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.
- Authors:
-
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- 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
- 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
- Publication Date:
- Research Org.:
- Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1817096
- Grant/Contract Number:
- SC0014664
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Viruses
- Additional Journal Information:
- Journal Volume: 12; Journal Issue: 11; Journal ID: ISSN 1999-4915
- Publisher:
- MDPI
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; rabies; lyssavirus; canine rabies elimination; portable sequencing; nanopore; MinION
Citation Formats
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., and Li, Yu. Portable Rabies Virus Sequencing in Canine Rabies Endemic Countries Using the Oxford Nanopore MinION. United States: N. p., 2020.
Web. doi:10.3390/v12111255.
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. Portable Rabies Virus Sequencing in Canine Rabies Endemic Countries Using the Oxford Nanopore MinION. United States. https://doi.org/10.3390/v12111255
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., and Li, Yu. Sun .
"Portable Rabies Virus Sequencing in Canine Rabies Endemic Countries Using the Oxford Nanopore MinION". United States. https://doi.org/10.3390/v12111255. https://www.osti.gov/servlets/purl/1817096.
@article{osti_1817096,
title = {Portable Rabies Virus Sequencing in Canine Rabies Endemic Countries Using the Oxford Nanopore MinION},
author = {Gigante, Crystal M. and Yale, Gowri and Condori, Rene Edgar and Costa, Niceta Cunha and Long, Nguyen Van and Minh, Phan Quang and Chuong, Vo Dinh and Tho, Nguyen Dang and Thanh, Nguyen Tat and Thin, Nguyen Xuan and Hanh, Nguyen Thi Hong and Wambura, Gati and Ade, Frederick and Mito, Oscar and Chuchu, Veronicah and Muturi, Mathew and Mwatondo, Athman and Hampson, Katie and Thumbi, Samuel M. and Thomae, Byron G. and de Paz, Victor Hugo and Meneses, Sergio and Munyua, Peninah and Moran, David and Cadena, Loren and Gibson, Andrew and Wallace, Ryan M. and Pieracci, Emily G. and Li, Yu},
abstractNote = {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.},
doi = {10.3390/v12111255},
journal = {Viruses},
number = 11,
volume = 12,
place = {United States},
year = {Sun Nov 01 00:00:00 EDT 2020},
month = {Sun Nov 01 00:00:00 EDT 2020}
}
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Zika virus in the Americas: Early epidemiological and genetic findings
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Haematophagous Bats in Brazil, Their Role in Rabies Transmission, Impact on Public Health, Livestock Industry and Alternatives to an Indiscriminate Reduction of Bat Population
journal, December 2003
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Difficulties in estimating the human burden of canine rabies
journal, January 2017
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Barriers to dog rabies vaccination during an urban rabies outbreak: Qualitative findings from Arequipa, Peru
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Control and prevention of canine rabies: The need for building laboratory-based surveillance capacity
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Application of high-throughput sequencing to whole rabies viral genome characterisation and its use for phylogenetic re-evaluation of a raccoon strain incursion into the province of Ontario
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Rabies virus glycoprotein. II. Biological and serological characterization
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