Targeted rapid testing for SARS-CoV-2 in the emergency department is associated with large reductions in uninfected patient exposure time

Hinson, Jeremiah S.; Rothman, Richard E.; Carroll, Karen C.; Mostafa, Heba H.; Ghobadi, Kimia; Smith, Arthur L.; Martínez, Diego A.; Shaw-Saliba, Kathryn; Klein, Eili Y.; Levin, Scott R.

doi:10.1016/j.jhin.2020.09.035

Cited by 18 publications

(19 citation statements)

References 12 publications

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“…The Xpert Xpress SARS-CoV-2 test received FDA EUA on 20 March 2020 and was the first assay authorized for use in Clinical and Laboratory Improvement Amendments (CLIA)-waived settings. The use of this sensitive test in the laboratory and point-of-care settings ( 8 , 28 , 35 , 36 ) has reduced health care workers’ exposure risk in emergency rooms due to the short turnaround time ( 37 ).…”

Section: Discussionmentioning

confidence: 99%

Multicenter Evaluation of the Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV Test

et al. 2021

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With the approach of respiratory virus season in the Northern Hemisphere, clinical microbiology and public health laboratories will need rapid diagnostic assays to distinguish SARS-CoV-2 from influenza and respiratory syncytial virus (RSV) infections for diagnosis and surveillance. In this study, the clinical performance of the Xpert® Xpress SARS-CoV-2/Flu/RSV test (Cepheid, Sunnyvale, CA, USA) for nasopharyngeal swab specimens was evaluated in four centers: Johns Hopkins Medical Microbiology Laboratory, Northwell Health Laboratories, NYC Public Health Laboratory, and Los Angeles County/University of Southern California (LAC+USC) Medical Center. A total of 319 nasopharyngeal swab specimens, positive for SARS-CoV-2 (n = 75), influenza A (n = 65), influenza B (n = 50), RSV (n = 38), or negative (n = 91) by the standard of care nucleic acid amplification tests at each site were tested using the Cepheid panel test. The overall positive percent agreement for the SARS-CoV-2 target was 98.7% (n= 74/75) and the negative agreement was 100% (n= 91) with all other analytes showing 100% total agreement (n= 153). Standard of care tests to which the Cepheid panel was compared included the Cepheid Xpert Xpress SARS-CoV-2, Cepheid Xpert Xpress Flu/RSV, the GenMark ePlex respiratory panel, the BioFire Respiratory panels 2.1 and v1.7, the DiaSorin Simplexa COVID-19 Direct, and the Hologic Panther Fusion SARS-CoV-2 assays. The Xpert Xpress SARS-CoV-2/Flu/RSV test showed high sensitivity and accuracy for all analytes included in the test. This test will provide a valuable clinical diagnostic and public health solution for detecting and differentiating SARS-CoV-2, influenza A and B, and RSV infections during the current respiratory virus season.

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Section: Discussionmentioning

confidence: 99%

Multicenter Evaluation of the Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV Test

et al. 2021

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“…This should be considered when applying hexamer only based amplification as it can result in low depth of coverage, making it impossible to perform viral genome assembly when the virus titre is low and thus pre-detection methods are required so mapping can be directed rather than de novo . As compared to other recently published studies that utilize PCR-based targeted enrichment and either Illumina or Oxford Nanopore sequencing [10, 63, 64] the main advantage of SISPA (and/or S-P) method presented in this study is its simplicity (e.g. only one K-8N primer used), and possibility to apply the method to any unknown samples as no prior knowledge about pathogen is needed.…”

Section: Discussionmentioning

confidence: 99%

A random priming amplification method for whole genome sequencing of SARS-CoV-2 and H1N1 influenza A virus

Chrząstek

Tennakoon

Bialy

et al. 2021

Preprint

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Background: Non-targeted whole genome sequencing is a powerful tool to comprehensively identify constituents of microbial communities in a sample. There is no need to direct the analysis to any identification before sequencing which can decrease the introduction of bias and false negatives results. It also allows the assessment of genetic aberrations in the genome (e.g., single nucleotide variants, deletions, insertions and copy number variants) including in noncoding protein regions. Methods: The performance of four different random priming amplification methods to recover RNA viral genetic material of SARS-CoV-2 were compared in this study. In method 1 (H-P) the reverse transcriptase (RT) step was performed with random hexamers whereas in methods 2-4 RT incorporating an octamer primer with a known tag. In methods 1 and 2 (K-P) sequencing was applied on material derived from the RT-PCR step, whereas in methods 3 (SISPA) and 4 (S-P) an additional amplification was incorporated before sequencing. Results: The SISPA method was the most effective and efficient method for non-targeted/random priming whole genome sequencing of COVID that we tested. The SISPA method described in this study allowed for whole genome assembly of SARS-CoV-2 and influenza A(H1N1)pdm09 in mixed samples. We determined the limit of detection and characterization of SARS-CoV-2 virus which was 103 pfu/ml (Ct, 22.4) for whole genome assembly and 101 pfu/ml (Ct, 30) for metagenomics detection. Conclusions: The SISPA method is predominantly useful for obtaining genome sequences from RNA viruses or investigating complex clinical samples as no prior sequence information is needed. It might be applied to monitor genomic virus changes, virus evolution and can be used for fast metagenomics detection or to assess the general picture of different pathogens within the sample.

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“…We identified three peer-reviewed studies that evaluated the impact of rapid NAAT performed at the POC, including one which involved the Xpert Xpress SARS-CoV-2 test. Hinson et al performed the Xpress SARS-CoV-2 test on demand in the Emergency Department and compared impact with batch RT-PCR testing in a central laboratory [89]. Rapid testing at the POC was associated with a significant reduction in the time to removal from isolation for patients with negative test results, an increase in COVID-19 treatment capacity, and conservation of personal protective equipment.…”

Section: Impact Of Sars-cov-2 Naats Performed At the Pocmentioning

confidence: 99%

“…Rapid testing at the POC was associated with a significant reduction in the time to removal from isolation for patients with negative test results, an increase in COVID-19 treatment capacity, and conservation of personal protective equipment. Another study compared the impact of a non-EUA NAAT performed at POC, to a batch-based RT-PCR performed in a central laboratory [89]. The time to result for the POC NAAT was significantly shorter than the standard lab RT-PCR, and POC testing resulted in faster time to final bed placement from the Emergency Room, increased isolation room availability, and faster patient discharge.…”

Section: Impact Of Sars-cov-2 Naats Performed At the Pocmentioning

confidence: 99%

Detection of Sars-Cov-2At the Point of Care

Loeffelholz¹,

Tang

2021

Bioanalysis

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of COVID-19. Testing for SARS-CoV-2 infection is a critical element of the public health response to COVID-19. Point-of-care (POC) tests can drive patient management decisions for infectious diseases, including COVID-19. POC tests are available for the diagnosis of SARS-CoV-2 infections and include those that detect SARS-CoV-2 antigens as well as amplified RNA sequences. We provide a review of SARS-CoV-2 POC tests including their performance, settings for which they might be used, their impact and future directions. Further optimization and validation, new technologies as well as studies to determine clinical and epidemiological impact of SARS-CoV-2 POC tests are needed.

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Targeted rapid testing for SARS-CoV-2 in the emergency department is associated with large reductions in uninfected patient exposure time

Cited by 18 publications

References 12 publications

Multicenter Evaluation of the Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV Test

Multicenter Evaluation of the Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV Test

A random priming amplification method for whole genome sequencing of SARS-CoV-2 and H1N1 influenza A virus

Detection of Sars-Cov-2At the Point of Care

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