Comparison of Two RNA Extraction Methods for the Molecular Detection of SARS-CoV-2 from Nasopharyngeal Swab Samples

Abstract

Background: Rapid diagnosis of COVID-19 is essential in order to restrict the spread of the pandemic, and different approaches for SARS-CoV-2 testing have been proposed as cost-effective and less time-consuming alternatives. For virus detection, the real-time reverse transcriptase–polymerase chain reaction (RT-PCR) technique is still the “gold standard” for accuracy and reliability, but its performance is affected by the efficiency of nucleic acid extraction methods. Objective: In order to improve the SARS-CoV-2 diagnostic workflow, we compared a “standard” commercially available kit, based on viral RNA extraction from human swab samples by magnetic beads, with its technological evolution. The two methods differ mainly in their time consumption (9 vs. 35 min). Methods: We adopted the MAGABIO PLUS VIRUS DNA/RNA PURIFICATION KIT II (BIOER), defined as “standard”, with the automatic extractor BIOER (GenePure Pro fully automatic nucleic acid purification system) to isolate RNA from nasopharyngeal swabs for the detection of SARS-CoV-2 by RT-PCR. We tested this kit with a new faster version of the first one, defined as “rapid” (MAGABIO PLUS VIRUS RNA PURIFICATION KIT II). Results and Conclusion: The two evaluated procedures provided similar analytical results, but the faster method proved to be a more suitable tool for the detection of SARS-CoV-2 from nasopharyngeal swabs, due to a more rapid availability of results, which may contribute to improving both clinical decision making and patient safety.

Direct capture and amplification of nucleic acids using a universal, elution-free magnetic bead-based method for rapid pathogen detection in multiple types of biological samples

“…Unfortunately, the products prepared by the elution-free MB-based method could not be used as templates for qPCR assays, as almost no fluorescence signal accumulation was observed in the reactions, which might be attributed to the inhibition of the reaction by the Fe 3+ released from the MBs during the high-temperature thermal cycling process, since this heavy metal ion can strongly inhibit qPCR at a concentration of 3 mg/L [31]. Therefore, only the nucleic acid products prepared by the commercial kit based on the traditional MB-based method were employed as templates for qPCR assays for the comparison, which is the most commonly used NAATs protocol at present [32]. As shown in Fig.…”

A semi-automated and high-throughput approach for the detection of honey bee viruses in bee samples

“…PCR remains one of the most favored and applied techniques for virus detection and disease diagnosis. It is routinely used for virus diagnostics in many research fields and is a standard for evaluating viral loads in biomedical research, agricultural and environmental sectors [33][34][35][36][37][38]. NGS technology is an additive and sometimes alternative method, capable of identifying unknown viruses in the sample, including variants and quasispecies [39][40][41], and is a reliable tool for validation of PCR results [32,39,40,41].…”

“…The magnetic beads-based technology has been widely used in biomedical research [33][34][35][36][37], and has become one of the most used methods to extract viral RNA for screening for SARS-CoV-2 [36], as rapid diagnosis of COVID-19 is essential to restrict its spreading. A same extraction method combined with an automated approach, which is rapid, high-throughput, uniform and bears low cross contamination risk [50][51][52] may be employed for honey bee research, in particular for virus screening surveys to screen multiple colonies in a limited timeframe.…”