Abstract
The GeXP-based assay has recently been developed for simultaneous detection of multiple pathogens. So far, the application of the GeXP assay to test larger clinical samples has hardly been reported. Community-acquired pneumonia (CAP) is the leading cause of death in children worldwide and a substantial proportion of childhood CAP is caused by viruses. Rapid and accurate diagnosis of virus infection is important for the clinical management of CAP. In this study, we explored the GeXP assay for simultaneous detection of 20 types/subtypes of viruses in hospitalized children with CAP. A total of 1699 nasopharyngeal swabs were prospectively collected and viral nucleic acid was extracted and assayed. Using viral genomic DNA or RNA as template, we showed that at the concentration of 104 copies of DNA or RNA of each virus/μl, all 20 target viruses were simultaneously identified by the GeXP assay. Fifteen control microorganisms, in contrast, failed to be amplified by the assay. About 65% of cases tested in this study had viral infection, with patients aged <3 years having a 70% positive rate, significantly higher than that in patients aged > 3 years (40%). The most frequently detected virus was RSV followed by PIV3, HRV, ADV and HBoV. Seasonal distribution analysis revealed that RSV was the most predominant in autumn and winter, while in spring and summer PIV3 and RSV were the most frequently identified with similar positive percentages. One hundred twenty randomly-chosen samples tested by the GeXP assay were re-evaluated by mono-RT-PCR, the results showed 97.5% diagnosis agreement between these 2 methods. Our findings suggest that the GeXP assay could be a valuable diagnostic tool for virus infection in pediatric patients with CAP.
Highlights
Community acquired pneumonia (CAP) in children can be potentially serious and often results in hospitalization [1,2,3]
Viruses discovered in the samples included respiratory syncytial virus (RSV), PIV3, human rhinovirus (HRV), ADV, human bocavirus (HBoV), PIV1, HMPV, FluA, HCoV, FluB, N1 and N2, among which RSV was the most detected followed by PIV3, HRV, ADV, and HBoV (Table 3)
Seasonal distribution analysis revealed that RSV was the most predominant in autumn and winter, while in spring and summer PIV3 and RSV were the most frequently identified with similar positive percentages (Table 5)
Summary
Community acquired pneumonia (CAP) in children can be potentially serious and often results in hospitalization [1,2,3]. It is the leading cause of respiratory morbidity and mortality in PLOS ONE | DOI:10.1371/journal.pone.0162411. Etiologic agents of CAP include bacteria and virus [6,7,8,9,10,11,12]. Viruses commonly detected in children with CAP include respiratory syncytial virus (RSV), influenza A and B (Flu A and B), parainfluenza viruses (PIV), adenovirus (ADV), human rhinovirus (HRV), and human metapneumovirus (HPMV) etc. Viruses commonly detected in children with CAP include respiratory syncytial virus (RSV), influenza A and B (Flu A and B), parainfluenza viruses (PIV), adenovirus (ADV), human rhinovirus (HRV), and human metapneumovirus (HPMV) etc. [7, 9,10,11,12]
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