Journal Article

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

Muturi, Mathew, Cadena, Loren, Li, Yu, Mwatondo, Athman, Pieracci, Emily G., Mito, Oscar, Hampson, Katie, Gigante, Crystal M., Gibson, Andrew, Wallace, Ryan M., Thumbi, Samuel M., Thomae, Byron G., Costa, Niceta Cunha, Thin, Nguyen Xuan, Hanh, Nguyen Thi Hong, Tho, Nguyen Dang, Chuchu, Veronicah, de Paz, Victor Hugo, Yale, Gowri, Long, Nguyen Van, Meneses, Sergio, Thanh, Nguyen Tat, Minh, Phan Quang, Ade, Frederick, Chuong, Vo Dinh, Moran, David, Condori, Rene Edgar, Wambura, Gati, Munyua, Peninah

2020

Overview

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.

• Publisher: MDPI,MDPI AG
• Subject: Animals / BASIC BIOLOGICAL SCIENCES / canine rabies elimination / Diagnostic Equipment / Dog Diseases - virology / Dogs / Endemic Diseases - prevention & control / Endemic Diseases - veterinary / genetic variation / geographical distribution / Guatemala / human diseases / Humans / India / Kenya / lyssavirus / MinION / nanopore / Nanopores / pathogens / Phylogeny / portable sequencing / Public Health / rabies / Rabies - veterinary / Rabies - virology / Rabies lyssavirus / Rabies virus - classification / Rabies virus - genetics / rural areas / Sequence Analysis, DNA - instrumentation / Sequence Analysis, DNA - methods / vaccination / Vietnam / viruses