key: cord-0857916-rbh02ktb
authors: Salcedo, N.; Nandu, N.; Boucau, J.; Herrera, B. B.
title: Detection of SARS-CoV-2 Omicron, Delta, Alpha and Gamma variants using a rapid antigen test
date: 2022-01-28
journal: nan
DOI: 10.1101/2022.01.27.22269299
sha: 87b92f28e1251eea201320d5c1d50fc3e0de1e35
doc_id: 857916
cord_uid: rbh02ktb

Throughout the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have emerged with different infection and disease dynamics. Testing strategies, including clinical diagnosis, surveillance, and screening, have been deployed to help limit the spread of SARS-CoV-2 variants. Rapid antigen tests, in particular, have been approved for self-testing in many countries and governments are supporting their manufacturing and distribution. However, studies demonstrating the accuracy of rapid antigen tests in detecting SARS-CoV-2 variants, especially the new Omicron variant, are limited. We determined the analytical sensitivity of a CE-marked rapid antigen test against the Omicron, Delta, Alpha and Gamma variants. The rapid antigen test had the most sensitive limit of detection (10 plaque forming units [PFU]/mL) when tested with the Alpha and Gamma variants, followed by the Omicron (100 PFU/mL) and Delta (1,000 PFU/mL) variants. Given the increasing numbers of breakthrough infections and the need to surveil infectiousness, rapid antigen tests are effective public health tools to detect SARS-CoV-2 variants.

primary clinical specimens. The viral titer (plaque forming unit (PFU)/mL) of each viral 91 stock was calculated by standard plaque assay using 5-fold serial dilution of the stock in 92 . CC-BY-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 (which was not certified by peer review)

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The rapid antigen test (E25Bio, Inc., Cambridge, MA and Perkin Elmer, Waltham, 106 MA) used for the study targets the SARS-CoV-2 nucleocapsid (N); the test is CE-107 marked. The test and the control line have immobilized antibodies that produce visible 108 results upon interaction with antigen and the nanoparticle conjugate. 100µL of the 10X 109 serial dilutions (100,000 to 1 PFU/mL) were applied to the antigen test in triplicates. 110

After 15 minutes, results were scored as positive or negative and images of the tests 111 were captured using an iPad (Apple, Inc, Cupertino, CA). 112 113 Image Analysis 114 . CC-BY-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)

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The images of the rapid antigen tests were analyzed using Image J (NIH, 115

Bethesda, MD) for quantitative analysis of the results. The software was used to 116 calculate the average pixels of the test line, control line and the background area. The 117 signal from the background was subtracted from the test and control line signals before 118 normalizing the test signal to the control signal. The resulting test signal expressed as 119 percent of control was used to determine the limit of detection for the rapid antigen test. To determine the analytical sensitivity of a rapid antigen test with SARS-CoV-2 127 variants, we utilized clinical isolates of Omicron, Delta, Alpha and Gamma. Each of the 128 variants were diluted to 100,000 PFU/mL test samples, followed by 10X serial dilutions 129 to obtain 10,000, 1,000, 100, 10, and 1 PFU/mL test samples. The limits of detection 130 were determined by applying to each rapid antigen test 100 μ L of the test samples. The 131

antigen tests reacted for 15 minutes before results were visually scored and images 132 were captured. 133

The rapid antigen test detected the Delta variant with the highest limit of 134 detection at 1,000 PFU/mL, followed by the Omicron variant at 100 PFU/mL ( Fig. 2A-D , 135 Table 1 ). The rapid antigen test had the lowest limits of detection against the Alpha and 136

Gamma variants at 10 PFU/mL ( Fig. 2A-E, Table 1 ). The rapid antigen test was 137 . CC-BY-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 28, 2022. ; https://doi.org/10.1101/2022.01.27.22269299 doi: medRxiv preprint negative when tested with the 1 PFU/mL test samples from the Alpha and Gamma 138 variants and the kit buffer alone (Fig. 2F -G, Table 1 ). Image analysis of test signal 139 intensities corroborated our visual scoring results (Fig. 3) . Omicron, Delta, Alpha, and Gamma. Our data show that the rapid antigen test has the 160 . CC-BY-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 28, 2022. ; https://doi.org/10.1101/2022.01.27.22269299 doi: medRxiv preprint 8 lowest limit of detection with Alpha and Gamma (10 PFU/mL), followed by Omicron (100 161 PFU/mL) and Delta (1,000 PFU/mL) (Fig. 2-3, Table 1) . 162 concern. Virus Evol. 7, veab091 (2021). 228 . CC-BY-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 28, 2022. ; https://doi.org/10.1101/2022.01.27.22269299 doi: medRxiv preprint . CC-BY-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 28, 2022. CC-BY-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 28, 2022. . CC-BY-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 28, 2022. CC-BY-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 28, 2022. Alpha, and Gamma variants recorded after 15 minutes. A) 100,000 PFU/mL. B) 10,000 316 PFU/mL. C) 1,000 PFU/mL. D) 100 PFU/mL. E) 10 PFU/mL. F) 1 PFU/mL. G) Kit buffer. 317

All tests were carried out in triplicates. 318 319 320 321 . CC-BY-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 28, 2022. ; https://doi.org/10.1101/2022.01.27.22269299 doi: medRxiv preprint 16 322 16 . CC-BY-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 28, 2022. ; https://doi.org/10.1101/2022.01.27.22269299 doi: medRxiv preprint 10,000 PFU/mL. C) 1,000 PFU/mL. D) 100 PFU/mL. E) 10 PFU/mL. F) 1 PFU/mL. G) 325

Kit buffer. The y-axis corresponds to the background subtracted test signal normalized 326 to the control line. Test results less than 10% of the control are considered negative 327 results, which is indicated by the black dashed line. 328 329 . CC-BY-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 28, 2022. ; https://doi.org/10.1101/2022.01.27.22269299 doi: medRxiv preprint

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