key: cord-0962224-hy8o6tc5
authors: Rodgers, Mary A; Olivo, Ana; Harris, Barbara J; Lark, Chris; Luo, Xinxin; Berg, Michael G; Meyer, Todd V; Mohaimani, Aurash; Orf, Gregory S; Goldstein, Yitz; Fox, Amy S; Hirschhorn, Julie; Glen, William B; Nolte, Frederick; Landay, Alan; Jennings, Cheryl; Moy, James; Servellita, Venice; Chiu, Charles; Batra, Rahul; Snell, Luke B; Nebbia, Gaia; Douthwaite, Sam; Tanuri, Amilcar; Singh, Lavanya; de Oliveira, Tulio; Ahouidi, Ambroise; Mboup, Souleymane; Cloherty, Gavin A
title: Detection of SARS-CoV-2 variants by Abbott molecular, antigen, and serological tests
date: 2022-01-20
journal: J Clin Virol
DOI: 10.1016/j.jcv.2022.105080
sha: a13735bb9c504b24da8847357bca06c86eb84978
doc_id: 962224
cord_uid: hy8o6tc5

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 circulating SARS-CoV-2 variants, including all current variants of concern (VOC): B.1.1.7 (alpha), B.1.351 (beta), P.1 (gamma) and B.1.617.2 (delta). STUDY DESIGN: : Dilutions of variant virus cultures (B.1.1.7, B.1.351, B.1.429, B.1.526.1, B.1.526.2, B.1.617.1, B.1.617.2, P.1, R.1 and control isolate WA1) and a panel of N = 248 clinical samples from patients with sequence confirmed variant infections (B.1.1.7, B.1.351, B.1.427, B.1.429, B.1.526, B.1.526.1, B.1.526.2, P.1, P.2, R.1) were evaluated on at least one assay: 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: : Consistent with in silico predictions, each molecular and antigen assay detected VOC virus cultures with equivalent sensitivity to the WA1 control strain. Notably, 100% of all tested variant patient specimens were detected by molecular assays (N = 197 m2000, N = 88 Alinity m, N = 99 ID NOW), and lateral flow assays had a sensitivity of >94% for specimens with genome equivalents (GE) per device above 4 log (85/88, Panbio; 54/57 Binax). Furthermore, Abbott antibody assays detected IgG and IgM in 94–100% of sera from immune competent B.1.1.7 patients 15–26 days after symptom onset. CONCLUSIONS: : These data confirm variant detection for 11 SARS-CoV-2 assays, which is consistent with each assay target region being highly conserved. Importantly, alpha, beta, gamma, and delta VOCs were detected by molecular and antigen assays, indicating that these tests may be suitable for widescale use where VOCs predominate.

Results: Consistent with in silico predictions, each molecular and antigen assay detected VOC 56 virus cultures with equivalent sensitivity to the WA1 control strain. Notably, 100% of all tested 57 variant patient specimens were detected by molecular assays (N=197 m2000, N=88 Alinity m, 58 N=99 ID NOW), and lateral flow assays had a sensitivity of >94% for specimens with genome 59 equivalents (GE) per device above 4 log (85/88, Panbio; 54/57 Binax). Furthermore, Abbott 60 antibody assays detected IgG and IgM in 94-100% of sera from immune competent B.1.1.7 61 patients 15-26 days after symptom onset. 62

Conclusions: These data confirm variant detection for 11 SARS-CoV-2 assays, which is 63 consistent with each assay target region being highly conserved. Importantly, alpha, beta, 64 gamma, and delta VOCs were detected by molecular and antigen assays, indicating that these 65 tests may be suitable for widescale use where VOCs predominate. 66 67 Keywords: SARS-CoV-2, molecular diagnostics, variant of concern, rapid antigen tests, 68 antibody assays 69

As viruses continue to evolve, diagnostic tests must keep pace to ensure accurate detection of 71 all circulating variants. While assay design can mitigate the impact of viral diversity, assay 72 performance must be continually monitored through variant testing and molecular surveillance. 73

To meet this challenge, the Abbott Global Surveillance program has been tracking the 74 sequences of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants that 75 have emerged throughout the pandemic, including variant of concern (VOC) lineages that have 76 The goal of this study was to evaluate the performance of Abbott SARS-CoV-2 molecular, 99 antigen, and serological assays to detect SARS-CoV-2 variants and variant-specific antibodies. 100 101

In silico analysis -Sequences containing lineage-defining mutations were obtained from 103 GISAID [11] for in silico analysis by customized application of the NextClade tool 104 (clades.nextstrain.org) to compare individual assay target sequences for Abbott ID NOW 105 COVID-19, m2000 RealTime SARS-CoV-2, Alinity m SARS-CoV-2, and Alinity m Resp-4-Plex 106 molecular assays; the BinaxNOW COVID-19 Ag Card and Panbio COVID-19 Ag Rapid Test 107

Device; and the ARCHITECT/Alinity i SARS-CoV-2 IgG and AdviseDx IgM assays, Panbio 108 COVID-19 IgG assay, and ARCHITECT/Alinity i AdviseDx SARS-CoV-2 IgG II assay. 109

Mismatches were considered significant if they were present in >75% of lineage sequences 110 and reduced the target region nucleotide identity or amino acid homology to less than 90%. Table 2 ). To evaluate these predictions for 173

Abbott's high throughput molecular assays, dilution series of heat-inactivated B. Table 3) . ARCHITECT/Alinity i, and Panbio IgG assays (Table 3) . Variant lineages will continue to emerge as the SARS-CoV-2 pandemic progresses, with the 294 pace at which they arise dependent upon the total number of infections and the mutation rate. 295

For context, SARS coronaviruses maintain a higher rate of replication fidelity during replication 296 due to an encoded proofreading mechanism in their RDRP [26] . As a result, SARS-CoV-2 297 variants are typically defined by a pattern of mutations totaling <30 nucleotides (0.1% 298 divergence), which is much lower than the divergence of 30% or more between HCV 299 genotypes, for example [11, 27, 28] 

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