False negative rate of COVID-19 PCR testing: a discordant testing analysis
| dc.contributor.author | Kanji, Jamil N | |
| dc.contributor.author | Zelyas, Nathan | |
| dc.contributor.author | MacDonald, Clayton | |
| dc.contributor.author | Pabbaraju, Kanti | |
| dc.contributor.author | Khan, Muhammad N | |
| dc.contributor.author | Prasad, Abhaya | |
| dc.contributor.author | Hu, Jia | |
| dc.contributor.author | Diggle, Mathew | |
| dc.contributor.author | Berenger, Byron M | |
| dc.contributor.author | Tipples, Graham | |
| dc.date.accessioned | 2021-01-10T01:02:53Z | |
| dc.date.available | 2021-01-10T01:02:53Z | |
| dc.date.issued | 2021-01-09 | |
| dc.date.updated | 2021-01-10T01:02:53Z | |
| dc.description.abstract | Abstract Background COVID-19 is diagnosed via detection of SARS-CoV-2 RNA using real time reverse-transcriptase polymerase chain reaction (rtRT-PCR). Performance of many SARS-CoV-2 rtRT-PCR assays is not entirely known due to the lack of a gold standard. We sought to evaluate the false negative rate (FNR) and sensitivity of our laboratory-developed SARS-CoV-2 rtRT-PCR targeting the envelope (E) and RNA-dependent RNA-polymerase (RdRp) genes. Methods SARS-CoV-2 rtRT-PCR results at the Public Health Laboratory (Alberta, Canada) from January 21 to April 18, 2020 were reviewed to identify patients with an initial negative rtRT-PCR followed by a positive result on repeat testing within 14 days (defined as discordant results). Negative samples from these discordant specimens were re-tested using three alternate rtRT-PCR assays (targeting the E gene and N1/N2 regions of the nucleocapsid genes) to assess for false negative (FN) results. Results During the time period specified, 95,919 patients (100,001 samples) were tested for SARS-CoV-2. Of these, 49 patients were found to have discordant results including 49 positive and 52 negative swabs. Repeat testing of 52 negative swabs found five FNs (from five separate patients). Assuming 100% specificity of the diagnostic assay, the FNR and sensitivity in this group of patients with discordant testing was 9.3% (95% CI 1.5–17.0%) and 90.7% (95% CI 82.6–98.9%) respectively. Conclusions Studies to understand the FNR of routinely used assays are important to confirm adequate clinical performance. In this study, most FN results were due to low amounts of SARS-CoV-2 virus concentrations in patients with multiple specimens collected during different stages of infection. Post-test clinical evaluation of each patient is advised to ensure that rtRT-PCR results are not the only factor in excluding COVID-19. | |
| dc.identifier.citation | Virology Journal. 2021 Jan 09;18(1):13 | |
| dc.identifier.doi | https://doi.org/10.1186/s12985-021-01489-0 | |
| dc.identifier.uri | http://hdl.handle.net/1880/112953 | |
| dc.identifier.uri | https://doi.org/10.11575/PRISM/44669 | |
| dc.language.rfc3066 | en | |
| dc.rights.holder | The Author(s) | |
| dc.title | False negative rate of COVID-19 PCR testing: a discordant testing analysis | |
| dc.type | Journal Article |