A six-plex droplet digital RT-PCR assay for seasonal influenza virus typing, subtyping, and lineage determination

Influenza Other Respir Viruses. 2020 Nov;14(6):720-729. doi: 10.1111/irv.12769. Epub 2020 Jun 10.


Background: There are two influenza A subtypes (H1 and H3) and two influenza B lineages (Victoria and Yamagata) that currently co-circulate in humans. In this study, we report the development of a six-plex droplet digital RT-PCR (ddRT-PCR) assay that can detect HA and M segments of influenza A (H1, H3, and M) and influenza B (Yamagata HA, Victoria HA, and M) viruses in a single reaction mixture. It can simultaneously detect six different nucleic acid targets in a ddRT-PCR platform.

Methods: The six-plex ddRT-PCR used in this study is an amplitude-based multiplex assay. The analytical performance of the assay was evaluated. Correlation with standard qRT-PCR methodology was assessed using 55 clinical samples.

Results: The assay has a wide dynamic range, and it has good reproducibility within and between runs. The limit of quantification of each target in this assay ranged from 15 copies/reaction for influenza B Victoria M gene to 45 copies/reaction for influenza B Yamagata M gene. In addition, this assay can accurately quantify each of these targets in samples containing viral RNAs from two different viruses that were mixed in a highly skewed ratio. Typing, subtyping, and lineage differentiation data of 55 tested clinical respiratory specimens were found to be identical to those deduced from standard monoplex qRT-PCR assays.

Conclusions: The six-plex ddRT-PCR test was demonstrated to be highly suitable for detecting dual influenza infection cases. This assay is expected to be a useful diagnostic tool for clinical and research use.

Keywords: RT-PCR; digital RT-PCR; influenza.

Publication types

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

MeSH terms

  • Humans
  • Influenza A virus / classification*
  • Influenza A virus / genetics
  • Influenza A virus / isolation & purification
  • Influenza B virus / classification*
  • Influenza B virus / genetics
  • Influenza B virus / isolation & purification
  • Influenza, Human / diagnosis
  • Influenza, Human / virology
  • Limit of Detection
  • Molecular Diagnostic Techniques*
  • Polymerase Chain Reaction*
  • RNA, Viral / genetics
  • Reproducibility of Results
  • Seasons
  • Viral Proteins / genetics


  • RNA, Viral
  • Viral Proteins