key: cord-1048185-ckimrtgc
authors: Silva, Lívia Mara; Riani, Lorena Rodrigues; Silvério, Marcelo Silva; Pereira-Júnior, Olavo dos Santos; Pittella, Frederico
title: Comparison of Rapid Nucleic Acid Extraction Methods for SARS-CoV-2 Detection by RT-qPCR
date: 2022-02-27
journal: Diagnostics (Basel)
DOI: 10.3390/diagnostics12030601
sha: 515a3f7c403a57ed25546bb50319ac152f785135
doc_id: 1048185
cord_uid: ckimrtgc

Since 2020, humanity has been facing the COVID-19 pandemic, a respiratory disease caused by the SARS-CoV-2. The world’s response to pandemic went through the development of diagnostics, vaccines and medicines. Regarding diagnostics, an enormous challenge was faced due to shortage of materials to collect and process the samples, and to perform reliable mass diagnosis by RT-qPCR. In particular, time-consuming and high cost of nucleic acid extraction procedures have hampered the diagnosis; moreover, several steps in the routine for the preparation of the material makes the extracted sample susceptible to contamination. Here two rapid nucleic acid extraction reagents were compared as extraction procedures for SARS-CoV-2 detection in clinical samples by singleplex and multiplex RT-qPCR analysis, using different transport media, samples with high and low viral load, and different PCR machines. As observed, rapid nucleic acid extraction procedures can be applied for reliable diagnosis using a TaqMan-based assay, over multiple platforms. Ultimately, prompt RNA extraction may reduce costs with reagents and plastics, the chances of contamination, and the overall time to diagnosis by RT-qPCR.

COVID-19, caused by SARS-CoV-2, became a global pandemic disease from March of 2020, when the World Health Organization (WHO) declared a "public health emergency of international concern" [1]. The first case was reported in 2019 in the city of Wuhan, China, after the emergence of symptoms similar to pneumonia in part of the population [2] . The most common clinical symptoms of COVID-19 are fever, cough, fatigue, chest pain, headache and shortness of breath, characteristic of other viral illnesses such as the flu [3] . In December 2021, there were over 200 million confirmed cases and over 5 million deaths worldwide from COVID-19 [4] .

The virus that causes the disease belongs to the Coronaviridae family, which has an RNA genome. Genetic sequencing showed that SARS-CoV-2 is 79% equivalent to SARS-CoV and 50% to MERS-CoV [1] . Thus far, there is no defined treatment to eliminate the virus, but vaccines are already available to control the disease progress [5] [6] [7] ; however, the transmission of SARS-CoV-2 is very fast, and the rate of vaccination is usually slow in several countries, allowing new variants of the virus to emerge around the world [8] . The diagnosis of the disease allows both the correct management of the patient and the biosafety strategic actions to avoid the dissemination of the disease [9] .

The most used methods for detecting or quantifying viruses nucleic acids in human biological samples are reverse transcription quantitative polymerase chain reaction (RT-qPCR) or real-time PCR. This technique detects a small segment of the viral genome, enabling rapid, sensitive and accurate strain-level detection of up to five targets in an assay. Several RT-qPCR assays have been designed for the detection of SARS-CoV-2 [10, 11] .

Currently, there are many WHO-approved commercial RT-qPCR kits for detecting SARS-CoV-2. In general, viral RNA is transcribed into cDNA, following the binding of the primers to newly synthesized cDNA. The primers usually target sequences that codify essential proteins from SARS-CoV-2, including the genes E, S, N, RdRp and Orf1ab [12] . Although it is a sensitive and accurate method for detecting viral genomes, it requires expensive sets of reagents, the availability of equipment and time to process the samples; moreover, there are several steps susceptible to mistakes that may impair the diagnosis of SARS-CoV-2, including sample collecting procedure and nucleic acid extraction [13] .

