key: cord-0956758-if33cjv0
authors: Fitoussi, Frédéric; Dupont, Raphaël; Tonen‐Wolyec, Serge; Bélec, Laurent
title: Performances of the VitaPCR™ SARS‐CoV‐2 Assay during the second wave of the COVID‐19 epidemic in France
date: 2021-04-01
journal: J Med Virol
DOI: 10.1002/jmv.26950
sha: 012f08fd3a4f03edfb080d167db02a898575c144
doc_id: 956758
cord_uid: if33cjv0

To assess the practicability (usability and satisfaction) and analytical performances of the VitaPCR™ SARS‐CoV‐2 Assay (Credo Diagnostics Biomedical Pte. Ltd.), a rapid point‐of‐care nucleic acid amplification test (NAAT), by reference to real‐time reverse‐transcription polymerase chain reaction (rRT‐PCR) for respiratory viruses. The practicability of the VitaPCR™ Assay and Instrument was assessed from usability evaluation and a satisfaction questionnaire. Nasopharyngeal swabs were collected from 239 patients with coronavirus disease 2019 (COVID‐19)‐like illness during the second epidemic wave, in Paris, France. Overall, the usability of the VitaPCR™ Instrument was high. The satisfaction questionnaire indicated a high appreciation of the VitaPCR™ NAAT mainly for the short duration of analysis in only 20 min. A total of 140 and 99 samples were positive and negative for SARS‐CoV‐2 RNA by rRT‐PCR, respectively. In the event of significant viral load (i.e., N gene C (t) values 33), the platform's analytical performances dropped significantly, with lower sensitivity, concordance, and accuracy, while its specificity remained high. The VitaPCR™ SARS‐CoV‐2 Assay is an accurate rapid point‐of‐care NAAT, suitable for clinical practice for the rapid diagnosis of COVID‐19, especially in patients with COVID‐19‐suspected symptoms.

Controlling the outbreak in the community and hospitals mainly relied on the availability of highly sensitive and specific nucleic acid amplification-based molecular testing for SARS-CoV-2, which is the gold standard for the diagnosis of SARS-CoV-2 in respiratory samples. 3, 4 Molecular assays are crucial for the rapid application of infection control measures, case identification, and contact tracing. 5 Several nucleic acid amplification test (NAAT) platforms are currently available to be used at central reference or hospital laboratory levels. These large platforms are not suitable for small laboratory structures such as district laboratory level, lacking high-level facilities and instruments, clinics, medical offices, and in general for decentralized diagnostics, as in establishments for the elderly, or even airports. Indeed, one of the major drawbacks of these assays is the need for viral nucleic acid extraction from clinical specimens. Furthermore, the assay run times of 1-3 h are still too long for timely decision support in a variety of important clinical situations (e.g., bed assignments for patients being admitted from the emergency department who may require cohorting by their COVID-19 status).

Thus, diagnostic tests specific to SARS-CoV-2 infection are urgently required to confirm suspected cases, screen patients, and conduct virus surveillance. In this scenario, a point-of-care, rapid, robust, and cost-efficient device is crucial and urgently needed for the detection of COVID-19. 6 Indeed, point-of-care tests are used to diagnose patients without sending samples to centralized facilities, thereby enabling communities without laboratory infrastructure to detect infected patients.

In search for a platform with a shorter turnaround time, we sought to evaluate the recently released VitaPCR™ SARS-CoV-2

Assay and Instrument (Credo Diagnostics Biomedical Pte. Ltd.). We report herein our field experience on the practicability and analytical performances of the VitaPCR™ SARS-CoV-2 Assay during the second wave of COVID-19 epidemic in Paris, France, from our continuous quality improvement program required by the accreditation of medical biology laboratories.

