Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay

Wong, River Chun-Wai; Wong, April S. Y.; Ho, Yolanda Iok-Ieng; Leung, Eddie Chi Man; Lai, Robin Kit-Ho

doi:10.1016/j.jcv.2020.104593

Cited by 25 publications

(33 citation statements)

References 12 publications

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“…however, an increasing number of institutions are using deep throat saliva (DTS) as an alternative specimen type for detecting influenza and SARS-CoV-2 (13,20,21). Studies have been performed for the use of DTS in the Xpert SARS-CoV-2 (10) and Xpert Flu/RSV assays (22).…”

Section: Downloaded Frommentioning

confidence: 99%

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

et al. 2021

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Patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A (flu A), influenza B (flu B), and respiratory syncytial virus (RSV) have overlapping clinical presentations, but the approaches to treatment and management of infections caused by these viruses are different. Therefore, rapid diagnosis in conjunction with infection prevention measures is important to prevent transmission of the diseases. Recently, a new Xpert Xpress SARS-CoV-2/Flu/RSV (Xpert 4-in-1) assay enables the detection and differentiation of SARS-CoV-2, flu A, flu B, and RSV in upper respiratory tract specimens. In this study, we evaluated the performance of the Xpert 4-in-1 assay by comparing it with the Xpert Xpress SARS-CoV-2 and Xpert Xpress Flu/RSV assays for the detection of the four viruses in nasopharyngeal (NP) specimens. A total of 279 NP specimens, including 66, 56, 64 and 53 positive specimens for SARS-CoV-2, flu A, flu B and RSV respectively, were included. The Xpert 4-in-1 assay demonstrated high concordance with the comparator assays, with overall agreement for SARS-CoV-2, flu A, flu B, and RSV at 99.64%, 100%, 99.64%, and 100%, respectively, and a high kappa value ranging from 0.99 to 1.00, indicating an almost perfect correlation between assays. The cycle threshold value association between positive samples also showed a good correlation between assays. In conclusion, the overall performance of the Xpert 4-in-1 assay was highly comparable to that of the Xpert SARS-CoV-2 and Xpert Flu/RSV assays for the detection and differentiation of SARS CoV-2, flu A, flu B, and RSV in NP specimens.

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confidence: 99%

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

et al. 2021

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“…For the Xpert Xpress assay, we identified 11 studies comprising 1734 participants. 13,[16][17][18][19][22][23][24][25]27,28 Four studies were designed as multicenter trials, 14,16,19,20 and 13 studies were conducted only in the United States. 12,14,15,17,18,[20][21][22][23][24][25][26]28 The number of patients in each trial ranged from 26 to 524.…”

Section: Study Search and Characteristics And Quality Of Included Stumentioning

confidence: 99%

Diagnostic accuracy of the Cepheid Xpert Xpress and the Abbott ID NOW assay for rapid detection of SARS‐CoV‐2: A systematic review and meta‐analysis

Lee

Song

2021

Journal of Medical Virology

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Rapid and accurate diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is essential to prevent the spread of the virus. We investigated the diagnostic accuracy of the Xpert Xpress and the ID NOW assays for rapid detection of SARS-CoV-2 using a systemic review and meta-analysis approach.A systematic literature search was performed using PubMed, Embase, and the Cochrane COVID-19 Study Register. The sensitivity and specificity of these tests for detecting viruses in patients with suspected SARS-CoV-2 infection were pooled. We used commercial and laboratory-developed reverse transcription-polymerase chain reactions as reference standards. The Quality Assessment of Diagnostic Accuracy Studies-2 tool was used to assess the risk of bias. We identified 11 studies involving 1734 subjects for the Xpert Xpress assay and 10 studies involving 1778 subjects for the ID NOW assay. The pooled sensitivity and specificity of the Xpert Xpress assay for detection of SARS-CoV-2 were 0.99 (95% confidence interval [CI], 0.97 to 0.99) and 0.97 (95% CI, 0.95 to 0.98), respectively. The pooled sensitivity and specificity of the ID NOW assay were 0.79 (95% CI, 0.69 to 0.86) and 1.00 (95% CI, 0.98 to 1.00), respectively. The studies included in our analysis seemed to have low methodological quality. The Xpert Xpress assay showed excellent diagnostic accuracy for rapid detection of SARS-CoV-2. However, as the ID NOW assay showed relatively low sensitivity, this test might miss several positive samples.

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“… Lippi et al (2020) suggested that sample collection errors and transportation factors also have an impact on assay detection accuracy. It has shown that liquid Amies medium, PBS, or maintenance medium can be used for homogenization of saliva samples ( Williams et al, 2020 ; Wong et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Comparison Between a Standard and SalivaDirect RNA Extraction Protocol for Molecular Diagnosis of SARS-CoV-2 Using Nasopharyngeal Swab and Saliva Clinical Samples

Flores

Rodríguez-Martínez

Reyes-Berrones

et al. 2021

Front. Bioeng. Biotechnol.

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During the COVID-19 pandemic, a certified laboratory of Tamaulipas, Mexico has processed over 100,000 samples of COVID-19 suspected patients, working a minimum of 100 tests daily. Thus, it would be beneficial for such certified laboratories nationwide to reduce the time and cost involved in performing the diagnosis of COVID-19, from sample collection, transportation to local lab, processing of samples, and data acquisition. Here, 30 nasopharyngeal swab and saliva samples from the same COVID-19 individuals were assessed by a standard nucleic acid extraction protocol, including protein lysis with proteinase K followed by binding to column, washing, and elution, and by the SalivaDirect protocol based on protein lysis, skipping the other steps to reduce processing time and costs. The genomic RNA was amplified using a SARS-CoV-2 Real-Time PCR kit. A variation (P > 0.05) in the 95% CIs = 72.6%–96.7% was noted by using the SalivaDirect protocol and saliva samples (sensitivity of 88.2%) in comparison to those of standard protocol with oropharyngeal swab samples (95% CIs = 97.5%–100%; sensitivity of 100%) as reported elsewhere. However, when using nasopharyngeal swab samples in the SalivaDirect protocol (sensitivity of 93.6%; 95% CIs = 79.2%–99.2%), it was in concordance (P < 0.05) with those of the standard one. The logical explanation to this was that two samples with Ct values of 38, and 40 cycles for gene E produced two false negatives in the SalivaDirect protocol in relation to the standard one; thus, there was a reduction of the sensitivity of 6.4% in the overall assay performance.

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Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay

Cited by 25 publications

References 12 publications

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

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

Diagnostic accuracy of the Cepheid Xpert Xpress and the Abbott ID NOW assay for rapid detection of SARS‐CoV‐2: A systematic review and meta‐analysis

Comparison Between a Standard and SalivaDirect RNA Extraction Protocol for Molecular Diagnosis of SARS-CoV-2 Using Nasopharyngeal Swab and Saliva Clinical Samples

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