scholarly journals Stability of SARS-CoV-2 RNA in Viral Lysis Buffer Stored at Different Temperatures

2020 ◽  
Vol 12 (04) ◽  
pp. 268-270
Author(s):  
Nagaraj Perumal ◽  
Rajeev Kumar Jain ◽  
Rakesh Shrivastava ◽  
Jaya Lalwani ◽  
Deepti Chaurasia
Keyword(s):  
Diagnostic Testing ◽  
Rna Extraction ◽  
Delayed Diagnosis ◽  
Viral Rna ◽  
Molecular Diagnostic ◽  
Viral Lysis ◽  
Specimen Processing ◽  
Different Temperatures ◽  
Lysis Buffer ◽  
The Stability

Abstract Objectives The present COVID-19 pandemic resulted in an increased need for molecular diagnostic testing. Delay in the specimen processing and suboptimal storage of suspected samples in laboratories leads to degradation of SARS-CoV-2 viral RNA. Viral lysis buffers from RNA extraction kits have the potential to stabilize RNA. Hence, this study aimed to investigate the stability of SARS-CoV-2 RNA in viral lysis buffer at different temperatures and time periods. Materials and Methods Aliquots of samples with known SARS-CoV-2 RNA were processed in viral lysis buffers simultaneously, stored separately at 2 to 8°C and 22 to 28°C for 24 hours, 48 hours and 72 hours. SARS-CoV-2 viral RNA was extracted from each aliquot and analyzed using multiplex real-time PCR. Results SARS-CoV-2 RNA in samples placed in viral lysis buffer was stable for 48 hours at both 2 to 8°C and 22 to 28°C temperatures. Slight decline in the viral RNA quantity was found on aliquots tested after 48 hours of both the temperatures. Conclusions Viral lysis buffer maintains the integrity of SARS-CoV-2 RNA for up to 48 hours even at room temperature and supports delayed diagnosis with an overwhelming sample load in testing laboratories.

scholarly journals Evaluation of Chemical Protocols for Inactivating SARS-CoV-2 Infectious Samples

Viruses ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 624 ◽  
Author(s):  
Boris Pastorino ◽  
Franck Touret ◽  
Magali Gilles ◽  
Lea Luciani ◽  
Xavier de Lamballerie ◽  
...  
Keyword(s):  
Culture Supernatant ◽  
Rna Extraction ◽  
Cell Culture Supernatant ◽  
Molecular Diagnostic ◽  
Clinical Samples ◽  
European Standard ◽  
Lysis Buffer ◽  
Level 2 ◽  
Biosafety Level ◽  
Chaotropic Agents

Clinical samples collected in coronavirus disease 19 (COVID-19), patients are commonly manipulated in biosafety level 2 laboratories for molecular diagnostic purposes. Here, we tested French norm NF-EN-14476+A2 derived from European standard EN-14885 to assess the risk of manipulating infectious viruses prior to RNA extraction. SARS-CoV-2 cell-culture supernatant and nasopharyngeal samples (virus-spiked samples and clinical samples collected in COVID-19 patients) were used to measure the reduction of infectivity after 10 min contact with lysis buffer containing various detergents and chaotropic agents. A total of thirteen protocols were evaluated. Two commercially available formulations showed the ability to reduce infectivity by at least 6 log 10, whereas others proved less effective.

scholarly journals Extraction-free rapid cycle RT-qPCR and extreme RT-PCR for SARS-CoV-2 virus detection

2021 ◽  
Vol 156 (Supplement_1) ◽  
pp. S139-S139
Author(s):  
J C Lownik ◽  
J S Farrar ◽  
G Way ◽  
R K Martin
Keyword(s):  
Supply Chain ◽  
Diagnostic Testing ◽  
Rna Extraction ◽  
Virus Detection ◽  
Detection Methods ◽  
Molecular Diagnostic ◽  
Sample Collection ◽  
Rt Pcr ◽  
Hydrolysis Probe ◽  
Time Requirements

Abstract Introduction/Objective Since the start of the coronavirus disease 2019 (COVID-19) pandemic, molecular diagnostic testing for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has faced substantial supply chain shortages and noteworthy delays in result reporting after sample collection. Supply chain shortages have been most evident in reagents for RNA extraction and rapid diagnostic testing. In this study, we explored the kinetic limitations of extraction-free rapid cycle RT-qPCR for SARS-CoV-2 virus detection using the commercially available capillary based LightCycler. Methods/Case Report We optimized reverse transcription and PCR under extraction-free and rapid thermocycling conditions utilizing hydrolysis probe-based detection methods using a Roche LightCycler. Results (if a Case Study enter NA) This protocol improves detection speed while maintaining the sensitivity and specificity of hydrolysis probe-based detection. Percentage agreement between the developed assay and previously tested positive patient samples was 97.6% (n= 40/41) and negative patient samples was 100% (40/40). We further demonstrate that using purified RNA, SARS-CoV-2 testing using extreme RT-PCR and product verification by melting can be completed in less than 3 minutes. Conclusion We developed a protocol for sensitive and specific RT-qPCR of SARS-CoV-2 RNA from nasopharyngeal swabs in less than 20 minutes, with minimal hands-on time requirements. Overall, these studies provide a framework for increasing the speed of SARS-CoV-2 and other infectious disease testing.

