Human alphacoronavirus replication and innate immune induction in airway culture systems

Compared with lethal betacoronaviruses, there is limited knowledge of how human alphacoronaviruses HCoV-NL63 (NL63) and HCoV-229E (229E) interact with host innate immune responses. We compared NL63 and 229E infections in human lung-derived cell lines, A549^ACE2 and MRC-5, and primary nasal epithelial air-liquid interface (ALI) cultures. We measured the infection rates and viral replication kinetics. Additionally, we assessed the activation of three dsRNA-induced pathways, interferon (IFN) production and signaling, oligoadenylate synthetase-ribonuclease L (OAS/RNase L), and protein kinase R (PKR), following infection with each virus. Although both 229E and NL63 replicated efficiently in nasal ALI cultures, NL63 replicated minimally in A549^ACE2 or MRC-5. In lung-derived cell lines, significant IFN mRNA induction as well as PKR activation was observed during NL63 but not during 229E infection. In contrast, in nasal ALI cultures, significant induction of both the IFN and PKR pathways was observed during 229E and NL63 infection. Notably, there was no evidence of RNase L activation during infection with either virus in cell lines or nasal ALI cultures. Infection with a recombinant 229E expressing an inactivated nsp15 endoribonuclease U (EndoU) led to increased dsRNA levels, stronger induction of all three antiviral pathways, and attenuation of replication relative to wild-type 229E. This indicates that 229E nsp15 EndoU regulates host dsRNA responses, as shown previously for porcine epidemic diarrhea virus (PEDV) and pathogenic betacoronaviruses. These findings demonstrate that NL63 and 229E differentially modulate host dsRNA-induced innate immune pathways and highlight the critical role of nsp15 EndoU in suppressing antiviral responses to facilitate efficient viral replication.

Seasonal human coronaviruses (HCoVs) are the causative agents of more than 15% of common cold cases each year. However, compared with more virulent HCoVs such as SARS-CoV-2, there has been limited research on these viruses. We compared the replication of HCoV-NL63 (NL63) and HCoV-229E (229E). Additionally, we examined their interactions with interferon signaling and related innate immune pathways in lung-derived cell lines and primary nasal epithelial cultures. 229E replicates efficiently in each of these culture systems, with significant dsRNA-induced pathway induction only in nasal cells. In contrast, NL63 replicates efficiently only in nasal cell cultures but induces innate immune pathways in all three culture systems. Moreover, the conserved CoV innate immune antagonist endoribonuclease U aids in evading these responses in 229E infection. This study expands our understanding of common-cold HCoV-host interactions and provides insight into differences between seasonal and lethal HCoVs.