Abstract
BackgroundThe ongoing SARS-CoV-2 pandemic requires the availability of accurate and rapid diagnostic tests, especially in such clinical settings as emergency and intensive care units. The objective of this study was to evaluate the diagnostic performance of the Vivalytic SARS-CoV-2 rapid PCR kit in lower respiratory tract (LRT) specimens.MethodsConsecutive LRT specimens (bronchoalveolar lavage and bronchoaspirates) were collected from Intensive Care Units of San Martino Hospital (Genoa, Italy) between November 2020 and January 2021. All samples underwent RT-PCR testing by means of the Allplex™ SARS-CoV-2 assay (Seegene Inc., South Korea). On the basis of RT-PCR results, specimens were categorized as negative, positive with high viral load [cycle threshold (Ct) ≤ 30] and positive with low viral load (Ct of 31–35). A 1:1:1 ratio was used to achieve a sample size of 75. All specimens were subsequently tested by means of the Vivalytic SARS-CoV-2 rapid PCR assay (Bosch Healthcare Solutions GmbH, Germany). The diagnostic performance of this assay was assessed against RT-PCR through the calculation of accuracy, Cohen’s κ, sensitivity, specificity and expected positive (PPV) and negative (NPV) predictive values.ResultsThe overall diagnostic accuracy of the Vivalytic SARS-CoV-2 was 97.3% (95% CI: 90.9–99.3%), with an excellent Cohen’s κ of 0.94 (95% CI: 0.72–1). Sensitivity and specificity were 96% (95% CI: 86.5–98.9%) and 100% (95% CI: 86.7–100%), respectively. In samples with high viral loads, sensitivity was 100% (Table 1). The distributions of E gene Ct values were similar (Wilcoxon’s test: p = 0.070), with medians of 35 (IQR: 25–36) and 35 (IQR: 25–35) on Vivalytic and RT-PCR, respectively (Fig. 1). NPV and PPV was 92.6% and 100%, respectively.ConclusionsVivalytic SARS-CoV-2 can be used effectively on LRT specimens following sample liquefaction. It is a feasible and highly accurate molecular procedure, especially in samples with high viral loads. This assay yields results in about 40 min, and may therefore accelerate clinical decision-making in urgent/emergency situations.
Highlights
The ongoing SARS-CoV-2 pandemic requires the availability of accurate and rapid diagnostic tests, especially in such clinical settings as emergency and intensive care units
Global research is committed to exploring every aspect of the coronavirus disease-2019 (COVID-19) outbreak and restoring the normal level of public health
During symptom onset in SARS-CoV-2 patients, high viral nucleic acid shedding patterns have been detected in upper-respiratory-tract (URT) specimens, nasopharyngeal swabs (NPS) or oropharyngeal swabs (OPS) [5]
Summary
The ongoing SARS-CoV-2 pandemic requires the availability of accurate and rapid diagnostic tests, especially in such clinical settings as emergency and intensive care units. The objective of this study was to evaluate the diagnostic performance of the Vivalytic SARS-CoV-2 rapid PCR kit in lower respiratory tract (LRT) specimens. The rapid identification and monitoring of COVID-19 patients is Molecular diagnostic assays, in combination with chest radiography, continue to be gold standard tests for the laboratory diagnosis of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia [3]. The critical conditions of patients with severe acute respiratory infection (SARI) who undergo mechanical ventilation do not usually allow the collection of URT specimens. To improve the detection rate and reduce the false-negative rate in these cases, lower respiratory tract (LRT) specimens (i.e. bronchoalveolar lavage, BAL; bronchoaspirates, BAS; sputum; tracheal aspirate) should be used for testing in highly suspect patients [7]. SARS-CoV-2 displays active replication in pulmonary sites, as is revealed by the higher excretion kinetics in sputum than in URT samples [8]
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