scholarly journals Performance of Abbott ID Now COVID-19 Rapid Nucleic Acid Amplification Test Using Nasopharyngeal Swabs Transported in Viral Transport Media and Dry Nasal Swabs in a New York City Academic Institution

2020 ◽  
Vol 58 (8) ◽  
Author(s):  
Atreyee Basu ◽  
Tatyana Zinger ◽  
Kenneth Inglima ◽  
Kar-mun Woo ◽  
Onome Atie ◽  
...  
Keyword(s):  
New York ◽  
The United States ◽  
Turnaround Time ◽  
Nucleic Acid Amplification ◽  
Molecular Diagnostic ◽  
Sample Type ◽  
Negative Results ◽  
Viral Transport ◽  
Recent Emergence ◽  
Nasal Swabs

ABSTRACT The recent emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has posed formidable challenges for clinical laboratories seeking reliable laboratory diagnostic confirmation. The swift advance of the crisis in the United States has led to Emergency Use Authorization (EUA) facilitating the availability of molecular diagnostic assays without the more rigorous examination to which tests are normally subjected prior to FDA approval. Our laboratory currently uses two real-time reverse transcription-PCR (RT-PCR) platforms, the Roche Cobas SARS-CoV2 and the Cepheid Xpert Xpress SARS-CoV-2. The two platforms demonstrate comparable performances; however, the run times for each assay are 3.5 h and 45 min, respectively. In search for a platform with a shorter turnaround time, we sought to evaluate the recently released Abbott ID Now COVID-19 assay, which is capable of producing positive results in as little as 5 min. We present here the results of comparisons between Abbott ID Now COVID-19 and Cepheid Xpert Xpress SARS-CoV-2 using nasopharyngeal swabs transported in viral transport media and comparisons between Abbott ID Now COVID-19 and Cepheid Xpert Xpress SARS-CoV-2 using nasopharyngeal swabs transported in viral transport media for Cepheid and dry nasal swabs for Abbott ID Now. Regardless of method of collection and sample type, Abbott ID Now COVID-19 had negative results in a third of the samples that tested positive by Cepheid Xpert Xpress when using nasopharyngeal swabs in viral transport media and 45% when using dry nasal swabs.

scholarly journals Performance of Abbott ID NOW COVID-19 rapid nucleic acid amplification test in nasopharyngeal swabs transported in viral media and dry nasal swabs, in a New York City academic institution

2020 ◽  
Author(s):  
Atreyee Basu ◽  
Tatyana Zinger ◽  
Kenneth Inglima ◽  
Kar-mun Woo ◽  
Onome Atie ◽  
...  
Keyword(s):  
New York ◽  
The United States ◽  
Turnaround Time ◽  
Nucleic Acid Amplification ◽  
Molecular Diagnostic ◽  
Sample Type ◽  
Negative Results ◽  
Viral Transport ◽  
Recent Emergence ◽  
Nasal Swabs

AbstractThe recent emergence of the SARS-CoV-2 pandemic has posed formidable challenges for clinical laboratories seeking reliable laboratory diagnostic confirmation. The swift advance of the crisis in the United States has led to Emergency Use Authorization (EUA) facilitating the availability of molecular diagnostic assays without the more rigorous examination to which tests are normally subjected prior to FDA approval. Our laboratory currently uses two real time RT-PCR platforms, the Roche Cobas SARS-CoV2 and the Cepheid Xpert Xpress SARS-CoV-2. Both platforms demonstrate comparable performance; however, the run times for each assay are 3.5 hours and 45 minutes, respectively. In search for a platform with shorter turnaround time, we sought to evaluate the recently released Abbott ID NOW COVID-19 assay which is capable of producing positive results in as little as 5 minutes. We present here the results of comparisons between Abbott ID NOW COVID-19 and Cepheid Xpert Xpress SARS-CoV-2 using nasopharyngeal swabs transported in viral transport media and comparisons between Abbott ID NOW COVID-19 and Cepheid Xpert Xpress SARS-CoV-2 using nasopharyngeal swabs transported in viral transport media for Cepheid and dry nasal swabs for Abbott ID NOW. Regardless of method of collection and sample type, Abbott ID NOW COVID-19 had negative results in a third of the samples that tested positive by Cepheid Xpert Xpress when using nasopharyngeal swabs in viral transport media and 45% when using dry nasal swabs.

