Evaluation of Manual, Automated, and Extraction-Free Workflows for SARS-CoV-2 RNA Recovery from Swab Samples

Aim: This study aimed to compare the performance of four RNA recovery approaches—two silica column-based kits, an extraction-free vNAT method, and an automated magnetic bead-based extraction system—for the recovery of SARS-CoV-2 RNA from nasopharyngeal, oropharyngeal, and intubated samples. Materials and Methods: Samples collected from 29 patients under biosafety conditions were processed within 12 hours. RNA yield and purity were quantified using A260/280 and A260/230 ratios measured by NanoDrop spectrophotometry. IBM SPSS 21.0 were used for statistical analyses. Normality was assessed with the Shapiro–Wilk test, Wilcoxon signed-rank and Friedman tests were applied. p<0.05 were considered as statistically significant. Results: Silica Column–Based Extraction Kit 1 showed low RNA isolation and low purity indices. Silica Column–Based Extraction Kit 2 produced the highest RNA yields but reflected by high A260/280 and low A260/230 ratios. The automated magnetic bead-based extraction method provided the most consistent purity profile with moderate RNA yield; notably, A260/280 ratios were closest to ideal values, although A260/230 ratios remained below optimal levels. Conclusion: RNA yield and purity differed significantly among the four workflows. The automated magnetic bead-based isolation method was the most suitable for obtaining high-quality RNA for research applications, whereas the extraction-free vNAT method was appropriate only for rapid RT-qPCR–based diagnostic use.