Abstract: Objective To investigate the consistency of the two assays for the testing of SARS-CoV-2 nucleic acid. Methods 2019-nCoV nucleic acid were parallelly tested in sputum, anal swabs and nasal swabs from COVID-19 confirmed cases by A assays and B assay in the third people's hospital of Shenzhen. 539 results were retrospectively analyzed using consistency test. Four samples with Ct value >36 parallelly tested by two assay were selected for sequencing. Results The Kappa values of nucleic acid results from the two assay were 0.49 in sputum, 0.55 in nasal swabs, and 0.71 in anal swabs, respectively.The consistency rates for the nucleic acid in sputum, nasal swabs, and anal swabs were 100% when the Ct values were <34 parallelly tested by two assay. While, the corresponding consistency rates were 0% in sputum, 45% in nasal swabs, and 57.1% in anal swabs, respectively, when the Ct values were ≥ 34 parallelly tested by two assay. Nucleic acid was tested positively by sequence in the four samples with Ct values >36 parallelly tested by two assay. Conclusions The consistency of nucleic acid results tested by the two assays was low when Ct value was high (≥34), which implies that using single assay of them has the risk of false-negative. Parallelly testing the nucleic acid of 2019-nCoV is an alternative to increase testing accuracy. It is urgent to optimize the efficacy for the two assays.

Key words: 2019-nCoV, Nucleic acid, Consistency test, Sequence