scholarly journals Virucidal efficacy of guanidine-free inactivants and rapid test buffers against SARS-CoV-2

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Katherine Davies ◽  
Ulrike Arnold ◽  
Hubert Buczkowski ◽  
Christopher Burton ◽  
Stephen R. Welch ◽  
...  
Keyword(s):  
Diagnostic Testing ◽  
Rapid Test ◽  
Diagnostic Procedures ◽  
Clinical Samples ◽  
Evidence Based ◽  
Acid Extraction ◽  
Antigen Test ◽  
Pathogen Inactivation ◽  
Nucleic Acid Extraction ◽  
Virucidal Efficacy

AbstractA pathogen inactivation step during collection or processing of clinical samples has the potential to reduce infectious risks associated with diagnostic procedures. It is essential that these inactivation methods are demonstrated to be effective, particularly for non-traditional inactivation reagents or for commercial products where the chemical composition is undisclosed. This study assessed inactivation effectiveness of twenty-four next-generation (guanidine-free) nucleic acid extraction lysis buffers and twelve rapid antigen test buffers against SARS-CoV-2, the causative agent of COVID-19. These data have significant safety implications for SARS-CoV-2 diagnostic testing and support the design and evidence-based risk assessment of these procedures.

scholarly journals Virucidal Efficacy of Guanidine-Free Inactivants and Rapid Test Buffers Against SARS-CoV-2: Implications for Risk Assessment of Diagnostic Procedures

2021 ◽  
Author(s):  
Katherine Davies ◽  
Ulrike Arnold ◽  
Hubert Buczkowski ◽  
Christopher Burton ◽  
Stephen R Welch ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Diagnostic Testing ◽  
Rapid Test ◽  
Diagnostic Procedures ◽  
Clinical Samples ◽  
Evidence Based ◽  
Acid Extraction ◽  
Pathogen Inactivation ◽  
Nucleic Acid Extraction ◽  
Virucidal Efficacy

Abstract A pathogen inactivation step during collection or processing of clinical samples has the potential to reduce infectious risks associated with diagnostic procedures. It is essential that these inactivation methods are demonstrated to be effective, particularly for non-traditional inactivation reagents or for commercial products where the chemical composition is undisclosed. This study assessed inactivation effectiveness of twenty-four next-generation (guanidine-free) nucleic acid extraction lysis buffers and twelve rapid antigen test buffers against SARS-CoV-2, the causative agent of COVID-19. These data have significant safety implications for SARS-CoV-2 diagnostic testing and support the design and evidence-based risk assessment of these procedures.

scholarly journals Optimization of magnetic bead-based nucleic acid extraction for SARS-CoV-2 testing using readily available reagents

2021 ◽  
Author(s):  
Simon Haile ◽  
Aidan M. Nikiforuk ◽  
Pawan K. Pandoh ◽  
David D. W. Twa ◽  
Duane E. Smailus ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Diagnostic Testing ◽  
Magnetic Bead ◽  
Acid Extraction ◽  
Flexible Systems ◽  
Nucleic Acid Extraction ◽  
Extraction Protocol

AbstractThe COVID-19 pandemic has highlighted the need for generic reagents and flexible systems in diagnostic testing. Magnetic bead-based nucleic acid extraction protocols using 96-well plates on open liquid handlers are readily amenable to meet this need. Here, one such approach is rigorously optimized to minimize cross-well contamination while maintaining sensitivity.Article SummaryA scalable, non-proprietary, magnetic bead-based automated nucleic acid extraction protocol optimised for minimum cross-well contamination

scholarly journals Evaluation of real-time nucleic acid sequence-based amplification for detection of Chikungunya virus in clinical samples

2009 ◽  
Vol 58 (9) ◽  
pp. 1168-1172 ◽  
Author(s):  
J.-N. Telles ◽  
K. Le Roux ◽  
P. Grivard ◽  
G. Vernet ◽  
A. Michault
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Chikungunya Virus ◽  
False Negative ◽  
Nucleic Acid Sequence ◽  
Clinical Samples ◽  
Acid Extraction ◽  
Plasma Samples ◽  
Rt Pcr ◽  
Nucleic Acid Extraction

