key: cord-0979762-qsc3nks6 authors: Wong, River Chun‐Wai; Wong, Ann Han; Ho, Yolanda Iok‐Ieng; Leung, Eddie Chi‐Man; Lai, Raymond Wai‐Man title: Performance evaluation of Panther Fusion SARS‐CoV‐2 assay for detection of SARS‐CoV‐2 from deep throat saliva, nasopharyngeal and lower‐respiratory‐tract specimens date: 2020-09-30 journal: J Med Virol DOI: 10.1002/jmv.26574 sha: 29016e882d198835fea88a76062440728ed9ff37 doc_id: 979762 cord_uid: qsc3nks6 Tremendous increase in workload due to COVID‐19 pandemic has caused intense strain on laboratory service. This article is protected by copyright. All rights reserved. throughput platform with short hands-on time becomes essential. The Panther Fusion SARS-CoV-2 assay (PF assay) (Hologic, Inc., San Diego, USA) operated in Panther Fusion system (PF system) is one of the options. It is validated with nasopharyngeal (NP), oropharyngeal and bronchoalveolar lavage (BAL) specimens while other sample types like deep throat saliva (DTS) and lower-respiratory-tract (LRT) specimens besides BAL are not validated. This study aims to evaluate the diagnostic performance of PF assay for detection of SARS-CoV-2 in comparison to the TIB-Molbiol LightMix® SarbecoV E-gene assay (TIB-Molbiol assay) (TIB-Molbiol, Berlin, Germany) using DTS, NP and LRT specimens. 158 specimens (87 positive and 71 negative specimens) collected from 142 patients with suspected COVID-19 disease were tested. These included 60 NP, 59 DTS and 39 LRT specimens (including 26 sputum, 12 tracheal aspirate and one BAL). The median age of patients was 49 (Interquartile Range (IQR), 32-70) with 47.2% of female and proportion of in-patients was 75.4%. 109 of them were prospective samples and the remaining ones were archived samples stored at -70℃. All positive samples were confirmed by reference laboratory as published previously (1, 2) . Results of PF assay were compared with TIB-Molbiol assay. Discordant results were resolved with Xpert Xpress SARS-CoV-2 assay (Xpert Xpress assay) (Cepheid, Sunnyale, CA, USA). Article DTS and LRT specimens were pre-treated as published previously (2) while NP specimens were tested without pre-treatment. TIB-Molbiol assay was performed as described previously (1) and PF assay was performed according to manufacturer's instruction except supernatant was used for DTS / LRT specimens. Positive Percent Agreement (PPA), Negative Percent Agreement (NPA) and Cohen's Kappa (κ) were determined by using consensus results as reference method. Statistical analysis was performed by MedCalc 19.4.1 (Ostend, Belgium). Cohen's Kappa value greater than 0.81 was interpreted as very good agreement. Results of PF assay were compared to those of TIB-Molbiol assay, there were eight samples with discrepancy and were resolved by testing with Xpert Xpress assay. Using consensus results as gold standard, PPA of NP, LRT & DTS specimens were 96.43%, 100% & 96.00% respectively. The overall PPA and NPA were 97.53% and 100% respectively and overall Cohen's Kappa value was 0.97 (Table 1) . Among the 8 samples with discrepancy, 6 of them initially tested positive by TIB Miobiol assay were tested negative by both PF and Xpert Xpress assay. These samples were hence regarded as false-positive. Despite the manufacturer of TIB Miobiol regarded results with Ct <36 as positive, when use as an initial screening test in our laboratory, sample with any Ct value will be tested supplementary with Xpert Xpress assay. The high Ct values of two discrepant samples (36.49 and 37.90 respectively) suggested that their viral loads were low. Studies have verified the LoD of PF assay ranged from 62.5 to 100 copies/mL (3) (4) (5) . When tested with SARS-CoV-2 synthetic quantified standard from Exact Diagnostics (BioRad, USA), we found that the LoD of both TIB-Molbiol and PF assays were 100 copies/mL while that of Xpert Xpress assay was 50 copies/mL (2) . This article is protected by copyright. All rights reserved. Detection of other respiratory viruses with the respiratory panels on PF System for upper and LRT samples including BAL have been evaluated in various studies (6) (7) (8) . For SARS-CoV-2, several studies have assessed the diagnostic performance of PF assay with NP specimens (4, (9) (10) (11) . Performance of PF assay with DTS and LRT samples other than BAL has not been reported. In this study, we demonstrated that in addition to NP specimens, performance of PF assay for DTS and various LRT specimens was good and comparable to reference method. Presence of mucus in the lysis tube will lead to pipetting errors and invalid results. Similar problem has been reported by Szymczak et al (3) . To resolve such problem, before adding sample into the lysis tube, we recommend to centrifuge the homogenized DTS & LRT specimens according to the pre-treatment protocol reported in our previous study (2) . In conclusion, the Panther Fusion SARS-CoV-2 assay has comparable performance with the reference method. With its capability of random access and high-throughput, it maximizes the flexibility of SARS-CoV-2 testing in clinical laboratories. Abbreviations: CI, confidence interval; PPA, positive percent agreement; NPA, negative percent agreement. Deep throat saliva as an alternative diagnostic specimen type for the detection of SARS-CoV-2 Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay Comparison of the performance of the Panther Fusion respiratory virus panel to R-Gene and laboratory developed tests for diagnostic and hygiene screening specimens from the upper and lower respiratory tract Evaluation of Performance Characteristics of Panther Fusion Assays for Detection of Respiratory Viruses from Nasopharyngeal and Lower Respiratory Tract Specimens Comparison of the Panther Fusion and a laboratory-developed test targeting the envelope gene for detection of SARS-CoV-2 Comparison of Two High-Throughput Reverse Transcription-PCR Systems for the Detection of Severe Acute Respiratory Syndrome Coronavirus 2