Fig. 4: Replication kinetics of SARS-CoV-2 spike recombinants in nasal epithelium.
From: Phenotypic evolution of SARS-CoV-2 spike during the COVID-19 pandemic
a, Replication kinetics of SARS-CoV-2 viruses in hNECs. For a and e, the light grey area indicates the replication curve of S:B.1 used as reference virus in all experiments. b, Heat map of relative viral loads to S:B.1 for all SARS-CoV-2 recombinant viruses expressed as log2(fold change) at each indicated timepoint. c, Replication kinetics of S:EG.5.1 and S:BA.2.86 compared to the parental S:BA.2 (dashed line). d, Replication kinetics of S:EG.5.1 and S:BA.2.86 compared to their corresponding wild-type clinical isolates (dashed line). e, Replication kinetics of pre-Omicron and post-Omicron spike recombinant viruses in reconstituted hBEC. For a, c, d and e, the copy numbers of viral RNA in the culture supernatant of infected hNECs were quantified by RT–qPCR at the indicated timepoints. Data are mean ± s.e.m.; n = 6. Statistical significance of differences between S:B.1 (a), S:BA.2 (c) or clinical isolates (d) and the spike recombinant viruses across timepoints was determined using one-way ANOVA with multiple comparisons between area under the curve of the different recombinant viruses using the Holm–SĂdák post hoc test. The calculated P values are indicated in the figures. f, Heat map of relative viral loads to S:B.1 for all recombinant viruses expressed as log2(fold change) at each indicated timepoint. For b and f, statistical significance of differences between S:B.1 and the other spike-bearing viruses at each timepoint was determined using one-sample t-test. *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001, ****P ≤ 0.0001. g, Photomicrographs showing RNA in situ hybridization of SARS-CoV-2 spike in hNECs infected with the indicated viruses. Sloughing of the top layers of the epithelium is evident at 4 dpi in cultures infected with post-Omicron viruses. h, Quantification of cell sloughing (n = 3) in hNECs using whole-section software-assisted imaging. i, Photomicrographs of cleaved caspase-3 detected in hNECs infected with the indicated viruses at 4 dpi. Apoptotic cells with cleaved caspase-3 are stained in brown. j, Quantification of caspase-3 cleavage in hNECs (n = 3). For h and j, statistical significance was determined using one-way ANOVA with multiple comparisons between S:B.1 and other viruses using the Holm–ŠĂdák post hoc test.
