A novel real-time RT-PCR assay for influenza C tested in Peruvian children

- We report a novel real-time RT-PCR assay for influenza C Virus (ICV).
- ICV was less common in young Peruvian children with respiratory illness than IAV.
- ICV was less associated with fever and more associated with co-infection than IAV.

BackgroundInfluenza C virus (ICV) is associated with acute respiratory illness. Yet ICV remains under recognized, with most previous studies using only culture to identify cases.ObjectivesTo develop a sensitive and specific real-time RT-PCR assay for ICV that allows for rapid and accurate detection in a clinical or research setting.Study designMultiple ICV sequences obtained from GenBank were analyzed, including 141 hemagglutinin-esterase (HE), 106 matrix (M), and 97 nucleoprotein (NP) sequences. Primers and probes were designed based on conserved regions. Multiple primer-probe sets were tested against multiple ICV strains.ResultsThe ICV M and NP genes offered the most conserved sequence regions. Primers and probes based on newer sequence data offered enhanced detection of ICV, especially for low titer specimens. An NP-targeted assay yielded the best performance and was capable of detecting 10-100 RNA copies per reaction. The NP assay detected multiple clinical isolates of ICV collected in a field epidemiology study conducted in Peru.ConclusionsWe report a new real-time RT-PCR assay for ICV with high sensitivity and specificity.