False negative rate of COVID-19 PCR testing: a discordant testing analysis
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...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-01-01
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| Series: | Virology Journal |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12985-021-01489-0 |
| _version_ | 1818728425569910784 |
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| author | Jamil N. Kanji Nathan Zelyas Clayton MacDonald Kanti Pabbaraju Muhammad Naeem Khan Abhaya Prasad Jia Hu Mathew Diggle Byron M. Berenger Graham Tipples |
| author_facet | Jamil N. Kanji Nathan Zelyas Clayton MacDonald Kanti Pabbaraju Muhammad Naeem Khan Abhaya Prasad Jia Hu Mathew Diggle Byron M. Berenger Graham Tipples |
| author_sort | Jamil N. Kanji |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-17T22:29:47Z |
| format | Article |
| id | doaj.art-b40a594772e64e66bd2df08231d5107b |
| institution | Directory Open Access Journal |
| issn | 1743-422X |
| language | English |
| last_indexed | 2024-12-17T22:29:47Z |
| publishDate | 2021-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Virology Journal |
| spelling | doaj.art-b40a594772e64e66bd2df08231d5107b2022-12-21T21:30:13ZengBMCVirology Journal1743-422X2021-01-011811610.1186/s12985-021-01489-0False negative rate of COVID-19 PCR testing: a discordant testing analysisJamil N. Kanji0Nathan Zelyas1Clayton MacDonald2Kanti Pabbaraju3Muhammad Naeem Khan4Abhaya Prasad5Jia Hu6Mathew Diggle7Byron M. Berenger8Graham Tipples9Public Health Laboratory, Alberta Precision Laboratories, University of Alberta HospitalPublic Health Laboratory, Alberta Precision Laboratories, University of Alberta HospitalDivision of Medical Microbiology and Infection Control, Vancouver Coastal Health Vancouver General HospitalPublic Health Laboratory, Alberta Precision Laboratories, Foothills HospitalHealth Protection and Communicable Disease Control, Public Health, Alberta Health ServicesHealth Protection and Communicable Disease Control, Public Health, Alberta Health ServicesMedical Officer of Health (MOH), Public Health, Alberta Health ServicesPublic Health Laboratory, Alberta Precision Laboratories, University of Alberta HospitalPublic Health Laboratory, Alberta Precision Laboratories, Foothills HospitalPublic Health Laboratory, Alberta Precision Laboratories, University of Alberta HospitalAbstract 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.https://doi.org/10.1186/s12985-021-01489-0SARS-CoV-2COVID-19Discordant testingFalse negative rate |
| spellingShingle | Jamil N. Kanji Nathan Zelyas Clayton MacDonald Kanti Pabbaraju Muhammad Naeem Khan Abhaya Prasad Jia Hu Mathew Diggle Byron M. Berenger Graham Tipples False negative rate of COVID-19 PCR testing: a discordant testing analysis Virology Journal SARS-CoV-2 COVID-19 Discordant testing False negative rate |
| title | False negative rate of COVID-19 PCR testing: a discordant testing analysis |
| title_full | False negative rate of COVID-19 PCR testing: a discordant testing analysis |
| title_fullStr | False negative rate of COVID-19 PCR testing: a discordant testing analysis |
| title_full_unstemmed | False negative rate of COVID-19 PCR testing: a discordant testing analysis |
| title_short | False negative rate of COVID-19 PCR testing: a discordant testing analysis |
| title_sort | false negative rate of covid 19 pcr testing a discordant testing analysis |
| topic | SARS-CoV-2 COVID-19 Discordant testing False negative rate |
| url | https://doi.org/10.1186/s12985-021-01489-0 |
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