scholarly journals Diagnostic Performance of Ag-RDTs and NAAT for SARS-CoV2 Identification in Symptomatic Patients in Catalonia

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 908
Author(s):  
Luca Basile ◽  
Víctor Guadalupe-Fernández ◽  
Manuel Valdivia Guijarro ◽  
Ana Martinez Mateo ◽  
Pilar Ciruela Navas ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Symptom Onset ◽  
Diagnostic Performance ◽  
Diagnostic Technique ◽  
Nucleic Acid Amplification ◽  
False Negatives ◽  
Early Stages ◽  
Virus Dissemination ◽  
Nucleic Acid Amplification Testing

The use of rapid antigenic tests (Ag-RDTs) to diagnose a SARS-CoV-2 infection has become a common practice recently. This study aimed to evaluate performance of Abbott PanbioTM Ag-RDTs with regard to nucleic acid amplification testing (NAAT) in the early stages of the disease. A cohort of 149,026 infected symptomatic patients, reported in Catalonia from November 2020 to January 2021, was selected. The positivity rates of the two tests were compared with respect to the dates of symptom onset. Ag-RDTs presented positivity rates of 84% in the transmission phases of the disease and 31% in the pre-symptomatic period, compared to 93% and 91%, respectively, for NAAT. The detection of many false negatives with Ag-RDTs during the pre-symptomatic period demonstrates the risk of virus dissemination with this diagnostic technique if used outside the symptomatic period.

scholarly journals Combined SARS-CoV-2 nucleic acid amplification testing and respiratory virus panel RT-PCR on the Hologic Panther Fusion system

2021 ◽  
Vol 138 ◽  
pp. 104792
Author(s):  
Bryan A. Stevens ◽  
Catherine A. Hogan ◽  
Kenji O. Mfuh ◽  
Ghazala Khan ◽  
Malaya K. Sahoo ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Respiratory Virus ◽  
Nucleic Acid Amplification ◽  
Fusion System ◽  
Rt Pcr ◽  
Nucleic Acid Amplification Testing

scholarly journals Nonconcordance of E, N, and RdRp Genes in SARS-Coronavirus-2 Nucleic Acid Amplification Test Among Patients Older than 60 Years

2020 ◽  
Vol 154 (Supplement_1) ◽  
pp. S126-S127
Author(s):  
H Caulkins ◽  
K Rand ◽  
N Harris ◽  
S Beal
Keyword(s):  
Nucleic Acid ◽  
Symptom Onset ◽  
Chart Review ◽  
Nucleic Acid Amplification ◽  
Onset Date ◽  
Sars Coronavirus ◽  
Future Directions ◽  
Systematic Processing ◽  
At Risk Populations ◽  
Processing Errors

Abstract Introduction/Objective During the COVID-19 pandemic, the FDA authorized emergency use of nucleic acid amplification (NAA) testing. Accurate and rapid testing identifies infected persons, especially among at-risk populations. In our institution, the InGenius platform detects three gene targets of SARS-Coronavirus-2: envelope (E), nucleocapsid (N), and RNA-dependent RNA polymerase (RdRp). Nonconcordance of these components present accuracy or precision errors or may correspond to varying expression of viral genes with disease progression. Methods We retrospectively analyzed the result components from 93 nasopharyngeal swabs from 50 patients older than 60 years and positive for SARS-Coronavirus-2 (SARS-CoV-2). The symptom onset date was determined by chart review. Results We found a significant 26% nonconcordance rate, with a predominant pattern demonstrating positive N with negative RdRp and E (χ2 = 27.25, P < 0.0005). This nonconcordant pattern was more prevalent at longer symptom durations. In 7 patients with serial testing, the transition from concordant to nonconcordant results occurred 12 days (95% CI 3.5 – 20.3 days) after symptom onset. Conclusion This may be caused by several mechanisms. Possibilities include decreased expression of E and RdRp over time, inhibition of expression by treatments or host immune response, or lower viral titers by clearance or migration to the lower respiratory tract. Presence of a different viral strain or systematic processing errors are less likely causes of nonconcordance. Future directions of study would determine whether a similar decline in RdRp and E detection is seen in tracheal samples or if this correlates with changes in symptom severity.

scholarly journals Comparative performance and cycle threshold values of 10 nucleic acid amplification tests for SARS-CoV-2 on clinical samples

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252757
Author(s):  
Miyuki Mizoguchi ◽  
Sohei Harada ◽  
Koh Okamoto ◽  
Yoshimi Higurashi ◽  
Mahoko Ikeda ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Diagnostic Performance ◽  
Nucleic Acid Amplification ◽  
Clinical Samples ◽  
Nucleic Acid Amplification Tests ◽  
Cycle Threshold ◽  
E Gene ◽  
Viral Copy Number ◽  
Gene Test ◽  
Positive Results

Background A number of nucleic acid amplification tests (NAATs) for SARS-CoV-2 with different reagents have been approved for clinical use in Japan. These include research kits approved under emergency use authorization through simplified process to stabilize the supply of the reagents. Although these research kits have been increasingly used in clinical practice, limited data is available for the diagnostic performance in clinical settings. Methods We compared sensitivity, specificity, and cycle threshold (Ct) values obtained by NAATs using 10 kits approved in Japan including eight kits those receiving emergency use authorization using 69 frozen-stored clinical samples including 23 positive samples with various Ct values and 46 negative samples. Results Viral copy number of the frozen-stored samples determined with LightMix E-gene test ranged from 0.6 to 84521.1 copies/μL. While no false-positive results were obtained by any of these tests (specificity: 100% [95% CI, 88.9%-100%]), sensitivity of the nine tests ranged from 68.2% [95% CI, 45.1%-86.1%] to 95.5% [95% CI, 77.2%-99.9%] using LightMix E-gene test as the gold standard. All tests showed positive results for all samples with ≥100 copies/μL. Significant difference of Ct values even among tests amplifying the same genetic region (N1-CDC, N2) was also observed. Conclusion Difference in the diagnostic performance was observed among NAATs approved in Japan. Regarding diagnostic kits for emerging infectious diseases, a system is needed to ensure both rapidity of reagent supply and accuracy of diagnosis. Ct values, which are sometimes regarded as a marker of infectivity, are not interchangeable when obtained by different assays.

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