Comparison of SARS-CoV-2 variants in primary human nasal cultures indicates Delta as most cytopathic and Omicron as fastest replicating

The ongoing SARS-CoV-2 pandemic has been marked with emerging viral variants, some of which were designated as variants of concern (VOCs) due to their selection and rapid circulation in the human population. Here we elucidate functional features of each VOC linked to variations in growth during infection. Patient-derived primary nasal cultures grown at air-liquid-interface (ALI) were used to model upper-respiratory infection, and human lung epithelial cell lines used to model lower-respiratory infection. All VOCs replicated to higher titers than the ancestral virus, suggesting a selection for replication efficiency. In primary nasal ALI cultures, Omicron replicated to the highest titers at early time points, followed by Delta, paralleling comparative studies of patient samples. All SARS-CoV-2 viruses entered the cell primarily via a transmembrane serine protease 2 (TMPRSS2)-dependent pathway, and Omicron was more likely to use an endosomal route of entry. All VOCs overcame dsRNA-activated cellular responses including interferon signaling, oligoadenylate ribonuclease L (OAS-RNase L) degradation and protein kinase R (PKR) activation. Infections in nasal ALI resulted in damage to nasal cells such as a compromise of cell-barrier integrity and loss of nasal cilia and ciliary beating function, especially with Delta infections. Overall, Omicron replication was optimized for growth in the upper-respiratory system and least-favorable in the lower-respiratory cell line; and Delta was the most cytopathic for both upper and lower respiratory cells. Our findings highlight the functional differences among VOCs and illuminate distinct mechanisms of pathogenesis in infected individuals. SIGNIFICANCE STATEMENT: In a comparative analysis of infections by SARS-CoV-2 ancestral virus and variants of concern including Alpha, Beta, Delta and Omicron, we found that variants are selected for efficiency in replication. In infections of patient-derived primary nasal cultures grown at air-liquid-interface (ALI) to model upper-respiratory infection, we show that Omicron reached highest titers at early time points, a finding that is confirmed by parallel studies of patient sampling. In both primary nasal cells and lower-respiratory cell lines infections by Delta are most damaging to the cells as indicated by syncytia formation and loss of nasal ciliary function.