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E-GEOD-81391 - DNA Microarray Platform for Detection and Surveillance of Viruses Transmitted by Small Mammals and Arthropods

Status
Released on 5 September 2016, last updated on 12 September 2016
Organism
Aedes aegypti, Aedes albopictus, Bussuquara virus, Cacipacore virus, Chikungunya virus, Chlorocebus sabaeus, Dengue virus, Dengue virus 1, Dengue virus 2, Dengue virus 3, Dengue virus 4, Flaviviridae, Flavivirus, Guaroa virus, Homo sapiens, Iguape virus, Ilheus virus, Mayaro virus, Mucambo virus, Oropouche virus, Piry virus, Rhabdoviridae, Rio Mamore virus, Rocio virus, St. Louis encephalitis virus, Togaviridae, West Nile virus, Yellow fever virus
Samples (80)
Array (1)
Protocols (6)
Description
Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. SMAvirusChip was designed with more than 15,000 oligonucleotide probes (60-mers), including viral and control probes. Two SMAvirusChip versions were designed: SMAvirusChip v1 contains 4209 viral probes for the detection of 409 viruses, while SMAvirusChip v2 contains 4943 probes for the detection of 416 viruses. SMAvirusChip was evaluated with 20 laboratory reference-strain viruses. These viruses could be specifically detected when alone in a sample or when artificially mixed within a single sample. The sensitivity of SMAvirusChip was evaluated using 10-fold serial dilutions of dengue virus (DENV). The results showed a detection limit as low as 2.6E3 RNA copies/mL. Additionally, the sensitivity was one log10 lower (2.6E2 RNA copies/mL) than quantitative real-time RT-PCR and sufficient to detect viral genomes in clinical samples. The detection of DENV in serum samples of DENV-infected patients (n= 6) and in a whole blood sample spiked with DENV confirmed the applicability of SMAvirusChip for the detection of viruses in clinical samples. In addition, in a pool of mosquito samples spiked with DENV, the virus was also detectable. SMAvirusChip was able to specifically detect viruses in cell cultures, serum samples, total blood samples and a pool of mosquitoes, confirming that cellular RNA/DNA did not interfere with the assay. Therefore, SMAvirusChip may represent an innovative surveillance method for the rapid identification of viruses transmitted by small mammals and arthropods. The SMAvirusChip v1 microarray includes more than 15,000 oligonucleotide probes (60-mers long) for the detection of viruses transmitted by small mammals and arthropods. The sequences of 4209 viral probes for the detection of 409 viruses (109 viruses transmitted by small mammals and 300 arboviruses) were included in this platform. Positive and negative control oligonucleotide probes were also included in the design.
Experiment type
transcription profiling by array 
Contacts
Victor Hugo Aquino <vhugo@fcfrp.usp.br>, Amanda C Trabuco, Helda L Alfonso, Luiz T Figueiredo, Marco A Lavrador, Mario L Figueiredo, Mohd J Khan, Soraya J Badra, Victor H Aquino, Weber C Batista
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-81391.idf.txt
Sample and data relationshipE-GEOD-81391.sdrf.txt
Raw data (1)E-GEOD-81391.raw.1.zip
Processed data (1)E-GEOD-81391.processed.1.zip
Array designA-GEOD-21870.adf.txt
Links