ABSTRACT
Testing for SARS-CoV-2 is crucial to tracking and controlling the pandemic. In particular, rapid testing in settings such as the emergency department (ED) could improve time to diagnosis and promote proper infection control measures. Early in the COVID-19 pandemic, we implemented the Abbott ID NOW COVID-19 method for screening symptomatic ED patients. However, due to concerns of suboptimal sensitivity, samples with a negative result were reflexed to the lab for confirmatory testing by the TaqPath COVID-19 Combo RT-PCR method. This study analyzed 6773 ID NOW results from April 2020 to September 2020 in the ED, of which 10% (n = 673) were positive and reported directly. The rest 90% (n = 6100) were negative and reflexed to RT-PCR. Among them, 3% (n = 175) turned positive on RT-PCR while 97% (n = 5925) of the results were consistently negative. The cycle threshold (Ct) values of the false-negative samples (n = 175) showed 90% (n = 158) of them with relatively low viral loads (Ct ≥ 30) with median Ct value at 35, while a number of samples (n = 17) had low Ct values (Ct < 30) and no clear explanation for false-negative results. Our study demonstrates that the Abbott ID NOW, despite it's sensitivity limitations, was capable of providing near real-time results for 10% of symptomatic patients presenting to the ED allowing for improved management and workflow. However, our study findings emphasize the need to reflex negative specimens to a higher sensitivity method when prevalence is high and false-negative results are intolerable.
ABSTRACT
In the context of SARS-CoV-2 pandemic, rapid and easy-to-perform diagnostic methods are essential to limit the spread of the virus and for the clinical management of COVID-19 patients. Although real-time polymerase chain reaction remains the "gold standard" to diagnose acute infections, this technique is expensive, requires trained personnel, well-equipped laboratory and is time-consuming. A prospective evaluation of the Abbott ID NOW COVID-19 point-of-care testing that uses isothermal nucleic acid amplification for the qualitative detection of SARS-CoV-2 RdRp gene was run in the Emergency Department during the third wave of COVID-19 pandemic. ID-NOW significantly simplified SARS-CoV-2 identification and COVID-19 patient triaging, being highly valuable in rapidly locating febrile patients in or out of COVID-19 areas, and can be considered as a first-line diagnostic test in the Emergency Room setting.
ABSTRACT
Rising SARS-CoV-2 cases, testing delays, and the risk of pre-symptomatic and asymptomatic transmission provided the impetus for an in-house rapid testing program. Employees and their household contacts were encouraged to self-collect saliva samples that were pooled for routine testing using an established colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay. In brief, individual or a maximum of four saliva samples were pooled and heat-inactivated to render microorganisms, especially SARS-CoV-2, non-infectious prior to being added to RT-LAMP assay tubes containing either the human sample control gene, RNase P, or a region of the SARS-CoV-2 gene, ORF1ab. During the second wave of SARS-CoV-2 infections in November 2020, two samples from an employee and a member of their household tested positive via RT-LAMP within two days of each other. A delayed clinical qRT-PCR test confirmation of both individuals 5 days later underscored the power of routine rapid testing with within-the-hour turnaround times. Workplace rapid testing programs using RT-LAMP are flexible in their design, have a reduced cost compared to qRT-PCR, may involve non-invasive self-saliva collection for increased safety for the testing personnel, and can be performed with minimal training.
ABSTRACT
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.
ABSTRACT
OBJECTIVES: The reliable identification of individuals with SARS-CoV-2 infection is the cornerstone for containing viral spread. Rapid molecular point-of-care testing (POCT) of saliva might reduce analysis time, thus increasing the efficacy of contact tracing. In this study, a new POCT RT-PCR assay for the detection of SARS-CoV-2 RNA in saliva was evaluated and compared with an already validated CE-IVD method. METHODS: An evaluation was made of 160 left-over salivary samples (27 frozen, kept at -80 °C and 133 fresh), collected using Salivette (Sarstedt, Germany). Samples were analyzed by TaqPath COVID-19 CE-IVD RT-PCR kit, QuantStudio5 Real-Time (Applied Biosystems, USA) (TaqPath) and bKIT Virus Finder COVID-19 Saliva (Hyris Global Diagnostics, Italy). Performances of three- and fivefold pooling strategies were also evaluated. Blood assay interference in saliva was also tested with Hyris. RESULTS: On using TaqPath, SARS-CoV-2 positivity was detected in 35 samples. Another 10 positive samples were artificially-generated by blind mixing of positive with negative samples. Hyris positive and negative percentages of agreement were 97.6 (95% CI: 87.2-99.9%) and 100 (95% CI: 97.0-100%), respectively. Seventeen positive pools, evaluated for threefold strategy, were all correctly determined by both systems. For the 5-pool strategy, 94.7% (18/19) of samples resulted positive with the Hyris system, and 100% with TaqPath. The presence of 1% of blood (v/v) in saliva did not interfere with the accuracy of Hyris assay. CONCLUSIONS: The sensitivity and specificity of the bKIT Virus Finder COVID-19 Saliva were optimal with respect to TaqPath. In view of the safe and straightforward pre-analytical procedure involved, and the small size of the Hyris bCube, the Hyris system can be used for POCT.