Patients who were suspected of COVID-19 attending the Centre Cardiologique du Nord-CCN, Saint-Denis, France, were prospectively included during the last second epidemic wave in France from October to November 2020. Patients were subjected to nasopharyngeal flocked swab (Copan) in one nostril, and to the dedicated nylon flocked swab of the VitaPCR™ SARS-CoV-2 kit in the other nostril. SARS-CoV-2 RNA detection was first carried out by our reference multiplex real-time reverse-transcription polymerase chain reaction (rRT-PCR) on native nasopharyngeal sample specimens. The swab specimens for VitaPCR™ testing were kept frozen at −20°C before use. In addition, the internal quality control (IQC) consisted of a synthetic DNA of the SARS-CoV-2 N gene segment, which sequence is used for both universal primer/probe and specific primer/probe set target (control set for SARS-CoV-2 PCR produced by Biosynex) Forty microlitres of IQC was added into the sample collection buffer tube of the VitaPCR™ SARS-CoV-2 Assay, to process the test procedure.

IQC was carried out twice a week.

The practicability evaluation of the study platform was divided into two sub-studies carried out by trained health care professionals.

The usability of the VitaPCR™ Instrument for the qualitative molecular diagnosis of SARS-CoV-2 was assessed among volunteer health workers from the laboratory, including six laboratory technicians and four biologists. The participants were first trained on both platforms, and every one carefully read the instructions for each kit. Afterwards, the volunteers performed at least five measurements with each system, then completed the usability grid comprising 11 items ( Figure 1 ).

Afterwards, the participants fulfilled the satisfaction questionnaire concerning their experiences with the VitaPCR™ platform, comprising 11 items (Figure 1 ).

Each usability and satisfaction item received a note using an arbitrary quantitative five-point Likert's scale 8 ranging from 1 (very difficult), 2 (difficult), 3 (relatively easy) to 4 (easy) to 5 (very easy or comfortable).

Data were entered into an Excel database and analyzed using IBM® SPSS® Statistics 20 software (IBM, SPSS Inc.). Means or medians were calculated for quantitative variables and proportions for categorical variables. The results were presented along with their 95% confidence interval (CI) using the Wilson score bounds for categorical variables. 9 The results of SARS-CoV-2 RNA detection by the multiplex rRT-PCR (Liferiver and Shanghai ZJ Bio-Tech Co., Ltd.) were used as the reference standard to estimate the sensitivity and specificity of the VitaPCR™ platform to detect SARS-CoV-2 RNA, with corresponding 95% CI. The concordance between the VitaPCR™ platform and multiplex molecular detection of SARS-CoV-2 RNA was assessed by percent agreement corresponding to the observed proportion of identical results between VitaPCR™ compared to rRT-PCR detection. The reliability between the VitaPCR™ and the multiplex molecular detection of SARS-CoV-2 RNA was estimated by Cohen's κ coefficient, 10 and the degree of agreement was determined as ranked by Landlis and Koch. 11 The accuracy of the VitaPCR™ platform to correctly diagnose SARS-CoV-2 infection was estimated by Youden's J index (J = sensitivity + specificity − 1). 12 | 4355 late phase of the infection typically associated with a low viral load.

Otherwise and remarkably, the high performances of the VitaPCR™ SARS-Cov-2 Assay were obtained with no requirement for prior RNA extraction. These performances are reminiscent to those obtained with other NAATs for SARS-CoV-2 RNA qualitative detection, [17] [18] [19] [20] [21] although there are sometimes significant analytical differences between the analyzers according to the populations tested and the quality and processing of sampling. 17, 18, 22 In addition, in our series, influenza as compared to laboratory testing. 25 The limitations of our study include a relatively small sample size, inability to control for sampling variability, and lack of an additional comparator method to discern the discrepancies between 

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The authors are grateful to Biosynex, for providing for the tests for the study. Dr. Serge Tonen-Wolyec was the recipient of the ERASMUS program between the University of Kisangani, and the University of Liège.

The authors declare that there are no conflict of interests. 

http://orcid.org/0000-0002-5001-0405