scholarly journals Investigation of pooling strategies using clinical COVID-19 samples for more efficient diagnostic testing

2020 ◽  
Author(s):  
Samantha H Adikari ◽  
Emily Z Alipio Lyon ◽  
Attelia D Hollander ◽  
Alina Deshpande ◽  
Elizabeth Hong-Geller
Keyword(s):  
Diagnostic Testing ◽  
Rna Extraction ◽  
Positive Sample ◽  
Viral Rna ◽  
Clinical Samples ◽  
Extraction Column ◽  
Diagnostic Assay ◽  
Significant Difference ◽  
Pooling Strategies ◽  
Single Positive

When testing large numbers of clinical COVID-19 samples for diagnostic purposes, pooling samples together for processing can offer significant reductions in the materials, reagents, time, and labor needed. We have evaluated two different strategies for pooling independent nasopharyngeal swab samples prior to testing with an EUA-approved SARS-CoV-2 RT-qPCR diagnostic assay. First, in the Dilution Study, we assessed the assay's ability to detect a single positive clinical sample diluted in multiple negative samples before the viral RNA extraction stage. We observed that positive samples with Ct values at ~30 can be reliably detected in pools of up to 30 independent samples, and positive samples with Ct values at ~35 can be detected in pools of 5 samples. Second, in the Reloading Study, we assessed the efficacy of reloading QIAamp viral RNA extraction columns numerous times using a single positive sample and multiple negative samples. We determined that one RNA extraction column can be reloaded with up to 20 clinical samples (1 positive and 19 negatives) sequentially without any loss of signal in the diagnostic assay. Furthermore, we found there was no significant difference in assay readout whether the positive sample was loaded first or last in a series of 20 samples. These results demonstrate that different pooling strategies can lead to increased process efficiencies for COVID-19 clinical diagnostic testing.

scholarly journals Optimizing PCR Detection of West Nile Virus from Body Fluid Specimens to Delineate Natural History in an Infected Human Cohort

2019 ◽  
Vol 20 (8) ◽  
pp. 1934 ◽  
Author(s):  
Rodion Gorchakov ◽  
Bonnie E. Gulas-Wroblewski ◽  
Shannon E. Ronca ◽  
Jeanne C. Ruff ◽  
Melissa S. Nolan ◽  
...  
Keyword(s):  
West Nile Virus ◽  
Natural History ◽  
Diagnostic Testing ◽  
Rna Extraction ◽  
Pcr Detection ◽  
Viral Rna ◽  
Health Concern ◽  
West Nile ◽  
Viral Loads ◽  
History Of

West Nile virus (WNV), a mosquito-borne arbovirus, remains a major global health concern. In this study, we optimized PCR methods then assessed serially-collected whole blood (WB), urine (UR), saliva, and semen specimens from a large cohort of WNV-positive participants to evaluate the natural history of infection and persistent shedding of WNV RNA. Viral RNA extraction protocols for frozen WB and UR specimens were optimized and validated through spiking experiments to maximize recovery of viral RNA from archived specimens and to assess the degradation of WNV RNA in stored UR specimens. The resultant procedures were used in conjunction with PCR detection to identify WNV-positive specimens and to quantify their viral loads. A total of 59 of 352 WB, 10 of 38 UR, and 2 of 34 saliva specimens tested positive for WNV RNA. Although a single semen specimen was positive 22 days post onset, we could not definitively confirm the presence of WNV RNA in the remaining specimens. WNV RNA-positive UR specimens exhibited profound loss of viral RNA during storage, highlighting the need for optimal preservation pre-storage. This study provides optimized methods for WNV RNA detection among different fluid types and offers alternative options for diagnostic testing during the acute stages of WNV.

scholarly journals Simplified Magnetic Bead Based Viral RNA Extraction for Rapid Detection of COVID-19

2021 ◽  
Author(s):  
Shashi Sharma ◽  
Deepak Pardasani ◽  
Pooja Yadav ◽  
Jyoti S Kumar ◽  
Suman Dhankher ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Extraction Method ◽  
Molecular Detection ◽  
Virus Disease ◽  
Detection System ◽  
Rna Extraction ◽  
Magnetic Bead ◽  
Viral Rna ◽  
Molecular Diagnostic ◽  
Magnetic Extraction

