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. 2023 Aug 23:2023:6624932.
doi: 10.1155/2023/6624932. eCollection 2023.

Dry Swab-Based Nucleic Acid Extraction vs. Spin Column-Based Nucleic Acid Extraction for COVID-19 RT-PCR Testing: A Comparative Study

Mohammed Faraaz Khan  1 , C Roopa  2
Affiliations

Dry Swab-Based Nucleic Acid Extraction vs. Spin Column-Based Nucleic Acid Extraction for COVID-19 RT-PCR Testing: A Comparative Study

Mohammed Faraaz Khan et al. Can J Infect Dis Med Microbiol. .

Abstract

Conventional nucleic acid extraction involves usage of spin columns to isolate the RNA, but this is labor intensive. This study compares the spin column method with a dry swab-based method of extraction using a proteinase K buffer and subsequent heat inactivation. A total of 56 subjects were tested for COVID-19 by RT-PCR with probes targeting the E and RdRp genes by collecting two nasopharyngeal and two oropharyngeal swabs and subjecting one set to nucleic acid extraction by spin column and the other set to dry swab-based methods. Out of the 56 samples tested, 27 were positive for VTM-based extraction and 29 were negative. Dry swab-based extraction produced 22 positive results (sensitivity = 81.48%) and 34 negative results. The E gene was detectable in 25 samples by the dry swab method out of 27 samples that tested positive by the VTM-based method (sensitivity = 92.5%). The RdRp gene was detectable in 22 samples by the dry swab method out of 27 samples that tested positive by the VTM-based method (sensitivity = 81.48%). Concordance was 91% with discordance at 9% and a Kappa value of 0.82, indicating almost perfect agreement between the two methods. Our findings indicate that the dry swab method of nucleic acid extraction is a useful alternative to conventional spin column-based extraction with comparable sensitivity and specificity. The trial was registered with the Clinical Trials Registry of India (CTRI) with a CTRI registration number of CTRI/2021/12/038792.

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Conflict of interest statement

The authors declare that there are no conflicts of interest.

Figures

Figure 1
Figure 1
Procedure for the dry swab-based nucleic acid extraction.
Figure 2
Figure 2
Heat map demonstrating the Ct values for RNase P (internal control), E gene, and RdRp genes in samples tested by the spin column-based extraction method. The green color indicates no Ct values for that particular gene.
Figure 3
Figure 3
Heat map demonstrating the Ct values for RNase P (internal control), E gene, and RdRp genes in samples tested by the dry swab-based extraction method. The green color indicates no Ct values for that particular gene.
Figure 4
Figure 4
Scatter plot showing the Ct values for internal controls extracted by the spin column method and dry swab method.
Figure 5
Figure 5
Scatter plot showing the Ct values for the E gene extracted by the spin column and dry swab-based method.
Figure 6
Figure 6
Scatter plot showing the Ct values for the RdRp gene extracted by the spin column and dry swab-based methods.
See this image and copyright information in PMC

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