scholarly journals Method versatility in RNA extraction-free PCR detection of SARS-CoV-2 in saliva samples

2021 ◽  
Author(s):  
Orchid M Allicock ◽  
Devyn Yolda-Carr ◽  
Rebecca Earnest ◽  
Mallery Breban ◽  
Noel Vega ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
Rna Extraction ◽  
Health And Safety ◽  
Virus Detection ◽  
Cost Effective ◽  
Proteinase K ◽  
Sample Treatment ◽  
Simplified Approach ◽  
Safety Requirements ◽  
Qpcr Analysis

Early in the pandemic, a simple, open-source, RNA extraction-free RT-qPCR protocol for SARS-CoV-2 detection in saliva was developed and made widely available. This simplified approach (SalivaDirect) requires only sample treatment with proteinase K prior to PCR testing. However, feedback from clinical laboratories highlighted a need for a flexible workflow that can be seamlessly integrated into their current health and safety requirements for the receiving and handling of potentially infectious samples. To address these varying needs, we explored additional pre-PCR workflows. We built upon the original SalivaDirect workflow to include an initial incubation step (95°C for 30 minutes, 95°C for 5 minutes or 65°C for 15 minutes) with or without addition of proteinase K. The limit of detection for the workflows tested did not significantly differ from that of the original SalivaDirect workflow. When tested on de-identified saliva samples from confirmed COVID-19 individuals, these workflows also produced comparable virus detection and assay sensitivities, as determined by RT-qPCR analysis. Exclusion of proteinase K did not negatively affect the sensitivity of the assay. The addition of multiple heat pretreatment options to the SalivaDirect protocol increases the accessibility of this cost-effective SARS-CoV-2 test as it gives diagnostic laboratories the flexibility to implement the workflow which best suits their safety protocols.

scholarly journals Direct diagnostic testing of SARS-CoV-2 without the need for prior RNA extraction

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shan Wei ◽  
Esther Kohl ◽  
Alexandre Djandji ◽  
Stephanie Morgan ◽  
Susan Whittier ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
Point Of Care ◽  
Diagnostic Testing ◽  
Rna Extraction ◽  
Cost Effective ◽  
Clinical Samples ◽  
Nasopharyngeal Swab ◽  
Percentage Agreement ◽  
Testing Method ◽  
Viral Transport

AbstractThe COVID-19 pandemic has resulted in an urgent need for a rapid, point of care diagnostic testing that could be rapidly scaled on a worldwide level. We developed and tested a highly sensitive and robust assay based on reverse transcription loop mediated isothermal amplification (RT-LAMP) that uses readily available reagents and a simple heat block using contrived spike-in and actual clinical samples. RT-LAMP testing on RNA-spiked samples showed a limit of detection (LoD) of 2.5 copies/μl of viral transport media. RT-LAMP testing directly on clinical nasopharyngeal swab samples in viral transport media had an 85% positive percentage agreement (PPA) (17/20), and 100% negative percentage agreement (NPV) and delivered results in 30 min. Our optimized RT-LAMP based testing method is a scalable system that is sufficiently sensitive and robust to test for SARS-CoV-2 directly on clinical nasopharyngeal swab samples in viral transport media in 30 min at the point of care without the need for specialized or proprietary equipment or reagents. This cost-effective and efficient one-step testing method can be readily available for COVID-19 testing world-wide, especially in resource poor settings.

scholarly journals Saline collection media and an extraction free workflow enables massively scalable, highly sensitive, and cost-effective SARS-CoV-2 testing

2020 ◽  
Author(s):  
Yan Wei Lim ◽  
Nicole Leonetti ◽  
Aakash Amin ◽  
Henrique Machado ◽  
Natasha Bonilla ◽  
...  
Keyword(s):  
Supply Chain ◽  
Sensitivity And Specificity ◽  
Limit Of Detection ◽  
Rna Extraction ◽  
Cost Effective ◽  
Scaling Up ◽  
Consumption Patterns ◽  
Highly Sensitive ◽  
Processing Steps

