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

J Clin Virol. 2017 Nov:96:12-16. doi: 10.1016/j.jcv.2017.08.014. Epub 2017 Sep 1.

Abstract

Background: Influenza C virus (ICV) is associated with acute respiratory illness. Yet ICV remains under recognized, with most previous studies using only culture to identify cases.

Objectives: To 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 design: Multiple 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.

Results: The 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.

Conclusions: We report a new real-time RT-PCR assay for ICV with high sensitivity and specificity.

Keywords: Diagnostics; Influenza C; Real-time RT-PCR.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Child, Preschool
  • Female
  • Gammainfluenzavirus / genetics
  • Gammainfluenzavirus / isolation & purification*
  • Humans
  • Infant
  • Influenza, Human / diagnosis*
  • Influenza, Human / virology*
  • Male
  • Molecular Diagnostic Techniques / methods*
  • Peru
  • Real-Time Polymerase Chain Reaction / methods*
  • Reverse Transcriptase Polymerase Chain Reaction / methods*
  • Sensitivity and Specificity