Application of digital PCR to determine the reliability of Xpert Xpress SARS-CoV-2 assay with envelope (E) gene negative and nucleocapsid (N2) gene positive results

•E gene negative & N2 gene positive (E-N+) result by Cepheid could be falsely positive.•Application of digital PCR (dPCR) to determine whether E-N+ result is reliable.•Two dPCR assays were compared in detection of SARS-CoV-2 in low viral load samples.•QX200 ddPCR confirmed 81.8% of the E-N+ samples by Cepheid were true positive. This study used digital polymerase chain reaction (dPCR) to determine whether envelope (E) gene-negative and nucleocapsid (N2) gene-positive (E-N+) results obtained with the Cepheid Xpert Xpress SARS-CoV-2 assay are reliable. Using droplet digital PCR results as a reference, 18 of 22 E-N+ samples with a low viral load (81.8%) were identified as true positives.