key: cord-1052574-3tlv2b5x
authors: Bekliz, M.; Adea, K.; Alvarez, C.; Essaidi-Laziosi, M.; Escadafal, C.; Kaiser, L.; Eckerle, I.
title: Analytical sensitivity of seven SARS-CoV-2 antigen-detecting rapid tests for Omicron variant
date: 2021-12-22
journal: nan
DOI: 10.1101/2021.12.18.21268018
sha: c1fca2cb2bcaa8f54ed09c3af40812dae53f5e77
doc_id: 1052574
cord_uid: 3tlv2b5x

The emergence of novel SARS-CoV-2 variants of concern (VOCs) requires investigation of a potential impact on diagnostic performance, especially on Antigen-detecting rapid antigenic tests (Ag-RDT). Although anecdotal reports have been circulating that Omicron is in principle detected by several Ag-RDTs, no published data are a yet available for the newly emerged Omicron variant. Here, we have performed an analytical sensitivity testing with cultured virus in seven Ag-RDTs for their sensitivity to Omicron compared to data earlier obtained on VOCs Alpha, Beta Gamma and Delta and a pre-VOC isolate of SARS-CoV-2. Overall, we have found a tendency towards lower sensitivity for Omicron compared to pre-VOC SARS-CoV-2 and the other VOCs across tests. Importantly, while analytical testing with cultured virus may be a proxy for clinical sensitivity, is not a replacement for clinical evaluations which are urgently needed for Ag-RDT performance in Omicron-infected individuals.

The emergence of novel SARS-CoV-2 variants of concern (VOCs) requires investigation of a 23 potential impact on diagnostic performance, such as Antigen-detecting rapid diagnostic tests 24 (Ag-RDT). Although anecdotal reports have been circulating that Omicron is in principle 25 detectable by Ag-RDTs, no published data are a yet available for the newly emerged Omicron 26 variant. Here, we have performed an analytical sensitivity testing with cultured virus in seven 27 Ag-RDTs for their sensitivity to Omicron compared to data earlier obtained on VOCs Alpha, 28 Beta, Gamma and Delta and a pre-VOC isolate of SARS-CoV-2. Overall, we have found a 29 tendency towards lower sensitivity for Omicron compared to pre-VOC SARS-CoV-2 and the 30 other VOCs across tests. Importantly, while analytical testing with cultured virus may be a 31 proxy for clinical sensitivity, is not a replacement for clinical evaluations which are urgently 32 needed for Ag-RDT performance in Omicron-infected individuals.

. CC-BY-ND 4.0 International license It is made available under a perpetuity.

is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted December 22, 2021. ; https://doi.org/10.1101 https://doi.org/10. /2021 The emergence of novel SARS-CoV-2 variants of concern (VOCs) requires investigation of a 34 potential impact on diagnostic performance. SARS-CoV-2 antigen-detecting rapid diagnostic 35 tests (Ag-RDT) offer quick, cheap and laboratory-independent results at the point of care. 1

Although sensitivity is lower compared to RT-PCR, they enable reliable detection of high viral 37 loads associated with infectious virus presence, making them important public health tools. 2,3 38 However, the majority of Ag-RDT validation studies were performed prior to the emergence 39 of SARS-CoV-2 variants of concern (VOC). 4

The VOC Omicron was first reported at the end of November from South Africa and is 41 characterized by a high number of mutations compared to earlier circulating SARS-CoV-2. 5

The majority of mutations are located in the Spike protein, that are, according to preliminary 43 data, associated with considerable escape from neutralization by both disease-and vaccine 44 derived antibodies, and probably also associated lower vaccine effectiveness. 6,7 ,8 ,9 ,10 Current 45 epidemiological data show that Omicron circulation is associated with a steep increase in case 46 numbers as well as an increased risk of reinfections. 11

