key: cord-0799101-w1jeb7hd authors: Jokela, Pia; Jääskeläinen, Anu E.; Jarva, Hanna; Holma, Tanja; Ahava, Maarit J; Mannonen, Laura; Lappalainen, Maija; Kurkela, Satu; Loginov, Raisa title: SARS-CoV-2 sample-to-answer nucleic acid testing in a tertiary care emergency department: evaluation and utility date: 2020-08-27 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104614 sha: bfa8241f9b63d3ceef1e5e2ad5e9529025fc3ea8 doc_id: 799101 cord_uid: w1jeb7hd BACKGROUND: Rapid sample-to-answer tests for detection of SARS-CoV-2 are emerging and data on their relative performance is urgently needed. OBJECTIVES: We evaluated the analytical performance of two rapid nucleic acid tests, Cepheid Xpert® Xpress SARS-CoV-2 and Mobidiag Novodiag® Covid-19, in comparison to a combination reference of three large-scale PCR tests. Moreover, utility of the Novodiag® test in tertiary care emergency departments was assessed. RESULTS: In the preliminary evaluation, analysis of 90 respiratory samples resulted in 100% specificity and sensitivity for Xpert®, whereas analysis of 107 samples resulted in 93.4% sensitivity and 100% specificity for Novodiag®. Rapid SARS-CoV-2 testing with Novodiag® was made available for four tertiary care emergency departments in Helsinki, Finland between 18 and 31 May, coinciding with a rapidly declining epidemic phase. Altogether 361 respiratory specimens, together with relevant clinical data, were analyzed with Novodiag® and reference tests: 355/361 of the specimens were negative with both methods, and 1/361 was positive in Novodiag® and negative by the reference method. Of the 5 remaining specimens, two were negative with Novodiag®, but positive with the reference method with late Ct values. On average, a test result using Novodiag® was available nearly 8 hours earlier than that obtained with the large-scale PCR tests. CONCLUSIONS: While the performance of novel sample-to-answer PCR tests need to be carefully evaluated, they may provide timely and reliable results in detection of SARS-CoV-2 and thus facilitate patient management including effective cohorting. Patients with COVID-19 disease can present with a number of unspecific symptoms. Thus, the diagnosis of COVID-19 relies on molecular testing of SARS-CoV-2, typically from respiratory specimens [1] . Several methods are available for this purpose [2] [3] [4] [5] [6] [7] , both largescale testing platforms and simple cartridge-based tests for rapid examination of one or few samples at a time. Rapid and reliable laboratory testing is essential for patient management and infection control of COVID-19 and it is a prerequisite for appropriate patient cohorting within hospitals. Rapid SARS-CoV-2 molecular testing that can be performed near the healthcare facility is urgently needed. A number of such tests have now become available, and variable performance values have been reported for them [8] [9] [10] [11] [12] [13] [14] [15] . We aimed to evaluate the analytical performance of two sample-to-answer rapid PCR tests for the detection of SARS-CoV-2 infection, Cepheid Xpert ® Xpress SARS-CoV-2 and Mobidiag Novodiag ® Covid-19, and to assess the usefulness of such tests at tertiary care emergency departments. Patients who become hospitalized through emergency departments are among those who will benefit the most from quickly available test results. Here we describe the utility of a rapid test compared to large-scale testing platforms in such a patient care setting. The study was conducted at the Helsinki University Hospital Laboratory (HUSLAB), Finland, according to permit HUS/157/2020 (Helsinki University Hospital, Finland). The evaluated tests were Cepheid Xpert ® Xpress SARS-CoV-2, software version 1.0, later referred to as Xpert ® , and Mobidiag Novodiag ® Covid-19, software version v1.0.1, later Novodiag ® . Both of these tests are cartridge-based platforms that perform sample preparation, nucleic acid extraction, amplification, and detection of the target sequences. The three platforms used in our laboratory for routine diagnostics of SARS-CoV-2 were deployed as reference tests: the WHO recommended laboratory-developed test (LDT), modified from Corman and others [2] , cobas ® SARS-CoV-2 test kit on the cobas ® 6800 platform (Roche Diagnostics, Basel, Switzerland), and Amplidiag ® COVID-19 test on the Amplidiag ® Easy platform (Mobidiag, Espoo, Finland). We have separately evaluated the performance of the three reference methods used in our laboratory, and shown a good agreement between them [7] . See Table 1 for the main features of the tests. 