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

Abstract

<ns4:p>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.</ns4:p>

Update on lyssaviruses and rabies: will past progress play as prologue in the near term towards future elimination?

“…Over the past 10 years, substantial progress has occurred on a global level regarding pathogen discovery, diagnostics, prophylaxis, and engagement of professionals in academia, government, industry, and international non-governmental organizations. Further success requires maintaining this transdisciplinary philosophy, with collaboration among virologists, immunologists, epidemiologists, veterinarians, physicians, producers, regulators, economists, and social scientists within an updated One Health approach in a common endeavor to better understand, communicate, detect, prevent, control, and eliminate lyssavirus infections in the next decade 170 – 183 ( Table 6 ). Supporting focus, enthusiasm, and momentum, based upon the evidence at hand, is critical but will not be simple, overly rapid, or inexpensive ( https://www.who.int/neglected_diseases/news/WHO-EB-commend-progress-against-NTDs-and-calls-roadmap-2021-2030/en/ ).…”

Portable Rabies Virus Sequencing in Canine Rabies Endemic Countries Using the Oxford Nanopore MinION

“…First, our method allowed for the use of degenerate primers that work broadly against several diverse lineages of rabies virus, meaning only one set of primers can be used for many samples. Because of the diversity across Rabies lyssavirus, whole genome tiled primers are limited to a given lineage, clade, or variant [90][91][92][93], meaning divergent, new, or imported rabies virus variants may be missed. Second, the partial genome method presented here costs much less per sample than a whole genome PCR approach with the MinION [93].…”

Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap

“…The problems around political buy-in and societal trust for WGS in public health and possible solutions have been discussed for TB surveillance in Jackson et al 63 , for human genome sequencing in Tekola-Ayele and Rotimi, 64 and for rabies surveillance in Brunker et al . 65 Instead, we focus on the logistic and operational aspects illustrated in figure 2 .…”