Viruses causing lower respiratory symptoms in young children: findings from the ORChID birth cohort

Sarna, Mohinder; Lambert, Stephen B; Sloots, Theo P; Whiley, David M; Alsaleh, Asma; Mhango, Lebogang; Bialasiewicz, Seweryn; Wang, David; Nissen, Michael D; Grimwood, Keith; Ware, Robert S

Viruses were identified from parent-collected anterior nose swabs at the infant's birth, and weekly thereafter. 18 Specimens were mailed to the laboratory, taking a median of 3 (IQR 2-4) days, and where they were processed and stored at −80°C until further analysis. 14 19 Swabs were batch-tested for 17 respiratory viruses: human rhinovirus (HRV), influenza A and B (IFV-A, IFV-B), respiratory syncytial virus A and B (RSV-A, RSV-B), parainfluenza viruses 1-3 (PIV-1, PIV-2, PIV-3), human coronaviruses (HCoV) OC43, NL63, 229E and HKU1, human metapneumovirus (HMPV), adenovirus (AdV), human polyomaviruses WU (WU-PyV) and KI (KI-PyV) and human bocavirus-1 (HBoV-1), using previously validated real-time PCR assays. 14 Details of sample collection, processing, PCR assay parameters, quality control measures and HRV typing into species A, B and C are outlined in the online supplementary text and E-table 1 . Specimen quality was assessed by testing for a marker of human genomic DNA, endogenous retrovirus-3 (ERV-3). 20 Swabs with ERV-3 cycle-threshold (Ct) values >38 (including undetectable Ct values) were deemed to be of lesser quality and excluded from parts of the analysis. 21