The sample collection period overlapped with the start of the COVID-19 pandemic in the UK. To determine the presence of coronavirus all samples were tested for the Beta-CoV E gene and SARS-CoV-2 S gene targets. A clinically validated 45-microbe low density TaqMan Array Card (TAC) (Applied Biosystems, Foster City, CA, USA) was used to detect common respiratory microbes, using exogenous controls (T4 and MS2 bacteriophage gene targets), endogenous human controls (human 18S rRNA and RNase-P gene targets), see supplementary Table S2 for a full list of microbe gene targets [38 (link)].
Samples were run in 3 batches, amplified, and analysed using a Life Technologies Custom TaqMan Low Density Array system on an Applied Biosystems Life Technologies ViiA-7TM real-time PCR system as described elsewhere [39 (link)]. A cycle threshold (Ct) value < 38 for any gene target was reported as a positive result. Incidence of microbe carriage prevalence was calculated as the number of positive results as a percentage of all positive results. The Pearson’s chi-squared test with a Bonferroni-adjusted P value was used to determine significance between observed proportions of microbial carriage.
Samples were run in 3 batches, amplified, and analysed using a Life Technologies Custom TaqMan Low Density Array system on an Applied Biosystems Life Technologies ViiA-7TM real-time PCR system as described elsewhere [39 (link)]. A cycle threshold (Ct) value < 38 for any gene target was reported as a positive result. Incidence of microbe carriage prevalence was calculated as the number of positive results as a percentage of all positive results. The Pearson’s chi-squared test with a Bonferroni-adjusted P value was used to determine significance between observed proportions of microbial carriage.
Free full text: Click here
