A method to validate viral copy-number assay involving a hybrid amplicon and duplex droplet digital PCR

Viral copy-number (VCN) assay is a powerful, effective method to quantify toxicity, cellular kinetics, and durability of virus-modified cell therapy products. The qualification and validation of assay requires reference control. Traditionally, plasmids and cell lines are used as reference controls, but development and qualification of those controls require considerable time and resources. We propose a reference synthetic DNA fragment containing amplicons of woodchuck hepatitis virus posttranscriptional regulatory element (WPRE) and ribonuclease P protein subunit p30 (RPP30), connected by HindIII restriction enzyme cutting site, as a useful tool to qualify and validate duplex droplet digital PCR (ddPCR) assays for VCN. Using this hybrid amplicon, we qualified the duplex WPRE/RPP30 ddPCR assay by determining range of quantification, precision, bias, and robustness of the assay. The varying amount of input DNA showed upper limit, lower limit, and linearity of the assay. Coefficient of variation (CV) and % recovery showed assay precision and accuracy, respectively. Furthermore, the hybrid amplicon was used to determine assay robustness with potential conditions of variability. The hybrid amplicon was a comparable alternative to cell reference standards for validating VCN assay. In conclusion, WPRE-RPP30 hybrid amplicon can be used as a routine quality control measure to validate digital PCR assays.