Antigen rapid tests, nasopharyngeal PCR and saliva PCR to detect SARS-CoV-2: A prospective comparative clinical trial
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Abstract
Nasopharyngeal antigen Rapid Diagnostic Tests (RDTs), saliva RT-PCR and nasopharyngeal (NP) RT-PCR have shown different performance characteristics to detect patients infected by SARS-CoV-2, according to the viral load (VL)—and thus transmissibility.
Methods
In October 2020, we conducted a prospective trial involving patients presenting at testing centres with symptoms of COVID-19. We compared detection rates and performance of RDT, saliva PCR and nasopharyngeal (NP) PCR, according to VL and symptoms duration.
Results
Out of 949 patients enrolled, 928 patients had all three tests performed. Detection rates were 35.2% (95%CI 32.2–38.4%) by RDT, 39.8% (36.6–43.0%) by saliva PCR, 40.1% (36.9–43.3%) by NP PCR, and 41.5% (38.3–44.7%) by any test. For those with viral loads (VL) ≥10 6 copies/ml, detection rates were 30.3% (27.3–33.3), 31.4% (28.4–34.5), 31.5% (28.5–34.6), and 31.6% (28.6–34.7%) respectively.
Sensitivity of RDT compared to NP PCR was 87.4% (83.6–90.6%) for all positive patients, 94.5% (91.5–96.7%) for those with VL≥10 5 and 96.5% (93.6–98.3%) for those with VL≥10 6 . Sensitivity of STANDARD-Q ® , Panbio™ and COVID-VIRO ® Ag tests were 92.9% (86.4–96.9%), 86.1% (78.6–91.7%) and 84.1% (76.9–89.7%), respectively. For those with VL≥10 6 , sensitivity was 96.6% (90.5–99.3%), 97.8% (92.1–99.7%) and 95.3% (89.4–98.5%) respectively. No patient with VL<10 4 was detected by RDT.
Specificity of RDT was 100% (99.3–100%) compared to any PCR. RDT sensitivity was similar <4 days (87.8%, 83.5–91.3%) and ≥4 days (85.7%, 75.9–92.6%) after symptoms onset (p = 0.6). Sensitivity of saliva and NP PCR were 95.7% (93.1–97.5%) and 96.5% (94.1–98.1%), respectively, compared to the other PCR.
Conclusions
RDT results allow rapid identification of COVID cases with immediate isolation of most contagious individuals. RDT can thus be a game changer both in ambulatory care and community testing aimed at stopping transmission chains, and even more so in resource-constrained settings thanks to its very low price. When PCR is performed, saliva could replace NP swabbing.
Trial registration
ClinicalTrial.gov Identifier: NCT04613310 (03/11/2020).
Article activity feed
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SciScore for 10.1101/2020.11.23.20237057: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IACUC: Ethic statement: The study protocol and related documents were approved by the ethical review committee of Canton Vaud (CER-VD 2020-02269). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Brand of Rapid Diagnostic Tests evaluated: Three antigen-based RDTs were assessed: 1) STANDARD Q® COVID-19 Ag Test from Biosensor/Roche, 2) Panbio™ COVID-19 Ag Test from Abbott and 3) COVID-VIRO® from AAZ-LMB. Abbottsuggested: (Abbott, RRID:SCR_010477)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers …
SciScore for 10.1101/2020.11.23.20237057: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IACUC: Ethic statement: The study protocol and related documents were approved by the ethical review committee of Canton Vaud (CER-VD 2020-02269). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Brand of Rapid Diagnostic Tests evaluated: Three antigen-based RDTs were assessed: 1) STANDARD Q® COVID-19 Ag Test from Biosensor/Roche, 2) Panbio™ COVID-19 Ag Test from Abbott and 3) COVID-VIRO® from AAZ-LMB. Abbottsuggested: (Abbott, RRID:SCR_010477)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Limitations: The present study was conducted in a well-defined outpatient population with usual testing criteria for COVID-19 and presenting within 7 days after symptom onset for most of them. Our results might not apply in a setting where patients would attend after one week of symptoms, keeping in mind that these outpatients would be much less likely to transmit.27 Our results might neither apply to hospitalized patients, who tend to present late in the course of the disease, thus with lower viral loads. We did not include children in the study; however, viral loads seem not to differ between children and adults,28 which suggests that RDT could perform similarly in younger age groups. We cannot infer the accurate diagnostic performance of saliva PCR and RDTs in an asymptomatic population that was not investigated here. The sufficient sensitivity (82%) in patients with viral loads between 105 and 106 suggests that RDTs can be safely used for screening schools, university students or contacts of SARS-CoV-2 positive patients. 29
Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
Identifier Status Title NCT04613310 Recruiting PCR and Rapid Diagnostic Test on Saliva and Nasopharyngeal S… Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a protocol registration statement.
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SciScore for 10.1101/2020.11.23.20237057: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Methods Ethic statement The study protocol and related documents were approved by the ethical review committee of Canton Vaud (CER-VD 2020-02269). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable Median age was 31 years (IQR 25-42; range 18-87) with 49% being female. Table 2: Resources
Software and Algorithms Sentences Resources Brand of Rapid Diagnostic Tests evaluated Three antigen-based RDTs were assessed: 1) STANDARD Q COVID-19 Ag Test from Biosensor/Roche , 2) PanbioTM COVID-19 Ag Test from Abbott and 3) COVID-VIRO® from AAZ-LMB. Abbottsu…SciScore for 10.1101/2020.11.23.20237057: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Methods Ethic statement The study protocol and related documents were approved by the ethical review committee of Canton Vaud (CER-VD 2020-02269). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable Median age was 31 years (IQR 25-42; range 18-87) with 49% being female. Table 2: Resources
Software and Algorithms Sentences Resources Brand of Rapid Diagnostic Tests evaluated Three antigen-based RDTs were assessed: 1) STANDARD Q COVID-19 Ag Test from Biosensor/Roche , 2) PanbioTM COVID-19 Ag Test from Abbott and 3) COVID-VIRO® from AAZ-LMB. Abbottsuggested: (Abbott, RRID:SCR_010477)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
Limitations The present study was conducted in a well-defined outpatient population with usual testing criteria for COVID-19 and presenting within 7 days after symptom onset for most of them. Our results might not apply in a setting where patients would attend after one week of symptoms, keeping in mind that these outpatients would be much less likely to transmit.27 Our results might neither apply to hospitalized patients, who tend to present late in the course of the disease, thus with lower viral loads. We did not include children in the study; however, viral loads seem not to differ between children and adults,28 which suggests that RDT could perform similarly in younger age groups. We cannot infer the accurate diagnostic performance of saliva PCR and RDTs in an asymptomatic population that was not investigated here. The sufficient sensitivity (82%) in patients with viral loads between 105 and 106 suggests that RDTs can be safely used for screening schools, university students or contacts of SARS-CoV-2 positive patients. 29
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
Results from JetFighter: We did not find any issues relating to colormaps.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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