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

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.

Figure 1

Procedure for the dry swab-based nucleic acid extraction.

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

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

Scatter plot showing the Ct values for internal controls extracted by the spin column method and dry swab method.

Figure 5

Scatter plot showing the Ct values for the E gene extracted by the spin column and dry swab-based method.

Figure 6

Scatter plot showing the Ct values for the RdRp gene extracted by the spin column and dry swab-based methods.