Airway epithelial interferon response to SARS-CoV-2 is inferior to rhinovirus and heterologous rhinovirus infection suppresses SARS-CoV-2 replication

Common alphacoronaviruses and human rhinoviruses (HRV) induce type I and III interferon (IFN) responses important to limiting viral replication in the airway epithelium. In contrast, highly pathogenic betacoronaviruses including SARS-CoV-2 may evade or antagonize RNA-induced IFN I/III responses. In airway epithelial cells (AECs) from children and older adults we compared IFN I/III responses to SARS-CoV-2 and HRV-16, and assessed whether pre-infection with HRV-16, or pretreatment with recombinant IFN-β or IFN-λ, modified SARS-CoV-2 replication. Bronchial AECs from children (ages 6–18 years) and older adults (ages 60–75 years) were differentiated ex vivo to generate organotypic cultures. In a biosafety level 3 (BSL-3) facility, cultures were infected with SARS-CoV-2 or HRV-16, and RNA and protein was harvested from cell lysates 96 h. following infection and supernatant was collected 48 and 96 h. following infection. In additional experiments cultures were pre-infected with HRV-16, or pre-treated with recombinant IFN-β1 or IFN-λ2 before SARS-CoV-2 infection. In a subset of experiments a range of infectious concentrations of HRV-16, SARS-CoV-2 WA-01, SARS-CoV-2 Delta variant, and SARS-CoV-2 Omicron variant were studied. Despite significant between-donor heterogeneity SARS-CoV-2 replicated 100 times more efficiently than HRV-16. IFNB1, INFL2, and CXCL10 gene expression and protein production following HRV-16 infection was significantly greater than following SARS-CoV-2. IFN gene expression and protein production were inversely correlated with SARS-CoV-2 replication. Treatment of cultures with recombinant IFNβ1 or IFNλ2, or pre-infection of cultures with HRV-16, markedly reduced SARS-CoV-2 replication. In addition to marked between-donor heterogeneity in IFN responses and viral replication, SARS-CoV-2 (WA-01, Delta, and Omicron variants) elicits a less robust IFN response in primary AEC cultures than does rhinovirus, and heterologous rhinovirus infection, or treatment with recombinant IFN-β1 or IFN-λ2, reduces SARS-CoV-2 replication, although to a lesser degree for the Delta and Omicron variants.

The novel coronavirus SARS-CoV-2 has rapidly infected humans across the globe, causing one of the most devastating pandemics in modern history, with over 240 million confirmed cases and nearly 5 million deaths worldwide by October 2021 1 . While most cases of the resulting coronavirus disease 2019  are mild, some cases are severe and complicated by respiratory and multi-organ failure 2 , with a fatality rate ranging from as low as 0.2% to as high as 27% depending on underlying medical co-morbidity and age 3 . For the first half of the pandemic, incidence of COVID-19 was surprisingly low among children 3 , however, there is evidence that SARS-CoV-2 infection rates are as high in children as older adults 3 and that children can shed SARS-CoV-2 while asymptomatic and for prolonged periods 4 . More recently, the incidence of COVID-19 in the United States has increased significantly among children and adolescents 5 . Understanding mechanisms that explain the heterogeneity of severity with SARS-CoV-2 infection between individuals and across different age groups may assist efforts to develop therapeutic interventions to treat and prevent COVID-19. One potential explanation for the wide variation in COVID-19 disease severity is the differences in the innate immunity between individuals, particularly the heterogeneity of type I and III interferon (IFN) responses. Innate immune sensing of coronaviruses, including SARS-CoV-2, is thought to occur primarily through pattern recognition receptors (PRRs) including the cytosolic RIG-I-like receptors, melanoma differentiation-associated protein 5 (MDA5; coded for by the gene IFIH1), and retinoic acid-inducible gene I (RIG-I) as well as cell surface or endosomal transmembrane toll-like receptors (TLRs) TLR3 and TLR7, which lead to the activation of signaling cascades that further induce type I and III IFN responses [6][7][8][9] . Common human coronavirus (HCoV) strains (e.g. alpha-coronavirus strain 229E) potently induce type I and III IFN, and their replication is susceptible to inhibition by IFN I/III, leading to suppression of the early phase of viral replication 10,11 . In contrast, previous highly pathogenic beta-HCoVs (e.g. SARS-CoV and MERS-CoV) encode viral proteins with a greater capability to antagonize RNA-induced type I and III IFN production through perturbation of RNA sensing [12][13][14][15][16][17] . Likewise, IFN responses at mucosal surfaces appear to be muted during SARS-CoV-2 infection as compared to other respiratory viruses, suggesting evasion of innate immune responses by SARS-CoV-2 18,19 . Data from our lab and others indicates that epithelial infection with human rhinovirus increases the expression of the entry receptors for SARS-CoV-2 20,21 , suggesting that when these two viruses concurrently infect individuals the response to one virus could modulate the response to the other.
