Extended Data Fig. 9: The spike N501Y substitution benefits viral infection of hamster upper airways.

a, Design of the hamster infection kinetic studies. The wt, N501Y and Alpha-spike viruses were intranasally inoculated into hamsters at a titer of 10⁴ PFU per hamster. Nine hamsters were utilized for the initial infection in each group. At 2 days post-infection, 4 hamsters were sacrificed for organ collections. The nasal washes of the hamsters were collected on days 1, 2, 3 and 5 post-infection or before sacrifice. b, Weight change in hamsters following infection by the N501Y (n = 5) and Alpha-spike (n = 5) mutants compared to the wt (n = 5). MOCK group (n = 4) served as the negative (uninfected) control. The body weights were measured form 1–7 days post-infection. The weight loss data are shown as mean ± standard deviation and statistically analyzed using two-factor analysis of variance (ANOVA) with Tukey’s post hoc test. No significant differences were seen between the N501Y/Alpha-spike and wt groups. c–h, The infection of N501Y and Alpha-spike mutants compared to the wt in the nasal washes (c–e) collected 1 (n = 9), 2 (n = 4), 3 (n = 5), or 5 (n = 5) days post-infection and in the organs (f–h) 2 days (n = 4) post-infection. The amounts of infectious virus (c, f) and genomic RNA (d, g) were quantified by plaque assay and RT–qPCR, respectively. The genomic RNA:PFU ratio (e, h) was calculated as an indication of virion infectivity. The values in the graph represent the mean ± standard error of the mean.A non-parametric two-tailed Mann-Whitney test was used to determine significant differences. P values were adjusted using the Bonferroni correction to account for multiple comparisons. Differences were considered significant if p<0.025.