scholarly journals Comparison of two commercial platforms and a laboratory developed test for detection of SARS-CoV-2 RNA

2020 ◽  
Author(s):  
Laura Mannonen ◽  
Hannimari Kallio-Kokko ◽  
Raisa Loginov ◽  
Anu Jaaskelainen ◽  
Pia Jokela ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
The Other ◽  
Nucleic Acid Testing ◽  
Reference Standard ◽  
Critical Importance ◽  
Clinical Laboratories ◽  
Percent Agreement ◽  
Hands On ◽  
Respiratory Specimens ◽  
Higher Sensitivity

Mitigation of the ongoing COVID-19 pandemic requires reliable and accessible laboratory diagnostic services. We evaluated the performance of one LDT and two commercial tests, cobas® SARS-CoV-2 (Roche) and Amplidiag® COVID-19 (Mobidiag), for the detection of SARS-CoV-2 RNA in respiratory specimens. 183 specimens collected from suspected COVID-19 patients were studied with all three methods to compare their performance. In relation to the reference standard, which was established as the result obtained by two of the three studied methods, the positive percent agreement (PPA) was highest for cobas® test (100%), followed by Amplidiag® test and the LDT (98.9%). The negative percent agreement (NPA) was lowest for cobas® test (89.4%), followed by Amplidiag® test (98.8%) and the highest value was obtained for LDT (100%). The dilution series conducted for specimens, however, suggests significantly higher sensitivity for the cobas® assay in comparison with the other two assays and the low NPA value may be due to the same reason. In general, all tested assays performed adequately. Both the time from sample to result and hands-on time per sample were shortest for cobas® test. Clinical laboratories need to be prepared for uninterrupted high-throughput testing during the coming months in mitigation of the pandemic. To secure that, it is of critical importance for clinical laboratories to maintain several simultaneous platforms in their SARS-CoV-2 nucleic acid testing.

scholarly journals Equipment-free detection of SARS-CoV-2 and Variants of Concern using Cas13

2021 ◽  
Author(s):  
Jon Arizti-Sanz ◽  
A'Doriann Bradley ◽  
Yibin B. Zhang ◽  
Chloe K. Boehm ◽  
Catherine A. Freije ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
State Of The Art ◽  
Test Procedure ◽  
Nucleic Acid Testing ◽  
Sample Processing ◽  
Important Advance ◽  
Clinical Laboratories ◽  
Antigen Capture ◽  
Alpha Beta ◽  
Temperature Sample

The COVID-19 pandemic, and the recent rise and widespread transmission of SARS-CoV-2 Variants of Concern (VOCs), have demonstrated the need for ubiquitous nucleic acid testing outside of centralized clinical laboratories. Here, we develop SHINEv2, a Cas13-based nucleic acid diagnostic that combines quick and ambient temperature sample processing and lyophilized reagents to greatly simplify the test procedure and assay distribution. We benchmarked a SHINEv2 assay for SARS-CoV-2 detection against state-of-the-art antigen-capture tests using 96 patient samples, demonstrating 50-fold greater sensitivity and 100% specificity. We designed SHINEv2 assays for discriminating the Alpha, Beta, Gamma and Delta VOCs, which can be read out visually using lateral flow technology. We further demonstrate that our assays can be performed without any equipment in less than 90 minutes. SHINEv2 represents an important advance towards rapid nucleic acid tests that can be performed in any location.

scholarly journals Diagnostic Performance of Multiplex Nucleic Acid Testing of Bronchoalveolar Lavage and Bronchial Wash Specimens for Respiratory Viral Pathogens

2018 ◽  
Vol 56 (10) ◽  
Author(s):  
Satish Munigala ◽  
Carey-Ann D. Burnham ◽  
Neil W. Anderson ◽  
Stephen Y. Liang ◽  
Steven J. Lawrence ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Bronchoalveolar Lavage ◽  
Individual Performance ◽  
Performance Characteristics ◽  
Respiratory Pathogens ◽  
Nucleic Acid Testing ◽  
Viral Pathogens ◽  
Percent Agreement ◽  
Single Instance ◽  
Bronchial Wash

