Fig. 1: Enhanced replication of Omicron-BA.1 in nasal but not bronchial epithelial cell cultures.
From: The spike gene is a major determinant for the SARS-CoV-2 Omicron-BA.1 phenotype
a Genome sequences were compared to the SARS-CoV-2D614G WT virus and lineage-defining mutations (LDM) are depicted. The D614G mutation is highlighted in red, while the mutations highlighted in orange are either present in both Delta and Omicron, or in Omicron, S-Omicron, RBD-Omicron, Delta, and S-Delta, but not in SARS-CoV-2D614G. b The plaque sizes of viruses in 6-well plates 2 dpi. Sizes of 10 plaques/wells from one biological replicate were measured in Adobe Illustrator. Data are presented as mean+/−SD. Statistical significance was determined using ordinary one-way Anova and p-values were adjusted using Tukey’s multiple-comparison test; *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. Statistical significance of the differences of each virus vs. SARS-CoV-2D614G WT virus are demarcated with the red asterisks, whereas the black asterisks indicate the comparison of the Omicron spike subdomain clones to Omicron. c, d Human nasal (NEC) (n = 3 donors) and bronchial epithelial cell (BEC) (n = 3) cultures were infected with 104 TCID50 of the SARS-CoV-2 variants from the apical side and incubated at 33 °C (NECs) or 37 °C (BECs) for 1 h. Virus titers were assessed by TCID50 assays on VeroE6/TMPRSS2 cells. The graph represents the titers obtained from three donors (mean+/−SD) from one biological replicate. Statistical significance was determined using two-way ANOVA and p-values were adjusted using Tukey’s multiple-comparison test; *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. e–g NECs (n = 3), BECs (n = 3), or PCLS (n = 3) were infected with virus mixtures at a 1:1 ratio based on genome equivalents (GE) calculated by qPCR. Apical washes were collected at 2 and 6 dpi for the NECs and BECs and 2 dpi for PCLS. RNA was extracted from apical washes and sequenced on the MinION platform (Oxford Nanopore Technologies). Virus ratios were calculated for each donor based on the mean frequency of unique LDM mutations for each virus present in the mixture (for more details: Supplementary Fig. 1). Values shown represent the mean ratio/donor (circles) and the mean ratio/time point (bars) for each virus mixture (mean+/−SD). Each data point represents one biological replicate. Source data for Fig. 1 are provided as a Source Data file 1.
