Discordant SARS-CoV-2 PCR and Rapid Antigen Test Results When Infectious: A December 2021 Occupational Case Series

Adamson, Blythe; Sikka, Robby; Wyllie, Anne L.; Premsrirut, Prem K.

doi:10.1101/2022.01.04.22268770

Cited by 77 publications

(113 citation statements)

References 4 publications

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“…On the other hand, in symptomatic non-hospitalized patients in South Africa, saliva samples detected Omicron more often than mid-turbinate swabs (100% vs. 86% respectively) 8 which was opposite from the performance reported for previously circulating variants. Similarly, in a pre-print non-peer reviewed publication of a small subset of individuals in a high-risk occupational case cohort, the viral load in saliva specimens peaked 1 to 2 days prior to those observed with nasal swab collections 23 . These early data suggest there may be a different tissue tropism for the Omicron variant compared to prior circulating lineages of SARS-CoV-2 7 .…”

Section: Discussionmentioning

confidence: 90%

“…Similarly, in a pre-print non-peer reviewed publication of a small subset of individuals in a high-risk occupational case cohort, the viral load in saliva specimens peaked 1 to 2 days prior to those observed with nasal swab collections 23 . These early data suggest there may be a different tissue tropism for the Omicron variant compared to prior circulating lineages of SARS-CoV-2 7 .…”

Section: Discussionmentioning

confidence: 90%

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Investigating sensitivity of nasal or throat (ISNOT): A combination of both swabs increases sensitivity of SARS-CoV-2 rapid antigen tests

Goodall

LeBlanc

Hatchette

et al. 2022

Preprint

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The COVID-19 pandemic has been hallmarked by several waves of variants of concern (VoCs), each with novel challenges. Currently, the highly transmissible Omicron VOC is predominant worldwide, and sore throat is common among other cold-like symptoms. Anecdotes on social media suggested sampling ones throat can increase sensitivity for Omicron detection by antigen-based rapid testing devices (Ag-RDTs). This work determines whether the sensitivity of Ag-RDTs designed for nasal sampling is altered with use of self-administered throat swabs in self-perceived asymptomatic individuals. This investigation compared results of a common Ag-RDT (i.e. Abbott Panbio COVID-19 Ag Rapid Test Device) using three sampling sites: nasal swab; throat swab and; combined nasal/throat. All Ag-RDT results were confirmed with molecular testing. Compared to RT-PCR, samples from nasal or throat swabs each detected 64.5% of SARS-CoV-2 cases; however, combining the contributions of each swab increased sensitivity to 88.7%. This trend was also evident with the Rapid Response Ag-RDT (BTNX), which uses a more flexible swabs than Panbio. When nasal swab collection was compared to paired sampling of the nasal/throat using a single swab with the Panbio Ag-RDT, the sensitivity of each was 68.4% and 81.6%, respectively. No false-positive results were observed with nasal, throat, or combined nasal/throat sampling. Self-administered throat and nasal/throat swabs both had >90% acceptability. These findings support the use of self-collected combined nasal/throat sampling for Ag-RDT based SARS-CoV-2 detection in self perceived asymptomatic individuals.

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Section: Discussionmentioning

confidence: 90%

Section: Discussionmentioning

confidence: 90%

Investigating sensitivity of nasal or throat (ISNOT): A combination of both swabs increases sensitivity of SARS-CoV-2 rapid antigen tests

Goodall

LeBlanc

Hatchette

et al. 2022

Preprint

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“…While we chose a Ct value cutoff of 30 as a proxy for infectiousness [13][14][15][16][17] , this threshold should not be considered a perfect predictor of infectiousness. Second, the Ct values reported here are from samples that each combined anterior nares and oropharyngeal swabs and were performed on the Roche Cobas platform; results may differ by anatomical site and by PCR platform [24][25][26][27] . Third, this relatively small sample set was obtained in a population that is not representative of the general population.…”

Section: Discussionmentioning

confidence: 99%

Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: a retrospective cohort study

