performance comparison and clinical evaluation of three extraction-free sars-cov-2 rt-pcr assays

Background: rt-pcr technology is the gold standard for the diagnosis of sars-cov-2 infection. it was important to evaluate the applicability of different sars-cov-2 rt-pcr kits. objectives: this study compared the performance of three rna extraction-free sars-cov-2 nucleic acid detection assays (sx002, sx08, and kyd) and a magnetic bead-based kit (ss). methods: the performance indicators such as linear quantification, accuracy, precision, and the low limit of detection (lod) were assessed. specificity was evaluated by detecting six common respiratory pathogens. four kits were utilized to test national quality control materials that contained different sars-cov-2 variants with varying viral loads to further compare the performance. the clinical utility of the different sars-cov-2 nucleic acid assays was evaluated by testing clinical nasopharyngeal swab samples. results: the linear regression analysis showed that the three rna extraction-free kits and the magnetic bead extraction kit (ss) had a good correlation (r² value ranged from 0.9838 to 0.9970). among the three extraction-free kits, sx08 exhibited the highest r² value and correlation coefficient (0.997). the intra-batch and inter-batch coefficient of variation (cv) for all the kits was less than 5%. accuracy was assessed based on the absolute value of deviation, with ss exhibiting the highest accuracy when the deviation was less than 0.1 log. the sx002 and sx08 kits were the most accurate for the n gene and the orf1ab gene, respectively. the ss kit had the lowest lod. the sx08 kit exhibited a 100% coincidence rate and a κ value of 1. the kyd kit had a coincidence rate of 90.91% and a κ value of 0.814. when detecting control materials with different viral loads and sars-cov-2 variants, all reagents yielded positive results, except for the kyd kit. conclusions: the three rna extraction-free nucleic acid detection kits showed differences in performance compared with the magnetic bead-based ss kit. the rna extraction-free kits offered advantages in simplicity, rapid detection, cost-effectiveness, and high compliance rates. however, relying solely on ct values for viral load determination may be challenging due to variations across different rt-pcr methods.