Abstract The challenges in scaling up SARS-CoV-2 testing capacity include shortages in the supply chain for consumables and reagents. Improvements in consumption patterns can be obtained through removal of key processing steps, including RNA extraction. Here, we present a scalable and validated extraction-free method for the detection of SARS-CoV-2 from swab specimens in saline, with a limit of detection at 1,000 GCE/mL and a sensitivity and specificity of 100%.

scholarly journals A faster and less costly alternative for RNA extraction of SARS-CoV-2 using proteinase k treatment followed by thermal shock

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248885
Author(s):  
Adolfo Marcelo Ñique ◽  
Fiorella Coronado-Marquina ◽  
Jairo Andrés Mendez Rico ◽  
María Paquita García Mendoza ◽  
Nancy Rojas-Serrano ◽  
...  
Keyword(s):  
Thermal Shock ◽  
Real Time ◽  
Internal Control ◽  
Rna Extraction ◽  
Cost Effective ◽  
Proteinase K ◽  
Rt Pcr ◽  
Critical Material ◽  
Proteinase K Treatment ◽  
Commercial Kit

One of the biggest challenges during the pandemic has been obtaining and maintaining critical material to conduct the increasing demand for molecular tests. Sometimes, the lack of suppliers and the global shortage of these reagents, a consequence of the high demand, make it difficult to detect and diagnose patients with suspected SARS-CoV-2 infection, negatively impacting the control of virus spread. Many alternatives have enabled the continuous processing of samples and have presented a decrease in time and cost. These measures thus allow broad testing of the population and should be ideal for controlling the disease. In this sense, we compared the SARS-CoV-2 molecular detection effectiveness by Real time RT-PCR using two different protocols for RNA extraction. The experiments were conducted in the National Institute of Health (INS) from Peru. We compared Ct values average (experimental triplicate) results from two different targets, a viral and internal control. All samples were extracted in parallel using a commercial kit and our alternative protocol–samples submitted to proteinase K treatment (3 μg/μL, 56°C for 10 minutes) followed by thermal shock (98°C for 5 minutes followed by 4°C for 2 minutes); the agreement between results was 100% in the samples tested. In addition, we compared the COVID-19 positivity between six epidemiological weeks: the initial two in that the Real time RT-PCR reactions were conducted using RNA extracted by commercial kit, followed by two other using RNA obtained by our kit-free method, and the last two using kit once again; they did not differ significantly. We concluded that our in-house method is an easy, fast, and cost-effective alternative method for extracting RNA and conducing molecular diagnosis of COVID-19.

scholarly journals A Streamlined Approach to Rapidly Detect SARS-CoV-2 Infection Avoiding RNA Extraction: Workflow Validation

2020 ◽  
Vol 2020 ◽  
pp. 1-5
Author(s):  
Catia Mio ◽  
Adriana Cifù ◽  
Stefania Marzinotto ◽  
Natascha Bergamin ◽  
Chiara Caldana ◽  
...  
Keyword(s):  
Large Scale ◽  
Rna Extraction ◽  
Cost Effective ◽  
Extraction Methods ◽  
Rapid Identification ◽  
Proteinase K ◽  
Rt Pcr ◽  
Isolation Method ◽  
Pcr Assay ◽  
Sensitivity Specificity

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has rapidly spread worldwide from the beginning of 2020. The presence of viral RNA in samples by nucleic acid (NA) molecular analysis is the only method available to diagnose COVID-19 disease and to assess patients’ viral load. Since the demand for laboratory reagents has increased, there has been a worldwide shortage of RNA extraction kits. We, therefore, developed a fast and cost-effective viral genome isolation method that, combined with quantitative RT-PCR assay, detects SARS-CoV-2 RNA in patient samples. The method relies on the addition of Proteinase K followed by a controlled heat-shock incubation and, then, E gene evaluation by RT-qPCR. It was validated for sensitivity, specificity, linearity, reproducibility, and precision. It detects as low as 10 viral copies/sample, is rapid, and has been characterized in 60 COVID-19-infected patients. Compared to automated extraction methods, our pretreatment guarantees the same positivity rate with the advantage of shortening the time of the analysis and reducing its cost. This is a rapid workflow meant to aid the healthcare system in the rapid identification of infected patients, such as during a pathogen-related outbreak. For its intrinsic characteristics, this workflow is suitable for large-scale screenings.

