scholarly journals Comparison of the Accula SARS-CoV-2 Test with a Laboratory-Developed Assay for Detection of SARS-CoV-2 RNA in Clinical Nasopharyngeal Specimens

2020 ◽  
Vol 58 (8) ◽  
Author(s):  
Catherine A. Hogan ◽  
Natasha Garamani ◽  
Andrew S. Lee ◽  
Jack K. Tung ◽  
Malaya K. Sahoo ◽  
...  
Keyword(s):  
Viral Load ◽  
Test Performance ◽  
Point Of Care ◽  
False Negative ◽  
False Negative Rate ◽  
Kappa Coefficient ◽  
Performance Characteristics ◽  
Nasopharyngeal Swab ◽  
Percent Agreement ◽  
Gene Assay

ABSTRACT Several point-of-care (POC) molecular tests have received emergency use authorization (EUA) from the Food and Drug Administration (FDA) for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The test performance characteristics of the Accula (Mesa Biotech) SARS-CoV-2 POC test need to be evaluated to inform its optimal use. The aim of this study was to assess the test performance of the Accula SARS-CoV-2 test. The performance of the Accula test was assessed by comparing results of 100 nasopharyngeal swab samples previously characterized by the Stanford Health Care EUA laboratory-developed test (SHC-LDT), targeting the envelope (E) gene. Assay concordance was assessed by overall percent agreement, positive percent agreement (PPA), negative percent agreement (NPA), and Cohen’s kappa coefficient. Overall percent agreement between the assays was 84.0% (95% confidence interval [CI], 75.3 to 90.6%), PPA was 68.0% (95% CI, 53.3 to 80.5%), and the kappa coefficient was 0.68 (95% CI, 0.54 to 0.82). Sixteen specimens detected by the SHC-LDT were not detected by the Accula test and showed low viral load burden, with a median cycle threshold value of 37.7. NPA was 100% (95% CI, 94.2 to 100%). Compared to the SHC-LDT, the Accula SARS-CoV-2 test showed excellent negative agreement. However, positive agreement was low for samples with low viral load. The false-negative rate of the Accula POC test calls for a more thorough evaluation of POC test performance characteristics in clinical settings and for confirmatory testing in individuals with moderate to high pretest probability of SARS-CoV-2 who test negative on Accula.

scholarly journals Comparison of the Accula SARS-CoV-2 Test with a Laboratory-Developed Assay for Detection of SARS-CoV-2 RNA in Clinical Nasopharyngeal Specimens

2020 ◽  
Author(s):  
Catherine A. Hogan ◽  
Natasha Garamani ◽  
Andrew S. Lee ◽  
Jack K. Tung ◽  
Malaya K. Sahoo ◽  
...  
Keyword(s):  
Viral Load ◽  
Test Performance ◽  
Point Of Care ◽  
False Negative ◽  
False Negative Rate ◽  
Kappa Coefficient ◽  
Performance Characteristics ◽  
Nasopharyngeal Swab ◽  
Percent Agreement ◽  
Gene Assay

AbstractBackgroundSeveral point-of-care (POC) molecular tests have received emergency use authorization (EUA) from the Food and Drug Administration (FDA) for diagnosis of SARS-CoV-2. The test performance characteristics of the Accula (Mesa Biotech) SARS-CoV-2 POC test need to be evaluated to inform its optimal use.ObjectivesThe aim of this study was to assess test performance of the Accula SARS-CoV-2 test.Study designThe performance of the Accula test was assessed by comparing results of 100 nasopharyngeal swab samples previously characterized by the Stanford Health Care EUA laboratory-developed test (SHC-LDT) targeting the envelope (E) gene. Assay concordance was assessed by overall percent agreement, positive percent agreement (PPA), negative percent agreement (NPA), and Cohen’s kappa coefficient.ResultsOverall percent agreement between the assays was 84.0% (95% confidence interval [CI] 75.3 to 90.6%), PPA was 68.0% (95% CI 53.3 to 80.5%) and the kappa coefficient was 0.68 (95% CI 0.54 to 0.82). Sixteen specimens detected by the SHC-LDT were not detected by the Accula test, and showed low viral load burden with a median cycle threshold value of 37.7. NPA was 100% (95% CI 94.2 to 100%).ConclusionCompared to the SHC-LDT, the Accula SARS-CoV-2 test showed excellent negative agreement. However, positive agreement was low for samples with low viral load. The false negative rate of the Accula POC test calls for a more thorough evaluation of POC test performance characteristics in clinical settings, and for confirmatory testing in individuals with moderate to high pre-test probability of SARS-CoV-2 who test negative on Accula.

scholarly journals Comparison of a Point-of-Care Assay and a High-Complexity Assay for Detection of SARS-CoV-2 RNA

2020 ◽  
Vol 5 (6) ◽  
pp. 1307-1312 ◽  
Author(s):  
Bryan Stevens ◽  
Catherine A Hogan ◽  
Malaya K Sahoo ◽  
ChunHong Huang ◽  
Natasha Garamani ◽  
...  
Keyword(s):  
Test Performance ◽  
Target Genes ◽  
Point Of Care ◽  
The United States ◽  
Kappa Coefficient ◽  
Nucleic Acid Amplification ◽  
Limited Data ◽  
Percent Agreement ◽  
United States Food ◽  
States Food

Abstract Background Numerous nucleic acid amplification assays utilizing different target genes of the SARS-CoV-2 genome have received emergency use authorization (EUA) by the United States Food and Drug Administration (FDA). Limited data are available comparing the test performance characteristics of these assays. Methods A diagnostic comparison study was performed to evaluate the performance of the Cepheid Xpert Xpress SARS-CoV-2 assay compared to the Hologic Panther Fusion SARS-CoV-2 assay using clinical nasopharyngeal specimens. Agreement between the two assays was assessed by overall, positive, and negative percent agreement and Cohen’s kappa coefficient. Results A total of 104 (54 positive and 50 negative) clinical nasopharyngeal samples were tested by both assays. Using the Panther Fusion as a reference standard, the Xpert demonstrated an overall agreement of 99.0% [95% confidence interval (CI): 94.8–100], positive percent agreement of 98.1% (95% CI: 90.1–100), and a negative percent agreement of 100% (95% CI: 94.2–100). The kappa coefficient was 0.98 (95% CI: 0.94–1.0). One sample positive by the Panther Fusion with a cycle threshold (Ct) of 38.6 was found to be reproducibly negative by the Xpert assay. Conclusions The Cepheid Xpert Xpress SARS-CoV-2 assay provides test performance comparable to the Hologic Panther Fusion SARS-CoV-2 assay while offering laboratories rapid, on-demand testing capacity.

scholarly journals Temporal dynamics of viral load and false negative rate influence the levels of testing necessary to combat COVID-19 spread

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Katherine F. Jarvis ◽  
Joshua B. Kelley
Keyword(s):  
Viral Load ◽  
Temporal Dynamics ◽  
Reproduction Number ◽  
False Negative ◽  
False Negative Rate ◽  
Agent Based Model ◽  
Agent Based ◽  
Viral Spread ◽  
Negative Rate

AbstractColleges and other organizations are considering testing plans to return to operation as the COVID-19 pandemic continues. Pre-symptomatic spread and high false negative rates for testing may make it difficult to stop viral spread. Here, we develop a stochastic agent-based model of COVID-19 in a university sized population, considering the dynamics of both viral load and false negative rate of tests on the ability of testing to combat viral spread. Reported dynamics of SARS-CoV-2 can lead to an apparent false negative rate from ~ 17 to ~ 48%. Nonuniform distributions of viral load and false negative rate lead to higher requirements for frequency and fraction of population tested in order to bring the apparent Reproduction number (Rt) below 1. Thus, it is important to consider non-uniform dynamics of viral spread and false negative rate in order to model effective testing plans.

scholarly journals Essential properties and pitfalls of colorimetric Reverse Transcription Loop-mediated Isothermal Amplification as a point-of-care test for SARS-CoV-2 diagnosis

2021 ◽  
Vol 27 (1) ◽  
Author(s):  
Bruna de Oliveira Coelho ◽  
Heloisa Bruna Soligo Sanchuki ◽  
Dalila Luciola Zanette ◽  
Jeanine Marie Nardin ◽  
Hugo Manuel Paz Morales ◽  
...  
Keyword(s):  
Viral Load ◽  
Internal Control ◽  
Reverse Transcription ◽  
Color Change ◽  
Point Of Care ◽  
Colorimetric Detection ◽  
False Negative ◽  
Isothermal Amplification ◽  
Clinical Samples ◽  
Loop Mediated Isothermal Amplification

