Abstract
To investigate the performance of laboratory methods and clinical case definitions in detecting the viral pathogens for acute respiratory infections (ARIs) from a prospective community cohort and hospital inpatients, nasopharyngeal swabs from cohort members reporting ARIs (community-ARI) and inpatients admitted with ARIs (inpatient-ARI) were tested by Singleplex Real Time-Polymerase Chain Reaction (SRT-PCR), multiplex RT-PCR (MRT-PCR) and pathogen-chip system (PathChip) between April 2012 and December 2013. Community-ARI and inpatient-ARI was also combined with mild and severe cases of influenza from a historical prospective study as mild-ARI and severe-ARI respectively to evaluate the performance of clinical case definitions. We analysed 130 community-ARI and 140 inpatient-ARI episodes (5 inpatient-ARI excluded because multiple pathogens were detected), involving 138 and 207 samples respectively. Detection by PCR declined with days post-onset for influenza virus; decrease was faster for community-ARI than for inpatient-ARI. No such patterns were observed for non-influenza respiratory virus infections. PathChip added substantially to viruses detected for community-ARI only. Clinical case definitions discriminated influenza from other mild-ARI but performed poorly for severe-ARI and for older participants. Rational strategies for diagnosis and surveillance of influenza and other respiratory virus must acknowledge the differences between ARIs presenting in community and hospital settings.
Highlights
Methods based on virus culture and isolation[13]
We investigated the performance of the singleplex RT-PCR (SRT-PCR) and multiplex RT-PCR (MRT-PCR), as well as explored the use of the Genome Institute of Singapore (GIS) PathChip for the detection of viral respiratory pathogens for mild and severe acute respiratory illness (ARI)
Of 507 participants from the community enrolled into a cohort, 99 reported having ARI episodes
Summary
Multiplex RT-PCR (MRT-PCR) assays, which allow for rapid detection of multiple types of known viral agents, are widely available[14]. Studies have evaluated the performance of PCR-based assays for diagnosing respiratory viruses[15,16,17], but were mostly restricted to either outpatients or inpatients, or to at-risk groups such as the elderly and young children. Large-scale pathogen detection technologies, like the Genome Institute of Singapore (GIS) PathChip, have recently been developed[18], and there is a need to rationalize how these could be integrated with routinely available assays. We investigated the performance of the singleplex RT-PCR (SRT-PCR) and MRT-PCR, as well as explored the use of the GIS PathChip for the detection of viral respiratory pathogens for mild and severe acute respiratory illness (ARI).
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