One of the bottlenecks to the diagnosis of COVID-19 by RT-qPCR is the limited availability of RNA extraction kits for preparing the samples collected from patients. The extraction is usually time-consuming and becomes a problem due to the urgency required for diagnosis [14] ; moreover, except for the major institutions, most of the diagnostic laboratories rely on manual extraction procedures which are prone to contamination, use large amounts of plastic materials (microtubes and pipette tips), or use toxic organic solvents. Thanks to the efforts of the scientific community, several nucleic acid extraction kits have been developed or improved. In this article, rapid nucleic acid extraction methods which speeds up SARS-CoV-2 detection by RT-qPCR were analyzed. In addition, the performance of two rapid nucleic acid extraction reagents, the Pi-Lise Nucleic Acid Extraction Reagent (Pi-Biotech Genética Avançada, Santos Dumont, MG, Brazil) , and the QuickExtract DNA Extraction Solution (Lucigen Corporation, Middleton, WI, USA), were compared on biological samples for investigation of COVID-19.

In this study, two rapid nucleic acid extraction reagents were used: Pi-Lise Nucleic Acid Extraction Reagent, by Pi-Biotech Genética Avançada Ltda (Santos Dumont, MG, Brazil) , and QuickExtract TM DNA Extraction Solution, by Lucigen Corporation (Middleton, WI, USA). Once thawed, aliquots were stored at −20 • C to avoid >3 freeze-thaw cycles.

To perform the RT-qPCR assays, a multiplex kit (Allplex SARS-CoV-2 Assay, by Seegene Inc., Seoul, Republic of Korea), and a singleplex set of reagents [iTaq Universal Probes One-Step Kit, by Bio-Rad Laboratories (Hercules, CA, USA),were used, together with primers and controls 2019-nCoV RUO by IDT Integrated DNA Technologies (Coralville, IA, USA)]. The analyses were run in two distinct equipment: QuantStudio ™ 3 and 7500Fast Real-Time PCR Systems, by Applied Biosystems (Foster, CA, USA).

Biological samples for this study were collected from patients suspected of COVID-19 between August 2020 and August 2021. A total of 50 respiratory samples (nasopharyngeal swab or endotracheal aspirate in viral transport medium or saline solution) with known results emitted by local diagnostic laboratories were included in the study. The positive samples were chosen to present both high and low viral load (CT < 30.0 and CT > 30.0, respectively).

The study was submitted and approved by the local ethics committee (CEP UFJF-CAAE: 48021321.3.0000.5147) and included written consent from all participants.

The method used to perform the extraction of nucleic acids from the samples was based in Ladha et al. [15] , with slight modifications according to the supplier's protocols. Important to note, viscous samples may require a pre-dilution with saline (NaCl 0.9%) prior to the extraction.

For the extraction, first the biological samples in viral transport medium (VTM) or saline (NaCl 0.9%) were diluted 1:1 with the extraction reagents. Here, a volume of 40 µL of sample was diluted with 40 µL of Pi-Lise or QuickExtract ( Figure 1 ) and homogenized. Then, the mixture was heated to 95 • C for 5 min in a dry block and incubated at −20 in a freezer for 2 min. Samples were then thawed at room temperature, quick spinned (10 s) and subjected to RT-qPCR assays.

For the extraction, first the biological samples in viral transport medium (VTM) or saline (NaCl 0.9%) were diluted 1:1 with the extraction reagents. Here, a volume of 40 µL of sample was diluted with 40 µL of Pi-Lise or QuickExtract ( Figure 1 ) and homogenized. Then, the mixture was heated to 95 °C for 5 min in a dry block and incubated at −20 in a freezer for 2 min. Samples were then thawed at room temperature, quick spinned (10 s) and subjected to RT-qPCR assays. 