Regulatory and sustainability initiatives lead to improved polyaminopolyamide epichlorohydrin (PAE) wet-strength resins and paper products

TAPPI Journal ◽  
2018 ◽  
Vol 17 (09) ◽  
pp. 519-532 ◽  
Author(s):  
Mark Crisp ◽  
Richard Riehle
Keyword(s):  
Health And Safety ◽  
Cost Effective ◽  
Worker Safety ◽  
Regulatory Requirements ◽  
Wet Strength ◽  
The Past ◽  
Consumer Safety ◽  
Federal Institute ◽  
Sustainability Initiatives ◽  
The Impact

Polyaminopolyamide-epichlorohydrin (PAE) resins are the predominant commercial products used to manufacture wet-strengthened paper products for grades requiring wet-strength permanence. Since their development in the late 1950s, the first generation (G1) resins have proven to be one of the most cost-effective technologies available to provide wet strength to paper. Throughout the past three decades, regulatory directives and sustainability initiatives from various organizations have driven the development of cleaner and safer PAE resins and paper products. Early efforts in this area focused on improving worker safety and reducing the impact of PAE resins on the environment. These efforts led to the development of resins containing significantly reduced levels of 1,3-dichloro-2-propanol (1,3-DCP) and 3-monochloropropane-1,2-diol (3-MCPD), potentially carcinogenic byproducts formed during the manufacturing process of PAE resins. As the levels of these byproducts decreased, the environmental, health, and safety (EH&S) profile of PAE resins and paper products improved. Recent initiatives from major retailers are focusing on product ingredient transparency and quality, thus encouraging the development of safer product formulations while maintaining performance. PAE resin research over the past 20 years has been directed toward regulatory requirements to improve consumer safety and minimize exposure to potentially carcinogenic materials found in various paper products. One of the best known regulatory requirements is the recommendations of the German Federal Institute for Risk Assessment (BfR), which defines the levels of 1,3-DCP and 3-MCPD that can be extracted by water from various food contact grades of paper. These criteria led to the development of third generation (G3) products that contain very low levels of 1,3-DCP (typically <10 parts per million in the as-received/delivered resin). This paper outlines the PAE resin chemical contributors to adsorbable organic halogens and 3-MCPD in paper and provides recommendations for the use of each PAE resin product generation (G1, G1.5, G2, G2.5, and G3).

Green Synthesis and Spectroscopic Studies of Ag-rGO Nanocomposites for Highly Selective Mercury (II) Sensing

2018 ◽  
Vol 9 (1) ◽  
pp. 101-108 ◽  
Author(s):  
Shubhangi J. Mane-Gavade ◽  
Sandip R. Sabale ◽  
Xiao-Ying Yu ◽  
Gurunath H. Nikam ◽  
Bhaskar V. Tamhankar
Keyword(s):  
Green Synthesis ◽  
Color Change ◽  
Limit Of Detection ◽  
Aqueous Media ◽  
Suitable Condition ◽  
Cost Effective ◽  
Spectroscopic Studies ◽  
Calibration Plot ◽  
First Time