Abstract Rapid and large-scale diagnosis has helped in mitigation the recent ongoing pandemic of corona virus disease of 2019 (COVID-19). The pandemic had a devastating effect on global economy. The molecular detection system has evolved over last two decades and is rapidly replacing the conventional confirmatory techniques in diagnostic virology. However the major limitation in implementation of available molecular detection assays is the non availability of field deployable nucleic acid isolation platform. The standard laboratory diagnosis rely on confirmation of presence of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in respiratory specimens of suspected patients. Preparation of viral nucleic acid is a critical step involved followed by downstream molecular diagnostic platforms. For good quality of viral RNA extraction many commercial extraction kits, are available. These are developed in a surge of pandemic scenario keeping in view the large demand for testing. The commercial RNA extraction kits available on either column based or magnetic extraction are limited and, alternative, non-commercial protocols are rapidly required. Here, we have standardized an in-house magnetic bead RNA extraction method which utilises simple in-house reagents and manual extraction method that doesn’t require any high-end equipments. The in-house assay was evaluated against the commercial available silica column and magnetic extraction kits using a panel of 100 throat /nasal swab samples. A high correlation in viral RNA detection with TaqMan qRT-PCR was observed with excellent sensitivity and specificity. Interestingly, the developed method is very simple, cost effective, rapid and can be quickly add up any downstream amplification platform for SARS-CoV-2 detection.

scholarly journals 458. Molecular SARS-CoV-2 Testing During the COVID-19 Outbreak: Experiences of a Hospital in Southeast Michigan, USA

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S296-S297
Author(s):  
Trini A Mathew ◽  
Jonathan Hopkins ◽  
Diane Kamerer ◽  
Shagufta N Ali ◽  
Daniel Ortiz ◽  
...  
Keyword(s):  
Clinical Features ◽  
Diagnostic Testing ◽  
Beaumont Hospital ◽  
High Capacity ◽  
Turnaround Time ◽  
Molecular Diagnostic ◽  
The Novel ◽  
Repeat Testing ◽  
Asymptomatic Patients ◽  
Novel Coronavirus

Abstract Background The novel Coronavirus SARS CoV-2 (COVID-19) outbreak was complicated by the lack of diagnostic testing kits. In early March 2020, leadership at Beaumont Hospital, Royal Oak Michigan (Beaumont) identified the need to develop high capacity testing modalities with appropriate sensitivity and specificity and rapid turnaround time. We describe the molecular diagnostic testing experience since initial rollout on March 16, 2020 at Beaumont, and results of repeat testing during the peak of the COVID-19 pandemic in MI. Methods Beaumont is an 1100 bed hospital in Southeast MI. In March, testing was initially performed with the EUA Luminex NxTAG CoV Extended Panel until March 28, 2020 when testing was converted to the EUA Cepheid Xpert Xpress SARS-CoV-2 for quicker turnaround times. Each assay was validated with a combination of patient samples and contrived specimens. Results During the initial week of testing there was > 20 % specimen positivity. As the prevalence grew the positivity rate reached 68% by the end of March (Figure 1). Many state and hospital initiatives were implemented during the outbreak, including social distancing and screening of asymptomatic patients to increase case-finding and prevent transmission. We also adopted a process for clinical review of symptomatic patients who initially tested negative for SARS-CoV-2 by a group of infectious disease physicians (Figure 2). This process was expanded to include other trained clinicians who were redeployed from other departments in the hospital. Repeat testing was performed to allow consideration of discontinuation of isolation precautions. During the surge of community cases from March 16 to April 30, 2020, we identified patients with negative PCR tests who subsequently had repeat testing based on clinical evaluation, with 7.1% (39/551) returning positive for SARS- CoV2. Of the patients who expired due to COVID-19 during this period, 4.3% (9/206) initially tested negative before ultimately testing positive. Figure 1 BH RO testing Epicurve Figure 2: Screening tool for repeat COVID19 testing and precautions Conclusion Many state and hospital initiatives helped us flatten the curve for COVID-19. Our hospital testing experience indicate that repeat testing may be warranted for those patients with clinical features suggestive of COVID-19. We will further analyze these cases and clinical features that prompted repeat testing. Disclosures All Authors: No reported disclosures

scholarly journals A Superhydrophobic, Antibacterial, and Durable Surface of Poplar Wood

Nanomaterials ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1885
Author(s):  
Xinyu Wu ◽  
Feng Yang ◽  
Jian Gan ◽  
Zhangqian Kong ◽  
Yan Wu
Keyword(s):  
Stearic Acid ◽  
Antibacterial Properties ◽  
Alkali Resistance ◽  
Poplar Wood ◽  
X Ray Diffraction ◽  
X Ray ◽  
Different Temperatures ◽  
Acid And Alkali Resistance ◽  
The Stability

