Clinical performance of the Xpert® Xpress Flu/RSV assay for the detection of Influenza A, B, and respiratory syncytial virus on ESwab™ medium

Background : Prior to the SARS-CoV-2 pandemic, the Xpert® Xpress Flu/RSV assay (GXA) was regularly used, while during the pandemic the Xpert® Xpress SARS-CoV-2/Flu/RSV plus assay was developed by Cepheid. In contrast to this new assay, the use of oropharyngeal ESwabs in combination with the Flu/RSV assay is designated as off CE-IVD label use, while these were used frequently in The Netherlands. Aim : To investigate the clinical performance of the GXA using 1,289 ESwab™ oropharyngeal samples for the detection of Influenza A virus, Influenza B virus and respiratory syncytial virus (RSV). Methods : The clinical performance of the GXA was prospectively investigated during the influenza seasons of 2017 and 2018 by testing fresh oropharyngeal samples, collected with ESwab™, contemporaneously with both the GXA and a laboratory developed Flu/RSV real time RT-PCR assay (LDA) (reference method). Results : 1,289 Samples from 1,213 patients (46% men, median age 73 (IQR 62-82)) were tested with both tests. Positive percent agreement (95% CI) was 98% (95%-99%) for Influenza A virus, 92% (88%-95%) for influenza B virus, and 88% (73%-96%) for RSV. Negative percent agreement was ≥ 99% for all three viruses. Ct-values of the GXA were on average higher than the LDA. Conclusion : This study showed a good clinical performance of the GXA in oropharyngeal samples for the detection of Influenza A and B virus. The positive percent agreement of the GXA for the detection of RSV in oropharyngeal samples was somewhat lower and in particular for the detection of RSV-A.

Clinical performance and sample freeze-thaw stability of the cobas®6800 SARS-CoV-2 assay for the detection of SARS-CoV-2 in oro-/nasopharyngeal swabs and lower respiratory specimens.

INTRODUCTION: Studies describing the performance characteristics of the cobas®6800 system for SARS-CoV-2 detection in deep respiratory specimens and freeze-thaw stability are limited. The current study compares the clinical performance of the automated SARS-CoV-2 assay on the cobas®6800 system to a lab-developed assay (LDA) and the cobas impact of freeze-thawing combined with lysis buffer. METHODS: Both retrospective and prospectively selected deep respiratory samples and oro- and nasopharyngeal samples in either E-swab® or GLY- were tested using the SARS-CoV-2 assay on the cobas®6800 System and compared to a lab developed assay. Additonally, SARS-CoV-2 RNA stability was assessed after one freeze-thaw cycle with or without lysis buffer. RESULTS: In total, 221 (58.3 %) oro- and nasopharyngeal swabs, 131 (34.6 %) deep respiratory specimens, and n = 25 (6.6 %) swabs of unknown origin were included to study clinical performance. Only 4 samples gave discrepant results, all being positive in the LDA and not the cobas®6800 system. For stability testing, 66 samples without and 110 with lysis buffer were included. No clinically significant difference was found in test results after one freeze-thaw cycle and addition of lysis buffer. CONCLUSION: Based on our findings, the cobas®6800 SARS-CoV-2 RNA assay yielded similar results as the LDA in oro-/nasopharyngeal swabs and deep respiratory specimens. Moreover, the cobas®6800 SARS-CoV-2 RNA assay yielded similar results before and after a freeze-thaw cycle, with better preservation of low viral loads in lysis buffer.

COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study.

BACKGROUND: 10 days after the first reported case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the Netherlands (on Feb 27, 2020), 55 (4%) of 1497 health-care workers in nine hospitals located in the south of the Netherlands had tested positive for SARS-CoV-2 RNA. We aimed to gain insight in possible sources of infection in health-care workers. METHODS: We did a cross-sectional study at three of the nine hospitals located in the south of the Netherlands. We screened health-care workers at the participating hospitals for SARS-CoV-2 infection, based on clinical symptoms (fever or mild respiratory symptoms) in the 10 days before screening. We obtained epidemiological data through structured interviews with health-care workers and combined this information with data from whole-genome sequencing of SARS-CoV-2 in clinical samples taken from health-care workers and patients. We did an in-depth analysis of sources and modes of transmission of SARS-CoV-2 in health-care workers and patients. FINDINGS: Between March 2 and March 12, 2020, 1796 (15%) of 12 022 health-care workers were screened, of whom 96 (5%) tested positive for SARS-CoV-2. We obtained complete and near-complete genome sequences from 50 health-care workers and ten patients. Most sequences were grouped in three clusters, with two clusters showing local circulation within the region. The noted patterns were consistent with multiple introductions into the hospitals through community-acquired infections and local amplification in the community. INTERPRETATION: Although direct transmission in the hospitals cannot be ruled out, our data do not support widespread nosocomial transmission as the source of infection in patients or health-care workers. FUNDING: EU Horizon 2020 (RECoVer, VEO, and the European Joint Programme One Health METASTAVA), and the National Institute of Allergy and Infectious Diseases, National Institutes of Health.