The Allplex 2019-nCoV (Seegene) assay: which performances are for SARS-CoV-2 infection diagnosis?
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The Allplex 2019-nCoV (Seegene) assay: which performances are for SARS-CoV-2 infection diagnosis? Eric Farfour 1 & Philippe Lesprit 1 & Benoit Visseaux 2 & Tiffany Pascreau 1 & Emilie Jolly 1 & Nadira Houhou 2 & Laurence Mazaux 1 & Marianne Asso-Bonnet 1 & Marc Vasse 1 & on behalf of the SARS-CoV-2 Foch Hospital study group Received: 26 April 2020 / Accepted: 13 May 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Several commercial assays for SARS-CoV-2 RT-PCR are available but few of them were assessed. We evaluate the Allplex 2019-nCoV (Seegene) assay using 41 nasopharyngeal samples. The rates of agreement were 92.7% and 100% with the GeneFinder COVID-19 plus (Elitech) and the diagnosis of the infectious disease specialist respectively. Four samples display a Ct < 22.0 for the E and RdRp genes while the N gene was not detected, suggesting a variability of the viral sequence. There was no cross-reactivity with other respiratory viruses. The Allplex 2019-nCoV appears as a reliable method, but additional evaluations using more samples are needed. RT-PCR assays should probably include at least 2 viral targets. Keywords SARS-CoV-2 . COVID-19 . RT-PCR . Allplex 2019-nCoV (Seegene) . Sensitivity . Nasopharyngeal swab
Introduction SARS-CoV-2 has rapidly spread, infecting more than 3.9 million people and causing more than 275,000 death 19 weeks after the WHO was alerted by Chinese health authority on December 31, 2019 [1]. As the clinical presentation of the disease is nonspecific and in order to improve the management of the patients and to limit the spread of the virus, a robust and accurate diagnosis is needed. According to the WHO, laboratory confirmation is required for suspicious cases [2]. Molecular methods performed on respiratory specimen are considered the gold standard as they are specific and viral excretion appears early, before the onset of the symptoms [3]. The Allplex 2019-nCoV assay (Seegene, Seoul, South Korea) was designed for amplifying three viral targets: the E gene (specific of the subgenus Sarbecovirus), the N and the RdRP genes (both specifics of the SARS-CoV-2). The assay is approved for in vitro diagnostic in several countries as South Korea and France. The first assessment of its performances by
* Eric Farfour [email protected]; [email protected] 1
Service de biologie Clinique, Hôpital Foch, Suresnes, France
2
Service de virologie, Hôpital Bichat, Saint-Ouen, France
the manufacturer demonstrates a specificity of 100% and a limit of detection of 100 RNA copies/PCR reactions. Following first manufacturer recommendations, samples with 1 or 2 viral targets were considered inconclusive and should be retested using a “higher concentration of sample” or a “gene sequencing” should be performed [4]. But, according to the revised recommendations issue in late April 2020, these profiles are considered positive. However, as the reagent was rapidly available in limited quantities and clinical laboratories were overwhelmed, no independent assessments
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