Abstract Background SARS-CoV-2 Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) colorimetric detection is a sensitive and specific point-of-care molecular biology technique used to detect the virus in only 30 min. In this manuscript we have described a few nuances of the technique still not properly described in the literature: the presence of three colors clusters; the correlation of the viral load with the color change; and the importance of using an internal control to avoid false-negative results. Methods To achieve these findings, we performed colorimetric RT-LAMP assays of 466 SARS-CoV-2 RT-qPCR validated clinical samples, with color quantification measured at 434 nm and 560 nm. Results First we determinate a sensitivity of 93.8% and specificity of 90.4%. In addition to the pink (negative) and yellow (positive) produced colors, we report for the first time the presence of an orange color cluster that may lead to wrong diagnosis. We also demonstrated using RT-qPCR and RT-LAMP that low viral loads are related to Ct values > 30, resulting in orange colors. We also demonstrated that the diagnosis of COVID-19 by colorimetric RT-LAMP is efficient until the fifth symptoms day when the viral load is still relatively high. Conclusion This study reports properties and indications for colorimetric RT-LAMP as point-of-care for SARS-CoV-2 diagnostic, reducing false results, interpretations and optimizing molecular diagnostics tests application.

scholarly journals False Negative Mitigation in Group Testing for COVID-19 Screening

2021 ◽  
Vol 8 ◽  
Author(s):  
Amir Reza Alizad Rahvar ◽  
Safar Vafadar ◽  
Mehdi Totonchi ◽  
Mehdi Sadeghi
Keyword(s):  
Viral Load ◽  
False Negative ◽  
Group Testing ◽  
False Negative Rate ◽  
Screening Strategy ◽  
Web Interface ◽  
Rt Pcr ◽  
Promising Candidate ◽  
Testing Method ◽  
High False Negative Rate

After lifting the COVID-19 lockdown restrictions and opening businesses, screening is essential to prevent the spread of the virus. Group testing could be a promising candidate for screening to save time and resources. However, due to the high false-negative rate (FNR) of the RT-PCR diagnostic test, we should be cautious about using group testing because a group's false-negative result identifies all the individuals in a group as uninfected. Repeating the test is the best solution to reduce the FNR, and repeats should be integrated with the group-testing method to increase the sensitivity of the test. The simplest way is to replicate the test twice for each group (the 2Rgt method). In this paper, we present a new method for group testing (the groupMix method), which integrates two repeats in the test. Then we introduce the 2-stage sequential version of both the groupMix and the 2Rgt methods. We compare these methods analytically regarding the sensitivity and the average number of tests. The tradeoff between the sensitivity and the average number of tests should be considered when choosing the best method for the screening strategy. We applied the groupMix method to screening 263 people and identified 2 infected individuals by performing 98 tests. This method achieved a 63% saving in the number of tests compared to individual testing. Our experimental results show that in COVID-19 screening, the viral load can be low, and the group size should not be more than 6; otherwise, the FNR increases significantly. A web interface of the groupMix method is publicly available for laboratories to implement this method.

Effects of environmental conditions on point-of-care cardiac biomarker test performance during a simulated rescue: Implications for emergency and disaster response

2013 ◽  
Vol 8 (3) ◽  
pp. 205-212 ◽  
Author(s):  
Richard F. Louie, PhD, FACB ◽  
William J. Ferguson, BS ◽  
Corbin M. Curtis, BS ◽  
John H. Vy, BS ◽  
Chloe S. Tang, BS ◽  
...  
Keyword(s):  
Test Performance ◽  
Troponin I ◽  
Point Of Care ◽  
False Negative ◽  
Environmental Stresses ◽  
Marshall Islands ◽  
Rank Test ◽  
Cardiac Biomarker ◽  
Mortality And Morbidity ◽  
The Impact

