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

Viruses

Oscar Mito¹  SamuelM. Thumbi¹  Frederick Ade¹  Gati Wambura¹  Veronicah Chuchu¹  NicetaCunha Costa²  Loren Cadena³  Peninah Munyua⁴  Katie Hampson⁵  ByronG. Thomae⁶  Gowri Yale⁷  NguyenDang Tho⁸  VictorHugo de Paz⁹  Sergio Meneses⁹  EmilyG. Pieracci^1,10  CrystalM. Gigante^1,10  RyanM. Wallace^1,10  ReneEdgar Condori^1,10  Yu Li^1,10  NguyenXuan Thin^1,11  NguyenTat Thanh^1,11  NguyenThi Hong Hanh^1,11  Andrew Gibson^1,12  David Moran^1,13  NguyenVan Long^1,14  VoDinh Chuong^1,14  PhanQuang Minh^1,14  Mathew Muturi^1,15  Athman Mwatondo^1,15 

[1] Center for Global Health Research, Kenya Medical Research Institute, Nairobi 00100, Kenya;Disease Investigation Unit, Directorate of Animal Health and Veterinary Services, Patto, Panjim, Goa 403001, India;Division of Global Health Protection, Centers for Disease Control, Guatemala City 01001, Guatemala;Division of Global Health Protection, Centers for Disease Control, Nairobi 00100, Kenya;Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK;Ministry of Agriculture Livestock and Food, Guatemala City 01013, Guatemala;Mission Rabies, Tonca, Panjim, Goa 403001, India;National Center for Veterinary Diseases, Hanoi 100000, Vietnam;National Health Laboratory, MSPAS, Villa Nueva 01064, Guatemala;Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA;Sub-Department of Animal Health, Phú Thọ Province 35000, Vietnam;The Roslin Institute and The Royal (Dick) School of Veterinary Studies, Division of Genetics and Genomics, The University of Edinburgh, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, UK;University del Valle de Guatemala, Guatemala City 01015, Guatemala;Vietnam Department of Animal Health, Hanoi 100000, Vietnam;Zoonotic Disease Unit, Ministry of Health, Ministry of Agriculture, Livestock and Fisheries, Nairobi 00100, Kenya;

关键词: rabies;    lyssavirus;    canine rabies elimination;    portable sequencing;    nanopore;    MinION;   

DOI  :  10.3390/v12111255

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown