Multi-Gene Detection and Identification of Mosquito-Borne RNA Viruses Using an Oligonucleotide Microarray
Abstract
Background: Arthropod-borne viruses are important emerging pathogens world-wide. Viruses transmitted by mosquitoes, such as dengue, yellow fever, and Japanese encephalitis viruses, infect hundreds of millions of people and animals each year. Global surveillance of these viruses in mosquito vectors using molecular based assays is critical for prevention and control of the associated diseases. Here, we report an oligonucleotide DNA microarray design, termed ArboChip5.1, for multi-gene detection and identification of mosquito-borne RNA viruses from the genera Flavivirus (family Flaviviridae), Alphavirus (Togaviridae), Orthobunyavirus (Bunyaviridae), and Phlebovirus (Bunyaviridae). Methodology/Principal Findings: The assay utilizes targeted PCR amplification of three genes from each virus genus for electrochemical detection on a portable, field-tested microarray platform. Fifty-two viruses propagated in cell-culture were used to evaluate the specificity of the PCR primer sets and the ArboChip5.1 microarray capture probes. The microarray detected all of the tested viruses and differentiated between many closely related viruses such as members of the dengue, Japanese encephalitis, and Semliki Forest virus clades. Laboratory infected mosquitoes were used to simulate field samples and to determine the limits of detection. Additionally, we identified dengue virus type 3, Japanese encephalitis virus, Tembusu virus, Culex flavivirus, and a Quang Binh-like virus from mosquitoes collected in Thailand inmore »
- Authors:
-
- US Army Medical Research Inst. of Infectious Diseases, Fort Detrick, MD (United States); Colorado State Univ., Fort Collins, CO (United States)
- US Army Medical Research Inst. of Infectious Diseases, Fort Detrick, MD (United States)
- US Army Medical Research Inst. of Infectious Diseases, Fort Detrick, MD (United States); Walter Reed Army Inst. of Research, Silver Spring, MD (United States)
- US Naval Medical Research Unit No. 2, Jakarta (Indonesia)
- Publication Date:
- Research Org.:
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1904914
- Grant/Contract Number:
- SC0014664
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS Neglected Tropical Diseases (Online)
- Additional Journal Information:
- Journal Name: PLoS Neglected Tropical Diseases (Online); Journal Volume: 7; Journal Issue: 8; Journal ID: ISSN 1935-2735
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Infectious diseases; Parasitology; Tropical medicine; Microarrays; Polymerase chain reactions; Mosquitoes; Rift Valley fever virus; RNA viruses; Gene pool; Dengue virus; Chikungunya virus
Citation Formats
Grubaugh, Nathan D., McMenamy, Scott S., Turell, Michael J., Lee, John S., and Williams, Maya. Multi-Gene Detection and Identification of Mosquito-Borne RNA Viruses Using an Oligonucleotide Microarray. United States: N. p., 2013.
Web. doi:10.1371/journal.pntd.0002349.
Grubaugh, Nathan D., McMenamy, Scott S., Turell, Michael J., Lee, John S., & Williams, Maya. Multi-Gene Detection and Identification of Mosquito-Borne RNA Viruses Using an Oligonucleotide Microarray. United States. https://doi.org/10.1371/journal.pntd.0002349
Grubaugh, Nathan D., McMenamy, Scott S., Turell, Michael J., Lee, John S., and Williams, Maya. Thu .
"Multi-Gene Detection and Identification of Mosquito-Borne RNA Viruses Using an Oligonucleotide Microarray". United States. https://doi.org/10.1371/journal.pntd.0002349. https://www.osti.gov/servlets/purl/1904914.
@article{osti_1904914,
title = {Multi-Gene Detection and Identification of Mosquito-Borne RNA Viruses Using an Oligonucleotide Microarray},
author = {Grubaugh, Nathan D. and McMenamy, Scott S. and Turell, Michael J. and Lee, John S. and Williams, Maya},
abstractNote = {Background: Arthropod-borne viruses are important emerging pathogens world-wide. Viruses transmitted by mosquitoes, such as dengue, yellow fever, and Japanese encephalitis viruses, infect hundreds of millions of people and animals each year. Global surveillance of these viruses in mosquito vectors using molecular based assays is critical for prevention and control of the associated diseases. Here, we report an oligonucleotide DNA microarray design, termed ArboChip5.1, for multi-gene detection and identification of mosquito-borne RNA viruses from the genera Flavivirus (family Flaviviridae), Alphavirus (Togaviridae), Orthobunyavirus (Bunyaviridae), and Phlebovirus (Bunyaviridae). Methodology/Principal Findings: The assay utilizes targeted PCR amplification of three genes from each virus genus for electrochemical detection on a portable, field-tested microarray platform. Fifty-two viruses propagated in cell-culture were used to evaluate the specificity of the PCR primer sets and the ArboChip5.1 microarray capture probes. The microarray detected all of the tested viruses and differentiated between many closely related viruses such as members of the dengue, Japanese encephalitis, and Semliki Forest virus clades. Laboratory infected mosquitoes were used to simulate field samples and to determine the limits of detection. Additionally, we identified dengue virus type 3, Japanese encephalitis virus, Tembusu virus, Culex flavivirus, and a Quang Binh-like virus from mosquitoes collected in Thailand in 2011 and 2012. Conclusions/Significance: We demonstrated that the described assay can be utilized in a comprehensive field surveillance program by the broad-range amplification and specific identification of arboviruses from infected mosquitoes. Furthermore, the microarray platform can be deployed in the field and viral RNA extraction to data analysis can occur in as little as 12 h. The information derived from the ArboChip5.1 microarray can help to establish public health priorities, detect disease outbreaks, and evaluate control programs.},
doi = {10.1371/journal.pntd.0002349},
journal = {PLoS Neglected Tropical Diseases (Online)},
number = 8,
volume = 7,
place = {United States},
year = {Thu Aug 15 00:00:00 EDT 2013},
month = {Thu Aug 15 00:00:00 EDT 2013}
}
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