Objective: To characterize the effects of environmental stress on point-of-care (POC) cardiac biomarker testing during a simulated rescue.Design: Multiplex test cassettes for cardiac troponin I (cTnI), brain natriuretic peptide (BNP), CKMB, myoglobin, and D-dimer were exposed to environmental stresses simulating a 24-hour rescue from Hawaii to the Marshall Islands and back. We used Tenney environmental chambers (T2RC and BTRC) to simulate flight conditions (20°C, 10 percent relative humidity) and ground conditions (22.3-33.9°C, 73-77 percent). We obtained paired measurements using stressed versus control (room temperature) cassettes at seven time points (T1-7 with T1,2,6,7 during flight and T3-5 on ground). We analyzed paired differences (stressed minus control) with Wilcoxon signed rank test. We assessed the impact on decision-making at clinical thresholds.Results: cTnI results from stressed test cassettes (n = 10) at T4 (p 0.05), T5 (p 0.01), and T7 (p 0.05) differed significantly from control, when testing samples with median cTnI concentration of 90 ng/L. During the ground rescue, 36.7 percent (11/30) of cTnI measurements from stressed cassettes generated significantly lowered results. At T5, 20 percent (2/10) of cTnI results were highly discrepant—stressed cassettes reported normal results, when control results were 100 ng/L. With sample median concentration of 108 pg/mL, BNP results from stressed test cassettes differed significantly from controls (p 0.05).Conclusion: Despite modest, short-term temperature elevation, environmental stresses led to erroneous results. False negative cTnI and BNP results potentially could miss acute myocardial infarction and congestive heart failure, confounded treatment, and increased mortality and morbidity. Therefore, rescuers should protect POC reagents from temperature extremes.

scholarly journals Rapid and quantitative detection of COVID-19 markers in micro-liter sized samples

2020 ◽  
Author(s):  
Xiaotian Tan ◽  
Cory Lin ◽  
Jie Zhang ◽  
Maung Kyaw Khaing Oo ◽  
Xudong Fan
Keyword(s):  
Point Of Care ◽  
False Negative ◽  
False Negative Rate ◽  
Quantitative Detection ◽  
Enzyme Linked Immunosorbent Assay ◽  
High False Negative Rate ◽  
Conventional Elisa ◽  
Assay Time ◽  
Specific Igg ◽  
Lateral Flow Test

AbstractCOVID-19 pandemic has caused tens of thousands of deaths and is now a severe threat to global health. Clinical practice has demonstrated that the SARS-CoV-2 S1 specific antibodies and viral antigens can be used as diagnostic and prognostic markers of COVID-19. However, the popular point-of-care biomarker detection technologies, such as the lateral-flow test strips, provide only yes/no information and have very limited sensitivities. Thus, it has a high false negative rate and cannot be used for the quantitative evaluation of patient’s immune response. Conventional ELISA (enzyme-linked immunosorbent assay), on the other hand, can provide quantitative, accurate, and sensitive results, but it involves complicated and expensive instruments and long assay time. In addition, samples need to be sent to centralized labs, which significantly increases the turn-around time. Here, we present a microfluidic ELISA technology for rapid (15-20 minutes), quantitative, sensitive detection of SARS-CoV-2 biomarkers using SARS-CoV-2 specific IgG and viral antigen – S protein in serum. We also characterized various humanized monoclonal IgG, and identified a candidate with a high binding affinity towards SARS-CoV-2 S1 protein that can serve as the calibration standard of anti-SARS-CoV-2 S1 IgG in serological analyses. Furthermore, we demonstrated that our microfluidic ELISA platform can be used for rapid affinity evaluation of monoclonal anti-S1 antibodies. The microfluidic ELISA device is highly portable and requires less than 10 μL of samples for each channel. Therefore, our technology will greatly facilitate rapid and quantitative analysis of COVID-19 patients and vaccine recipients at point-of-care.

scholarly journals Clinical performance of the point-of-care cobas Liat for detection of SARS-CoV-2 in 20 minutes: A multicenter study

2020 ◽  
Author(s):  
Glen Hansen ◽  
Jamie Marino ◽  
Zi-Xuan Wang ◽  
Kathleen G. Beavis ◽  
John Rodrigo ◽  
...  
Keyword(s):  
Influenza A ◽  
Clinical Performance ◽  
Point Of Care ◽  
Nasopharyngeal Swab ◽  
Molecular Testing ◽  
Rt Pcr ◽  
Percent Agreement ◽  
Individual Care ◽  
Pcr Technology ◽  
Acid Test

