These diverse mechanisms act within seconds or minutes and are most effective with small inocula of bacteria. Abnormally high glucose concentration in the ASL could both directly promote bacterial growth and impair antimicrobials. When bacteria are not eliminated, growth can be exponential and virulence factors of pathogenic and nonpathogenic bacteria can play a role. Thus, in the airways, the timedependent balance between bacterial killing and growth determine the outcome. Our data suggest that carbon source deprivation in airway surface liquid helps tip the balance towards airway sterility. Respiratory tract infection is the most common cause of hospitalization of children below the age of 5 years. In 5-40% of these hospitalizations no infectious agent can be identified but it is suspected that a viral infection is involved. In these cases a yet unknown virus might be the cause of respiratory illness. In the last decades several viral discovery methods have been developed which can detect viruses without knowledge of the genome sequence. We have previously used virus discovery cDNA-AFLP to PI-103 citations discover the human coronavirus NL63 and we were the first to describe human parechovirus type 5 and 6 in the Netherlands using the same technique. In the VIDISCA assay viral genomes transcribed into double stranded DNA are digested with restriction enzymes. The enzymes digest short recognition sequences that are present in virtually all viruses. After ligation of adaptors. The assay is user-friendly however the sensitivity of the assay is low. At least E6 genome copies/ml of a virus in a background that is low in competitor RNA/DNA are needed. These conditions are generally only met when virus culture supernatant is used. In clinical respiratory samples like nasopharyngeal swabs in universal transport medium various amounts of competitor RNA/DNA from disrupted cells/ bacteria can be present. Ribosomal RNA, which is,80% of the total cellular RNA, is one of the biggest problems due to its high copy number and its stability within ribosomes. In particular RNA viruses are difficult to discover since in these cases a reverse transcription is needed, which will enable rRNA to act as competiting nucleic acid sequences. One research group has addressed the problem of competing rRNA. Endoh et al showed that reverse transcription with 96 hexamers that can not anneal to rRNA, decreases the amount of background amplification and enhances the sensitivity of a virus discovery assay. We evaluated the benefit of the non-rRNAhexamers in VIDISCA. Furthermore, we evaluated whether the choice of the restriction enzyme can decrease rRNA amplification. Finally, specific blocking of rRNA reverse transcription by rRNA recognizing oligo’s that contain a 39 dideoxy-C6 modification, further inhibits cDNA synthesis of the target. All three steps to decrease the effect of inhibitor rRNA are presented in this paper.