The Chikungunya virus (CHIKV) is a member of the genus Alphavirus that is transmitted to humans by Aedes mosquitoes. In 2005 and 2006, the Indian Ocean island of La Réunion was hit with an unprecedented CHIKV fever outbreak that infected 300 000 people. In the present study, we describe the evaluation of real-time nucleic acid sequence-based amplification (RT-NASBA) for the detection of CHIKV in clinical samples. A co-extracted and co-amplified chimerical CHIKV RNA sequence was used as an internal control to eliminate false-negative results. The detection threshold of the assay was determined from quantified CHIKV-positive plasma, and estimated to be 200 copies per NASBA reaction. The specificity of the assay was determined using blast analyses and non-cross-reactivity using an O'nyong-nyong virus culture and 250 CHIKV RT-PCR-negative plasma samples. A 100 % specificity was found and no invalid result was obtained, showing the good quality of the nucleic acid extraction. The assay was then evaluated using 252 CHIKV-positive RT-PCR plasma samples. The samples were all tested positive, including those with low viral load. This evaluation showed that the RT-NASBA is a rapid (5 h from sample nucleic acid extraction to detection), sensitive, specific and reliable method for the routine diagnosis of CHIKV in clinical samples.

scholarly journals Towards a “Sample-In, Answer-Out” Point-of-Care Platform for Nucleic Acid Extraction and Amplification: Using an HPV E6/E7 mRNA Model System

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Anja Gulliksen ◽  
Helen Keegan ◽  
Cara Martin ◽  
John O'Leary ◽  
Lars A. Solli ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Sample Preparation ◽  
Clinical Sample ◽  
Point Of Care ◽  
Fluorescent Detection ◽  
Clinical Samples ◽  
Microfluidic Channels ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Hpv E6

The paper presents the development of a “proof-of-principle” hands-free and self-contained diagnostic platform for detection of human papillomavirus (HPV) E6/E7 mRNA in clinical specimens. The automated platform performs chip-based sample preconcentration, nucleic acid extraction, amplification, and real-time fluorescent detection with minimal user interfacing. It consists of two modular prototypes, one for sample preparation and one for amplification and detection; however, a common interface is available to facilitate later integration into one single module. Nucleic acid extracts (n=28) from cervical cytology specimens extracted on the sample preparation chip were tested using the PreTect HPV-Proofer and achieved an overall detection rate for HPV across all dilutions of 50%–85.7%. A subset of 6 clinical samples extracted on the sample preparation chip module was chosen for complete validation on the NASBA chip module. For 4 of the samples, a 100% amplification for HPV 16 or 33 was obtained at the 1 : 10 dilution for microfluidic channels that filled correctly. The modules of a “sample-in, answer-out” diagnostic platform have been demonstrated from clinical sample input through sample preparation, amplification and final detection.

scholarly journals Optimizing nucleic acid extraction and transcriptome evaluation from low-input, fixed clinical samples

2020 ◽  
Author(s):  
Katie M. Campbell ◽  
Egmidio Medina ◽  
Ignacio Baselga Carretero ◽  
Yaroslav Teper ◽  
Rangasamy Elumalai ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Rna Sequencing ◽  
Clinical Samples ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Sequencing Library ◽  
Ffpe Samples ◽  
Agilent Sureselect ◽  
Downstream Analysis ◽  
The Impact

AbstractTumor biopsies are commonly formalin-fixed and paraffin-embedded (FFPE) for long-term and efficient storage. However, FFPE preservation can greatly compromise the quality of samples, the extraction of nucleic acids, and feasibility of downstream studies, including RNA sequencing. These challenges are especially evident in the studies of clinical trial samples, where the sizes of biopsies often limit the amount of material available for study. Here, we evaluate two nucleic acid extraction kits (Covaris truXTRAC FFPE tNA Plus, QIAGEN miRNeasy FFPE) and three hybridized-capture-based RNA sequencing library preparations (Agilent SureSelect XT RNA Direct, Agilent SureSelect XT HS, and Illumina TruSeq RNA Exome) to evaluate the impact of these sample processing steps on transcriptome evaluation in a melanoma biopsy procured in a clinical setting and preserved by FFPE. While there exist many options for extraction and library preparation that are appropriate for RNA sequencing from FFPE samples, we observed that combinations of experimental approaches may have subtle impacts on downstream analysis, including gene expression quantification and fusion detection.

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