key: cord-289947-z2dw2eaz
authors: Wong, River Chun-Wai; Wong, Ann Han; Ho, Yolanda Iok-Ieng; Leung, Eddie Chi-Man; Lai, Raymond Wai-Man
title: Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay
date: 2020-08-16
journal: J Clin Virol
DOI: 10.1016/j.jcv.2020.104593
sha: 
doc_id: 289947
cord_uid: z2dw2eaz

BACKGROUND: Xpert® Xpress SARS-CoV-2 assay is only validated on nasopharyngeal specimens for detection of SARS-CoV-2. Other specimen types such as deep throat saliva (DTS), also known as posterior oropharyngeal saliva and lower-respiratorytract specimens (LRT) including sputum, tracheal aspirate and bronchoalveolar lavage are not validated. These non-validated specimen types, however, do have significant diagnostic value. OBJECTIVE: Evaluate the performance of Xpert Xpress SARS-CoV-2 assay for detection of SARS-CoV-2 from DTS and LRT specimens. METHODS: 162 specimens from 158 patients with suspected COVID-19 disease were tested with Xpert Xpress SARS-CoV-2 assay. These included 120 DTS and 42 LRT specimens i.e. 35 sputum, 6 tracheal aspirate and one bronchoalveolar lavage. Results were compared to those by the TIB-Molbiol LightMix® SarbecoV E-gene assay. RESULTS: Xpert Xpress SARS-CoV-2 assay has satisfactory performance when compared with reference method. The positive percent agreement (PPA) of DTS and LRT specimens were 98.86% & 100% respectively while the negative percent agreement (NPA) was 100% for both DTS and LRT specimens. CONCLUSIONS: This study demonstrated with appropriate sample pre-treatment, Xpert Xpress SARS-CoV-2 assay can be used to test on non-validated specimen types including DTS & LRT specimens.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus responsible for cluster of atypical pneumonia outbreak in Wuhan, China Table 1 Overall agreements between Xpert Xpress SARS-CoV-2 assay and reference method among 162 deep throat saliva and lower-respiratory-tract specimens for detection of SARS-CoV-2.

The SOC NAAT only allows batch testing. With the use of Xpert Xpress SARS-CoV-2 assay as a complementary test, it will allow rapid testing of ad-hoc samples received from AED & intensive care unit and provide round-the-clock service for samples received after batch testing cut-time. Similar testing algorithm has been adopted in our laboratory for testing of influenza [10].

The overall performance of Xpert Xpress SARS-CoV-2 assay was satisfactory when tested with DTS and LRT specimens. Review of the sample with discrepancy showed that it was sent from a known positive COVID-19 patient for disease monitoring.

Such discrepancy might be attributed to the low viral load in this sample (Ct = 34.47) as well as potential RNA degradation due to repeated freeze and thaw.

With the use of Exact Diagnostics SARS-CoV-2 reference standard (BioRad, USA), the analytical 95% lower limit of detection of Xpert Xpress SARS-CoV-2 assay and TIB-Molbiol LightMix® SarbecoV E-gene assay was determined as 50 and 100 copies/mL respectively.

To our knowledge, this is the first report to evaluate the use of PBS for sample homogenization of DTS prior to testing with Xpert Xpress SARS-CoV-2 assay.

Previous study used viral transport medium (VTM) for sample homogenization [1] .

One study recommended direct transfer of the liquid, non-viscous part of neat sample into the cartridge without pre-treatment [3] . Our previous experience with Xpert

Xpress Flu/RSV assay showed that direct transfer of LRT samples, in particular sputum, into the cartridge resulted in a high error frequency. This study was the first to evaluate the testing of LRT specimens (mainly sputum) with pre-treatment to minimize potential invalid results or instrument error. These procedures can minimize the mucus and viscous substances among non-validated specimen types and broaden the testing scope of Xpert Xpress SARS-CoV-2 assay. [4] . In this study, we demonstrated that both PBS and MM can be used for sample homogenization. LRT samples were suspended with MM for virus isolation in our routine practice, however, this service was obsoleted in February 2020. As in-

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We would like to thank all the technical staff who provide technical assistance and contribute to SARS-CoV-2 testing in our department.J o u r n a l P r e -p r o o f