ABSTRACTThere is limited knowledge on the yield of performing multiplex nucleic acid testing (NAT) on multiple lower respiratory tract specimens from a single patient with a single instance of infection. We evaluated the performance characteristics of multiplex NAT assays performed concurrently on bronchoalveolar lavage (BAL) and bronchial wash (BW) specimens to detect respiratory pathogens. A retrospective study of admitted patients from March 2013 through December 2016 was performed. Individual performance characteristics of BAL and BW specimens were compared to positive results from either set of specimens. Only contemporaneous BAL and BW specimens (received by the laboratory within 4 h of each other) were included. The final cohort included 170 patients, with 184 contemporaneous BAL and BW specimens submitted for multiplex NAT (median age, 58 years; 62% male). Of the patients with positive NAT results, 38 of 40 BW specimens tested positive (overall percent agreement with combined testing, 98.9%; 95% confidence interval [CI], 95.5 to 98.9%), and 34 of 40 BAL specimens tested positive (overall percent agreement with combined testing, 96.7%; 95% CI, 93.0 to 96.7%). Assays performed on BW specimens identified 4 additional specimens and had a higher positive percent agreement (95.0%) with combined testing results compared to those performed on BAL specimens (85.0%). There was exact concordance in 174 specimens (94.6%; negative and positive for respiratory pathogens, 144 and 34 specimens, respectively). We observed high concordance (95%) between multiplex NAT results from contemporaneous BAL and BW specimens. Performance characteristics of BW specimen testing were equivalent to those of BAL specimen testing. The benefit of performing additional testing should be carefully considered against the potential complications and health care costs.

Infection of Escherichia coli with bacteriophages

1969 ◽  
Vol 27 ◽  
pp. 370-371
Author(s):  
Manfred E. Bayer
Keyword(s):  
Escherichia Coli ◽  
Nucleic Acid ◽  
Cell Surface ◽  
Virus Type ◽  
Infection Process ◽  
Adsorption Site ◽  
The Other ◽  
Specific Receptors ◽  
Bacterial Receptors

The first step in the infection of a bacterium by a virus consists of a collision between cell and bacteriophage. The presence of virus-specific receptors on the cell surface will trigger a number of events leading eventually to release of the phage nucleic acid. The execution of the various "steps" in the infection process varies from one virus-type to the other, depending on the anatomy of the virus. Small viruses like ØX 174 and MS2 adsorb directly with their capsid to the bacterial receptors, while other phages possess attachment organelles of varying complexity. In bacteriophages T3 (Fig. 1) and T7 the small conical processes of their heads point toward the adsorption site; a welldefined baseplate is attached to the head of P22; heads without baseplates are not infective.

scholarly journals Atomic Force Microscopy Investigation of the Interactions between the MCM Helicase and DNA

Materials ◽  
2021 ◽  
Vol 14 (3) ◽  
pp. 687
Author(s):  
Amna Abdalla Mohammed Khalid ◽  
Pietro Parisse ◽  
Barbara Medagli ◽  
Silvia Onesti ◽  
Loredana Casalis
Keyword(s):  
Atomic Force Microscopy ◽  
Nucleic Acid ◽  
Single Molecule ◽  
Protein Complex ◽  
The Other ◽  
Contour Length ◽  
Force Microscopy ◽  
Atomic Force ◽  
Mcm Complex ◽  
Dna Double Helix

The MCM (minichromosome maintenance) protein complex forms an hexameric ring and has a key role in the replication machinery of Eukaryotes and Archaea, where it functions as the replicative helicase opening up the DNA double helix ahead of the polymerases. Here, we present a study of the interaction between DNA and the archaeal MCM complex from Methanothermobacter thermautotrophicus by means of atomic force microscopy (AFM) single molecule imaging. We first optimized the protocol (surface treatment and buffer conditions) to obtain AFM images of surface-equilibrated DNA molecules before and after the interaction with the protein complex. We discriminated between two modes of interaction, one in which the protein induces a sharp bend in the DNA, and one where there is no bending. We found that the presence of the MCM complex also affects the DNA contour length. A possible interpretation of the observed behavior is that in one case the hexameric ring encircles the dsDNA, while in the other the nucleic acid wraps on the outside of the ring, undergoing a change of direction. We confirmed this topographical assignment by testing two mutants, one affecting the N-terminal β-hairpins projecting towards the central channel, and thus preventing DNA loading, the other lacking an external subdomain and thus preventing wrapping. The statistical analysis of the distribution of the protein complexes between the two modes, together with the dissection of the changes of DNA contour length and binding angle upon interaction, for the wild type and the two mutants, is consistent with the hypothesis. We discuss the results in view of the various modes of nucleic acid interactions that have been proposed for both archaeal and eukaryotic MCM complexes.

