Fig. 1: Intrinsic ISGs expression analysis in embryonic stem cells identifies VAMP5 as a host restriction factor for SARS-CoV-2 infection.

a Representative heatmap of ISGs profiles of endoderm (END, n = 3 biological replicates), mesoderm (MES, n = 3 biological replicates) and ectoderm (ECT, n = 3 biological replicates). b Scatterplot of ISGs-wise log₂ fold change from this study analysis. c Venn diagram of the top 16 host factors significantly enriched in hESCs and MES but lowly in END and ECT from our own RNAseq data. Selected: selecting 24 ISGs enriched in MES compared to END and ECT. d Screen the influence of top 16 ISGs from (b) by siRNA in hESCs on SARS-CoV-2 replication (MOI = 0.05, 24 hpi). e Representative western blot image of VAMP5 expression in hESCs, END, MES and ECT. The results are representative of three independent experiments. f–k VAMP5 WT and KO (n = 2 cell lines) hESCs infected with SARS-CoV-2 (MOI = 0.05, 24hpi) WT (f) and variants of Alpha (g), Delta (h), Gamma (i), Kappa (j) and Omicron (k) with viral infection in cells at MOI of 1 for 24h. Virus strain is also indicated in the figure. ESC, embryonic stem cells; MES, mesoderm; END, endoderm; ECT, ectoderm; VAMP5, vesicle-associated membrane protein 5; KO, knock-out; OE, overexpression; WT, wild-type; ACE2, Angiotensin-converting enzyme 2. Data are represented as mean ± SEM, n = 3 biological replicates in each group. Student’s two tailed t test was used. *p < 0.05, **p < 0.01, ***p < 0.001.