Hay

Kissler

Fauver

et al. 2022

Preprint

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Background. The Omicron SARS-CoV-2 variant is responsible for a major wave of COVID-19, with record case counts reflecting high transmissibility and escape from prior immunity. Defining the time course of Omicron viral proliferation and clearance is crucial to inform isolation protocols aiming to minimize disease spread. Methods. We obtained longitudinal, quantitative RT-qPCR test results using combined anterior nares and oropharyngeal samples (n = 10,324) collected between July 5th, 2021 and January 10th, 2022 from the National Basketball Association's (NBA) occupational health program. We quantified the fraction of tests with PCR cycle threshold (Ct) values <30, chosen as a proxy for potential infectivity and antigen test positivity, on each day after first detection of suspected and confirmed Omicron infections, stratified by individuals detected under frequent testing protocols and those detected due to symptom onset or concern for contact with an infected individual. We quantified the duration of viral proliferation, clearance rate, and peak viral concentration for individuals with acute Omicron and Delta variant SARS-CoV-2 infections. Results. A total of 97 infections were confirmed or suspected to be from the Omicron variant and 107 from the Delta variant. Of 27 Omicron-infected individuals testing positive ≤1 day after a previous negative or inconclusive test, 52.0% (13/25) were PCR positive with Ct values <30 at day 5, 25.0% (6/24) at day 6, and 13.0% (3/23) on day 7 post detection. Of 70 Omicron-infected individuals detected ≥2 days after a previous negative or inconclusive test, 39.1% (25/64) were PCR positive with Ct values <30 at day 5, 33.3% (21/63) at day 6, and 22.2% (14/63) on day 7 post detection. Overall, Omicron infections featured a mean duration of 9.87 days (95% CI 8.83-10.9) relative to 10.9 days (95% CI 9.41-12.4) for Delta infections. The peak viral RNA based on Ct values was lower for Omicron infections than for Delta infections (Ct 23.3, 95% CI 22.4-24.3 for Omicron; Ct 20.5, 95% CI 19.2-21.8 for Delta) and the clearance phase was shorter for Omicron infections (5.35 days, 95% CI 4.78-6.00 for Omicron; 6.23 days, 95% CI 5.43-7.17 for Delta), though the rate of clearance was similar (3.13 Ct/day, 95% CI 2.75-3.54 for Omicron; 3.15 Ct/day, 95% CI 2.69-3.64 for Delta). Conclusions. While Omicron infections feature lower peak viral RNA and a shorter clearance phase than Delta infections on average, it is unclear to what extent these differences are attributable to more immunity in this largely vaccinated population or intrinsic characteristics of the Omicron variant. Further, these results suggest that Omicron's infectiousness may not be explained by higher viral load measured in the nose and mouth by RT-PCR. The substantial fraction of individuals with Ct values <30 at days 5 of infection, particularly in those detected due to symptom onset or concern for contact with an infected individual, underscores the heterogeneity of the infectious period, with implications for isolation policies.

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“…This is because the clinical sensitivity of an assay is influenced by factors inherent to the virus as well as host factors such as pre-existing immunity. For instance, Abramson et al reported the propensity for the BinaxNOW™ and the Quidel Quickvue™ LFIAs to be falsely negative early in infection despite very high viral loads detected concomitantly from saliva samples 11 . Antigen detection from nasal swab samples eventually turned positive several days after symptom onset, suggesting that viral replication may initially localize to the oropharynx prior to transitioning to the nasopharynx.…”

Section: Discussionmentioning

confidence: 99%

Analytic sensitivity of the Abbott BinaxNOW™ lateral flow immunochromatographic assay for the SARS-CoV-2 Omicron variant

Kanjilal

Chalise

Shah

et al. 2022

Preprint

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The emergence of the SARS-CoV-2 Omicron variant has motivated a re-evaluation of the test characteristics for lateral flow immunochromatographic assays (LFIAs), commonly referred to as rapid antigen tests. To address this need, we evaluated the analytic sensitivity of one of the most widely used LFIAs in the US market, the Abbott BinaxNOW COVID-19 Ag At-Home Card using 32 samples of Omicron and 30 samples of the Delta variant. Samples were chosen to intentionally over-represent the range of viral loads where differences are most likely to appear. We found no changes in the analytic sensitivity of the BinaxNOW assay by variant even after controlling for variation in cycle threshold values in the two populations. Similar to prior studies, the sensitivity of the assay is highly dependent on the amount of virus present in the sample. While the analytic sensitivity of the BinaxNOW LFIA remains intact versus the Omicron variant, its clinical sensitivity is influenced by the interaction between viral replication, the dynamics of tissue tropism and the timing of sampling. Further research is necessary to optimally adapt current testing strategies to robustly detect early infection by the Omicron variant to prevent transmission.

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Discordant SARS-CoV-2 PCR and Rapid Antigen Test Results When Infectious: A December 2021 Occupational Case Series

Cited by 77 publications

References 4 publications

Investigating sensitivity of nasal or throat (ISNOT): A combination of both swabs increases sensitivity of SARS-CoV-2 rapid antigen tests

Investigating sensitivity of nasal or throat (ISNOT): A combination of both swabs increases sensitivity of SARS-CoV-2 rapid antigen tests

Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: a retrospective cohort study

Analytic sensitivity of the Abbott BinaxNOW™ lateral flow immunochromatographic assay for the SARS-CoV-2 Omicron variant

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