Colorimetric Nucleic Acid Testing Assay for RNA Virus Detection Based on Circle-to-Circle Amplification of Padlock Probes

A large-scale (>20,000 tests per day) standardized and fully-automated laboratory (Huo-Yan) was built as an ad-hoc measure to meet the requirement of virus detection after the novel coronavirus (COVID-19) outbreak in Wuhan, China. We integrated the brief data from Health Commission of Hubei Province and the real-world operation data of Huo-Yan laboratory, into a novel differential model with non-linear transfer coefficients and competitive compartments, to evaluate the trend of suspected cases under different nucleic acid testing capacities, including suspected cases with/without coronavirus infection, to evaluate the achievement of “daily settlement” condition of suspected cases and the control of the epidemic under different nucleic acid testing capacities.

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Potential False-Negative Nucleic Acid Testing Results for Severe Acute Respiratory Syndrome Coronavirus 2 from Thermal Inactivation of Samples with Low Viral Loads

Clinical Chemistry ◽

10.1093/clinchem/hvaa091 ◽

2020 ◽

Vol 66 (6) ◽

pp. 794-801 ◽

Cited By ~ 76

Author(s):

Yang Pan ◽

Luyao Long ◽

Daitao Zhang ◽

Tingting Yuan ◽

Shujuan Cui ◽

...

Keyword(s):

Nucleic Acid ◽

Severe Acute Respiratory Syndrome ◽

Thermal Inactivation ◽

Rna Virus ◽

False Negative ◽

Heat Inactivation ◽

Nucleic Acid Testing ◽

Rt Pcr ◽

False Negatives ◽

Viral Loads

Abstract Background Coronavirus disease-2019 (COVID-19) has spread widely throughout the world since the end of 2019. Nucleic acid testing (NAT) has played an important role in patient diagnosis and management of COVID-19. In some circumstances, thermal inactivation at 56°C has been recommended to inactivate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) before NAT. However, this procedure could theoretically disrupt nucleic acid integrity of this single-stranded RNA virus and cause false negatives in real-time polymerase chain reaction (RT-PCR) tests. Methods We investigated whether thermal inactivation could affect the results of viral NAT. We examined the effects of thermal inactivation on the quantitative RT-PCR results of SARS-CoV-2, particularly with regard to the rates of false-negative results for specimens carrying low viral loads. We additionally investigated the effects of different specimen types, sample preservation times, and a chemical inactivation approach on NAT. Results Our study showed increased Ct values in specimens from diagnosed COVID-19 patients in RT-PCR tests after thermal incubation. Moreover, about half of the weak-positive samples (7 of 15 samples, 46.7%) were RT-PCR negative after heat inactivation in at least one parallel testing. The use of guanidinium-based lysis for preservation of these specimens had a smaller impact on RT-PCR results with fewer false negatives (2 of 15 samples, 13.3%) and significantly less increase in Ct values than heat inactivation. Conclusion Thermal inactivation adversely affected the efficiency of RT-PCR for SARS-CoV-2 detection. Given the limited applicability associated with chemical inactivators, other approaches to ensure the overall protection of laboratory personnel need consideration.

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RNA polymerization actuating nucleic acid membrane (RANAM)-based biosensing for universal RNA virus detection

Biosensors and Bioelectronics ◽

10.1016/j.bios.2021.113880 ◽

2021 ◽

pp. 113880

Author(s):

Dajeong Kim ◽

Sangwoo Han ◽

Yoonbin Ji ◽

Heejeong Youn ◽

Hyejin Kim ◽

...

Keyword(s):

Nucleic Acid ◽

Rna Virus ◽

Virus Detection ◽

Rna Polymerization

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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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