Data from clinical studies increasingly support a hypothesis that deficiency of initial IFN responses to SARS-CoV-2 may allow for increased viral replication that then supports systemic inflammatory responses that contribute to COVID-19 pathology and severity 19,[22][23][24] . Ziegler et al. recently performed scRNA-seq on nasopharyngeal swabs from 15 healthy adults, 14 adults with mild COVID-19 and 21 adults with severe COVID-19, and observed that epithelial cells from patients with severe COVID-19 had less robust expression of anti-viral interferon response genes as compared to patients with mild COVID-19 and healthy controls supporting their conclusion that a "failed" nasal epithelial innate anti-viral response may be a risk factor for severe COVID-19 25 .
The objectives of our study were to determine if heterogeneity in bronchial epithelial type I and III IFN responses to SARS-CoV-2 between individual pediatric and adult donors was associated with SARS-CoV-2 replication, to compare airway epithelial IFN responses between SARS-CoV-2 and human rhinovirus-A16 (HRV- 16), and to determine the effects of HRV pre-infection or exogenous IFN treatment on SARS-CoV-2 replication in organotypic airway epithelial cell (AEC) cultures from children and adults. We hypothesized that type I and III IFN responses would be less vigorous to SARS-CoV-2 than to HRV infection, that IFN responses would be associated with SARS-CoV-2 replication, and that HRV pre-infection and/or recombinant IFN treatment of airway epithelial cultures would decrease replication of SARS-CoV-2. Some of the results of these studies have been previously reported in the form of an abstract 26 .

Methods
Bronchial AECs from children ages 6-18 years (n = 15) and older adults ages 60-75 years (n = 10) were differentiated ex vivo at an air-liquid interface (ALI) to generate organotypic cultures. AECs from children were obtained under study #12490 approved by the Seattle Children's Hospital Institutional Review Board and in accordance with the Declaration of Helsinki, and all experiments were performed in accordance with relevant guidelines and regulations. Written informed consent was obtained from parents of subjects and children over 7 years of age provided written assent. Primary bronchial AECs from adults were purchased from Lonza ® or obtained from a tracheal segment lung transplant donor lung tissue. AECs were differentiated ex vivo for 21 days at an ALI on 12-well collagen-coated Corning ® plates with permeable transwells in PneumaCult™ ALI media (Stemcell™) at 37 °C in an atmosphere of 5% CO 2 as we have previously described, producing an organotypic differentiated epithelial culture with mucociliary morphology [27][28][29][30] 31 .
Expression of IFNB1, IFNL2, CXCL10, IFIH1, ACE2, and GAPDH were measured by quantitative polymerase chain reaction (qPCR) using Taqman ® probes. To measure SARS-CoV-2 replication in AEC cultures we used the Genesig ® Coronavirus Strain 2019-nCoV Advanced PCR Kit (Primerdesign ® ), with duplicate assays of harvested RNA from each SARS-CoV-2-infected AEC experimental condition. The viral copy number used in analyses of each experimental condition was the mean of duplicate assays from each experimental condition. Similarly, to measure HRV-16 replication in AEC cultures we used the Genesig ® Human Rhinovirus Subtype 16 PCR Kit (Primerdesign ® ).
To extract protein from the cell layer of SARS-CoV-2-infected AEC cultures, media was first removed from the basolateral chamber of transwells. Next, 100 µL of cold PBS was added to the apical surface of cultures and 1 mL was added to the basolateral chamber of cultures as a wash step. Next, 50 μL of RIPA buffer for protein extraction ready-to-use-solution (Sigma-Aldrich ® , Product No. R0278) containing Triton X100 1% and SDS 0.1% was added to the apical surface of AECs and incubated for 15 min on ice. A pipet tip was then used to gently scratch each apical well in a crosshatch pattern to loosen AECs from the transwell membrane. Material was collected, centrifuged at 10,000 rpm at 4 °C for 10 min, then supernatant containing isolated protein was collected. IFNβ1, IFNλ2, and CXCL-10 protein concentrations in cell lysates, and IFNβ1, IFNλ3, and CXCL-10 concentrations were measured in cell culture supernatants, via a Human Luminex ® Assay (R&D ® ), with protein concentrations normalized to total protein levels in lysate (BCA assay; Sigma-Aldrich ® ).
Statistical analysis. Gene expression and protein levels are presented as means ± standard deviation (SD) when data were normally distributed, and as medians with interquartile range if one or more groups were not normally distributed. To determine if data was normally distributed the Kolmogorov-Smirnov test was used (alpha = 0.05). IFNB1, IFNL2, IFIH1 and CXCL10 relative expression were standardized using GAPDH as a nonregulated housekeeping gene. GenEx version 5.0.1 was used to quantify gene expression from qPCR normalized to GAPDH (MultiD Analyses AB, Göteborg, Sweden) based on methods described by Pfaffl 32 . Data in at least one group or condition in each experiment analyzed were determined to be non-normally distributed, therefore nonparametric tests were used for analyses. To compare gene expression data and distributions of protein concentrations in cell lysates and supernatants between paired groups the Wilcoxon matched-pairs signed rank test was used. For unpaired data the Mann-Whitney test was used for analyses. For experiments with three or more conditions the Kruskal-Wallis or Friedman one-way ANOVA on ranks tests were used, and post hoc comparisons between pairs of subject groups were made using Dunn's multiple comparisons test (significance level set at p < 0.05). Correlations were determined using the Spearman's rank correlation coefficient. Data was analyzed using Prism ® 9.0 software (GraphPad Software Inc., San Diego, CA, USA). Statistical significance was set at p < 0.05. Ethics approval. Airway epithelial cells from children were obtained under study #12490 approved by the Seattle Children's Hospital IRB. Parents of subjects provided informed written consent and children over 7 years of age provided assent. Airway epithelial cells from adults were purchased from Lonza ® without personal identifiers. The Seattle Children's Hospital IRB determined that use of de-identified adult airway epithelial cells purchased from Lonza ® did not require ethics approval or consent.

