title: DNA microarray for detection of gastrointestinal viruses.
abstract: Gastroenteritis is a clinical illness of humans and other animals that is characterized by vomiting and diarrhea and caused by a variety of pathogens, including viruses. An increasing number of viral species have been associated with gastroenteritis or have been found in stool samples as new molecular tools have been developed. In this work, a DNA microarray capable in theory of parallel detection of more than 100 viral species was developed and tested. Initial validation was done with 10 different virus species, and an additional 5 species were validated using clinical samples. Detection limits of 1 × 10(3) virus particles of Human adenovirus C (HAdV), Human astrovirus (HAstV), and group A Rotavirus (RV-A) were established. Furthermore, when exogenous RNA was added, the limit for RV-A detection decreased by one log. In a small group of clinical samples from children with gastroenteritis (n = 76), the microarray detected at least one viral species in 92% of the samples. Single infection was identified in 63 samples (83%), and coinfection with more than one virus was identified in 7 samples (9%). The most abundant virus species were RV-A (58%), followed by Anellovirus (15.8%), HAstV (6.6%), HAdV (5.3%), Norwalk virus (6.6%), Human enterovirus (HEV) (9.2%), Human parechovirus (1.3%), Sapporo virus (1.3%), and Human bocavirus (1.3%). To further test the specificity and sensitivity of the microarray, the results were verified by reverse transcription-PCR (RT-PCR) detection of 5 gastrointestinal viruses. The RT-PCR assay detected a virus in 59 samples (78%). The microarray showed good performance for detection of RV-A, HAstV, and calicivirus, while the sensitivity for HAdV and HEV was low. Furthermore, some discrepancies in detection of mixed infections were observed and were addressed by reverse transcription-quantitative PCR (RT-qPCR) of the viruses involved. It was observed that differences in the amount of genetic material favored the detection of the most abundant virus. The microarray described in this work should help in understanding the etiology of gastroenteritis in humans and animals.
authors.affiliation: Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, Mexico.
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Martínez
authors.affiliation: Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, Mexico.
authors.forename: María de Los Dolores
authors.initials: Mde L
authors.lastname: Soto-Del Río
authors.affiliation: Departamento de Microbiología Molecular, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, Mexico.
authors.forename: Rosa María
authors.initials: RM
authors.lastname: Gutiérrez
authors.affiliation: Department of Laboratory Medicine, University of California-San Francisco, San Francisco, California, USA UCSF-Abbott Viral Diagnostics and Discovery Center, University of California-San Francisco, San Francisco, California, USA.
authors.forename: Charles Y
authors.initials: CY
authors.lastname: Chiu
authors.affiliation: Department of Biochemistry and Biophysics, University of California-San Francisco, San Francisco, California, USA.
authors.forename: Alexander L
authors.initials: AL
authors.lastname: Greninger
authors.affiliation: Departamento de Microbiología e Inmunología, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico.
authors.forename: Juan Francisco
authors.initials: JF
authors.lastname: Contreras
authors.affiliation: Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, Mexico.
authors.forename: Susana
authors.initials: S
authors.lastname: López
authors.affiliation: Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, Mexico.
authors.forename: Carlos F
authors.initials: CF
authors.lastname: Arias
authors.affiliation: Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, Mexico pavel@ibt.unam.mx.
authors.forename: Pavel
authors.initials: P
authors.lastname: Isa
mesh_terms: D002675:Child, Preschool; D005759:Gastroenteritis / Q000175:diagnosis* / Q000453:epidemiology / Q000821:virology*; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D015995:Prevalence; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012680:Sensitivity and Specificity; D014777:Virus Diseases / Q000175:diagnosis* / Q000453:epidemiology / Q000821:virology*; D014780:Viruses / Q000145:classification* / Q000235:genetics*