Sensitive detection and differentiation of rhinoviruses and enteroviruses by a nested real-time RT-PCR assay

We describe a real-time nested reverse transcription-PCR assay that enables us to differentially detect rhinoviruses and enteroviruses. Differential diagnosis of rhinovirus and enterovirus infections has not been succeeded because of their genetic diversities and similarities. We resolved this problem by using specific PCR primers that were designed by in silico analysis of all rhinovirus and enterovirus sequences obtained from GenBank. The developed method was validated by applying to more than 100 nasopharyngeal swab specimens from pediatric patients in Keio University Hospital in Japan and analyzing with the BLAST algorithm. The assay may be suitable for routine diagnosis and surveillance of rhinovirus and enterovirus infections.