Dataset Information

Comparison of 6 SARS-CoV-2 Molecular Methods and Correlation With the Cycle Threshold Distribution in Clinical Specimens.

ABSTRACT:

Background

The detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patient samples is of critical importance in the management of patients and monitoring transmission in the population. However, data on the analytical performance characteristics for detection of SARS-CoV-2 in clinical specimens between individual targets within the same platform, and among different analytical platforms, are limited.

Methods

Here we evaluated the performance of 6 different sample-to-answer SARS-CoV-2 detection methods-Roche cobas 6800, Cepheid GeneXpert, Diasorin Simplexa, Luminex Aries emergency use authorization (EUA), Luminex Aries research use only (RUO), and bioMérieux BioFire-in clinical specimens with a range of viral loads.

Results

The positive percentage agreement between the Roche cobas 6800 and GeneXpert was 100%, Diasorin 95%, Aries EUA 74%, Aries RUO 83%, and BioFire 97%. Notably, in samples with cycle threshold (Ct) values below 30 for the E gene on the Roche cobas 6800 platform, we found 100% positive agreement among all platforms. Given these results, we examined the distribution of over 10 000 Ct values of all positive specimens from individuals at our institution on the Roche cobas platform. Nearly 60% of specimens from asymptomatic individuals had a PCR Ct value >30 as measured using the cobas 6800 assay E gene.

Conclusions

Our results demonstrate performance characteristics between different platforms by Ct value and provide data regarding the distribution of viral RNA present in positive specimens.

SUBMITTER: Raju S

PROVIDER: S-EPMC8436400 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature

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Publications

Comparison of 6 SARS-CoV-2 Molecular Methods and Correlation With the Cycle Threshold Distribution in Clinical Specimens.

Raju Saravanan S Anderson Neil W NW Robinson Elizabeth E Squires Crystal C Wallace Meghan A MA Zhang Ray R Burnham Carey-Ann D CD Parikh Bijal A BA

The journal of applied laboratory medicine 20211101 6

<h4>Background</h4>The detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patient samples is of critical importance in the management of patients and monitoring transmission in the population. However, data on the analytical performance characteristics for detection of SARS-CoV-2 in clinical specimens between individual targets within the same platform, and among different analytical platforms, are limited.<h4>Methods</h4>Here we evaluated the performance of 6 different ...[more]

PMID: 34289054

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Project description:BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cycle threshold (Ct) has been suggested as an approximate measure of initial viral burden. The utility of cycle threshold, at admission, as a predictor of disease severity has not been thoroughly investigated.Methods and findingsWe conducted a retrospective study of SARS-CoV-2 positive, hospitalized patients from 3/26/2020 to 8/5/2020 who had SARS-CoV-2 Ct data within 48 hours of admission (n = 1044). Only patients with complete survival data, discharged (n = 774) or died in hospital (n = 270), were included in our analysis. Laboratory, demographic, and clinical data were extracted from electronic medical records. Multivariable logistic regression was applied to examine the relationship of patient mortality with Ct values while adjusting for established risk factors. Ct was analyzed as continuous variable and subdivided into quartiles to better illustrate its relationship with outcome. Cumulative incidence curves were created to assess whether there was a survival difference in the setting of the competing risks of death versus patient discharge. Mean Ct at admission was higher for survivors (28.6, SD = 5.8) compared to non-survivors (24.8, SD = 6.0, P<0.001). In-hospital mortality significantly differed (p<0.05) by Ct quartile. After adjusting for age, gender, BMI, hypertension and diabetes, increased cycle threshold was associated with decreased odds of in-hospital mortality (0.91, CI 0.89-0.94, p<0.001). Compared to the 4th Quartile, patients with Ct values in the 1st Quartile (Ct <22.9) and 2nd Quartile (Ct 23.0-27.3) had an adjusted odds ratio of in-hospital mortality of 3.8 and 2.6 respectively (p<0.001). The discriminative ability of Ct to predict inpatient mortality was found to be limited, possessing an area under the curve (AUC) of 0.68 (CI 0.63-0.71).ConclusionSARS-CoV-2 Ct was found to be an independent predictor of patient mortality. However, further study is needed on how to best clinically utilize such information given the result variation due to specimen quality, phase of disease, and the limited discriminative ability of the test.

Project description:Dogs can discriminate between people infected with SARS-CoV-2 from those uninfected, although their results vary depending on the settings in which they are exposed to infected individuals or samples of urine, sweat or saliva. This variability likely depends on the viral load of infected people, which may be closely associated with physiological changes in infected patients. Determining this viral load is challenging, and a practical approach is to use the cycle threshold (Ct) value of a RT-qPCR test. The hypothesis was that dogs should have a specific Ct range at which they could detect people infected with SARS-CoV-2. Therefore, the objective was to determine this Ct range. Sweat samples and epidemiological data were collected from 89 infected and 289 non-infected individuals at real life settings (e.g. health centers, offices, football fields). To determine each person's infection status, the Norgen Biotek kit for RT-qPCR was used; targeting the N1 and N2 regions of the SARS-CoV-2 nucleocapsid N gene. The performance of 11 trained dogs was evaluated on sweat samples of 379 individuals to determine their sensitivity and specificity (± 95% Confidence Intervals; CI) in detecting SARS-CoV-2 infections. Additionally, the SARS-CoV-2 viral load was calculated from Ct values using a reference curve, and the Ct range at which dogs showed optimal performance was determined. Six dogs exhibited a marginal performance, as their sensitivity 95% CI overlapped with the region of randomness (50%). The remaining five dogs demonstrated sensitivity values between 67% and 87%, with none of their 95% CIs overlapping the randomness region. Regarding specificity, three dogs showed values between 87% and 92%, while all other dogs exhibited values of ≥ 90%. Dogs demonstrated higher detection accuracy in a range of Ct values between 18.49 and 29.17 for the N1 region and between 24.07 and 26.69 for the N2 region of the SARS-CoV-2 nucleocapsid gene. Detection significantly decreases for Ct values greater than 30 or less than 16, indicating an optimal range in which dogs are most effective. These performance values concur well with those reported for commercial rapid antigen tests for detecting SARS-CoV-2. Consequently, it is considered that using properly trained animals could offer a viable option to supplement existing diagnostic methods, allowing for rapid diagnosis while optimizing time and economic resources. Moreover, this approach is ecologically sustainable, as it generates less waste compared to the use of rapid tests, while continuing to confirm positive cases.

Dataset Information

Comparison of 6 SARS-CoV-2 Molecular Methods and Correlation With the Cycle Threshold Distribution in Clinical Specimens.

Background

Methods

Results

Conclusions

Publications

Comparison of 6 SARS-CoV-2 Molecular Methods and Correlation With the Cycle Threshold Distribution in Clinical Specimens.

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