scholarly journals Trends in Testing for Mycobacterium tuberculosis Complex From US Public Health Laboratories, 2009–2013

2016 ◽  
Vol 132 (1) ◽  
pp. 56-64 ◽  
Author(s):  
Frances Tyrrell ◽  
Cortney Stafford ◽  
Mitchell Yakrus ◽  
Monica Youngblood ◽  
Andrew Hill ◽  
...  
Keyword(s):  
Public Health ◽  
Mycobacterium Tuberculosis ◽  
Mycobacterium Tuberculosis Complex ◽  
The United States ◽  
Drug Susceptibility ◽  
Turnaround Time ◽  
Nucleic Acid Amplification ◽  
Tuberculosis Complex ◽  
Complex Detection ◽  
Susceptibility Tests

Objective: We investigated data from US public health laboratories funded through the Centers for Disease Control and Prevention’s Tuberculosis Elimination and Laboratory Cooperative Agreement to document trends and challenges in meeting national objectives in tuberculosis (TB) laboratory diagnoses. Methods: We examined data on workload and turnaround time from public health laboratories’ progress reports during 2009-2013. We reviewed methodologies, laboratory roles, and progress toward rapid detection of Mycobacterium tuberculosis complex through nucleic acid amplification (NAA) testing. We compared selected data with TB surveillance reports to estimate public health laboratories’ contribution to national diagnostic services. Results: During the study period, culture and drug susceptibility tests decreased, but NAA testing increased. Public health laboratories achieved turnaround time benchmarks for drug susceptibility tests at lower levels than for acid-fast bacilli smear and identification from culture. NAA positivity in laboratories among surveillance-reported culture-positive TB cases increased from 26.6% (2355 of 8876) in 2009 to 40.0% (2948 of 7358) in 2013. Public health laboratories provided an estimated 50.9% (4285 of 8413 in 2010) to 57.2% (4210 of 7358 in 2013) of culture testing and 88.3% (6822 of 7727 in 2011) to 94.4% (6845 of 7250 in 2012) of drug susceptibility tests for all US TB cases. Conclusions: Public health laboratories contribute substantially to TB diagnoses in the United States. Although testing volumes mostly decreased, the increase in NAA testing indicates continued progress in rapid M tuberculosis complex detection.

scholarly journals Evaluation of symptomatic patient saliva as a sample type for the Abbott ID NOW COVID-19 assay

2020 ◽  
Author(s):  
Jeffrey A. SoRelle ◽  
Lenin Mahimainathan ◽  
Clare McCormick-Baw ◽  
Dominick Cavuoti ◽  
Francesca Lee ◽  
...  
Keyword(s):  
False Negative ◽  
Symptomatic Patient ◽  
Sample Type ◽  
Sample Collection ◽  
Cycle Number ◽  
Negative Results ◽  
Percent Agreement ◽  
False Negative Results ◽  
Nasal Swabs ◽  
Comparable Performance

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has presented significant challenges for laboratories including supply chain limitations with restricted access to reagents and sample collection materials (i.e. swabs, viral transport media (VTM)) for patients testing. Therefore, saliva has been evaluated as an alternative specimen for COVID-19 diagnosis. comparable performance between dry nasal swabs (NS) and nasopharyngeal swabs (NPS) collected in VTM has been observed with the ID NOW for SARS-CoV-2; the majority of false-negative results occur with higher cycle number (CN) or cycle threshold (Ct) values suggesting low viral load in these specimens. We performed clinical validation of saliva specimens on the ID NOW molecular platform to detect SARS-CoV-2. Saliva was compared to nasopharyngeal swabs tested on the ID NOW and the Cepheid molecular assay. We also performed stability studies of saliva samples over 5 days. A total of 96 saliva samples and 64 paired NPS were analyzed. We observed 78% (18/23) positive percent agreement (PPA) and 100% (44/44) negative percent agreement (NPA) between matched saliva and nasopharyngeal specimens performed on ID NOW. We found 83% (19/23) PPA and 100% NPA (25/25) between saliva run on the ID NOW and Cepheid assay. Six saliva specimens positive for SARS-CoV-2 were continuously positive for five days when stored at room temperature. Therefore, we propose further investigation of saliva as an alternative sample type for testing symptomatic patients with ID NOW as a promising method to address COVID-19 testing.