Introduction: Herein we report the green synthesis and characterization of silverreduced graphene oxide nanocomposites (Ag-rGO) using Acacia nilotica gum for the first time. Experimental: We demonstrate the Hg2+ ions sensing ability of the Ag-rGO nanocomposites form aqueous medium. The developed colorimetric sensor method is simple, fast and selective for the detection of Hg2+ ions in aqueous media in presence of other associated ions. A significant color change was noticed with naked eye upon Hg2+ addition. The color change was not observed for cations including Sr2+, Ni2+, Cd2+, Pb2+, Mg2+, Ca2+, Fe2+, Ba2+ and Mn2+indicating that only Hg2+ shows a strong interaction with Ag-rGO nanocomposites. Under the most suitable condition, the calibration plot (A0-A) against concentration of Hg2+ was linear in the range of 0.1-1.0 ppm with a correlation coefficient (R2) value 0.9998. Results & Conclusion The concentration of Hg2+ was quantitatively determined with the Limit of Detection (LOD) of 0.85 ppm. Also, this method shows excellent selectivity towards Hg2+ over nine other cations tested. Moreover, the method offers a new cost effective, rapid and simple approach for the detection of Hg2+ in water samples.

scholarly journals Pitfalls in the Immunochemical Determination of β‑Lactam Antibiotics in Water

Antibiotics ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 298
Author(s):  
Alexander Ecke ◽  
Rudolf J. Schneider
Keyword(s):  
Limit Of Detection ◽  
Cost Effective ◽  
Enzyme Linked Immunosorbent Assay ◽  
Degree Of Hydrolysis ◽  
Site Analysis ◽  
Antibody Recognition ◽  
Immunochemical Determination ◽  
Key Factor ◽  
Lactam Ring

Contamination of waters with pharmaceuticals is an alarming problem as it may support the evolution of antimicrobial resistance. Therefore, fast and cost-effective analytical methods for potential on-site analysis are desired in order to control the water quality and assure the safety of its use as a source of drinking water. Antibody-based methods, such as the enzyme-linked immunosorbent assay (ELISA), can be helpful in this regard but can also have certain pitfalls in store, depending on the analyte. As shown here for the class of β-lactam antibiotics, hydrolysis of the β‑lactam ring is a key factor in the immunochemical analysis as it influences antibody recognition. With the antibody used in this study, the limit of detection (LOD) in the immunoassay could be significantly reduced by hydrolysis for the five tested penicillins, with the lowest LOD for carbenicillin (0.2 nmol/L) and the greatest impact on penicillins G and V (reduction by 85%). In addition to enhanced quantification, our strategy also provides access to information about the degree of hydrolysis in water samples as shown for the most abundant penicillin amoxicillin.

scholarly journals Urine lipoarabinomannan in HIV uninfected, smear negative, symptomatic TB patients: effective sample pretreatment for a sensitive immunoassay and mass spectrometry

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Anita G. Amin ◽  
Prithwiraj De ◽  
Barbara Graham ◽  
Roger I. Calderon ◽  
Molly F. Franke ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
Sample Pretreatment ◽  
Positive Association ◽  
Proteinase K ◽  
Clinical Samples ◽  
Sputum Smear ◽  
Smear Negative ◽  
Tuberculostearic Acid ◽  
Negative Sputum ◽  
Adult Culture

AbstractOur study sought to determine whether urine lipoarabinomannan (LAM) could be validated in a sample cohort that consisted mainly of HIV uninfected individuals that presented with tuberculosis symptoms. We evaluated two tests developed in our laboratory, and used them on clinical samples from Lima, Peru where incidence of HIV is low. ELISA analysis was performed on 160 samples (from 140 adult culture-confirmed TB cases and 20 symptomatic TB-negative child controls) using 100 μL of urine after pretreatment with Proteinase K. Two different mouse monoclonal antibodies-CS35 and CHCS9-08 were used individually for capture of urine LAM. Among cases, optical density (OD450) values had a positive association with higher bacillary loads. The 20 controls had negative values (below the limit of detection). The assay correctly identified all samples (97–100% accuracy confidence interval). For an alternate validation of the ELISA results, we analyzed all 160 urine samples using an antibody independent chemoanalytical approach. Samples were called positive only when LAM surrogates—tuberculostearic acid (TBSA) and d-arabinose (d-ara)—were found to be present in similar amounts. All TB cases, including the 40 with a negative sputum smear had LAM in detectable quantities in urine. None of the controls had detectable amounts of LAM. Our study shows that urinary LAM detection is feasible in HIV uninfected, smear negative TB patients.

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