Extended Data Fig. 1: Replication measurements of SARS-CoV-2 variants.
From: Evolution of enhanced innate immune suppression by SARS-CoV-2 Omicron subvariants
(a) Calu-3 and (b) Hela-ACE2 were infected with 1000 E copies/cell in the presence of DMSO (-), 25 μM E64d or 25 μM Camostat. Infection levels at 24hpi by nucleocapsid expression, one of two independent experiments shown. (c) Quantification of viral stocks used in Figs. 1 and 2 by TCID50/ml on Hela-ACE2. Each symbol indicates an independent virus stock. (d) Ratio of TCID50/ml over E copies/ml for virus stocks from (d). (e) TCID50/ml over E copies/ml of virus stocks measured on Hela-ACE2 or Calu-3 cells. (f) Western blot of purified SARS-CoV-2 virions, n = 2. (g) Calu-3 infection with 200 E copies/cell of Delta (yellow; Ο), BA.1 (blue; Ο), BA.2 (blue; Δ), BA.4 (purple; Ο) and BA.5 (purple; Δ). Viral replication at 2hpi. (h) Nsp12 copies/μg RNA or (i) Orf1a gRNA/GAPDH in cells from Fig. 1a. Viral replication measured by (j) E copies/μg RNA, (k) Nsp12 copies/μg RNA or (l) Orf1a gRNA/GAPDH in cells infected with 200 E copies/ml. (m) E copies/Nsp12 copies in Calu-3 cells. Nine replicates from three independent experiments shown. (n-p) Calu-3 cells were infected with 2000 E copies/cell. (n) Intracellular replication (Cell) and viral release (Supernatant) was determined by quantification of E copies at 24hpi. (o) Correlation graph of intracellular E copies and virus released into supernatant at 24hpi. (p) Nsp12 and E gene copies correlation in supernatants from (n). (q) Correlation of Nsp12 and E copies in apical washes from HAEs infected with BA.2 (blue) or BA.5 (purple) (samples from Fig. 4). (r) Infections levels measured by nucleocapsid expression in cells from (j). For a, b, h-l, r, one-way ANOVA with a Dunnett post-test was used. For a, b, groups were compared to DMSO. For e, paired Student’s t-Test was used. For h-m, groups were compared to BA.2 and colors indicate comparator (Delta, yellow; BA.1, blue; BA.4, purple; BA.5, pink). For m, n.s. is not significant at P > 0.05 for all comparisons. For o,p,q, simple linear regression was used. Triplicate measurements from representative experiments. Mean + /-SEM or individual datapoints shown. hpi, hours post infection. gRNA, genomic RNA.