scholarly journals Evaluation of specimen types and saliva stabilization solutions for SARS-CoV-2 testing

2021 ◽  
Author(s):  
Sara B Griesemer ◽  
Greta Van Slyke ◽  
Dylan Ehrbar ◽  
Klemen Strle ◽  
Tugba Yildirim ◽  
...  
Keyword(s):  
New York ◽  
Room Temperature ◽  
Nasal Swab ◽  
Diagnostic Testing ◽  
New York State ◽  
Detection Sensitivity ◽  
Sample Type ◽  
Total N ◽  
Nasal Swabs ◽  
Alternative Specimen

Identifying SARS-CoV-2 infections through aggressive diagnostic testing remains critical in tracking and curbing the spread of the COVID-19 pandemic. Collection of nasopharyngeal swabs (NPS), the preferred sample type for SARS-CoV-2 detection, has become difficult due to the dramatic increase in testing and consequential supply strain. Therefore, alternative specimen types have been investigated, that provide similar detection sensitivity with reduced health care exposure and potential for self-collection. In this study, the detection sensitivity of SARS-CoV-2 in nasal swabs (NS) and saliva was compared to that of NPS, using matched specimens from two outpatient cohorts in New York State (total n = 463). The first cohort showed only a 5.4% positivity but the second cohort (n=227) had a positivity rate of 41%, with sensitivity in NPS, NS and saliva of 97.9%, 87.1%, and 87.1%, respectively. Whether the reduced sensitivity of NS or saliva is acceptable must be assessed in the settings where they are used. However, we sought to improve on it by validating a method to mix the two sample types, as the combination of nasal swab and saliva resulted in 94.6% SARS-CoV-2 detection sensitivity. Spiking experiments showed that combining them did not adversely affect the detection sensitivity in either. Virus stability in saliva was also investigated, with and without the addition of commercially available stabilizing solutions. The virus was stable in saliva at both 4°C and room temperature for up to 7 days. The addition of stabilizing solutions did not enhance stability and in some situations reduced detectable virus levels.

scholarly journals Evaluation of specimen types and saliva stabilization solutions for SARS-CoV-2 testing

2020 ◽  
Author(s):  
Sara B Griesemer ◽  
Greta Van Slyke ◽  
Dylan Ehrbar ◽  
Klemen Strle ◽  
Tugba Yildirim ◽  
...  
Keyword(s):  
New York ◽  
Room Temperature ◽  
Nasal Swab ◽  
Diagnostic Testing ◽  
New York State ◽  
Detection Sensitivity ◽  
Sample Type ◽  
Total N ◽  
Nasal Swabs ◽  
Alternative Specimen

AbstractIdentifying SARS-CoV-2 infections through aggressive diagnostic testing remains critical in tracking and curbing the spread of the COVID-19 pandemic. Collection of nasopharyngeal swabs (NPS), the preferred sample type for SARS-CoV-2 detection, has become difficult due to the dramatic increase in testing and consequential supply strain. Therefore, alternative specimen types have been investigated, that provide similar detection sensitivity with reduced health care exposure and potential for self-collection. In this study, the detection sensitivity of SARS-CoV-2 in nasal swabs (NS) and saliva was compared to that of NPS, using matched specimens from two outpatient cohorts in New York State (total n = 463). The first cohort showed only a 5.4% positivity but the second cohort (n=227) had a positivity rate of 41%, with sensitivity in NPS, NS and saliva of 97.9%, 87.1%, and 87.1%, respectively. Whether the reduced sensitivity of NS or saliva is acceptable must be assessed in the settings where they are used. However, we sought to improve on it by validating a method to mix the two sample types, as the combination of nasal swab and saliva resulted in 94.6% SARS-CoV-2 detection sensitivity. Spiking experiments showed that combining them did not adversely affect the detection sensitivity in either. Virus stability in saliva was also investigated, with and without the addition of commercially available stabilizing solutions. The virus was stable in saliva at both 4°C and room temperature for up to 7 days. The addition of stabilizing solutions did not enhance stability and in some situations reduced detectable virus levels.

scholarly journals Comparative study of four SARS-CoV-2 Nucleic Acid Amplification Test (NAAT) platforms demonstrates that ID NOW performance is impaired substantially by patient and specimen type