Results
In organotypic primary bronchial AEC cultures from children (n = 15) and older adults (n = 10) we observed marked heterogeneity in SARS-CoV-2 replication between human donors (Fig. 1). The clinical characteristics of human airway epithelial donors included in these experiments is summarized in Table 1. Despite the significant between-subject heterogeneity in SARS-CoV-2 replication, we observed that SARS-CoV-2 replicated approximately 100 times more efficiently than HRV-16 in these primary bronchial AEC cultures ( Fig. 1A; SARS-CoV-2 median copy number 215,387 vs. HRV-16 median copy number 2211; p < 0.0001) when parallel cultures from each donor were infected with each virus at the same MOI of 0.5. When data from pediatric and adult cultures were analyzed separately SARS-CoV-2 replication was also markedly greater than HRV- 16  www.nature.com/scientificreports/   For primary bronchial epithelial cultures wherein SARS-CoV-2 WA-01 and HRV-16 infection was compared in parallel, RNA harvested 96 h following infection was available from 22 donor cultures (n = 14 children, n = 8 adults) to allow measurement of IFNB1, IFNL2, and CXCL10 gene expression, and protein was available from cell lysate collected 96 h following infection from 20 donor cultures (n = 12 children, n = 8 adults) to allow for measurement of IFNβ1, IFNλ2 (IL-28A), and CXCL-10 protein levels. As compared to uninfected cultures, the relative increase in expression of IFNB1 following infection with HRV-16 was significantly greater than following infection with SARS-CoV-2 WA-01 (median increase expression 4.4-fold vs. 1.4-fold, p < 0.0001; Fig. 2A). Similarly, the relative increase in expression of IFNL2 following infection with HRV-16 was significantly greater than following infection with SARS-CoV-2 (median increase expression 21.2-fold vs. 4.3-fold, p < 0.0001; Fig. 2C), as was the increase in expression of CXCL10 (median increase expression 9.8-fold vs. 5.4-fold, p = 0.003; Fig. 2E). The expression of these three genes was significantly greater following HRV-16 infection than following SARS-CoV-2 WA-01 in cultures from both children and adults when analyzed separately (data not shown). The concentrations of IFNβ1, IFNλ2 (IL-28A), and CXCL-10 protein, normalized to total protein concentration, in cell lysates collected 96 h following infection with HRV-16 were also significantly greater than in parallel cultures following SARS-CoV  Fig. 6C). An HRV-16 pre-infection with MOI of 0.5 or 0.1 reduced replication of the Omicron variant at an MOI of 0.1 (Fig. 6C). We also measured expression of IFNB1 and IFNL2 in these different combinations of HRV-16 infectious doses and SARS-CoV-2 variants and infectious doses. We observed that IFNB1 and IFNL2 expression were significantly greater following HRV-16 than following infection with SARS-CoV-2 WA-01, SARS-CoV-2 Delta variant, or SARS-CoV-2 Omicron variant at equivalent MOIs ( Supplementary Fig. 1A,B). Furthermore,   Fig. 1D).
Given that SARS-CoV and MERS have been noted to evade innate antiviral defenses at various steps between viral sensing and transcription and translational of type I and III interferons, and ultimately transcription of an array antiviral genes 12-17 , we assessed one potential proximal step where SARS-CoV-2 may evade sensing of viral nucleic acids by comparing gene expression of the pattern-recognition receptor and RNA viral sensor IFIH1/ MDA5 between primary bronchial AEC cultures infected in parallel with SARS-CoV-2 (MOI = 0.5) or HRV-16 (MOI = 0.5). We observed that IFIH1 expression was more than twofold greater following infection with HRV-16 as compared to following SARS-CoV-2 infection (Fig. 7; p = 0.003). www.nature.com/scientificreports/

Discussion
A growing body of literature suggests that beta-HCoVs, including SARS-CoV-2 appear able to antagonize type I and III IFN responses at mucosal surfaces at multiple steps between viral sensing and production of interferon induced antiviral proteins 18,19,33 . In this study we directly compared type I and III IFN responses to SARS-CoV-2 and HRV-16 infection by primary organotypic bronchial AEC cultures from children and adults, and assessed the impact of exogenous treatment with recombinant IFNβ1 or IFNλ2 on SARS-CoV-2 replication as well as the impact of heterologous infection with HRV-16 prior to SARS-CoV-2. We observed significant heterogeneity in SARS-CoV-2 replication between primary AEC lines from different human donors, however, despite between donor heterogeneity we also observed that SARS-CoV-2 replicated approximately 100 times more efficiently than HRV-16 in these primary bronchial AEC cultures. As compared to uninfected cultures, the relative increase in expression of IFNB1, INFL2, and CXCL10 following infection with HRV-16 was significantly greater than following infection with SARS-CoV-2, and the protein concentrations of type I and III IFN and the IFN stimulated chemokine CXCL10 in both cell lysates and supernatant were significantly greater in AEC cultures following infection with HRV-16 as compared to SARS-CoV-2. In SARS-CoV-2 infected AEC cultures type I and III IFN gene expression and protein production were inversely correlated with viral replication. Furthermore, treatment of AEC cultures with recombinant IFNβ1 or IFNλ2, or pre-infection of AEC cultures with HRV-16, markedly reduced SARS-CoV-2 replication. Sensing of beta-HCoVs by the innate immune system is believed to be primarily through pattern recognition receptors (PRRs), including cell surface or endosomal transmembrane TLRs TLR3 and TLR7, the cytosolic RIG-I-like receptors melanoma differentiation-associated protein 5 (MDA5), as well as retinoic acid-inducible gene I (RIG-I) [6][7][8][9] . PRR's then mediate activation of signaling cascades leading to induction of type I and III IFN responses [6][7][8][9] . Recently Sampaio et al. reported that in the lung cancer cell line Calu-3 the cytosolic RNA sensor MDA5 was required for type I and III IFN induction when cells were infected with SARS-CoV-2 infection 6 .
