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Article

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

1
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
2
Mission Rabies, Tonca, Panjim, Goa 403001, India
3
Disease Investigation Unit, Directorate of Animal Health and Veterinary Services, Patto, Panjim, Goa 403001, India
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Vietnam Department of Animal Health, Hanoi 100000, Vietnam
5
National Center for Veterinary Diseases, Hanoi 100000, Vietnam
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Sub-Department of Animal Health, Phú Thọ Province 35000, Vietnam
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Center for Global Health Research, Kenya Medical Research Institute, Nairobi 00100, Kenya
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Department of Public Health, Pharmacology and Toxicology, University of Nairobi, Nairobi 00100, Kenya
9
Zoonotic Disease Unit, Ministry of Health, Ministry of Agriculture, Livestock and Fisheries, Nairobi 00100, Kenya
10
Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
11
University of Nairobi Institute of Tropical and Infectious Diseases, Nairobi 00100, Kenya
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Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA 99164, USA
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Ministry of Agriculture Livestock and Food, Guatemala City 01013, Guatemala
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National Health Laboratory, MSPAS, Villa Nueva 01064, Guatemala
15
Division of Global Health Protection, Centers for Disease Control, Nairobi 00100, Kenya
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University del Valle de Guatemala, Guatemala City 01015, Guatemala
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Division of Global Health Protection, Centers for Disease Control, Guatemala City 01001, Guatemala
18
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
*
Author to whom correspondence should be addressed.
Viruses 2020, 12(11), 1255; https://doi.org/10.3390/v12111255
Received: 15 September 2020 / Revised: 21 October 2020 / Accepted: 26 October 2020 / Published: 4 November 2020
(This article belongs to the Special Issue Lyssaviruses and Other Bat Rhabdoviruses)
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. View Full-Text
Keywords: rabies; lyssavirus; canine rabies elimination; portable sequencing; nanopore; MinION rabies; lyssavirus; canine rabies elimination; portable sequencing; nanopore; MinION
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MDPI and ACS Style

Gigante, C.M.; Yale, G.; Condori, R.E.; Costa, N.C.; Long, N.V.; Minh, P.Q.; Chuong, V.D.; Tho, N.D.; Thanh, N.T.; Thin, N.X.; Hanh, N.T.H.; Wambura, G.; Ade, F.; Mito, O.; Chuchu, V.; Muturi, M.; Mwatondo, A.; Hampson, K.; Thumbi, S.M.; Thomae, B.G.; de Paz, V.H.; Meneses, S.; Munyua, P.; Moran, D.; Cadena, L.; Gibson, A.; Wallace, R.M.; Pieracci, E.G.; Li, Y. Portable Rabies Virus Sequencing in Canine Rabies Endemic Countries Using the Oxford Nanopore MinION. Viruses 2020, 12, 1255. https://doi.org/10.3390/v12111255

AMA Style

Gigante CM, Yale G, Condori RE, Costa NC, Long NV, Minh PQ, Chuong VD, Tho ND, Thanh NT, Thin NX, Hanh NTH, Wambura G, Ade F, Mito O, Chuchu V, Muturi M, Mwatondo A, Hampson K, Thumbi SM, Thomae BG, de Paz VH, Meneses S, Munyua P, Moran D, Cadena L, Gibson A, Wallace RM, Pieracci EG, Li Y. Portable Rabies Virus Sequencing in Canine Rabies Endemic Countries Using the Oxford Nanopore MinION. Viruses. 2020; 12(11):1255. https://doi.org/10.3390/v12111255

Chicago/Turabian Style

Gigante, Crystal M.; Yale, Gowri; Condori, Rene E.; Costa, Niceta C.; Long, Nguyen V.; Minh, Phan Q.; Chuong, Vo D.; Tho, Nguyen D.; Thanh, Nguyen T.; Thin, Nguyen X.; Hanh, Nguyen T.H.; Wambura, Gati; Ade, Frederick; Mito, Oscar; Chuchu, Veronicah; Muturi, Mathew; Mwatondo, Athman; Hampson, Katie; Thumbi, Samuel M.; Thomae, Byron G.; de Paz, Victor H.; Meneses, Sergio; Munyua, Peninah; Moran, David; Cadena, Loren; Gibson, Andrew; Wallace, Ryan M.; Pieracci, Emily G.; Li, Yu. 2020. "Portable Rabies Virus Sequencing in Canine Rabies Endemic Countries Using the Oxford Nanopore MinION" Viruses 12, no. 11: 1255. https://doi.org/10.3390/v12111255

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