2020 ◽  
Author(s):  
Paul R. Lephart ◽  
Michael Bachman ◽  
William LeBar ◽  
Scott McClellan ◽  
Karen Barron ◽  
...  
Keyword(s):  
Nasal Swab ◽  
The United States ◽  
Nucleic Acid Amplification Test ◽  
Nucleic Acid Amplification ◽  
Molecular Diagnostic ◽  
Nasopharyngeal Swab ◽  
Diagnostic Assays ◽  
Comparable Performance ◽  
Indications For Use ◽  
Significant Factors

AbstractThe advent of the COVID-19 pandemic in the United States created a unique situation where multiple molecular diagnostic assays with various indications for use in the detection of SARS-CoV-2 rapidly received Emergency Use Authorization by the FDA, were validated by laboratories and utilized clinically, all within a period of a few weeks. We compared the performance of four of these assays that were being evaluated for use at our institution: Abbott RealTime m2000 SARS-CoV-2 Assay, DiaSorin Simplexa COVID-19 Direct, Cepheid Xpert Xpress SARS-CoV-2 and Abbott ID NOW COVID-19. Nasopharyngeal and nasal specimens were collected from 88 ED and hospital-admitted patients and tested by the four methods in parallel to compare performance. ID NOW performance stood out as significantly worse than the other three assays despite demonstrating comparable analytic sensitivity. Further study determined that the use of a foam nasal swab compared to a nylon flocked nasopharyngeal swab, as well as use in a population chronically vs. acutely positive for SARS-CoV-2, were significant factors in the poor comparable performance.

scholarly journals iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2

2020 ◽  
Author(s):  
Zahir Ali ◽  
Rashid Aman ◽  
Ahmed Mahas ◽  
Gundra Sivakrishna Rao ◽  
Muhammad Tehseen ◽  
...  
Keyword(s):  
Point Of Care ◽  
Human Life ◽  
Virus Detection ◽  
Turnaround Time ◽  
Nucleic Acid Amplification ◽  
Molecular Diagnostic ◽  
Amplification Method ◽  
Single Temperature ◽  
User Friendly ◽  
And Control

AbstractThe COVID-19 pandemic caused by SARS-CoV-2 affects all aspects of human life. Detection platforms that are efficient, rapid, accurate, specific, sensitive, and user friendly are urgently needed to manage and control the spread of SARS-CoV-2. RT-qPCR based methods are the gold standard for SARS-CoV-2 detection. However, these methods require trained personnel, sophisticated infrastructure, and a long turnaround time, thereby limiting their usefulness. Reverse transcription-loop-mediated isothermal amplification (RT-LAMP), a one-step nucleic acid amplification method conducted at a single temperature, has been used for colorimetric virus detection. CRISPR-Cas12 and CRISPR-Cas13 systems, which possess collateral activity against ssDNA and RNA, respectively, have also been harnessed for virus detection. Here, we built an efficient, rapid, specific, sensitive, user-friendly SARS-CoV-2 detection module that combines the robust virus amplification of RT-LAMP with the specific detection ability of SARS-CoV-2 by CRISPR-Cas12. Furthermore, we combined the RT-LAMP-CRISPR-Cas12 module with lateral flow cells to enable highly efficient point-of-care SARS-CoV-2 detection. Our iSCAN SARS-CoV-2 detection module, which exhibits the critical features of a robust molecular diagnostic device, should facilitate the effective management and control of COVID-19.

scholarly journals The PRONTO study: Clinical performance of ID NOW in individuals with compatible SARS-CoV-2 symptoms in walk-in centres—accelerated turnaround time for contact tracing

2021 ◽  
Vol 47 (12) ◽  
pp. 534-542
Author(s):  
Isabelle Goupil-Sormany ◽  
Jean Longtin ◽  
Jeannot Dumaresq ◽  
Marieve Jacob-Wagner ◽  
Frédéric Bouchard ◽  
...  
Keyword(s):  
Clinical Performance ◽  
Point Of Care ◽  
Standard Of Care ◽  
Turnaround Time ◽  
Nucleic Acid Amplification ◽  
Contact Tracing ◽  
Test Results ◽  
Predictive Values ◽  
Negative Results ◽  
Paired Samples