Studies using immortalized cell lines (e.g. Vero, HeLa, Calu-3, 293 T) in vitro, as well as murine in vivo studies, have suggested a number of potential mechanisms by which beta-HCoVs (e.g. SARS-CoV, MERS-CoV, and SARS-CoV-2) may evade IFN responses at the level of the airway epithelium. Prior to the onset of the COVID-19 pandemic, these mechanisms were investigated extensively for SARS-CoV and MERS-CoV. One group of  19 , raising the possibility that a deficient epithelial IFN response to SARS-CoV-2 may facilitate enhanced local viral replication that ultimately might lead to a dysregulated systemic pro-inflammatory response. Data from several clinical studies have provided additional support for the hypothesis that a muted initial local IFN response to SARS-CoV-2 in the airway epithelium, at least in some hosts, allows the virus to replicate unimpeded which then sets up the host for potential systemic inflammatory responses that contribute to COVID-19 pathology and severity 19,[22][23][24] . Recently, Ziegler et al. published transcriptomics results from nasopharyngeal swabs from 15 healthy adults, 14 adults with mild COVID-19 and 21 adults with severe COVID-19, and observed that nasal epithelial cells from patients with severe COVID-19 exhibited less robust expression of anti-viral IFN response genes as compared to patients with mild COVID-19 and healthy adults, supporting their conclusion that a "failed" nasal epithelial innate anti-viral response may be a risk factor for severe COVID-19 25 .
Mechanisms underlying the marked increase in transmissibility of the SARS-CoV-2 Delta and Omicron variants respectively, and the progressively larger worldwide surges caused by these variants, has been of great interest. Much research has focused on how mutations in the SARS-CoV-2 spike protein enhanced transmission and replication of the Delta and Omicron variants. However, our experimental data demonstrating that across a range pre-infection doses HRV-16 was less effective at reducing replication of Delta and Omicron or boosting type I and III interferon responses as compared to HRV-16 pre-infection prior to SARS-CoV-2 WA-01 strongly suggest that the Delta and Omicron variants also interfere with interferon responses in human primary airway epithelium. Future studies are needed to further elucidate how these variants dampen interferon responses.
In the early stages of the pandemic, morbidity and mortality was skewed toward older patients with significant underlying comorbidities, however, over time it has become increasingly clear that clinical outcomes with COVID-19 following infection with SARS-CoV-2 is heterogeneous with outcomes even in young adults and children without medical comorbidities unpredictably ranging from ranging from asymptomatic infection to death 57 . An objective of our study was to determine if heterogeneity in airway epithelial IFN responses to SARS-CoV-2 between individual pediatric and adult donors was associated with SARS-CoV-2 replication. A striking observation in our data is the marked between-donor heterogeneity in the replication of SARS-CoV-2 in organotypic AEC cultures using standardized protocols and uniform viral inoculation doses. A potential important future area of investigation will be to investigate possible genetic and epigenetic factors that may partially explain heterogeneity in SARS-CoV-2 replication in airway epithelium.
