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Evaluation of the SARS-CoV-2 Inactivation Efficacy Associated With Buffers From Three Kits Used on High-Throughput RNA Extraction Platforms.

ABSTRACT: Rapid and demonstrable inactivation of SARS-CoV-2 is crucial to ensure operator safety during high-throughput testing of clinical samples. The inactivation efficacy of SARS-CoV-2 was evaluated using commercially available lysis buffers from three viral RNA extraction kits used on two high-throughput (96-well) RNA extraction platforms (Qiagen QIAcube HT and the Thermo Fisher KingFisher Flex) in combination with thermal treatment. Buffer volumes and sample ratios were chosen for their optimised suitability for RNA extraction rather than inactivation efficacy and tested against a representative sample type: SARS-CoV-2 spiked into viral transport medium (VTM). A lysis buffer mix from the MagMAX Pathogen RNA/DNA kit (Thermo Fisher), used on the KingFisher Flex, which included guanidinium isothiocyanate (GITC), a detergent, and isopropanol, demonstrated a minimum inactivation efficacy of 1 × 10⁵ tissue culture infectious dose (TCID)₅₀/ml. Alternative lysis buffer mixes from the MagMAX Viral/Pathogen Nucleic Acid kit (Thermo Fisher) also used on the KingFisher Flex and from the QIAamp 96 Virus QIAcube HT Kit (Qiagen) used on the QIAcube HT (both of which contained GITC and a detergent) reduced titres by 1 × 10⁴ TCID₅₀/ml but did not completely inactivate the virus. Heat treatment alone (15 min, 68°C) did not completely inactivate the virus, demonstrating a reduction of 1 × 10³ TCID₅₀/ml. When inactivation methods included both heat treatment and addition of lysis buffer, all methods were shown to completely inactivate SARS-CoV-2 inactivation against the viral titres tested. Results are discussed in the context of the operation of a high-throughput diagnostic laboratory.

SUBMITTER: Thom RE

PROVIDER: S-EPMC8481894 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:OBJECTIVE:To evaluate the effects of heat inactivation of blood samples at 56? for 30 min on the results of SARS-CoV-2 antibody detection using different methods. METHODS:This retrospective study was conducted in 11 patients with established diagnosis of COVID-19 and 10 patients with diseases other than COVID- 19 in our hospital. We collected samples of serum, plasma and whole blood from each patient between February, 12 and 18, 2020, and with a double- blind design, the samples were examined for SARS-CoV-2 antibodies before and after heat inactivation at 56 ? for 30 min. In all the samples, the total SARS-CoV-2 antibodies were detected using immunochromatography, and the IgM antibodies were detected using fluorescence immunochromatography; the IgM and IgG antibodies in the serum and plasma samples detected with chemiluminescence immunoassay. We compared the detection results and analyzed the correlation of semi-quantitative detection results of IgM and IgG antibodies before and after heat inactivation of the samples. RESULTS:With immuno-chromatography, the coincidence rate of the total SARS-CoV-2 antibody detection before and after heat inactivation of the serum and plasma samples was 90.0% in COVID-19 cases and 100.0% in the negative cases, resulting in a total coincidence rate 95.2%; for the whole blood samples, the total coincidence rates of the total SARS-CoV-2 antibodies were 100.0%. For detection of IgM antibodies in the serum, plasma and whole blood samples using fluorescence immunochromatography, the coincidence rates in SARS-CoV-2-positive and negative cases and the total coincidence rate before and after inactivation were 100.0%, 0 and 47.6%, respectively. For detection of serum IgM and IgG antibodies and plasma IgG antibodies with chemiluminescence immunoassay, the coincidence rates in SARS-CoV-2-positive and negative cases and the total coincidence rate before and after inactivation were all 100.0%, and the total coincidence rate of plasma IgM antibodies was 95.2%. Pearson correlation analysis of the semi-quantitative results of IgM and IgG detection in the serum and plasma samples showed a correlation coefficient of 0.9999 (95%CI: 0.9998-1.000, P < 0.001) between the results before and after sample inactivation. CONCLUSIONS:Heat inactivation of blood samples at 56 ? for 30 min does not obviously affect the results of immunochromatography and chemiluminescent immunoassay for detection of SARS-COV-2 antibodies but can reduce the risk of infection for the operators. Heat-inactivated samples can not be used in fluorescence immunochromatography for SARS-CoV-2 antibody detection.

Project description:Next-generation sequencing (NGS) studies are becoming routinely used for the detection of novel and clinically actionable DNA variants at a pangenomic scale. Such analyses are now used in the clinical practice to enable precision medicine. Formalin-fixed paraffin-embedded (FFPE) tissues are still one of the most abundant source of cancer clinical specimen, unfortunately this method of preparation is known to degrade DNA and therefore compromise subsequent analysis. Some studies have reported that variant detection can be performed on FFPE samples sequenced with NGS techniques, but few or none have done an in-depth coverage analysis and compared the influence of different state-of-the-art FFPE DNA extraction kits on the quality of the variant calling. Here, we generated 42 human whole-exome sequencing data sets from fresh-frozen (FF) and FFPE samples. These samples include normal and tumor tissues from two different organs (liver and colon), that we extracted with three different FFPE extraction kits (QIAamp DNA FFPE Tissue kit and GeneRead DNA FFPE kit from Qiagen, Maxwell™ RSC DNA FFPE Kit from Promega). We determined the rate of concordance of called variants between matched FF and FFPE samples on all common variants (representing at least 86% of the total number of variants for SNVs). The concordance rate is very high between all matched FF / FFPE pairs, with equivalent values for the three kits we analyzed. On the other hand, when looking at the difference between the total number of variants in FF and FFPE, we find a significant variation for the three different FFPE DNA extraction kits. Coverage analysis shows that FFPE samples have less good indicators than FF samples, yet the coverage quality remains above accepted thresholds. We detect limited but statistically significant variations in coverage indicator values between the three FFPE extraction kits. Globally, the GeneRead and QIAamp kits have better variant calling and coverage indicators than the Maxwell kit on the samples used in this study, although this kit performs better on some indicators and has advantages in terms of practical usage. Taken together, our results confirm the potential of FFPE samples analysis for clinical genomic studies, but also indicate that the choice of a FFPE DNA extraction kit should be done with careful testing and analysis beforehand in order to maximize the accuracy of the results.

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Evaluation of the SARS-CoV-2 Inactivation Efficacy Associated With Buffers From Three Kits Used on High-Throughput RNA Extraction Platforms.

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