The real-time PCR assay was performed using multiplexed and singleplexed approaches: the Allplex™ SARS-CoV-2 Assay (Seegene Inc., Seoul, Republic of Korea), and iTaq Universal Probes One-Step Kit (Bio-Rad Laboratories, Hercules, CA, USA), with primers, probes and controls 2019-nCoV RUO (IDT Integrated DNA Technologies).

Allplex™ SARS-CoV-2 Assay is a multiplexed RT-qPCR assay that detects and identifies in a single sample three target: RdRp and N genes (specific for SARS-CoV-2) and gene E (for all Sarbecoviruses, including SARS-CoV-2) [16, 17] . On the other hand, the IDT panel corresponds to the primers and probes developed by the US CDC (Centers for Disease Control and Prevention, Atlanta, GA, USA); it was developed for singleplex analysis for RT-qPCR, with the detection of three genes: regions of the virus nucleocapsid gene (N1 and N2 targets) and an additional primer-probe set to detect the human RNase P gene (RP) as endogenous control [18] . It was combined with iTaq Universal Probes One-

Step Kit (Bio-Rad Laboratories) for the singleplex analysis.

The real-time PCR was carried out in the 7500 Fast Real-Time (Applied Biosystems) for the multiplex assay. The final 25 µL reaction mixture contained 3.0 µL of extracted sample, 5.0 µL of primers and probes, 7.0 µL of enzyme mix and reaction buffer and 10.0 µL of nuclease-free water. The thermocycling conditions consisted of 50 °C for 20 min for reverse transcription, followed by 95 °C for 15 min and then 45 cycles of 95 °C for 15 s, 58 °C for 30 s.

The following reactions were performed using Bio-Rad Laboratories singleplex kit and IDT primers in a QuanStudio3 Real-Time PCR System (Applied Biosystems). The final 20 uL reaction mixture contained 3.0 µL of extracted sample, 0.5 µL of iScript enzyme mix, 10 µL of 2x iTaq PCR reaction mix and the combination of primers/probes and water (for N1 and RNaseP: 0.8 µL of primers and probes and 5.7 µL of nuclease-free water; for N2: 0.47 µL of primers and probes, and 6.03 of µL of nuclease-free water). Cycling was performed at 50 °C for 15 min for reverse transcription, followed by 95 °C for 3 min and then 40 cycles of 95 °C for 15 s, 60 °C for 1 min [19] .

All runs included a positive SARS-CoV-2 genomic control and a negative control for the PCR amplification step. Fluorescence measurements were taken, and the threshold cycle (CT) value was calculated by determining the point at which fluorescence exceeded a defined threshold of the mean plus 10 standard deviations above baseline [20, 21] , according to the manufacturer's recommendation. Clinical specimens were considered 

The real-time PCR assay was performed using multiplexed and singleplexed approaches: the Allplex™ SARS-CoV-2 Assay (Seegene Inc., Seoul, Republic of Korea), and iTaq Universal Probes One-Step Kit (Bio-Rad Laboratories, Hercules, CA, USA), with primers, probes and controls 2019-nCoV RUO (IDT Integrated DNA Technologies).

Allplex™ SARS-CoV-2 Assay is a multiplexed RT-qPCR assay that detects and identifies in a single sample three target: RdRp and N genes (specific for SARS-CoV-2) and gene E (for all Sarbecoviruses, including SARS-CoV-2) [16, 17] . On the other hand, the IDT panel corresponds to the primers and probes developed by the US CDC (Centers for Disease Control and Prevention, Atlanta, GA, USA); it was developed for singleplex analysis for RT-qPCR, with the detection of three genes: regions of the virus nucleocapsid gene (N1 and N2 targets) and an additional primer-probe set to detect the human RNase P gene (RP) as endogenous control [18] . It was combined with iTaq Universal Probes One-Step Kit (Bio-Rad Laboratories) for the singleplex analysis.

