Rapid Diagnosis of SARS-CoV-2 Pneumonia on Lower Respiratory Tract Specimens

Abstract

Background: The ongoing pandemic of SARS-CoV-2 requires the availability of accurate and rapid diagnostic tests, especially in some clinical settings like emergency and intensive care units. The objective of this study was to evaluate the diagnostic performances of rapid PCR kit Vivalytic SARS-CoV-2 in lower respiratory tract (LRT) specimens.Methods: A consecutive sample of LRT specimens (bronchoalveolar lavage and bronchoaspirates) was collected from Intensive Care Units of San Martino Hospital (Genoa, Italy) between November 2020 and January 2021. All samples were tested in RT-PCR by using Allplex™ SARS-CoV-2 assay (Seegene Inc., South Korea). Based on RT-PCR results, specimens were categorized into negative, positive with high viral load [cycle threshold (Ct) ≤30] and positive with low viral load (Ct of 31–35). A quota 1:1:1 sampling was used to achieve a sample size of 75. Then, all specimens were tested in the rapid PCR assay Vivalytic SARS-CoV-2 (Bosch Healthcare Solutions GmbH, Germany). The diagnostic performance of the rapid PCR against RT-PCR was assessed through calculation of accuracy, Cohen’s κ, sensitivity, specificity and expected positive (PPV) and negative (NPV) predictive values.Results: The 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). The sensitivity and specificity were 96% (95% CI: 86.5–98.9%) and 100% (95% CI: 86.7–100%), respectively. Samples with high viral loads had a sensitivity of 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), respectively (Figure 1). NPV and PPV was 92.6% and 100%, respectively.Conclusions: This study shows Vivalytic SARS-CoV-2 can be used following the sample liquefaction on LRT specimens. It’s a feasible and highly accurate molecular procedure especially in high viral load samples. This assay allows having a result in about 40 min and therefore may accelerate the clinical decision making in urgent/emergency situations.

Lung donation and SARS‐CoV‐2 transmission: Missed detection versus missed opportunity?

“…They include rapid antigen tests (RATs) and various types of nucleic acid amplification tests (NAATs). The performance of POCTs in BAL samples has not been reported except for one NAAT (Bosch Vivalytic), which showed a sensitivity of 96% and specificity of 100% 16 …”

“…However, to date we do not know the specificity of most POCTs for LRT samples. Only for the Bosch Vivalytic, specificity for LRT samples (100%) has been reported 16 . Validation of other POCTs for the detection of SARS‐CoV‐2 in LRT samples would increase their usability in the setting of lung donation.…”

“…Several NAATs consisting of a disposable cassette that is inserted in a portable analyzer have been developed for detection of SARS‐CoV‐2 RNA including the Roche cobas Liat System, 19 Abbott ID NOW, 19 Mesa Biotech Accula, 20 Cue Health, 21 and Lucira Check It 22 . For NP swabs, sensitivity for these NAATs is higher compared to RATs and specificity >95% 16,19–22 . The better performance of NAATs compared to RATs comes with a higher cost and more logistical requirements (transport of analyzer and cassettes, longer set‐up time, more experience required).…”

Diagnostic and prognostic role of the SARS-COV-2-specific IgA antibody: an updated systematic review and meta-analysis

“…CoV-2 RNA in respiratory samples. However, a number of variables have been found to significantly impact the performance of RT-PCR tests, including i m p r o p e r s p e c i m e n c o l l e c t i n g procedures, viral load, time since exposure, and specimen source, all of which might lead to false-negative tests 4,5 findings. As a result, more diagnostic tests are urgently required to reduce the risk of misdiagnosis or developing critical illness, which may lead to hospitalization and even death.…”