Rhinovirus detection by real-time RT-PCR in children with acute respiratory infection in Buenos Aires, Argentina.

Marcone, Débora N; Videla, Cristina; Ricarte, Carmen; Carballal, Guadalupe; Vidaurreta, Santiago; Echavarría, Marcela

Human rhinoviruses (HRV), the major cause of common colds, have a significant genetic diversity and are classified into 3 species (A, B, C) with more than 100 serotypes. HRV species C, described in 2006, can only be detected using molecular methods. The objectives of this paper were to adapt a real-time reverse transcription-polymerase chain reaction (RT-PCR) assay for HRV detection and to further determine the frequency of HRV in respiratory samples from children under 2 years of age, with acute respiratory infection (ARI), from Buenos Aires, Argentina. Two real-time RT-PCR assays amplifying the 207 base pair of the 5' non-coding region were compared. The original protocol includes locked nucleic acid analogues and a pyrimidine derivative in the forward primer, while the adapted protocol avoided those molecules. Of 67 respiratory samples, 17 (25.4 %) were positive with the original protocol, and 20 (29.9 %) with the adapted one. Discrepant results were confirmed by sequencing analysis. An expanded gold standard was defined to determine the performance of both assays, and was used to describe the clinical characteristics of positive patients. Better sensitivity and specificity were obtained with the adapted protocol. Considering the expanded gold standard, HRV were detected in 23/67 (34.3 %) patients with ARI: 8/18 (44.4 %) outpatients and 15/49 (30.6 %) hospitalized. Wheezing episodes were more frequent in HRV positive patients (43.5 %) than in HRV negative patients (18.2 %) (p = 0.041). This study describes the utility and clinical sensitivity of an adapted real-time RT-PCR assay for HRV detection.