In this study, based on an existing reverse transcriptase real-time PCR (RT-qPCR) assay, we developed a reverse transcriptase droplet digital PCR assay (RT-ddPCR) to detect and quantify the frequency of the E119V-NA mutation. Once a mutation such as E119V-NA is known, highly sensitive PCR-based genotypic assays can be used to identify the prevalence of such mutant influenza viruses in clinical samples. The neuraminidase inhibition assay allows the phenotypical identification of resistant strains however, this test often has limited sensitivity with high variability depending on the virus strain, drugs and assays. Early detection of resistant influenza viruses is important for patient management and for the rapid containment of antiviral resistance.

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