Efficacy of Nucleic Acid Extraction by Manual versus Automated Magnetic Bead-based Method to Detect SARS-CoV-2

Abstract

Introduction: In December 2019, a rapid spread of highly infectious, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), was reported in Wuhan, China. The gold standard for diagnosis of SARS-CoV-2 infection is nucleic acid amplification technology by detecting its viral Ribonucleic Acid (RNA) from respiratory swabs (oropharyngeal and nasopharyngeal) by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) whose specificity is approximately 95%. Magnetic bead RNA extraction was benchmarked against the commercial QIAcube extraction platform. Aim: To compare the efficacy of nucleic acid extraction by manual method and automated magnetic bead-based method to detect SARS-CoV-2. Materials and Methods: The present observational comparative study was conducted in the Department of Microbiology, Autonomous State Medical College, Firozabad, Uttar Pradesh, India. Duration of the study was from February to March 2022. A total of 470 oropharyngeal and nasopharyngeal samples were included in this study to observe the efficacy of nucleic acid extraction by manual extraction and automated extraction for SARS-CoV-2. Data were entered in Microsoft Excel software and analysed using Statistical Package for the Social Sciences (SPSS) version 26.0. Results: During this study period, a total of 470 individual samples were tested in 94 pools. Out of these 470 individuals, 331 were males (70.5%) and 139 were females (29.5%). All 94 pools were found negative by both automatic and manual extraction methods. Envelope (E) gene was found in one pool (1.06%) by the manual RNA extraction method. E gene was absent in 93 pools (98.94%) by manual method. Internal control was found highest in 88 pools (93.62%) by the automated extraction method. Conclusion: Automated workflows avoid human error from the sample processing pipeline and also ensure as well as enhance the meaningful output, diagnostic precision, and testing capacity. Automated instruments are in wide usage because of their capability of processing thousands of samples per day with the support of minimal staff.