The real-time PCR was carried out in the 7500 Fast Real-Time (Applied Biosystems) for the multiplex assay. The final 25 µL reaction mixture contained 3.0 µL of extracted sample, 5.0 µL of primers and probes, 7.0 µL of enzyme mix and reaction buffer and 10.0 µL of nuclease-free water. The thermocycling conditions consisted of 50 • C for 20 min for reverse transcription, followed by 95 • C for 15 min and then 45 cycles of 95 • C for 15 s, 58 • C for 30 s.

The following reactions were performed using Bio-Rad Laboratories singleplex kit and IDT primers in a QuanStudio3 Real-Time PCR System (Applied Biosystems). The final 20 µL reaction mixture contained 3.0 µL of extracted sample, 0.5 µL of iScript enzyme mix, 10 µL of 2x iTaq PCR reaction mix and the combination of primers/probes and water (for N1 and RNaseP: 0.8 µL of primers and probes and 5.7 µL of nuclease-free water; for N2: 0.47 µL of primers and probes, and 6.03 of µL of nuclease-free water). Cycling was performed at 50 • C for 15 min for reverse transcription, followed by 95 • C for 3 min and then 40 cycles of 95 • C for 15 s, 60 • C for 1 min [19] .

All runs included a positive SARS-CoV-2 genomic control and a negative control for the PCR amplification step. Fluorescence measurements were taken, and the threshold cycle (CT) value was calculated by determining the point at which fluorescence exceeded a defined threshold of the mean plus 10 standard deviations above baseline [20, 21] , according to the manufacturer's recommendation. Clinical specimens were considered positive if two or more of the SARS-CoV-2 genomic targets showed positive results and all positive and negative control reactions resulted as expected.

To investigate the interference of Pi-Lise reagent on RT-qPCR activity, RT-qPCR reactions using SARS-CoV-2 synthetic gene fragment dissolved in nuclease-free water or in a Diagnostics 2022, 12, 601 4 of 12 50:50 nuclease-free water:Pi-Lise mixture were compared, as described by Ladha et al. for QuickExtract reagent [15] . Each RT-qPCR reaction was prepared using the Seegene kit in 7500 Fast system, and a total volume of 25 µL (3.0 µL of extracted sample, 5.0 µL of primers and probes, 7.0 µL of enzyme mix and reaction buffer and 10.0 µL of nuclease-free water).

Statistical analysis was performed using GraphPad Prism version 8.0.1 (USA). Differences in the mean of cycle threshold (CT) values of genes were compared between the rapid extraction reagents by the T-Student test. Values with p < 0.05 were considered statistically significant. Graphs were prepared using GraphPad Prism version 8.0.1 (USA).

Initially, the analyses were performed using the Allplex kit (Seegene), on the 7500 Fast Real-Time. The results presented in Table 1 show that the analyses with Pi-Lise and QuickExtract were the same regarding the final outcome (detected or not detected) for individual samples; moreover, both reagents presented 100% compatibility to the original results emitted after first analysis for diagnosis. The original Ct values used for diagnosis are shown in Supplementary Tables S1 and S2, and were obtained using PureLink RNA Mini Kit (Invitrogen). The CT values for gene N were similar in most samples, without statistical variations between the mean of the values of the two reagents ( Figure 2 ). For the analysis of gene E, QuickExtract showed lower CT values with a significant difference (p < 0.05). As for the RdRp gene, there was no statistical significant difference between the mean CT values of Pi-Lise and QuickExtract. Ultimately, the obtained results showed that Pi-Lise and QuickExtract were effective in providing nucleic acid from samples in the different media tested. The detection of genes N, E and RdRp was viable in biological samples regardless of the transport media used (viral transport medium, saline and clinical samples of endotracheal aspirate) ( Table 1) . A singleplex analysis (Bio-rad kit, with IDT primer-probes) was also performed after the extraction with both reagents. For this analysis, the QuantStudio 3 equipment was used. The results show that there was no significant difference in the final outcome when the samples were processed with Pi-Lise or QuickExtract (Table 2 and Figure 3 ). The process including both reagents provided compatible results using a different equipment and singleplex kit. As in the multiplex kit analysis, the singleplex results also show that Pi-Lise and QuickExtract are effective for extracting nucleic acids with different media. A singleplex analysis (Bio-rad kit, with IDT primer-probes) was also performed after the extraction with both reagents. For this analysis, the QuantStudio 3 equipment was used. The results show that there was no significant difference in the final outcome when the samples were processed with Pi-Lise or QuickExtract (Table 2 and Figure 3 ). The process including both reagents provided compatible results using a different equipment and singleplex kit. As in the multiplex kit analysis, the singleplex results also show that Pi-Lise and QuickExtract are effective for extracting nucleic acids with different media. 

