Viral metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA283035 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2010685_1.fastq.gz | Fastqsanger.gz | |||
| SRR2010685_2.fastq.gz | Fastqsanger.gz | |||
| SRR2010686_1.fastq.gz | Fastqsanger.gz | |||
| SRR2010686_2.fastq.gz | Fastqsanger.gz | |||
| SRR2040553_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
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Project description:This series includes 278 microarrays used to detect respiratory viruses in a set of nasopharyngeal lavage specimens from children with respiratory tract infections Objective: To assess the utility of a pan-viral DNA microarray platform (Virochip) in the detection of viruses associated with pediatric respiratory tract infections. Study Design: The Virochip was compared to conventional clinical direct fluorescent antibody (DFA) and PCR-based testing for the detection of respiratory viruses in 278 consecutive nasopharyngeal aspirate samples from 222 children. Results: The Virochip was superior in performance to DFA, showing a 19% increase in the detection of 7 respiratory viruses included in standard DFA panels, and was similar to virus-specific PCR (sensitivity 85-90%, specificity 99%, PPV 94-96%, NPV 97-98%) in the detection of respiratory syncytial virus, influenza A, and rhino-/enteroviruses. The Virochip also detected viruses not routinely tested for or missed by DFA and PCR, as well as double infections and infections in critically ill patients that DFA failed to detect. Conclusions: Given its favorable sensitivity and specificity profile and greatly expanded spectrum of detection, microarray-based viral testing holds promise for clinical diagnosis of pediatric respiratory tract infections. Keywords: viral detection The series includes 278 clinical specimens
2010-05-26 | E-GEOD-10294 | biostudies-arrayexpress
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Project description:This was a prospective observational cohort study involving a convenience sample of previously healthy children <2 years of age with acute RSV infection as well as healthy non-infected age matched controls. The study was conducted at Nationwide Children’s Hospital (NCH; Columbus, OH) during four respiratory seasons, from 2011 to 2015. Children were enrolled at the NCH urgent care clinics, the emergency department or in the inpatient ward or intensive care unit (PICU). For the inpatients enrolled at ward or PICU the median time from admission to sample collection was 21.3h (interquartile range [IQR] 16.7 -37.6h). The majority of children had a confirmatory RSV test (either rapid antigen testing or PCR based) at enrollment per standard of care. In addition, the presence of RSV was confirmed by quantitative real time (qRT)-PCR in all study subjects. Healthy age-matched controls were enrolled during well-child visits or minor elective surgical procedures not involving the respiratory tract as described [Mejias 2013]. Exclusion criteria were as follows: documented bacterial co-infections, premature birth (<36 weeks of gestation), chronic or congenital medical conditions, and immunodeficiency. For healthy controls, additional exclusion criteria included: presence of fever or symptoms of respiratory tract infection within two weeks of enrollment.
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Project description:This series includes 278 microarrays used to detect respiratory viruses in a set of nasopharyngeal lavage specimens from children with respiratory tract infections Objective: To assess the utility of a pan-viral DNA microarray platform (Virochip) in the detection of viruses associated with pediatric respiratory tract infections. Study Design: The Virochip was compared to conventional clinical direct fluorescent antibody (DFA) and PCR-based testing for the detection of respiratory viruses in 278 consecutive nasopharyngeal aspirate samples from 222 children. Results: The Virochip was superior in performance to DFA, showing a 19% increase in the detection of 7 respiratory viruses included in standard DFA panels, and was similar to virus-specific PCR (sensitivity 85-90%, specificity 99%, PPV 94-96%, NPV 97-98%) in the detection of respiratory syncytial virus, influenza A, and rhino-/enteroviruses. The Virochip also detected viruses not routinely tested for or missed by DFA and PCR, as well as double infections and infections in critically ill patients that DFA failed to detect. Conclusions: Given its favorable sensitivity and specificity profile and greatly expanded spectrum of detection, microarray-based viral testing holds promise for clinical diagnosis of pediatric respiratory tract infections. Keywords: viral detection
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