The silver particles were grown in situ on the surface of wood by the silver mirror method and modified with stearic acid to acquire a surface with superhydrophobic and antibacterial properties. Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), and X-ray energy spectroscopy (XPS) were used to analyze the reaction mechanism of the modification process. Scanning electron microscopy (SEM) and contact angle tests were used to characterize the wettability and surface morphology. A coating with a micro rough structure was successfully constructed by the modification of stearic acid, which imparted superhydrophobicity and antibacterial activity to poplar wood. The stability tests were performed to discuss the stability of its hydrophobic performance. The results showed that it has good mechanical properties, acid and alkali resistance, and UV stability. The durability tests demonstrated that the coating has the function of water resistance and fouling resistance and can maintain the stability of its hydrophobic properties under different temperatures of heat treatment.

scholarly journals An assessment of methanolysis and other factors used in the analysis of carbohydrate-containing materials

1971 ◽  
Vol 125 (4) ◽  
pp. 1009-1018 ◽  
Author(s):  
R. E. Chambers ◽  
J. R. Clamp
Keyword(s):  
Hydrochloric Acid ◽  
Analytical Procedure ◽  
Internal Standard ◽  
Inorganic Contaminants ◽  
Rotary Evaporation ◽  
Silver Salts ◽  
Methanolic Hydrochloric Acid ◽  
Different Temperatures ◽  
The Stability ◽  
Analytical System

The stability of monosaccharides in methanolic hydrochloric acid of different strengths and at different temperatures was determined. They are generally stable for 24h in methanolic 1m- and 2m-hydrochloric acid at both 85°C and 100°C, but undergo considerable destruction in methanolic 4m- and 6m-hydrochloric acid at 100°C. Analysis of glycopeptides and oligosaccharides of known composition showed that release of carbohydrate was complete within 3h in methanolic 1m-hydrochloric acid at 85°C. Removal of methanolic hydrochloric acid by rotary evaporation resulted in considerable losses of monosaccharides, which could be prevented by prior neutralization. Methanolysis caused extensive de-N-acetylation of acetamidohexoses, so that a re-N-acetylation step is necessary in the analytical procedure. The addition of acetic anhydride for this purpose also prevented loss of internal standard by adsorption on the insoluble silver salts used in neutralization. Several trimethylsilylating agents were studied and suitable conditions are recommended. The effects on the analytical system of water and some common organic and inorganic contaminants are assessed.

scholarly journals Influence of study model, baseline catalytic concentrations and analytical system on the stability of serum alanine aminotransferase

2020 ◽  
Vol 1 (2) ◽  
Author(s):  
Josep Miquel Bauça ◽  
Andrea Caballero ◽  
Carolina Gómez ◽  
Débora Martínez-Espartosa ◽  
Isabel García del Pino ◽  
...  
Keyword(s):  
Alanine Aminotransferase ◽  
Experimental Models ◽  
Individual Variability ◽  
Serum Samples ◽  
Multicentric Study ◽  
Different Temperatures ◽  
The Stability ◽  
Analytical System ◽  
Definition Of ◽  
Analytical Platforms

AbstractObjectivesThe stability of the analytes most commonly used in routine clinical practice has been the subject of intensive research, with varying and even conflicting results. Such is the case of alanine aminotransferase (ALT). The purpose of this study was to determine the stability of serum ALT according to different variables.MethodsA multicentric study was conducted in eight laboratories using serum samples with known initial catalytic concentrations of ALT within four different ranges, namely: <50 U/L (<0.83 μkat/L), 50–200 U/L (0.83–3.33 μkat/L), 200–400 U/L (3.33–6.67 μkat/L) and >400 U/L (>6.67 μkat/L). Samples were stored for seven days at two different temperatures using four experimental models and four laboratory analytical platforms. The respective stability equations were calculated by linear regression. A multivariate model was used to assess the influence of different variables.ResultsCatalytic concentrations of ALT decreased gradually over time. Temperature (−4%/day at room temperature vs. −1%/day under refrigeration) and the analytical platform had a significant impact, with Architect (Abbott) showing the greatest instability. Initial catalytic concentrations of ALT only had a slight impact on stability, whereas the experimental model had no impact at all.ConclusionsThe constant decrease in serum ALT is reduced when refrigerated. Scarcely studied variables were found to have a significant impact on ALT stability. This observation, added to a considerable inter-individual variability, makes larger studies necessary for the definition of stability equations.

Sign in / Sign up

Export Citation Format

Share Document