key: cord-1050805-i3bvwbnh
authors: Nchioua, Rayhane; Schundner, Annika; Klute, Susanne; Noettger, Sabrina; Zech, Fabian; Koepke, Lennart; Graf, Alexander; Krebs, Stefan; Blum, Helmut; Kmiec, Dorota; Frick, Manfred; Kirchhoff, Frank; Sparrer, Konstantin M.J.
title: The Delta variant of SARS-CoV-2 maintains high sensitivity to interferons in human lung cells
date: 2021-11-17
journal: bioRxiv
DOI: 10.1101/2021.11.16.468777
sha: a8bcdd9c0fb92b78e351181d807546881b2a5ec3
doc_id: 1050805
cord_uid: i3bvwbnh

Interferons are a major part of the anti-viral innate defense system. Successful pathogens, including the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), need to overcome these defenses to establish an infection. Early induction of interferons (IFNs) protects against severe coronavirus disease 2019 (COVID-19). In line with this, SARS-CoV-2 is inhibited by IFNs in vitro, and IFN-based therapies against COVID-19 are investigated in clinical trials. However, SARS-CoV-2 continues to adapt to the human population resulting in the emergence of variants characterized by increased transmission fitness and/or decreased sensitivity to preventive or therapeutic measures. It has been suggested that the efficient spread of these so-called “Variants of Concern” (VOCs) may also involve reduced sensitivity to IFNs. Here, we examined whether the four current VOCs (Alpha, Beta, Gamma and Delta) differ in replication efficiency or IFN sensitivity from an early isolate of SARS-CoV-2. All viruses replicated in a human lung cell line and in iPSC-derived alveolar type II cells (iAT2). The Delta variant showed accelerated replication kinetics and higher infectious virus production compared to the early 2020 isolate. Replication of all SARS-CoV-2 VOCs was reduced in the presence of exogenous type I, II and III IFNs. On average, the Alpha variant was the least susceptible to IFNs and the Alpha, Beta and Gamma variants show increased resistance against type III IFN. Although the Delta variant has outcompeted all other variants in humans it remained as sensitive to IFNs as an early 2020 SARS-CoV-2 isolate. This suggests that increased replication fitness rather than IFN resistance may be a reason for its dominance. Our results may help to understand changes in innate immune susceptibility of VOCs, and inform clinical trials exploring IFN-based COVID-19 therapies.

The IFN system constitutes a potent barrier against viral infections [1] [2] [3] . After recognition 42 of viral pathogen-associated molecular patterns by germ-line encoded pattern recognition 43 receptors, signaling cascades are activated. This results in the induction and secretion of IFNs as 44 well as other pro-inflammatory cytokines [1] . The secreted IFNs can act in an autocrine or Interleukin 10 receptor β-subunit (IL10R2) and the Interleukin 28 receptor α-subunit (IFNLR1). 52 Type I and III IFNs may be secreted by almost any cell type, whereas type II IFN production is 53 restricted to immune cells, particularly T and Natural Killer (NK) cells. Innate immunity plays a 54 major role in defending against emerging pathogens like SARS-CoV-2, the causative agent of 55 COVID-19 [7] [8] [9] [10] [11] . This respiratory virus has a profound global impact both on a socioeconomic 56 level and as a major threat to human health. To date (November 4th, 2021), more than 240 million 57 SARS-CoV-2 infections were reported worldwide, resulting in over 4.9 million deaths. 58 To be able to replicate in the presence of a functioning innate immune system, SARS-CoV- 59 2 utilizes more than half of its about 30 proteins to suppress IFN induction and signaling [12] [13] [14] [15] . 60 However, despite these evasion mechanisms SARS-CoV-2 still remains sensitive towards all types 61 of IFNs, with types II and III being most effective [12, [16] [17] [18] [19] . Importantly, early induction of high 62 levels of IFNs in patients were reported to prevent severe COVID-19 [8, 9] Currently, it is poorly understood whether they also evolved increased resistance towards innate 80 immune defenses.

Next-generation sequencing of an early SARS-CoV-2 isolate from February 2020 (NL-02-83 2020) and four VOC isolates revealed amino acid changes in the S glycoprotein, as well as in 84 proteins involved in replication and innate immune escape, compared to the first available 85 sequence of the Wuhan-Hu-1isolate ( Fig 1A) . The impact of mutations in the S protein of VOCs 86 has been the focus of many studies. Some of them are known to affect the affinity between S and 87 the cellular receptor ACE2 and/or alter proteolytic activation of S, resulting in increased Hu-1 reference strain (Fig. 1A) . These include mutations in Nsp3, ORF6 and N, which were 94 reported to be crucial for IFN escape [12, 25, 26] . The consequence of these alterations is, however, 95 unknown.

Cells of the respiratory tract are primary targets of SARS-CoV-2 infection. We found that 97 the Delta variant replicated with higher efficiency (Fig 1B, Figs S1A and S1B) and produced ~24- respectively. In comparison to the early NL-02-2020 isolate the Beta, Alpha and Gamma VOCs 142 were 3-5-fold less susceptible to inhibition by type III IFN (Fig 2F) . In line with the results in 143 Calu-3 cells, the Delta variant was still sensitive towards IFN, even more so in the case of IFNβ. 

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