Background: The persistence of the rapid spread of the COVID-19 pandemic is linked to the appearance of several variants of SARS-CoV2 with an impact on biological diagnosis, treatment and vaccination. The United States Food and Drug Administration (FDA) has granted several SARS-CoV-2 detection tests Emergency Use Authorization (EUA) for diagnosis and better epidemiological surveillance. Thus, multiple RT-PCR tests have been developed and brought to market in order to meet the urgent need for the diagnosis of COVID-19. However, comparative data between these tests in clinical laboratories are scarcely available to assess their performance. Objective: To compare two molecular methods for detecting SARS-CoV-2: the RT-PCR, Allplex™ 2019-nCoV tests on CFX96 Bio-Rad and the Abbott m2000sp/rt RealTime SARS-CoV-2. Materials andMethods: Nasopharyngeal and oropharyngeal swabs were taken from patients to diagnose SARS-CoV-2 infection. For each sample, we searched for the virus with two different RT-PCR tests: 1) first on Abbott m2000 SARS-CoV-2 targeting the N and RdRp genes, 2) then on Allplex™ 2019-nCoV Assay looking for the E, N and RdRp genes. Results: Percentages of the agreement were calculated. A total of 100 samples that tested negative and 90 positives on Abbott m2000 SARS-CoV-2 were retested on Allplex™ 2019-nCoV. Overall agreement was 74.74% on all samples. The specific agreement was 84% and 64.4% respectively for negative and positive samples with the RealTime SARS-CoV-2 test. A positive correlation (r2 = 0.63; p < 0.0001) was found between the two tests associated with a kappa coefficient of 0.5, thus demonstrating an acceptable concordance between the two methods. However, 48 samples gave discordant results, in particular those whose Ct (Cycle threshold) was high (low viremia). A comparison by Cts found that concordance was higher for lower Cts (high viremia) which would indicate the acute phase of the disease. Note that our study revealed a possible cross-reaction with the E gene of a Sarbecovirus. It is a subgenus of Betacoronavirus grouping coronaviruses linked to severe acute respiratory syndromes such as SARS-CoV and SARS-CoV-2. Conclusion: Our results showed good overall agreement between RT-PCR, Allplex™ 2019-nCoV and
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