Comparison of PCR primer pairs in the detection of human rhinoviruses in nasopharyngeal aspirates

The development of a rapid and highly sensitive PCR assay for the detection of human rhinoviruses (HRVs) in nasopharyngeal aspirates is described. Two simple and fast commercial RNA extraction methods and four primer pairs were compared. The most sensitive RNA extraction method (Ultraspec®) and primer pair (A) were applied to detection of HRV RNA in 49 nasopharyngeal aspirates, of which 31 had previously been found culture-positive for HRVs. All culture-positive specimens were found positive by PCR. In addition, four of the 18 culture-negative samples were positive by PCR. Primer pair A, however, is not specific for rhinoviruses; it also amplifies enteroviruses, and thus an additional hybridization step with an HRV-specific probe is needed for group-specific diagnosis. The assay was able to detect an amount of HRV-1B RNA corresponding to 0.01 infected cells. In addition, about 50 ag (about 10 genomes) of purified HRV-1B and CBV-3 RNA still gave a signal with this primer pair.