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Series GSE81393 Query DataSets for GSE81393
Status Public on Sep 06, 2016
Title DNA Microarray Platform for Detection and Surveillance of Viruses Transmitted by Small Mammals and Arthropods
Platform organism Viruses
Sample organisms Aedes aegypti; Aedes albopictus; Homo sapiens; Togaviridae; Flaviviridae; Flavivirus; dengue virus type 1; dengue virus type 2; dengue virus type 3; dengue virus type 4; St. Louis encephalitis virus; West Nile virus; Yellow fever virus; Rhabdoviridae; Piry virus; Dengue virus; Chikungunya virus; Rio Mamore hantavirus; Mayaro virus; Ilheus virus; Chlorocebus sabaeus; Mucambo virus; Bussuquara virus; Cacipacore virus; Iguape virus; Rocio virus; Zika virus; Guaroa virus; Oropouche virus
Experiment type Expression profiling by array
Summary 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.
 
Overall design Refer to individual Series
 
Citation(s) 27654806
Submission date May 12, 2016
Last update date Dec 06, 2016
Contact name Victor Hugo Aquino
E-mail(s) vhugo@fcfrp.usp.br
Phone 55-16-33154510
Organization name University of Sao Paulo
Department Fculty of Pharmaceutical Sciences
Lab Laboratory of Virology
Street address Avenida do Cafe, s/n
City Ribeirao Preto
State/province Sao Paulo
ZIP/Postal code 14040-903
Country Brazil
 
Platforms (2)
GPL21870 Agilent-048715 RoboArboChip V1
GPL21871 Agilent-062039 RoboArbovirusChip V2
Samples (87)
GSM2151705 Bussuquara virus
GSM2151706 Cacipacore virus
GSM2151707 Chikungunya virus
This SuperSeries is composed of the following SubSeries:
GSE81391 DNA Microarray Platform for Detection and Surveillance of Viruses Transmitted by Small Mammals and Arthropods
GSE81392 DNA Microarray Platform for Detection and Surveillance of Viruses Transmitted by Small Mammals and Arthropods
Relations
BioProject PRJNA321493

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE81393_RAW.tar 43.6 Mb (http)(custom) TAR (of GPR)

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