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

Öz

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.

Anahtar Kelimeler

• SARS-CoV-2
• RNA isolation
• nasopharyngeal
• oropharyngeal

Destekleyen Kurum

There is no organization supporting our research.

Etik Beyan

Ethical approval was obtained from the Clinical Research Ethics Committee of Istanbul Medeniyet University (Date: 18.11.2020; Approval No: 2020/06/56). Informed consent to participate was obtained from all individual participants included in the study. All procedures involving human participants were conducted in accordance with the ethical standards of the institutional and national research committees and with the principles outlined in the Declaration of Helsinki (as revised in 2013).

Teşekkür

The author would like to acknowledge Prof. Dr. Güler Öztürk and Prof. Dr. Sadrettin Pençe for their contributions. While their support was appreciated, their involvement did not fulfill the criteria for authorship and is therefore recognized in the acknowledgments.

Kaynakça

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