key: cord-0685537-9w80nsq8
authors: Rodgers, M. A.; Batra, R.; Snell, L. B.; Daghfal, D. J.; Roth, R.; Huang, S.; Kovacs, S.; Nebbia, G.; Douthwaite, S.; Cloherty, G. A.
title: Detection of SARS-CoV-2 variants by Abbott molecular, antigen, and serological tests
date: 2021-04-26
journal: nan
DOI: 10.1101/2021.04.24.21256045
sha: e449cfb04129d1e8d27e368c7fac95bd073e49ab
doc_id: 685537
cord_uid: 9w80nsq8

Background: Viral diversity presents an ongoing challenge for diagnostic tests, which need to accurately detect all circulating variants. The Abbott Global Surveillance program monitors severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants and their impact on diagnostic test performance. Objectives: To evaluate the capacity of Abbott molecular, antigen, and serologic assays to detect the SARS-CoV-2 B.1.1.7, B.1.351 and the P.1 variants. Study design: Virus variant culture stock dilutions (B.1.1.7, BEI NR-54011; B.1.351, BEI NR-54008 and 54009; P.1, BEI NR-54982) and clinical samples from patients with confirmed B.1.1.7 variant infection were run on the Abbott ID NOW COVID-19, m2000 RealTime SARS-CoV-2, Alinity m SARS-CoV-2, and Alinity m Resp-4-Plex molecular assays; the BinaxNOW COVID-19 Ag Card and Panbio COVID-19 Ag Rapid Test Device; and the ARCHITECT/Alinity i SARS-CoV-2 IgG and AdviseDx IgM assays, Panbio COVID-19 IgG assay, and ARCHITECT/Alinity i AdviseDx SARS-CoV-2 IgG II assay. Results: Cultured virus stocks and B.1.1.7 clinical samples were detected with molecular, antigen, and serologic assays in the expected ranges, confirming in silico predictions. The ratio between genome equivalents (GE) and calculated median tissue culture infectious dose (TCID50) were 31- to 83-fold higher for B.1.1.7 cultures compared to B.1.351 and P.1 cultures, demonstrating that GE are more consistent units between cultures than TCID50. Conclusions: Abbott molecular and antigen assays effectively detect B.1.1.7, B.1.351, and P.1 variant infections and Abbott serologic assays detect B.1.1.7 antibodies in patient sera. Future studies with SARS-CoV-2 virus cultures should use quantitative viral load values to compare detection of variants.

As viruses continue to evolve, diagnostic tests must keep pace to ensure accurate detection of 47

Plex, BinaxNOW COVID-19 Ag Card, Panbio COVID-19 Ag Rapid Test Device, 98 ARCHITECT/Alinity i SARS-CoV-2 IgG, and Panbio COVID-19 IgG), and spike region 99 (ARCHITECT/Alinity i AdviseDx SARS-CoV-2 IgM, ARCHITECT/Alinity i AdviseDx SARS-CoV-100 2 IgG II). To evaluate these predictions for Abbott's molecular and antigen assays, dilution series VTM samples were run on the m2000 and both Alinity m SARS-CoV-2 assays; the sample 119 volume from patient #19 was not sufficient for any molecular testing. The B.1.1.7 variant was 120 detected in all 19 samples by the m2000 and both Alinity m assays and was detected in all 13 121 samples with sufficient volume by the Alinity Resp-4-Plex assay (Table 1) . Three samples had 122 sufficient volume for testing with ID NOW; the B.1.1.7 variant was detected in all three (Table 2) . 123 . CC-BY 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) which is much lower than the divergence of 30% or more between HCV genotypes, for example 146 (Table 4 ). This observation is consistent with recent studies reporting that 149 . CC-BY 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. CC-BY 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 April 26, 2021. 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 April 26, 2021. ; https://doi.org/10.1101/2021.04.24.21256045 doi: medRxiv preprint CC-BY 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 April 26, 2021. ; https://doi.org/10.1101/2021.04.24.21256045 doi: medRxiv preprint 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 April 26, 2021. 

SARS-CoV-2 analytical limits of detection across seven molecular assays

Performance 203 characteristics of a rapid SARS-CoV-2 antigen detection assay at a public plaza testing site

SARS-CoV-2 Lateral Flow Antigen Tests Evaluation of VUI-20201201

Field performance evaluation of the PanBio rapid 210

SARS-CoV-2 antigen assay in an epidemic driven by 501Y.v2 (lineage B.1.351) in the Eastern 211

Insights into RNA synthesis, capping, 213 and proofreading mechanisms of SARS-coronavirus

Global 217 epidemiology of hepatitis C virus infection: An up-date of the distribution and circulation of 218 hepatitis C virus genotypes

Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding 222

This study was funded by Abbott Laboratories. 155

* Genome equivalents (GE)/mL were calculated from a standard curve plot of TCID 50 vs GE with an R 2 value of 0.99. 253