key: cord-0748470-ztnjvamo authors: Quinton, Mikayla; Geahr, Melissa; Gluck, Linda; Jarrett, Junko; Mostafa, Heba H. title: Evaluation of the Respiratory NeuMoDx(TM) Flu A-B/RSV/SARS-CoV-2 Vantage and Alinity m Resp-4-Plex Assays date: 2022-04-18 journal: J Clin Virol DOI: 10.1016/j.jcv.2022.105164 sha: a8ccc2f974d2ca4b1160b564334e99352dff211d doc_id: 748470 cord_uid: ztnjvamo BACKGROUND: December 2021 witnessed an unprecedented increase in SARS-CoV-2 infections in addition to the circulation of influenza A and respiratory syncytial viruses (RSV). Due to increased testing demands for SARS-CoV-2, influenza, and RSV associated with the overall increase in symptomatic respiratory infections, there is an urgent need for multiplex, automated, and high throughput assays in the diagnostic laboratories. METHODS: We compared the performance of the NeuMoDx(TM) Flu A-B/RSV/SARS-CoV-2 Vantage and the Alinity m Resp-4-Plex to the standard of care influenza A, B, RSV, and SARS-CoV-2 assays used at the Johns Hopkins Microbiology Laboratory. A total of 181 remnant nasopharyngeal swab (NPS) specimens positive for influenza A (n = 30), influenza B (n = 34), RSV (n = 40), SARS-CoV-2 (n = 33), and negatives (n = 44) were tested by either or both assays. RESULTS: Both the NeuMoDx(TM) Flu A-B/RSV/SARS-CoV-2 Vantage and the Alinity m Resp-4-Plex assays showed 100% total agreement for all the tested analytes. For samples with available cycle threshold (Ct) values, comparable ranges were noted for all targets between the two assays and to the standard of care Ct values as well. CONCLUSION: The NeuMoDx(TM) Flu A-B/RSV/SARS-CoV-2 Vantage and the Alinity m Resp-4-Plex assays showed high sensitivity and accuracy for all the analytes included in both tests. Implementing these assays will assist the diagnostic laboratories with the surge of testing during the 2021- 2022 influenza season. The diagnostic laboratory testing of influenza and RSV increases during the seasons of their circulation. The COVID-19 pandemic impacted the circulation of respiratory viruses, including influenza and RSV, associated with measures of mitigating the spread of SARS-CoV-2 (1). May 2021 with marked increases in enterovirus/rhinovirus and RSV (1) . The first detection of influenza in our system in 2021 was on October 27 th followed by a slow increase in the number of cases to reach an average positivity of 3% in the month of December. The circulation of influenza in December correlated with a large increase in the circulation of SARS-CoV-2 that correlated with the introduction of the variant of concern Omicron (2). This increase in symptomatic infections warranted an increase in the capacity of testing of SARS-CoV-2, influenza, and RSV to reveal the need for batched, fully automated, and multiplexed approaches for the three viruses under such circumstances. We hence evaluated the performance of the NeuMoDx TM Flu A-B/RSV/SARS-CoV-2 Vantage and the Alinity m Resp-4-Plex assays compared to the standard of care methods for the detection and differentiation of influenza A, B, RSV, and SARS-CoV-2. The research was conducted with a waiver of consent under the Johns Hopkins IRB protocol IRB00246024. Remnant nasopharyngeal swabs (NPS) were collected after the standard of care diagnostic testing was performed. A total of 181 NPS specimens were randomly selected (based on the availability) from archived samples stored at -80°C after the standard of care (SOC) testing for influenza A, influenza B, RSV, and/ or SARS-CoV-2. SOC testing included the Xpert® Xpress SARS-CoV-2/Flu/RSV (3, Table 1 summarizes the gene targets of the main evaluated and SOC assays. Notably, the two evaluated assays use one channel for detecting each virus and hence each virus has only one cycle threshold (Ct) value. Assays were run following the manufacturers' package inserts. (Table S1, and Table 2 total agreement for all targets tested with both assays (Table S1 ). For samples with SOC Ct, we correlated the Cts for each target with Cts from the NeuMoDx™ (Table S1) . Notably, the SOC assays use a different gene target for RSV (Table 1) . Resp-4-Plex assays. To assess the intra and inter-assay precision of both the NeuMoDx™ Flu operators. An overall precision of 100 % was noted for both assays for all tested analytes (Tables 3 and 4 ). The The limitations of our report include using retrospective SOC results and archived frozen specimens. In addition, the Ct value comparisons might be biased by the gene targets used by each platform, the chemistry behind each technology, as well as the use of archived rather than fresh samples. The Ct analyses though showed the comparable trends of the two evaluated assays in different ranges of Ct values as well as to the standard of care methods. Circulation of Non-SARS-CoV-2 Respiratory Pathogens and Coinfection with SARS-CoV-2 Amid the COVID-19 Pandemic A Quick Displacement of the SARS-CoV-2 variant Delta with Omicron Cases Associated with Fewer Admissions and Comparable Upper Respiratory Viral Loads Multi-center Evaluation of the Cepheid Xpert(R) Xpress SARS-CoV-2/Flu/RSV Test Evaluation of the Xpert Xpress SARS-CoV-2/Flu/RSV Assay for Simultaneous Detection of SARS-CoV-2, Influenza A and B Viruses, and Respiratory Syncytial Virus in Nasopharyngeal Specimens Multicenter Evaluation of the Cepheid Xpert Xpress SARS-CoV-2 Test We thank the entire Medical Microbiology division for their assistance with this study. We also thank Qiagen and Abbott Molecular for their scientific and technical support during the assays' evaluations. The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.