Beyond the Spike mutations, Omicron has also mutations in the nucleocapsid, which is the 48 target of almost all Ag-RDTs. Two mutations found in Omicron are R203K and G204R that 49 have been described already before Omicron in some SARS-CoV-2 sequences, were linked to 50 increased sub-genomic RNA and increased viral loads. 12-14 In addition, a deletion (Del31-33) 51 is found in the nucleocapsid of Omicron, as well as another mutation P13L, which is present 52 in some, but not all Omicron sequences. No information on a potential impact of these 53 mutations on Ag-RDTs performance is available so far. Anecdotal reports were circulating on 54 positive detection of Omicron-confirmed patient samples by Ag-RDTs but no published data 55 on Ag-RDT sensitivity for Omicron is available so far. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted December 22, 2021. ; https://doi.org/10.1101 https://doi.org/10. /2021 Here, we have evaluated test analytical sensitivity using cultured SARS-CoV-2 Omicron 57 variant, in comparison with earlier data on isolates of the other VOCs (Alpha, Beta, Gamma 58 and Delta) and an early-pandemic (pre-VOC) SARS-CoV-2 isolate (B.1.610) in seven Ag-59 RDTs, three of them WHO-EUL approved. 15-17 All viruses were isolated from clinical samples.

Isolates were grown in Vero-E6 cells as described previously. 16 When assessing by infectious virus titers (PFU/mL) (Fig 1) , analytical sensitivity to detect 79 Omicron was lower than for the other VOCs in most of the tests evaluated. One test, Flowflex is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted December 22, 2021. ; https://doi.org/10.1101 https://doi.org/10. /2021 (ACON biotech) showed the highest overall sensitivity for all SARS-CoV-2 isolates used 81 compared to the others, and here, Omicron was detected with even slightly higher sensitivity 82 than Delta but still lower than Alpha, Beta, Gamma and pre-VOC SARS-CoV-2.

Of note, while in this analysis the previous VOCs Alpha, Beta, Gamma and Delta were mainly 84 detected with comparable or even higher sensitivity compared to pre-VOC SARS-CoV-2, here 85 Omicron is the first VOC which showed a tendency towards lower analytical sensitivity across 86 assays. However, we have also observed considerable heterogeneity in sensitivity patterns 87 across variants and between individual assays in this analytical testing using cultured virus. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted December 22, 2021. ; https://doi.org/10.1101 https://doi.org/10. /2021 

SARS-CoV-2 rapid antigen test: High sensitivity to 116 detect infectious virus

Infection Using Rapid Immunoassays

Rethinking Covid-19 Test Sensitivity -A Strategy for 122 Containment

Reduced Neutralization of SARS-CoV-2 Omicron 129 Variant by Vaccine Sera and monoclonal antibodies

SARS-CoV-2 Omicron has extensive but incomplete escape 131 of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection

SARS-CoV-2 B.1.1.529 variant (Omicron) 134 evades neutralization by sera from vaccinated and convalescent individuals

1.1.529 variant by post-immunisation serum

Estimates of reduced vaccine effectiveness against hospitalization, 139 infection, transmission and symptomatic disease of a new SARS-CoV-2 variant, Omicron 140 (B.1.1.529), using neutralizing antibody titers

Increased risk of SARS-CoV-2 reinfection 142 associated with emergence of the Omicron variant in South Africa

Generation of a novel SARS-CoV-2 sub-genomic RNA 146 due to the R203K/G204R variant in nucleocapsid

Saudi Arabian SARS-CoV-2 genomes implicate a mutant 148 Nucleocapsid protein in modulating host interactions and increased viral load in COVID-19 149 patients

SARS-CoV-2 antigen-detecting rapid tests for the

This work was supported by the Swiss National Science Foundation (grant number 196383) , 103 the Fondation Ancrage Bienfaisance du Groupe Pictet, and FIND, the global alliance for 104 diagnostics. The Swiss National Science Foundation and the Fondation Ancrage Bienfaisance 105 du Groupe Pictet had no role in data collection, analysis, or interpretation. Antigen rapid 106 diagnostic tests were provided by FIND and FIND was involved in methodology, data analysis 107 and interpretation. CE is an employee of FIND. 

The authors declare no competing interests. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprintThe copyright holder for this this version posted December 22, 2021. ; https://doi.org/10.1101 https://doi.org/10. /2021