key: cord-0324021-u08yfr58 authors: Kanjilal, S.; Chalise, S.; Shami Shah, A.; Cheng, C.-A.; Senussi, Y.; Springer, M.; Walt, D. R. title: Analytic sensitivity of the Abbott BinaxNOW lateral flow immunochromatographic assay for the SARS-CoV-2 Omicron variant date: 2022-01-11 journal: nan DOI: 10.1101/2022.01.10.22269033 sha: cf0bcd29c71feba6eec306ae1c43efff06eabe5d doc_id: 324021 cord_uid: u08yfr58 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. The identification of infection by severe acute respiratory syndrome coronavirus-2 (SARS-CoV- 2 2), the virus that causes coronavirus disease 2019 (COVID-19), aids the individual by prompting 3 timely initiation of treatment and aids the public by allowing for separation of contagious hosts 4 from susceptible secondary contacts. Lateral flow immunochromatographic (LFIAs) assays, 5 commonly referred to as rapid antigen tests, are an important element of pandemic containment 6 as they provide results within 15 minutes and can be performed by the public without supervision. 7 However, a drawback is their lower analytic sensitivity relative to nucleic acid amplification based 8 assays like the reverse transcriptase polymerase chain reaction (RT-PCR). In practice, the impact 9 of this drop in sensitivity is limited to the brief window during which a person is efficiently 10 transmitting live virus but still has viral loads below the limit of detection (LoD) of the LFIA. In prior 11 waves of COVID-19, this time period is estimated to be days 1 to 2 post-infection 1 . Tests taken 12 during that time window have a risk of being falsely negative and can lead individuals to transmit 13 the virus to others unbeknownst to them. The COVID-19 pandemic has spread in a series of waves due to the successive emergence of 16 variants of concern (VOCs) that contain sets of mutations that confer selective advantages over 17 prior lineages due to improved transmissibility, immune escape, and more efficient viral The N protein is the target analyte for the majority of LFIAs currently approved for emergency use 25 by the US Food and Drug Administration (FDA). These assays typically use monoclonal 26 antibodies coupled to nanoparticles to bind epitopes present on the SARS-CoV-2 N protein, which The precise epitopes targeted by the commercially-available LFIAs are proprietary, therefore 32 independent evaluation is necessary to evaluate whether changes to nucleocapsid protein in the 33 Omicron variant affect the analytic sensitivity of the test. Given the critical role that LFIAs play in 34 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted January 11, 2022. ; https://doi.org/10.1101/2022.01.10.22269033 doi: medRxiv preprint early case detection and return to work assessments, quantifying changes in test performance is 35 of high value to the scientific community, policy makers and the public. In this study we report the analytic sensitivity of the widely used Abbott BinaxNOW™ COVID-19 38 Ag Card against the Omicron variant, using the Delta variant as a reference. Our primary 39 hypothesis is that the analytic sensitivity of the Abbott BinaxNOW™ LFIA will be unaffected by 40 the nucleocapsid mutations specific to the Omicron variant. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. Samples were genotyped using a multiplex PCR assay with primers specific to both variants. After RT-PCR analysis, the specimens selected for this analysis were frozen once at -20°C. For 64 LFIA testing, 50μl of each sample was placed in a 1.5ml microcentrifuge tube into which the kit-65 supplied swab was placed and rotated for 15 seconds. This volume was chosen based on a prior 66 study that determined 50μl to be the optimal volume for balancing the ratio of analyte to kit- cards were then sealed and read twice after 15 minutes by two independent readers blinded to 73 the identity of the sample. A third reader was used for any discordant reads and a photo was 74 taken of the card after the completion of the incubation period. All samples were run in triplicate. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted January 11, 2022. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted January 11, 2022. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted January 11, 2022. ; https://doi.org/10.1101/2022.01.10.22269033 doi: medRxiv preprint . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted January 11, 2022. ; https://doi.org/10.1101/2022.01.10.22269033 doi: medRxiv preprint The emergence of the Omicron variant in mid-November 2021 was followed by many anecdotal 115 reports of false negative LFIA tests. In this study, we found no significant difference in the analytic 116 sensitivity of the widely used Abbott BinaxNOW™ COVID-19 Ag Card LFIA for the N protein of 117 the SARS-CoV-2 Omicron variant with respect to the Delta variant. We noted a greater proportion 118 of negative samples containing viral loads above the assay's LoD for Omicron specimens than 119 for Delta specimens, but this finding did not reach statistical significance, possibly due to our 120 study's small sample size. Given that N protein mutations have been shown to impact LFIA 121 performance in the past 6 , these findings provide a degree of reassurance that the assay is 122 performing as expected. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted January 11, 2022. ; https://doi.org/10.1101/2022.01.10.22269033 doi: medRxiv preprint Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies Emergency Use Authorization Summary: Quaeris SARS-CoV-2 Assay Analytical Sensitivity of the Abbott BinaxNOW COVID-19 Ag Card Abbott BinaxNOW COVID-19 Ag At-Home Card -Instructions For Use A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance Detection of the omicron variant virus with the Abbott BinaxNow SARS-CoV-2 Rapid Antigen Assay Assessment of the analytical sensitivity of ten lateral flow devices against the SARS-CoV-2 omicron variant Direct Comparison of SARS Co-V-2 Nasal RT-PCR and Rapid Antigen Test (BinaxNOWTM) at a Community Testing Site During an Omicron Surge Discordant SARS-CoV-2 PCR and Rapid Antigen Test Results When Infectious: A December 2021 Occupational Case Series Saliva swabs are the preferred sample for Omicron detection . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted January 11, 2022. ; https://doi.org/10.1101/2022.01.10.22269033 doi: medRxiv preprint