. Czupryna³  Fred Ade^1,17  Gati Wambura^1,17  Veronicah Chuchu^1,17  Rachel Steenson³  Chanasa Ngeleja^2,21  Criselda Bautista¹ 

[1] Research Institute for Tropical Medicine;Field Epidemiology Training Program Alumni Foundation;Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow;The Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, School of Life Sciences and Mathematical Institute, University of Warwick;Department of Agriculture Regional Field Office 5, Regional Animal Disease, Diagnostic Laboratory;Albay Veterinary Office, Provincial Government of Albay, Albay Farmers' Bounty Village;Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency;Institute of Infection and Global Health,, University of Liverpool;Department of Pathology, University of Cambridge;University of Oxford;Institute of Microbiology and Infection, School of Biosciences, University of Birmingham;Advanced Research Computing, University of Birmingham;MRC-University of Glasgow Centre for Virus Research ,(CVR), University of Glasgow;Zoonotic Disease Unit, Ministry of Health, Ministry of Agriculture;The Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow;University of Nairobi Institute of Tropical and Infectious Diseases;Center for Global Health Research, Kenya Medical Research Institute;Paul G. Allen School for Global Animal Health, Washington State University;Ifakara Health Institute;Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture;Tanzania Veterinary Laboratory Agency, Ministry of Livestock and Fisheries Development

关键词: dog-mediated rabies;    field sequencing;    lyssavirus;    MinION;    nanopore;    neglected tropical diseases;    phylogenetic;    rabies virus;    whole genome sequencing;    zoonoses;    surveillance;   

DOI  :  10.12688/wellcomeopenres.15518.2

学科分类：内科医学

来源: Wellcome

【 摘 要 】

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.

【 授权许可】

CC BY