Fig. 5: Determinants of SARS-CoV-2 nasal tropism.
From: Phenotypic evolution of SARS-CoV-2 spike during the COVID-19 pandemic
a, Ribbon diagram of the molecular structure of spike (based on PDB:6VSB, one RBD ‘up’ conformation98,99,100) illustrating the location of the stated residues, colour-coded as shown in the key. The approximate location of the viral membrane is shown as a dashed line. b, Schematic representation of the spike recombinant mutants used in this study. S:BA.1 spike amino acid residues in the RBD, RBM, S1/S2 junction and S2 domain have been reverted to the corresponding S:B.1 residues (top) or inserted in the S:B.1 backbone (bottom) in combination or individually as indicated. c,d, Replication kinetics of the SARS-CoV-2 S:BA.1 (c) and S:B.1 wt (d) spike mutants in hNECs. S:B.1 (indicated by light grey area) and S:BA.1 (dashed purple line) viruses were used as reference viruses. 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. of 3 biological replicates. e,f, Replication kinetics of the SARS-CoV-2 S:BA.1 (e) and S:B.1 wt (f) spike mutants in Calu-3 cells. The copy numbers of viral RNA in the culture supernatant of infected Calu-3 cells were quantified by RT–qPCR at the indicated timepoints. g,h, Live virus-based fusion assay in AAT-GFP10/AAT-GFP11 cells. The fusion activity of SARS-CoV-2 S:BA.1 (g) and S:B.1 wt (h) spike mutants was measured over time and expressed as a percentage of maximum fluorescence over S:B.1. The light grey area indicates S:B.1, while the purple dashed line represents S:BA.1; both recombinant viruses were used as reference viruses in all experiments. In e–h, data are mean ± s.e.m. of 3 independent experiments each performed in triplicate (n = 3). For c–h, statistical significance of differences between S:B.1 and the mutant spike virus panel across timepoints was determined using one-way ANOVA with multiple comparisons between area under the curve of the different viruses and S:B.1 using the Holm–Šídák post hoc test. Mutants were also compared to S:BA.1+WT-13 (c) or S:B.1+BA.1-13 (d). The calculated P values are indicated in the figure.