Our group and others have demonstrated that the SARS-CoV-2 entry receptor ACE2 is an ISG 20,21 . We have demonstrated that HRV-16 infection induces a type I and III interferon response, and increases ACE2 expression 21 , leading us to originally speculate that HRV pre-infection of AECs might increase replication of SARS-CoV-2 through greater expression of the entry receptor and be a clinical risk factor for acquisition of COVID-19. However, our results demonstrate that even though baseline expression of the SARS-CoV-2 entry factor ACE2 is positively correlated with SARS-CoV-2 replication, and though ACE2 is an ISG, HRV-16 infection induces much more potent type I and III IFN responses than SARS-CoV-2 and heterologous infection of organotypic AEC cultures with HRV-16 three days prior to inoculation with SARS-CoV-2 markedly reduces replication   60 . However, that study lacked reporting of whether any subjects that experienced severe clinical outcomes were children, multivariate models used did not adjust for subject age, and the study was limited by a lack of data to determine the timing of HRV vs. SARS-CoV-2 infection. It is likely that host co-morbidities, timing of a HRV pre-infection, as well as co-infection with other pathogens, all significantly impact the clinical manifestations of SARS-CoV-2 infection. Given the steady evolution of new SARS-CoV-2 variants through 2021 and continued significant resistance to vaccination among a sizable minority of people with access to vaccines, the pandemic has continued to result in high levels of morbidity and mortality in many areas of the world, fueling an ongoing need for therapeutics to treat COVID-19. Our results demonstrating marked reduction in SARS-CoV-2 replication in AEC cultures treated with recombinant IFNβ1 or IFNλ2 provides further mechanistic evidence to support the possible use of inhaled interferon as a possible treatment option if initiated early enough during COVID-19. A recent randomized, double-blind, placebo-controlled, phase 2 trial of inhaled nebulized interferon beta-1a (SNG001) for treatment of SARS-CoV-2 infection demonstrated that patients who received SNG001 early in their disease course had greater odds of improvement and recovered more rapidly from SARS-CoV-2 infection than patients who received placebo, providing a strong rationale for further trials of this agent 61 .
We are not aware of other studies to date that have directly compared innate immune responses between SARS-CoV-2 and HRV in organotypic AEC cultures from many pediatric and adult donors. However, there are several limitations of our primary airway epithelial model system. First, our ex vivo system lacks interaction with immune cells and the complex immune responses that occur in vivo in the context of COVID-19, and therefore we cannot assess how heterogeneity in interferon responses to SARS-CoV-2 at the level of the airway epithelium relate to systemic immune responses or clinical outcomes in vivo. Second, in this study we did not investigate potential genetic or epigenetic factors that may explain the between subject heterogeneity in interferon responses and viral replication that we observed. Finally, given the limitations posed by the complex logistics of completing these experiments in a biosafety level 3 (BSL-3) facility, together with limitations in available material from organotypic cultures from a sizeable number of human donors, we were constrained in the number of feasible sample harvesting timepoints which prevented us from conducting a high resolution assessment of the time kinetics of viral infection and interferon responses in the present study; however, our choice to harvest supernatant 48 h following SARS-CoV-2 infection and RNA 96 h following infection was informed by both our prior work with RSV 29 and preliminary experiments with SARS-CoV-2 (data not shown) where we observed that in organotypic primary ALI cultures type I and III interferon responses peak between 24 and 48 h while expression of downstream ISGs peak between 72 and 96 h.
In conclusion, in this study we have demonstrated that in addition to remarkable between subject heterogeneity in interferon responses and viral replication, SARS-CoV-2 WA-01, SARS-CoV-2 Delta variant, and SARS-CoV-2 Omicron variant all elicit a less robust type I and III interferon response in organotypic primary bronchial AEC cultures than does human rhinovirus, and that pre-infection of AECs with HRV-16, or pre-treatment with recombinant IFN-β1 or IFN-λ2, markedly reduces SARS-CoV-2 replication. www.nature.com/scientificreports/

Data availability
The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request. www.nature.com/scientificreports/ Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http:// creat iveco mmons. org/ licen ses/ by/4. 0/.