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

Vo Dinh Chuong,Yu Li,Gati Wambura,Loren Cadena,Victor Hugo De Paz,Rene Edgar Condori,Peninah Munyua,Samuel M Thumbi,Athman Mwatondo,Katie Hampson,Nguyen Tat Thanh,Crystal M Gigante,Nguyen Xuan Thin,Veronicah Chuchu,Oscar Mito,Emily G Pieracci,Byron G Thomae ,Phạm Quang Minh ,David Morán ,Nguyen Van Duc Long ,Andrew D Gibson ,Nguyễn Thị Hồng Hạnh ,Sergio Meneses,Niceta Cunha Costa,Mathew Muturi,Gowri Yale,Frederick Ade,Nguyen Dang Tho

doi:10.3390/v12111255

Abstract

As countries with endemic canine rabies progress towards elimination by 2030, it will become necessary to employ techniques to help plan, monitor, and confirm canine rabies elimination. Sequencing can provide critical information to inform control and vaccination strategies by identifying genetically distinct virus variants that may have different host reservoir species or geographic distributions. However, many rabies testing laboratories lack the resources or expertise for sequencing, especially in remote or rural areas where human rabies deaths are highest. We developed a low-cost, high throughput rabies virus sequencing method using the Oxford Nanopore MinION portable sequencer. A total of 259 sequences were generated from diverse rabies virus isolates in public health laboratories lacking rabies virus sequencing capacity in Guatemala, India, Kenya, and Vietnam. Phylogenetic analysis provided valuable insight into rabies virus diversity and distribution in these countries and identified a new rabies virus lineage in Kenya, the first published canine rabies virus sequence from Guatemala, evidence of rabies spread across an international border in Vietnam, and importation of a rabid dog into a state working to become rabies-free in India. Taken together, our evaluation highlights the MinION’s potential for low-cost, high volume sequencing of pathogens in locations with limited resources.

Highlights

Rabies is a progressive, fatal encephalitis caused by members of 17 different viral species within the Lyssavirus genus of rhabdoviruses [1]
We developed and validated a portable strategy to sequence rabies virus nucleoprotein and glycoprotein genes in rabies diagnostic laboratories in canine rabies endemic countries using the Oxford Nanopore MinION sequencer
We developed a rabies virus sequencing strategy focused on low cost and high throughput

Summary

Introduction

Fatal encephalitis caused by members of 17 different viral species within the Lyssavirus genus of rhabdoviruses [1]. The vast majority of human rabies deaths are caused by a virus in the species Rabies lyssavirus [2], commonly referred to as rabies virus. Canine rabies has been effectively controlled and even eliminated in several countries through coordinated surveillance and canine vaccination campaigns [2,4,5,6,7,8,9]. The World Health Organization (WHO), the World Organization for Animal Health (OIE) and the Food and Agriculture Organization (FAO) have set a goal to eliminate dog-mediated human rabies deaths by 2030 [10]. Many countries with endemic canine rabies are in the early stages of planning control efforts and face barriers including limited understanding of rabies prevalence, logistical challenges, and competition for limited resources [9,11]

Methods

Results

Conclusion