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

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.

Mathematical modelling and phylodynamics for the study of dog rabies dynamics and control: A scoping review

“…Genomic surveillance relies on laboratory infrastructures, supply chains and expertise, all of which are costly and generally lacking in low- and middle-income countries. New portable sequencing technologies combined with bioinformatics workflows could accelerate capacity building through portability and affordability [ 94 , 95 ]. In parallel, potential sampling bias effects should not be overlooked [ 53 , 96 ] since they may hide a part of disease dynamics such as silent spread in deprived rural areas.…”

A cocktail of human monoclonal antibodies broadly neutralizes North American rabies virus variants as a promising candidate for rabies post-exposure prophylaxis

“…RABISHIELD © is the first anti-rabies monoclonal antibody product commercially available in the world and is fully licensed for human PEP in India. It was proven to be safe and effective against RABV exposures in India where circulating arctic-like and Indian subcontinent RABV variants are the primary sources of rabies 32 , 33 .…”

Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea

“…In contrast, the MinION device, a compact portable sequencer, offers the application of real-time sequencing in point-of-care tests for infectious diseases, including identification of CHIKV, EBOV, and ZIKV from clinical blood samples [ 26 , 59 , 60 ]. The major advantages of the MinION system are the reasonable price, the ability to produce real-time data, and portability, which would make it an appropriate device to be used in a hospital or field for rapid diagnosis [ 24 ]. In previous studies, a genomic surveillance system based on phylogenetic analyses provided an effective prevention strategy against emerging orthohantavirus outbreaks for mitigating HFRS incidences, such as the restriction of field activities and environmental cleaning to eliminate rodents in endemic areas [ 37 , 39 ].…”

“…MinION (Oxford Nanopore Technologies) is a palm-sized portable sequencer that is smaller and cheaper than conventional sequencing platforms; it allows real-time sequencing in field situations or hospitals [ 22 , 23 ]. The nanopore sequencing has allowed researchers to reveal the dynamic genetic diversity and geographic distribution of the rabies virus in field [ 24 ]. Previous studies have used nanopore sequencing in point-of-care testing for the real-time identification of infectious agents, including severe acute respiratory syndrome coronavirus 2, Chikungunya virus (CHIKV), Ebola virus (EBOV), Zika virus (ZIKV), and hepatitis C virus in clinical samples [ 25 , 26 , 27 ].…”