107 nasopharyngeal or oropharyngeal swab specimens were included in the evaluation: all were tested with Novodiag ® , and 90 with Xpert ® , as well. Of the 107 specimens, 97 were sent to HUSLAB for SARS-CoV-2 testing between March and May 2020, and 10 were sent due to suspicion of other respiratory virus infection in 2019 or early 2020. Sixty-one were SARS-CoV-2 positive and 46 negative in the reference SARS-CoV-2 PCR tests. All specimens were analyzed by at least one of our reference tests. Those specimens that gave discrepant results were analyzed with at least the cobas ® SARS-CoV-2 test. Of the 10 samples originally sent for other than SARS-CoV-2 testing To assess the comparative sensitivity of the two tests, we pooled positive patient samples and made a dilution series in a pool of negative samples. All were nasopharyngeal swabs in 0.9% NaCl. We tested triplicates of dilution 10 -3 , 10 -4 and 10 -5 , and dublicates of dilution 10 -6 with Novodiag ® and Xpert ® , and dublicates of dilution 10 -7 and one sample of 10 -8 with Xpert ® . The results of the analytical evaluation are summarized in In the analytical performance assessment of this study, Xpert ® showed complete concordance of results with the reference and the kappa value of 1.00 implied an almost perfect agreement. The high sensitivity and specificity observed for Xpert ® in this study has also been shown in previous reports [8] [9] [10] . For Novodiag ® , the results obtained were 96.2% concordant with the reference. The kappa value of 0.924 also referred to an almost perfect agreement, which was further supported by McNemar's test. Together with the two false negative low-concentration proficiency samples, the high median Ct value of 31.9 for the false negative patient samples may point towards a limited ability of the Novodiag ® to detect positive samples with low viral loads, which was further supported by the dilution series experiment (Tables 3, 4 and 6 ). Another weakness of Novodiag ® system is that it does not easily enable evaluation of the amplification curves nor other data from the analysis. It would be of high importance especially now, when diagnostic tests worldwide have been set up so promptly [7] . Nonetheless, with specificity of 100% and sensitivity of 93.4%, and low invalid rate of 0.9%, the Novodiag ® was chosen for the utility assessment of rapid SARS-CoV-2 testing in the clinical setting of emergency departments. Due to the inactivation protocol included in the sample preparation step of the Novodiag ® , there is no need for placing the Novodiag ® instrument inside a biosafety cabinet. This, together with potentially foreseeable challenges in the availability of Xpert ® test cassettes, encouraged us to choose Novodiag ® for the clinical utility study. The utility of rapid SARS-CoV-2 testing with Novodiag ® was assessed prospectively in the analysis of 362 samples from four tertiary care emergency departments in Helsinki, Finland, in May 2020. At that time, the number of new cases was declining (on the average 28 cases per day in the Helsinki and Uusimaa hospital district (incidence 11.6/100000)) [16] and approximately 2% of all specimens sent to HUSLAB were positive [17] . In conclusion, the Xpert ® showed high sensitivity and specificity, and a reasonable sensitivity and high specificity was achieved for the Novodiag ® assay. The possible limited ability of the Novodiag ® to detect low viral load samples is a drawback, which may be overcome by Table 4 . Dilution series of positive patient sample pool. C Table 5 . Clinical characteristics of the adult patients at the first evaluation at the emergency department. Some patients presented with multiple symptoms. 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Evaluation of the QIAstat-Dx Respiratory SARS-CoV-2 Panel, the first rapid multiplex PCR commercial assay for SARS-CoV-2 detection Comparison of two commercial molecular tests and a laboratory-developed modification of the CDC 2019-nCoV RT-PCR assay for the detection of SARS-CoV-2 Performance evaluation of the point-of-care SAMBA II SARS-CoV-2 Test for detection of SARS-CoV-2 Performance characteristics of the ID NOW COVID-19 assay: A regional health care system experience Institute for Health and Welfare: COVID-19-epidemian Hybridistrategian seuranta Finnish. Updated 25 Laboratory-based surveillance of COVID-19 in Greater Helsinki area OUCRU COVID-19 research group. 2020. The natural history and transmission potential of asymptomatic SARS-CoV-2 infection No/reference Agreement % (95% CI) No/reference Agreement % (95% CI) We would like to thank the nursing staff at our laboratory, especially Jonna Keijama, for the valuable technical assistance.J o u r n a l P r e -p r o o f . LDT; laboratory developed test; Pos, positive; Neg, negative, Inv, invalid, CI, confidence interval.