Elevated white blood cell count does not predict Clostridium difficile nucleic acid testing results

2021 ◽  
Author(s):  
Dustin E Bosch ◽  
Patrick C Mathias ◽  
Niklas Krumm ◽  
Andrew Bryan ◽  
Ferric C Fang ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Clostridium Difficile ◽  
Blood Cell ◽  
Cell Count ◽  
Prognostic Marker ◽  
White Blood Cell Count ◽  
White Blood Cell ◽  
Inpatient Setting ◽  
Nucleic Acid Testing ◽  
Blood Cell Count

Abstract Background An elevated white blood cell count (>15 thousand/μL) is an established prognostic marker in patients with Clostridium difficile infection (CDI). Small observational studies have suggested that a markedly elevated WBC should prompt consideration of CDI. However, there is limited evidence correlating WBC elevation with the results of C. difficile nucleic acid testing (NAAT). Methods Retrospective review of laboratory testing, outcomes, and treatment of 16,568 consecutive patients presenting to 4 hospitals over four years with NAAT and WBC testing on the same day. Results No significant relationship between C. difficile NAAT results and concurrent WBC in the inpatient setting was observed. Although an elevated WBC did predict NAAT results in the outpatient and emergency department populations (p<0.001), accuracy was poor, with receiver-operator areas under the curve of 0.59 and 0.56. An elevated WBC (>15 thousand/μL) in CDI was associated with a longer median hospital length of stay (15.5 vs. 11.0 days, p<0.01), consistent with leukocytosis as a prognostic marker in CDI. NAAT-positive inpatients with elevated WBC were more likely to be treated with metronidazole and/or vancomycin (relative ratio 1.2, 95% confidence interval 1.1–1.3) and die in the hospital (relative ratio 2.9, 95% CI 2.0–4.3). Conclusions Although WBC is an important prognostic indicator in patients with CDI, an isolated WBC elevation has low sensitivity and specificity as a predictor of fecal C. difficile NAAT positivity in the inpatient setting. A high or rising WBC in isolation is not a sufficient indication for CDI testing.

scholarly journals Are RNA-Based Tests Sufficient for COVID-19 Diagnosis? An Inspiration of Three Asymptomatic Cases

2021 ◽  
Vol 30 ◽  
pp. 096368972098545
Author(s):  
Tao Hu ◽  
Xiao Liu ◽  
Qinan Yin ◽  
Xingting Duan ◽  
Li Yan
Keyword(s):  
Computed Tomography ◽  
Nucleic Acid ◽  
Virus Infection ◽  
Severe Acute Respiratory Syndrome ◽  
The Other ◽  
Computed Tomography Scan ◽  
Health Authorities ◽  
History Of ◽  
Tomography Scan ◽  
Nucleic Acid Tests

In this work, we discovered a new phenomenon—asymptomatic COVID-19 infection, or covert case, during the pandemic. All the 3 patients had a history of exposure, with no symptoms, and no abnormalities were found in computed tomography scan or lab tests. Except for case 2, the other patients’ severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) nucleic acid tests were negative. But their anti-SARS-COV-2 nucleocapsid antibody showed a dynamic trend, consistent with the process of virus infection and clearance. A growing number of asymptomatic or covert cases need more attention. Lack of surveillance may lead to another outbreak. We hope to demonstrate our cases to attract the attention of governments or health authorities that covert cases should be the focus as well.

scholarly journals Comprehensive large-scale nucleic acid–testing strategies support China’s sustained containment of COVID-19

2021 ◽  
Author(s):  
Zhongjie Li ◽  
Fengfeng Liu ◽  
Jinzhao Cui ◽  
Zhibin Peng ◽  
Zhaorui Chang ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Large Scale ◽  
Nucleic Acid Testing ◽  
Testing Strategies

Peptide synthesis in bone marrow: insulin and thyroxin effects

1962 ◽  
Vol 203 (4) ◽  
pp. 693-696 ◽  
Author(s):  
Thomas F. Necheles
Keyword(s):  
Bone Marrow ◽  
Nucleic Acid ◽  
Peptide Synthesis ◽  
Ribonucleic Acid ◽  
Deoxyribonucleic Acid ◽  
Optimum Concentration ◽  
The Other ◽  
Anabolic Effect ◽  
Oxygen Buffer

Myeloid marrow was rapidly removed from femurs of fasting young rabbits, sectioned, and incubated in Krebs-bicarbonate-CO2-oxygen buffer with appropriate C14-labeled precursors. All manipulations were designed to preserve the architecture of the tissue. After 1 hr the protein or nucleic acid-adenine was isolated and purified. Insulin, 0.01 U/ml added in vitro, stimulated histidine-2(ring)-C14 incorporation into protein by 26 ± 1.4%; alkali-treated insulin was inactive. Thyroxin elicited a 49.4 ± 2.1% stimulation at an optimum concentration of 10–7 m. Triiodothyronine, but not diiodothyronine, also had a significant effect. Insulin increased incorporation of carbon from adenosine-8-C14 into adenine of ribonucleic acid and deoxyribonucleic acid. Thyroxin, on the other hand, was without consistent effect on this process. Thyroxin stimulated significantly the incorporation of C14 of glycine-2-C14 into adenine. The possibility that part of the anabolic effect of thyroxin on bone marrow may arise from a stimulus to incorporation of precursors into purines is suggested.

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