SARS-CoV-2 Omicron Induces Enhanced Mucosal Interferon Response Compared to other Variants of Concern, Associated with Restricted Replication in Human Lung Tissues

Abstract

SARS-CoV-2 Omicron variant has been characterized by decreased clinical severity, raising the question of whether early variant-specific interactions within the mucosal surfaces of the respiratory tract could mediate its attenuated pathogenicity. Here, we employed ex vivo infection of native human nasal and lung tissues to investigate the local-mucosal susceptibility and innate immune response to Omicron compared to Delta and earlier SARS-CoV-2 variants of concern (VOC). We show that the replication of Omicron in lung tissues is highly restricted compared to other VOC, whereas it remains relatively unchanged in nasal tissues. Mechanistically, Omicron induced a much stronger antiviral interferon response in infected tissues compared to Delta and earlier VOC-a difference, which was most striking in the lung tissues, where the innate immune response to all other SARS-CoV-2 VOC was blunted. Notably, blocking the innate immune signaling restored Omicron replication in the lung tissues. Our data provide new insights to the reduced lung involvement and clinical severity of Omicron.

Keywords: COVID-19; Omicron; SARS-CoV-2; interferon response; lung organ culture; nasal organ culture; organ culture.

Figure 1

SARS-CoV-2 Omicron and Delta replication kinetics in human nasal and lung tissues. Nasal (A) and lung (B) organ cultures were (each) infected in parallel with Omicron and Delta (10⁵ PFU/well). The levels of tissue-associated viral sub-genomic (sg)-mRNA (left panels) and infectious virus progeny released from the same infected tissues (right panels) represent mean values (±SEM) of four and five independent nasal and lung tissues, respectively, each tested in four biological replicates. (C) Representative confocal micrographs of whole-mount lung tissues at 72 h post-infection. Whole-mount tissues were visualized using a Nikon A1R confocal microscope and were analyzed using NIS Elements software (Nikon). Scale bar = 100 μm. **, p < 0.01. Statistics were performed using multiple paired, two-tailed Student’s t-test.

Figure 2

Lung tissue interferon response to SARS-CoV-2 Omicron and Delta. Lung organ cultures were infected in parallel with Omicron and Delta (10⁵ PFU/well), and the effect of infection on the expression of the indicated innate immunity genes, measured by RT-qPCR at 24h post-infection, is presented as fold-change from mock-infection. (A) the mean values (±SEM) in 8 independent tissues, each tested in 4 biological replicates. (B) the mean values (±SEM) in a representative tissue (tested in 4 biological replicates) exposed in parallel to infectious versus UV-inactivated viruses. The results shown in panel B represent at least three independent tissues. *, p < 0.05; **, p < 0.01; ***, p < 0.001; ****, p < 0.0001.

Figure 3

Ruxolitinib treatment restores Omicron replication in human lung tissues. Lung organ cultures were pretreated with 5 uM Ruxolitinib (Ruxo) 16 h when indicated. Treated and non-treated tissues were infected in parallel with Omicron and Delta (10⁵ PFU/well). The levels of tissue-associated viral sub-genomic (sg)-mRNA (left panel) and infectious virus progeny released from the same infected tissue (right panel) represent mean values (±SEM) of four biological replicates. **, p < 0.01; ***, p < 0.001.