Background: Highly accurate testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the point of care (POC) is an unmet diagnostic need in emergency care and time-sensitive outpatient care settings. Reverse transcription-polymerase chain reaction (RT-PCR) technology is the gold-standard for SARS-CoV-2 diagnostics. Methods: We performed a multi-site United States (US) study comparing the clinical performance of the first US Food and Drug Administration (FDA) authorized POC RT-PCR test for detection of SARS-CoV-2 in 20 minutes, the cobas® Liat SARS-CoV-2 & Influenza A/B nucleic acid test, to the most widely used RT-PCR laboratory test, the cobas® 68/8800 SARS-CoV-2 test. Results: Clinical nasopharyngeal swab specimens from 444 patients with 357 evaluable specimens at five US clinical laboratories were enrolled from September 21, 2020 to October 23, 2020. The overall agreement between the Liat and 68/8800 systems for SARS-CoV-2 diagnostics was 98.6% (352/357). Using Liat, positive percent agreement for SARS-CoV-2 was 100% (162/162) and the negative percent agreement was 97.4% (190/195). Conclusion: The Liat is an RT-PCR POC test that provides highly accurate SARS-CoV-2 results in 20 minutes with equivalent performance to high-throughput laboratory molecular testing. Rapid RT-PCR testing at the POC can enable more timely infection control and individual care decisions for Coronavirus Disease 2019.

scholarly journals Sample Pooling as a Strategy of SARS-COV-2 Nucleic Acid Screening Increases the False-negative Rate

2020 ◽  
Author(s):  
Yichuan Gan ◽  
Lingyan Du ◽  
Oluwasijibomi Damola Faleti ◽  
Jing Huang ◽  
Gang Xiao ◽  
...  
Keyword(s):  
Viral Load ◽  
Nucleic Acid ◽  
Large Scale ◽  
False Negative ◽  
False Negative Rate ◽  
High Viral Load ◽  
Careful Consideration ◽  
The World ◽  
Sample Pooling ◽  
Pooling Strategy

SummaryBackgroundIdentification of less costly and accurate methods for monitoring novel coronavirus disease 2019 (CoViD-19) transmission has attracted much interest in recent times. Here, we evaluated a pooling method to determine if this could improve screening efficiency and reduce costs while maintaining accuracy in Guangzhou, China.MethodsWe evaluated 8097 throat swap samples collected from individuals who came for a health check-up or fever clinic in The Third Affiliated Hospital, Southern Medical University between March 4, 2020 and April 26, 2020. Samples were screened for CoViD-19 infection using the WHO-approved quantitative reverse transcription PCR (RT-qPCR) primers. The positive samples were classified into two groups (high or low) based on viral load in accordance with the CT value of COVID-19 RT-qPCR results. Each positive RNA samples were mixed with COVID-19 negative RNA or ddH2O to form RNA pools.FindingsSamples with high viral load could be detected in pool negative samples (up to 1/1000 dilution fold). In contrast, the detection of RNA sample from positive patients with low viral load in a pool was difficult and not repeatable.InterpretationOur results show that the COVID-19 viral load significantly influences in pooling efficacy. COVID-19 has distinct viral load profile which depends on the timeline of infection. Thus, application of pooling for infection surveillance may lead to false negatives and hamper infection control efforts.FundingNational Natural Science Foundation of China; Hong Kong Scholars Program, Natural Science Foundation of Guangdong Province; Science and Technology Program of Guangzhou, China.Research in contextEvidence before this studySince it emergence in late 2019, CoViD-19 has dramatically increased the burden healthcare system worldwide. A research letter titled “Sample Pooling as a Strategy to Detect Community Transmission of SARS-CoV-2” which was recently published in JAMA journal proposed that sample pooling could be used for SARS-COV-2 community surveillance. Currently, the need for large-scale testing increases the number of 2019-nCOV nucleic acid analysis required for proper policy-making especially as work and normal school resumes. As far as we know, there are many countries and regions in the world, who are beginning to try this strategy for nucleic acid screening of SARS-CoV-2.Added value of this studyWe carried out a study using pooled samples formed from SARS-COV-2 negative samples and positive samples with high or low viral and assessed detection rate for the positive samples. We found that positive sample with high viral load could be detected in pools in a wide range of dilution folds (ranging from1/2 to 1/50). On the contrary, the sample with low viral load could only be detected in RNA “pools” at very low dilution ratio, and the repeatability was unsatisfactory. Our results show the application of the “pooling” strategy for large-scale community surveillance requires careful consideration and depends on the viral load of the positive samples.Implications of all the available evidenceAlthough the number of newly diagnosed cases has been reducing in some parts of the world, the possibility of a second wave of infection has made quick and efficient data gathering essential for policy-making, isolation and treatment of patients. Fast and efficient nucleic acid detection methods are encouraged, but sample pooling as a strategy of SARS-COV-2 nucleic acid screening increased the false-negative rate, especially those with asymptomatic infections have lower viral load. Therefore, the application of the “pooling” strategy for large-scale community surveillance requires careful consideration by policy makers.

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