Updated February 2021 – QIAGEN response to the SARS-CoV-2 variants with increased infectivity

It is well established that RNA viruses frequently mutate due to erroneous or ineffective replication of the virus genome (1). As an RNA virus, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) lacks a robust proofreading mechanism increasing the likelihood of mutants. Usually these mutations are innocuous, but can sometimes lead to viruses with altered properties or even new strains. During February 2021, data on novel SARS-CoV-2 variants added to the Variants of Concern (VOC) list (2) due to potentially increased transmissibility includes the SARS-CoV-2 A.23.1-Uganda and the B.1.525-Nigeria variants.

To address the possible impact on the genetic variability of SARS-CoV-2, QIAGEN keeps continuous surveillance on the sequences uploaded to public databases (GISAID and GenBank) to assess the effect of the mutations of the SARS-CoV-2 genome. In particular, we periodically perform an in silico analysis on how these mutations could affect the sensitivity of the QIAGEN assays currently used in the fight against COVID-19: QIAstat-Dx® Respiratory SARS-CoV-2 Panel*, NeuMoDx™ SARS-CoV-2 Assay*, and NeuMoDx Flu A-B/RSV/SARS- CoV-2 Vantage Test Strip*.

Specifically, upon the in silico analysis, following our published methodology (3), of the strains under investigation by the European Center for Disease Control (ECDC)(4) and the cov-lineages.org website (2) listed on the table below, we can conclude that none of the recorded mutations (captured on GISAID and GenBank) on the listed strains affects the sensitivity of the assays in the QIAGEN products detecting SARS-CoV-2 (5).

Sample to Insight Impact on sensitivity of SARS-CoV-2 detection by Reported Public Mutations QIAstat-Dx NeuMoDx Flu SARS-CoV-2 Variant NeuMoDx Health Impact (amino acid change) Respiratory A-B/RSV/ SARS-CoV-2 Assay SARS-CoV-2 Panel SARS-CoV-2

Substitution (nsp3): E95K (nsp6): M86I L98F, M183I Report of increased (Spike): R102I, F157L, V367F, A.23.1 transmissibility from Kampala Q613H, P681R No impact No impact No impact region from Uganda (Nucleocapsid): S202N, Q418H (ORF8): L84S, E92K Deletion (pp1a(b)): ∆3675-3678 Emerged in Nigeria, but (Spike) ∆68-69 with no reported increased (Nucleocapsid) ∆2 tranmissibility or more B.1.525 No impact No impact No impact virulant. Predicted to possibly Substitution (orf1ab): L4715F surpass previous immunity or (Spike): Q52R, E484K, Q677H, vaccination F888L (Nucleocapsid): L21F, I82T Deletion (Spike): ∆69-70, Report of increased ∆144,Substitution (Spike): N501Y, VOC 202012/01 No impact No impact No impact transmissibility from the UK A570D, P681H, T716I, S982A, D1118 H Report of increased Substitution (Spike): D80A, 501.V2 transmissibility from South D215G, E484K, N501Y No impact No impact No impact Africa and A701V Transmission from mink to humans and community Deletion (Spike): ∆69-70 Danish Mink Variant No impact No impact No impact spread confirmed, no changes Substitution (Spike):Y453F in transmissibility reported. Preliminary report of moderate Deletion (Spike): ∆69-70 Danish Mink Cluster 5 reduction of neutralization by Substitution (Spike): Y453F, No impact No impact No impact convalescent sera I692V, M1229I Reports of minor reduction of Deletion (Spike): Variants with N439K neutralization by convalescent No impact No impact No impact Often ∆69-70 sera Rapid increase in Spain and then the rest of the EU/EEA at Nextstrain Cluster the start of the second wave, Substitution (Spike): A222V No impact No impact No impact 20A.EU1 probably due to random events and travel patterns Rapid increase in France at Nextstrain Cluster the start of the second wave, Substitution (Spike): S477N No impact No impact No impact 20A.EU2 probably due to founder (Nucleocapsid): A376T effects Rapid increase during the early stages of the pandemic in the EU/EEA and then Variants with D614G Substitution (Spike): D614G No impact No impact No impact worldwide, probably due to a mix of founder effects and increased transmissibility Spike L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, Manaus B.1.1.128 P1 Emergent lineage in Manaus H655Y, T1027I6S, D138Y, No impact No impact No impact (Brazilian variant) (Brazil) R190S, K417T, E484K, N501Y, H655Y, T1027I

The majority of the listed variants above concentrate the highest incidence of genetic variability on the S-gene that encodes for the Spike protein. None of the assays included on the QIAGEN products targets the S-gene to detect SARS-CoV-2. The few mutations that occur within the nucleocapsid and other ORF regions are not predicted to alter the annealing efficiency of the oligonucleotides used in the QIAGEN assays. QIAstat-Dx Respiratory SARS-CoV-2 Panel NeuMoDx SARS-CoV-2 Assay NeuMoDx Flu A-B/RSV/SARS-CoV-2

Genomic regions targeted E-gene & Orf1ab gene N- gene & Nsp2 gene Nsp2 gene by the QIAGEN products

From the onset of the novel coronavirus outbreak, QIAGEN’s dedicated global teams have been working around the clock to support the worldwide fight against COVID-19. We will continue with our genetic variation surveillance on a regular basis. Please do not hesitate to reach out to your local QIAstat-Dx or NeuMoDx specialist with questions.

References: 1. Shen Z, et al. (2020) Genomic Diversity of Severe Acute Respiratory Syndrome-Coronavirus 2 in Patients With Coronavirus Disease 2019. Clin Infect Dis 71, 713-20. 2. Global Report Investigating Novel Coronavirus Haplotypes. https://cov-lineages.org/global_report.html (accessed Feb 22nd 2021) 3. Peñarrubia, Luis, et al. (2020) Multiple assays in a real-time RT-PCR SARS-CoV-2 panel can mitigate the risk of loss of sensitivity by new genomic variants during the COVID-19 outbreak. Int J Infect Dis. 97, 225-9 4. European Centre for Disease Prevention and Control. (2020) Risk related to spread of new SARSCoV-2 variants of concern in the EU/EEA. https://www.ecdc.europa.eu/sites/default/files/documents/COVID-19-risk-related-to-spread-of-new-SARS-CoV-2-variants-EU-EEA.pdf 5. Penarrubia L, et al. (2021) In Response to: Multiple assays in a real-time RT-PCR Severe Acute Respiratory Syndrome Coronavirus-2 (SARS- CoV-2) panel can mitigate the risk of loss of sensitivity by new genomic variants during the COVID-19 outbreak. Int J Infect Dis https://doi.org/10.1016/j.ijid.2021.01.049

* Products and product claims may differ from country to country based on regulations and approvals. Contact your country representative for further details.

Trademarks: QIAGEN®, Sample to Insight®, QIAstat-Dx®, NeuMoDx™ (QIAGEN Group). Registered names, trademarks, etc. used in this document, even when not specifically marked as such, are not to be considered unprotected by law. PROM-17719-002 02/2021 © QIAGEN 2021, all rights reserved.

Ordering www.qiagen.com/shop Technical Support support.qiagen.com Website www.qiagen.com