Fig. 1: Study design and Viral-Track method for identification and characterization of HBV infection in scRNA-Seq data.

A Schematic representation of the experimental strategy. B Results of doublet and singlet cells by scDblFinder. C The characteristic variance diagram was drawn for 4000 genes with significant cell-cell variations. D HBV transcripts identification and quality control metrics: (left panel) overall mapping quality of sequencing reads, including both host and viral transcripts; (middle panel). After removing human sequences, the percentage of mapped viral contigs and the entropy-based sequence complexity (right panel). E A viral genome coverage map of 5′ scRNAseq data from Viral-Track analysis shows the HBV gene locations from the NCBI database (left panel), and the HBV genome coverage map of 5′ scRNAseq data of validation cohort 1 (right panel). F Histogram shows the percentage (%) of infected and non-infected cells in each patient’s tumor tissue. G HBV reads in HCC tissues were detected by the Viral-Track method (left panel), and a pie chart of viral reads in each infected patient in the HBV tumour (right panel). H Uniform Manifold Approximation and Projection (UMAP) plot of the liver HBV data. Infected cells are red, and non-infected cells are green (left panel)-pie chart of infected and non-infected cells in HBV tumor (right panel). I The ratio of HBV-infected cells relative to the total cell populations defines the HBV transcript enrichment factor in each cell type. J Histogram of each analysed patient’s infected immune and non-immune cells in tumor tissue. See also Supplementary Figs. 1 and 2.