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Updated: May 2, 2026
High-throughput Detection of Respiratory Pathogens in Animal Specimens by Nanoscale PCR
Published on: November 28, 2016
Clinical utility of PCR for common viruses in acute respiratory illness
Samuel Rhedin1, Ann Lindstrand, Maria Rotzén-Östlund
1Department of Medicine Solna, Unit of Infectious Diseases, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden;
Insights
Quantitative real-time polymerase chain reaction (qPCR) detected respiratory viruses in children with acute respiratory illness (ARI). Some viruses like RSV, metapneumovirus, and parainfluenza are likely causative, while others require cautious interpretation.
Area of Science:
- Pediatric infectious diseases
- Virology
- Molecular diagnostics
Background:
- Acute respiratory illness (ARI) is a common reason for pediatric healthcare visits.
- Quantitative real-time polymerase chain reaction (qPCR) detects viral nucleic acids but interpretation is challenging due to asymptomatic carriage.
- Understanding viral contributions to ARI is crucial for appropriate antibiotic use.
Purpose of the Study:
- To compare qPCR findings in children with ARI against asymptomatic controls.
- To identify viruses significantly associated with ARI in young children.
Main Methods:
- Nasopharyngeal aspirates collected from children ≤5 years with ARI and matched asymptomatic controls.
- Analysis of samples using qPCR for 16 common respiratory viruses.
- Study conducted during a noninfluenza season.
Main Results:
- Respiratory viruses detected in 72.3% of ARI cases vs. 35.4% of controls (P = .001).
- Rhinovirus was most common in both groups; RSV, metapneumovirus, and parainfluenza viruses were overrepresented in ARI cases.
- Bocavirus was associated with ARI and severe disease; enterovirus and coronavirus detection rates were similar between groups.
Conclusions:
- qPCR detection of RSV, metapneumovirus, or parainfluenza viruses in children with ARI suggests causality.
- Interpretation of other detected respiratory viruses requires caution due to high prevalence in asymptomatic children.
- This study aids in distinguishing causative pathogens from incidental findings in pediatric ARI.
Background:
Acute respiratory illness (ARI) accounts for a large proportion of all visits to pediatric health facilities. Quantitative real-time polymerase chain reaction (qPCR) analyses allow sensitive detection of viral nucleic acids, but it is not clear to what extent specific viruses contribute to disease because many viruses have been detected in asymptomatic children. Better understanding of how to interpret viral findings is important to reduce unnecessary use of antibiotics.
Objective:
To compare viral qPCR findings from children with ARI versus asymptomatic control subjects.
Methods:
Nasopharyngeal aspirates were collected from children aged ≤5 years with ARI and from individually matched, asymptomatic, population-based control subjects during a noninfluenza season. Samples were analyzed by using qPCR for 16 viruses.
Results:
Respiratory viruses were detected in 72.3% of the case patients (n = 151) and 35.4% of the control subjects (n = 74) (P = .001). Rhinovirus was the most common finding in both case patients and control subjects (47.9% and 21.5%, respectively), with a population-attributable proportion of 0.39 (95% confidence interval: 0.01 to 0.62). Metapneumovirus, parainfluenza viruses, and respiratory syncytial virus were highly overrepresented in case patients. Bocavirus was associated with ARI even after adjustment for coinfections with other viruses and was associated with severe disease. Enterovirus and coronavirus were equally common in case patients and control subjects.
Conclusions:
qPCR detection of respiratory syncytial virus, metapneumovirus, or parainfluenza viruses in children with ARI is likely to be causative of disease; detection of several other respiratory viruses must be interpreted with caution due to high detection rates in asymptomatic children.
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