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

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.

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

10.1101/2020.07.03.20144758 ◽

2020 ◽

Cited By ~ 3

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.

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Spanish society of laboratory medicine external quality assurance programmes: evolution of the analytical performance of clinical laboratories over 30 years and comparison with other programmes

Advances in Laboratory Medicine / Avances en Medicina de Laboratorio ◽

10.1515/almed-2020-0019 ◽

2020 ◽

Vol 1 (2) ◽

Author(s):

Carmen Perich ◽

Carmen Ricós ◽

Fernando Marqués ◽

Joana Minchinela ◽

Angel Salas ◽

...

Keyword(s):

Quality Assurance ◽

State Of The Art ◽

Laboratory Medicine ◽

Analytical Performance ◽

External Quality Assurance ◽

Biological Variability ◽

External Quality ◽

Spanish Society ◽

Clinical Laboratories ◽

Quality Specifications

AbstractThe purpose of this study is to understand the evolution of the analytical performance of the laboratories participating in the Spanish society of laboratory medicine (SEQCML) external quality assurance (EQA) programmes during its 30 years of operation and to compare it with the performance of other EQA programmes to establish whether the results are similar. The results obtained during this period are evaluated by applying the biological variability (BV) and state of the art-derived quality specifications. In addition, the results are compared with those obtained by other EQA programme organisations. It is noted that the laboratories participating in the EQA–SEQCML programmes have improved their performance over 30 years of experience and that the specifications derived from biological variation are achievable. It is difficult to compare EQA programmes, due to lack of accessibility and the differences in the design of these programmes (control materials, calculations used and analytical specifications established). The data from this study show that for some biological magnitudes the results obtained by the programmes are not yet harmonised, although efforts are being made to achieve this. Organisers of EQA programmes should also join the harmonisation effort by providing information on their results to enable comparison.

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Diagnostic Challenges on the Laboratory Detection of Lupus Anticoagulant

Biomedicines ◽

10.3390/biomedicines9070844 ◽

2021 ◽

Vol 9 (7) ◽

pp. 844

Author(s):

Armando Tripodi

Keyword(s):

Lupus Anticoagulant ◽

Clinical Laboratory ◽

External Quality Assessment ◽

State Of The Art ◽

Diagnostic Procedures ◽

External Quality ◽

Glycoprotein I ◽

Current State ◽

Clinical Laboratories

Lupus anticoagulant (LA) is one of the three laboratory parameters (the others being antibodies to either cardiolipin or β2-glycoprotein I) which defines the rare but potentially devastating condition known as antiphospholipid syndrome (APS). Testing for LA is a challenging task for the clinical laboratory because specific tests for its detection are not available. However, proper LA detection is paramount for patients’ management, as its persistent positivity in the presence of (previous or current) thrombotic events, candidate for long term anticoagulation. Guidelines for LA detection have been established and updated over the last two decades. Implementation of these guidelines across laboratories and participation to external quality assessment schemes are required to help standardize the diagnostic procedures and help clinicians for appropriate management of APS. This article aims to review the current state of the art and the challenges that clinical laboratories incur in the detection of LA.

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

Clinical Infectious Diseases ◽

10.1093/cid/ciab106 ◽

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.

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