Extended Data Fig. 1: Construction and characterization of SARS-CoV-2s with variant spikes.

a, Diagram of engineered variant spike mutations. Mutations from variant spikes were engineered into isolate USA-WA1/2020. Mutations and deletions are indicated in red and by dotted lines, respectively. Nucleotide and amino acid positions are also indicated. Different regions of SARS-CoV-2 genome are indicated: L (leader sequence), ORF (open reading frame), RBD (receptor binding domain), S (spike glycoprotein), S1 (N-terminal furin cleavage fragment of S), S2 (C-terminal furin cleavage fragment of S), E (envelope protein), M (membrane protein), N (nucleoprotein), and UTR (untranslated region). b, Plaque morphologies of recombinant SARS-CoV-2s. Plaque assays were performed on Vero E6 cells in six-well plates. c, Comparison of viral genomic RNA-to-PFU ratios (log₁₀[RNA/PFU]) of recombinant SARS-CoV-2s. The genomic RNA and PFU of individual virus stocks were measured by RT–qPCR and plaque assay, respectively. The RNA/PFU ratios were calculated to determine specific infectivities. Dots represent individual biological replicates from four aliquots of viruses (n = 4, one experiment). Bars and error bars show means with 95% confidence intervals. A non-parametric two-tailed Mann–Whitney test was used to determine the significance of differences between USA-WA1/2020 and variant viruses. P values were adjusted using the Bonferroni correction to account for multiple comparisons. Differences were considered significant if P < 0.05; n.s., no statistical difference.