Background: This PRONTO study investigated the clinical performance of the Abbott ID NOWTM (IDN) COVID-19 diagnostic assay used at point of care and its impact on turnaround time for divulgation of test results. Methods: Prospective study conducted from December 2020 to February 2021 in acute symptomatic participants presenting in three walk-in centres in the province of Québec. Results: Valid paired samples were obtained from 2,372 participants. A positive result on either the IDN or the standard-of-care nucleic acid amplification test (SOC-NAAT) was obtained in 423 participants (prevalence of 17.8%). Overall sensitivity of IDN and SOC-NAAT were 96.4% (95% CI: 94.2–98.0%) and 99.1% (95% CI: 97.6–99.8), respectively; negative predictive values were 99.2% (95% CI: 98.7–99.6%) and 99.8% (95% CI: 99.5–100%), respectively. Turnaround time for positive results was significantly faster on IDN. Conclusion: In our experience, IDN use in symptomatic individuals in walk-in centres is a reliable sensitive alternative to SOC-NAAT without the need for subsequent confirmation of negative results. Such deployment can accelerate contact tracing, reduce the burden on laboratories and increase access to testing.

scholarly journals 366. Abbott BinaxNOW Rapid Antigen Test Performance in Detecting SARS-CoV-2 Infections in a COVID-19 Outbreak Among Horse Racetrack Workers

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S286-S286
Author(s):  
Krishna Surasi ◽  
Kristin J Cummings ◽  
Carl V Hanson ◽  
Mary Kate Morris ◽  
Maria Salas ◽  
...  
Keyword(s):  
Test Performance ◽  
Predictive Value ◽  
Nucleic Acid Amplification ◽  
Rt Pcr ◽  
Ct Value ◽  
Negative Results ◽  
Percent Agreement ◽  
Nasal Swabs ◽  
Antigen Tests ◽  
Positive Results

Abstract Background Rapid antigen tests (e.g., Abbott’s BinaxNOW) are cheaper and faster than nucleic acid amplification tests (e.g., real-time reverse transcription polymerase chain reaction [RT-PCR]) for SARS-CoV-2 infection, with variable reported sensitivity. A horse racetrack in California experienced a COVID-19 outbreak among staff and used BinaxNOW to supplement RT-PCR. Utility of BinaxNOW in detecting SARS-CoV-2 infection in a workplace outbreak was assessed. Methods Between November 25–December 22, 2020, anterior nasal swabs were collected from racetrack staff for six rounds of paired BinaxNOW and RT-PCR tests. BinaxNOW tests were interpreted according to manufacturer instructions. RT-PCR was performed at the state public health lab using the ThermoFisher TaqPath COVID-19 Combo Kit. Staff with positive results on either test were isolated and removed from subsequent testing. Viral cultures were attempted on specimens with cycle threshold (Ct) < 30. Results Overall, 769 paired results from 342 staff were analyzed. Most were of Hispanic ethnicity (62.0%) and ages ranged from 18 to 92 years (median 52). BinaxNOW performance compared to RT-PCR (95% CI) was as follows: positive percent agreement (PPA) 43.3% (34.6%–52.4%); negative percent agreement (NPA) 100% (99.4%–100%); positive predictive value (PPV) 100% (93.5%–100%); negative predictive value 89.9% (87.5%–92.0%). Among 127 RT-PCR-positive specimens, those with paired BinaxNOW-positive results (n = 55) had a lower mean Ct value than those with paired BinaxNOW-negative results (n = 72) (17.8 vs. 28.5) (p < 0.001). In dual positive pairs, median time from specimen collected to RT-PCR result reported was 4 days (range 1-6), compared to the 15-minute BinaxNOW reporting time. Of 100 Ct < 30 specimens, 51 resulted in positive virus isolation, 45 (88.2%) of which were BinaxNOW-positive. Conclusion High NPA and PPV support immediate isolation of BinaxNOW-positive individuals, while low PPA supports confirmatory testing following BinaxNOW-negative results. BinaxNOW performed better in paired specimens with lower Ct value and positive viral cultures, which could suggest that among RT-PCR-positive specimens, those that are BinaxNOW-negative may be less likely to contain infectious virus than those that are BinaxNOW-positive. Disclosures David Seftel, M.D., M.D., M.B.A., Enable Biosciences, Inc (Board Member, Employee, Scientific Research Study Investigator, Shareholder)

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