As of February 2024, the COVID-19 pandemic caused by spread of the coronavirus SARS-CoV-2 had led to more than 770 million cases, with 7 million deaths reported worldwide. Age remains the greatest risk factor leading to mortality after SARS-CoV-2 encounter1. In their work published in Nature Microbiology, Woodall et al.2 demonstrate that the capacity of SARS-CoV-2 to spread and grow in nasal epithelial cells (NECs) depends on the age of the individual.

Fig. 1: Distinct responses to SARS-CoV-2 of NECs of children and older adults.
figure 1

In pediatric NECs, goblet cells are the main port of entry of SARS-CoV-2. The virus leads to the expansion of the group of goblet inflammatory cells that produce and respond to IFNs, decreasing viral replication and spread. Older adult NECs show expanded basal cells that are infected by SARS-CoV-2, leading to the expansion of a basaloid cell type with increased repair and fibrotic functions. Aged NECs are characterized by increased viral spread, augmented extrusion of dying cells and expanded production of infectious viral particles.

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The nasal mucosa is composed by multiple different cell types that have different functions during homeostasis or in the presence of a pathogen. By culturing ex vivo NECs isolated from children (<12 years), adults (30–50 years) and older adults (>70 years), the authors show that NECs differ in their cellular composition across age groups before their encounter with the virus. After infection with SARS-CoV-2, pediatric NECs show a strong antiviral response, whereas NECs derived from elderly people present heightened epithelial repair programs that facilitate virus growth and spread.

The upper airway is the port of entry for respiratory viruses. Most of these viruses, including SARS-CoV-2, become life-threatening only once they reach the lower airways. The damage caused in the lower airways by virus replication, as well as the immune response elicited by the host against the virus, can alter the functionality of the lungs and cause an exaggerated inflammatory response that drives a lethal acute respiratory distress syndrome (ARDS). Indeed, severe COVID-19 was initially characterized for the excessive presence of inflammatory mediators in the lung3. The antiviral response that takes place in the nasal mucosa plays central roles in preventing the escape of the virus to the bronchial and alveolar space, avoiding the development of ARDS. Beyond immune cells residing in the respiratory tract, NECs are crucial in the response to SARS-CoV-2. The capacity of NECs to orchestrate a local intrinsic antiviral response that determines disease severity in patients with COVID-19 was proposed in two independent studies4,5. Both studies showed that COVID-19 severity depends on the capacity to mount an effective interferon (IFN) response in the upper airways. IFNs are a group of antiviral and antibacterial cytokines and are divided into three major families: type I IFNs (mostly represented by a dozen IFNα subtypes, along with IFNβ); type II IFNs (IFNγ); and type III IFNs (IFNλ1–IFNλ4 in humans). Type I and type III IFNs are recognized as the most potent antiviral effectors produced by our immune system and control the induction of hundreds of antiviral genes, called interferon-stimulated genes (ISGs). Both studies found elevated levels of ISGs, and/or of the IFNs themselves, in the nasopharyngeal swabs of patients with COVID-19 with mild, but not severe, disease4,5. These studies were based on samples derived from patients with COVID-19, and they could not take into consideration the precise timing of encounter with the virus or how the cells of the immune system affected the responses of the NECs. Also, the samples analyzed came mostly from adult and older adult individuals, leaving the impact of age in children on the local intrinsic immune response of the upper airways unclear.

In their work, Woodall et al.2 isolated NECs from healthy individuals across different ages, and cultured them in vitro in an organoid model at the air–liquid interface (ALI) that allows the differentiation of different subtypes of NECs. Using single-cell RNA sequencing (scRNA-seq) analyses, the authors confirmed that their ALI cultures contained the three major groups of NECs — basal, secretory and ciliated cell — and further differentiated these three major types into distinct subtypes. They also found that the proportions of the different cell types varied depending on the age of the donor, and that a set of secretory cells called goblet cells was expanded in pediatric cultures. The distribution among cell types of the major known receptors for the entry of SARS-CoV-2 (ACE2 and TMPRSS2) also differed across age groups, with higher expression of these receptors in pediatric goblet cells, whereas in adult and older adult cultures the receptors were present in the secretory and basal cell groups. The different distribution of the entry receptors for SARS-CoV-2 suggests that the specific cell types of the NECs of children that can be infected are different from those of more adult populations.