A series of reagent dilutions were evaluated to identify one that would achieve efficient lysis of the enveloped virus while preserving the activity of the RT-qPCR reaction. The results (Figure 4) show that Pi-Lise at a final concentration of 6.0% v/v did not interfere 

A series of reagent dilutions were evaluated to identify one that would achieve efficient lysis of the enveloped virus while preserving the activity of the RT-qPCR reaction. The results ( Figure 4) show that Pi-Lise at a final concentration of 6.0% v/v did not interfere with the RT-qPCR reaction. 

This study compared two commercially available reagents on the extraction of nucleic acid from biological samples for COVID-19 diagnostic by RT-qPCR. The reagents Pi- 

This study compared two commercially available reagents on the extraction of nucleic acid from biological samples for COVID-19 diagnostic by RT-qPCR. The reagents Pi-Lise and QuickExtract promoted rapid extraction of nucleic acids, without the application of columns and organic solvents [22] , for the use in TaqMan-based RT-qPCR.

The results obtained in this study show that SARS-CoV-2 was identified in different clinical samples after nucleic acid extraction by both reagents used separately. In addition, Pi-Lise and QuickExtract were effective in extracting viral RNA from endotracheal aspirate. These results demonstrate that the reagents are effective in complex matrices.

In nasopharyngeal swab samples, transported in viral transport medium and/or saline solution, Pi-Lise and QuickExtract were also efficient for nucleic acid extraction from samples with high viral load (CT ≤ 30.0) and for samples with low viral load (CT ≥ 30.0). In a study by Komiazyk et al., difficulty in extracting RNA from samples with low viral load was reported, in particular, due to operational difficulties in conventional extraction techniques (by column or organic solvents) [23] . Due to several steps in the extraction using column or solvent, and also the final eluting step in which the final concentration is dependent on the water volume added, the viral RNA concentration may be reduced, impairing the detection by RT-qPCR. The result obtained in this work demonstrates that rapid extraction reagents are effective in samples with low viral load, such as samples S7, S26 and S37. Patients with a low viral load are usually in the initial or final stage of the disease, which is a serious problem in case of a wrong diagnosis. Analyzing the compatibility of the original results emitted for diagnosis and the result obtained using either Pi-Lise or QuickExtract in the process, there was full compatibility among the reagents and the original diagnosis (detected and not detected). This indicates that both fast extracting reagents were effective in promoting the lysis and extraction of the SARS-CoV-2 nucleic acids, while preserving it from nucleases for a successful and reliable PCR reaction.

Based on the CT values obtained, both reagents showed similar results for gene N. Gene N is part of the viral nucleocapsid and has been reported as a long region of the viral gene sequence, highly conserved among Sarbecoviruses [24] . According to previous studies, results from RT-q-PCR using the N gene were more sensitive than those using other genes [12] . Therefore, the similarity in the values obtained demonstrates that both reagents do not interfere in the enzyme reaction with the gene N, validating the use of Pi-Lise and QuickExtract reagents for the detection kits comprising gene N, based on TaqMan reaction.

