Article: Analytic Sensitivity of 3 Nucleic Acid Detection Assays in Diagnosis of SARS-CoV-2 Infection.
The journal of applied laboratory medicine
2021 Volume 6, Issue 2, Page(s) 421–428
Abstract: Background: Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by reverse transcription PCR is the primary method to diagnose coronavirus disease 2019 (COVID-19). However, the analytic sensitivity required is not well defined and ... ...
| Abstract | Background: Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by reverse transcription PCR is the primary method to diagnose coronavirus disease 2019 (COVID-19). However, the analytic sensitivity required is not well defined and it is unclear how available assays compare. Methods: For the Abbott RealTime SARS-CoV-2 assay (m2000; Abbott Molecular), we determined that it could detect viral concentrations as low as 26 copies/mL, we defined the relationship between cycle number and viral concentrations, and we tested naso- and oropharyngeal swab specimens from 8538 consecutive individuals. Using the m2000 as a reference assay method, we described the distribution of viral concentrations in these patients. We then used selected clinical specimens to determine the positive percent agreement of 2 other assays with more rapid turnaround times [Cepheid Xpert Xpress (GeneXpert; Cepheid); n = 27] and a laboratory developed test on the Luminex ARIES system [ARIES LDT (Luminex); n = 50] as a function of virus concentrations, from which we projected their false-negative rates in our patient population. Results: SARS-CoV-2 was detected in 27% (95% CI: 26%-28%) of all specimens. Estimated viral concentrations were widely distributed, and 17% (95% CI: 16%-19%) of positive individuals had viral concentrations <845 copies/mL. Positive percent agreement was strongly related to viral concentration, and reliable detection (i.e., ≥95%) was observed at concentrations >100 copies/mL for the GeneXpert but not the ARIES LDT, corresponding to projected false-negative rates of 4% (95% CI: 0%-21%) and 27% (95% CI: 11%-46%), respectively. Conclusions: Substantial proportions of clinical specimens have low to moderate viral concentrations and may be missed by methods with less analytic sensitivity. |
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| MeSH term(s) | Adult ; Aged ; Aged, 80 and over ; COVID-19/diagnosis ; COVID-19/virology ; COVID-19 Nucleic Acid Testing/instrumentation ; False Negative Reactions ; Female ; Humans ; Limit of Detection ; Male ; Middle Aged ; RNA, Viral/isolation & purification ; Reagent Kits, Diagnostic ; Real-Time Polymerase Chain Reaction/instrumentation ; Reproducibility of Results ; Retrospective Studies ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification |
| Chemical Substances | RNA, Viral ; Reagent Kits, Diagnostic |
| Language | English |
| Publishing date | 2021-03-05 |
| Publishing country | England |
| Document type | Journal Article |
| ISSN | 2576-9456 |
| ISSN | 2576-9456 |
| DOI | 10.1093/jalm/jfaa187 |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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