The authors next infected their ALI cultures with an ancestral lineage of SARS-CoV-2 and found that older adult cultures secreted greater amounts of infectious viruses compared to pediatric NECs. Pediatric cultures infected with SARS-CoV-2 showed the expansion of a distinct goblet cell population, the goblet inflammatory cells. The presence of these cells was associated with a strong induction of ISGs. Intriguingly, the authors showed that several type I and III IFNs were also induced in the same NECs that had upregulated ISGs, suggesting that autonomous IFN induction by NECs, independently of immune cells, can participate in the protective immune response also reported previously in individuals with mild COVID-19 disease4,5. The population of goblet inflammatory cells in the pediatric NEC culture also showed a high abundance of viral reads, which was potentially contradictory to the protective role of this cell type and the lower production of infective viral particles in pediatric compared to older adult cultures. The authors refined their analyses to demonstrate that the goblet inflammatory cell population mostly harbors noncanonical subgenomic SARS-CoV-2 RNAs that can result in defective viral genomes, previously associated with the induction of IFNs6.

In contrast to these changes, older adult NEC cultures infected with SARS-CoV-2 showed decreased thickness and integrity, accompanied by an augmented mobilization of basal cells and the extrusion from the apical side of cells that can potentially produce infective viruses. Older adult NECs were characterized by the expansion of a specific basal cell population, the basaloid-like cells, that express integrin β6 (ITGB6). The ITGB6-positive cells have been previously associated with wound healing and fibrosis7, and ITGB6 expression was confirmed at the protein level in the basaloid-like cell population, together with other pro-fibrotic and epithelial–mesenchymal transition markers, often associated with altered repair. The authors speculate that this basaloid-like cell population might be involved in favoring the severe disease that characterizes older individuals with COVID-19.

Finally, to prove that the emergence of the different subtypes of NECs in pediatric or older adult cultures differentially affects repair, the authors used a wound-healing assay that stimulate epithelial repair pathways. Whereas uninfected ALI cultures, across age groups, did not show any difference in their repair capacity, after SARS-CoV-2 infection, older adult cultures showed a faster wound-healing rate that correlated with increased NEC infection, as well as augmented infectious viral particle production compared to pediatric NECs.

The authors proposed that these differences are due to a more pro-repair and pro-fibrotic cellular landscape of older adult NECs after infection with SARS-CoV-2. A non–mutually exclusive explanation for the delayed repair in the pediatric ALI culture is the increased activity of IFNs, previously identified by the authors. Data from the upper and lower airways of individuals infected with SARS-CoV-2 who have severe disease suggest that IFN signaling can decrease cell proliferation and increase apoptotic cell death of the epithelial layer5. That IFN signaling may delay repair in the airways has also been shown in two independent mouse models of lung viral encounter8,9. Both papers support a major role for type III IFNs in driving these detrimental roles. Indeed, individuals with mild or severe COVID-19 present unique patterns of IFNs and ISGs5. Which specific IFNs are produced by the NECs across ages remains an open question that will require further investigation. One can speculate that the presence of pediatric NEC populations that produce strong IFN responses on the one side limits viral spread, but on the other side delays repair functions. It will be important to assess in the future whether other stromal or immune factors may compensate in vivo for the reduced intrinsic repair capacity of pediatric NECs, explaining the overall advantage of children during the SARS-CoV-2 infection. Regarding this point, the authors also found that publicly available scRNA-seq datasets spanning the lower and upper airways of COVID-19 patients across ages 0–90 years showed the presence of the goblet inflammatory cells and basaloid-like populations identified in their in vitro cultures. Nevertheless, the distribution across ages of these populations was slightly different from that in the in vitro cultures. These discrepancies may be due to differences present in the upper and lower airways that were analyzed as a unique dataset. Alternatively, other factors that alter the proportions and differentiation of these cell populations may exist in vivo. Similarly, the older adult population has been characterized for the presence of autoreactive antibodies directed against IFNs10. These antibodies have been associated with severe COVID-19 in 2–12% of the overall adult population11 but in up to 20% of older adults10. Whether inhibition of IFN signaling by these autoantibodies may affect repair in the context of SARS-CoV-2 infection remains to be investigated.

Of note, all the experiments by Woodall et al.2 were performed using an early-lineage SARS-CoV-2 isolate. This leaves unanswered the important question of whether more recent variants of concern (VOCs) of SARS-CoV-2 may differentially affect NEC responses across age groups. Beyond a high escape capacity from antibodies elicited against previous SARS-CoV-2 lineages, the newest VOCs have acquired changes in their capacity to enter the cells and to inhibit the innate immune signaling cascades that lead to virus recognition and antiviral responses12. These differences warrant future studies to evaluate whether the same cellular and transcriptional processes described for an ancestral isolate of SARS-CoV-2 also apply to newer VOCs.

Overall, the data presented by Woodall et al.2 reinforce the concept of intrinsic immunity and open the door to future studies aimed at better understanding epithelial cell intrinsic and extrinsic factors that regulate antiviral responses along the respiratory tract and across age groups.