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

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

doi:10.3390/v12111255

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

Journal Article · Sun Nov 01 00:00:00 EDT 2020 · Viruses

DOI:https://doi.org/10.3390/v12111255· OSTI ID:1817096

^[1]; ^[2]; ^[3]; Costa, Niceta Cunha ^[4]; Long, Nguyen Van ^[5]; Minh, Phan Quang ^[5]; Chuong, Vo Dinh ^[5]; Tho, Nguyen Dang ^[6]; Thanh, Nguyen Tat ^[7]; Thin, Nguyen Xuan ^[7]; Hanh, Nguyen Thi Hong ^[7]; Wambura, Gati ^[8]; Ade, Frederick ^[8]; Mito, Oscar ^[8]; Chuchu, Veronicah ^[8]; ^[9]; Mwatondo, Athman ^[9]; ^[10]; ^[11]; Thomae, Byron G. ^[12] more »

Centers for Disease Control and Prevention (CDC), Atlanta, GA (United States). National Center for Emerging and Zoonotic Infectious Diseases. Division of High-Consequence Pathogens and Pathology. Poxvirus and Rabies Branch; OSTI
Mission Rabies, Tonca, Panjim, Goa (India)
Centers for Disease Control and Prevention (CDC), Atlanta, GA (United States). National Center for Emerging and Zoonotic Infectious Diseases. Division of High-Consequence Pathogens and Pathology. Poxvirus and Rabies Branch
Directorate of Animal Health and Veterinary Services, Patto, Panjim, Goa (India). Disease Investigation Unit
Vietnam Dept. of Animal Health, Hanoi (Vietnam)
National Center for Veterinary Diseases, Hanoi (Vietnam)
Sub-Dept. of Animal Health, Phú Thọ Province (Vietnam)
Kenya Medical Research Inst., Nairobi (Kenya)
Ministry of Health, Nairobi (Kenya). Ministry of Agriculture, Livestock and Fisheries. Zoonotic Disease Unit
Univ. of Glasgow, Scotland (United Kingdom). Inst. of Biodiversity, Animal Health and Comparative Medicine
Kenya Medical Research Inst., Nairobi (Kenya); Univ. of Nairobi (Kenya). Inst. of Tropical and Infectious Diseases; Washington State Univ., Pullman, WA (United States). Paul G. Allen School for Global Animal Health
Ministry of Agriculture Livestock and Food, Guatemala City (Guatemala)
National Health Lab., MSPAS, Villa Nueva (Guatemala)
Centers for Disease Control, Nairobi (Kenya). Division of Global Health Protection
University del Valle de Guatemala, Guatemala City (Guatemala)
Centers for Disease Control, Guatemala City (Guatemala). Division of Global Health Protection
Univ. of Edinburgh, Scotland (United Kingdom). Easter Bush Veterinary Centre

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 Accepted Manuscript (DOE)

Research Organization:: Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: SC0014664

OSTI ID:: 1817096

Journal Information:: Viruses, Journal Name: Viruses Journal Issue: 11 Vol. 12; ISSN 1999-4915

Publisher:: MDPICopyright Statement

Country of Publication:: United States

Language:: English

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Vaccinate-assess-move method of mass canine rabies vaccination utilising mobile technology data collection in Ranchi, India Gibson, Andrew; Ohal, Praveen; Shervell, Kate Figshare https://doi.org/10.6084/m9.figshare.c.3600026	collection	January 2015
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Performance of neural network basecalling tools for Oxford Nanopore sequencing Wick, Ryan; Judd, Louise; Holt, Kathryn Figshare https://doi.org/10.6084/m9.figshare.c.4553849.v1	collection	January 2019
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59 BASIC BIOLOGICAL SCIENCES
MinION
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lyssavirus
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Portable Rabies Virus Sequencing in Canine Rabies Endemic Countries Using the Oxford Nanopore MinION

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