Abstract
BackgroundCarefully conducted, community-based, longitudinal studies are required to gain further understanding of the nature and timing of respiratory viruses causing infections in the population. However, such studies pose unique challenges for field specimen collection, including as we have observed the appearance of mould in some nasal swab specimens. We therefore investigated the impact of sample collection quality and the presence of visible mould in samples upon respiratory virus detection by real-time polymerase chain reaction (PCR) assays.MethodsAnterior nasal swab samples were collected from infants participating in an ongoing community-based, longitudinal, dynamic birth cohort study. The samples were first collected from each infant shortly after birth and weekly thereafter. They were then mailed to the laboratory where they were catalogued, stored at -80°C and later screened by PCR for 17 respiratory viruses. The quality of specimen collection was assessed by screening for human deoxyribonucleic acid (DNA) using endogenous retrovirus 3 (ERV3). The impact of ERV3 load upon respiratory virus detection and the impact of visible mould observed in a subset of swabs reaching the laboratory upon both ERV3 loads and respiratory virus detection was determined.ResultsIn total, 4933 nasal swabs were received in the laboratory. ERV3 load in nasal swabs was associated with respiratory virus detection. Reduced respiratory virus detection (odds ratio 0.35; 95% confidence interval 0.27-0.44) was observed in samples where the ERV3 could not be identified. Mould was associated with increased time of samples reaching the laboratory and reduced ERV3 loads and respiratory virus detection.ConclusionSuboptimal sample collection and high levels of visible mould can impact negatively upon sample quality. Quality control measures, including monitoring human DNA loads using ERV3 as a marker for epithelial cell components in samples should be undertaken to optimize the validity of real-time PCR results for respiratory virus investigations in community-based studies.
Highlights
Conducted, community-based, longitudinal studies are required to gain further understanding of the nature and timing of respiratory viruses causing infections in the population
Understanding more fully the Acute respiratory infection (ARI) disease burden in the community is important for developing public health interventions, such as vaccination programs [6], and for understanding the role respiratory viruses may play in the pathogenesis of certain chronic pulmonary disorders, such as asthma [7,8,9]
This shows the importance of measuring human deoxyribonucleic acid (DNA) as a marker for epithelial cells in swab samples, which if tested and monitored in real time during the study, can identify problems associated with collection that can be addressed quickly
Summary
Community-based, longitudinal studies are required to gain further understanding of the nature and timing of respiratory viruses causing infections in the population. Understanding more fully the ARI disease burden in the community is important for developing public health interventions, such as vaccination programs [6], and for understanding the role respiratory viruses may play in the pathogenesis of certain chronic pulmonary disorders, such as asthma [7,8,9] This has led to the instigation of community-based studies. Cost and feasibility of using healthcare workers are important when large longitudinal, community-based cohort studies, involving frequent specimen collections, are planned To help address these limitations, we and others have begun testing parentcollected, anterior nasal swab specimens that have been transported to the research laboratory using the standard mail [13,14,15,16]. This approach is considered to be safe, convenient and cost-effective [17]
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