For the elaboration of the E gene primer-probe, a region of the viral structural protein envelope was used [25] . Although the mean CT values for gene E were different between the reagents, there was no change in the final qualitative result. The RdRp primer-probe is also able to detect the viral RNA-dependent RNA polymerase sequence [26] . The results obtained for this gene showed that there was no significant difference between the reagents in the mean CT values, indicating similar sensitivity.

In the analysis using a singleplex test, the extraction process employing Pi-Lise or QuickExtract was also satisfactory for the final detection of SARS-CoV-2 in different samples. In these reactions, the panel of primers used was that of the US CDC, which contained the genes N1 and N2, specific to SARS-CoV-2 and the RNAseP gene, as endogenous control [18] . According to the results, the viral genes that are pivotal for diagnosis were fully compatible between reagents. The virus was identified in 40% samples from varied biological matrices and was also 100% compatible with the original results emitted for diagnosis. The CT values observed for the viral genes were similar in the extractions performed with Pi-Lise and QuickExtract, proving the efficiency of lysis and extraction of viral nucleic acids and demonstrating the stability of the reagents in RT-qPCR reactions.

The Pi-Lise interference analysis in the RT-qPCR reaction showed that the reagent does not harm the PCR assay. The reaction volume was 25 µL, with 3 µL of sample. Among the samples containing Pi-Lise:Water mixture (50:50), the largest volume of Pi-Lise analyzed was 1.5 µL (6.0% v/v). In these samples, amplification was not observed in samples without positive control and the virus was detected at all concentrations tested. This result shows that Pi-Lise does not interfere in RT-qPCR reactions.

Nucleic acid extraction methods are of great importance for the diagnosis of several diseases, including COVID-19 [27] . In addition to easing the extraction process and requiring less instrumentation, the rapid extraction reagents proved to be effective in extracting and preserving the genetic material, enabling its safe use in a subsequent step of RT-qPCR based on TaqMan. It is important to note that the rapid method reduces the time of the extraction process to up to 7 min, which is of great importance in diagnosis using molecular biology tools.

Despite the efforts of the academic community being enormous, the control of COVID-19 is still a considerable challenge. New mutations are appearing periodically, with new cycles of dissemination, presenting significant difficulties in detecting and controlling the virus. Therefore, adequate diagnostic processes will still be essential for the correct management of infected people. The faster the diagnosis, the better the virus-fighting response; thus, nucleic acid extraction reagents are great allies in the control of COVID-19.

Many laboratories around the world are already using rapid nucleic acid extraction reagents to promptly obtain nucleic acids for RT-qPCR assay of SARS-CoV-2. Fast RNA extraction reduces costs with reagent and plastics, reduces the overall time to diagnosis by RT-qPCR and consequently reduces the enormous pressure that the technicians suffer during routine assays. Our study demonstrates that the Pi-Lise and QuickExtract reagents are effective in extracting and preserving viral and human nucleic acids to further detection of SARS-CoV-2 virus by TaqMan-based RT-qPCR in biological samples from diverse matrices (nasopharynx swabs, salive and endotracheal aspirates), using different equipment and diagnostic sets. Reliable results can be obtained using rapid nucleic acid extraction reagents and methods, with a positive impact on time and cost of analysis.

Supplementary Materials: The following supporting information can be downloaded at: https: //www.mdpi.com/article/10.3390/diagnostics12030601/s1, Table S1 : RT-qPCR results of reactions performed with Allplex kit after extraction with PureLink RNA Mini Kit (original Ct values used for diagnosis); Table S2 : RT-qPCR results of reactions performed with Bio-rad kit and IDT primers-probes after extraction with PureLink RNA Mini Kit (original Ct values used for diagnosis). Acknowledgments: The authors would like to thank the support from UFJF regarding infrastructure, and everyone else who collaborated with this work.

Conflicts of Interest: F.P. is cofounder of Pi-Biotech Genetica Avancada. This does not alter our adherence to Diagnostics policies on sharing data and materials.

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