Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus — Worldwide, 2021

Chen, Ziwei; Shen, Xinxin; Wang, Ji; Zhao, Xiang; Gao, Yuan; Zhang, Ruiqin; Wang, Jinrong; Liu, Leping; Nie, Xinmin; Ma, Xuejun

Background: COVID-19 infection is a major public health problem worldwide, and the D614G mutation enhances the infectivity of COVID-19. Methods: A probe-directed recombinase amplification (PDRA) assay was discussed to detect the D614G mutation at 39 ℃ for 30 min. The sensitivity, specificity, and reproducibility of the PDRA were evaluated by D614 and G614 recombinant plasmids. The clinical performance of PDRA assay was validated by testing of 53 previously confirmed COVID-19 positive RNAs and 10 negative samples. Direct sequencing was carried out in parallel for comparison. Result: With good reproducibility and specificity, the PDRA assay worked well with the concentration in the range of 10(3)–10(7) copies/reaction. Compared with direct sequencing as a reference, the recombinase-aided amplification (RAA) assay obtained 100% sensitivity and 100% specificity using clinical samples. Conclusions: A rapid, convenient, sensitive, and specific method to detect D614G mutation was developed, which offers a useful tool to monitor mutations in COVID-19 virus RNA.