Protocol for quantifying hepatitis B virus transcript abundance and genomic segment distribution from single-cell RNA-seq

Hepatitis B virus (HBV) drives liver disease progression. Here, we present a protocol for sequencing single cells from HBV-infected liver tissue, producing two complementary outputs: quantitative per-cell HBV transcript abundance and a genome-wide map of read distribution. We describe steps for tissue dissociation and purification, single-cell RNA sequencing (RNA-seq), library construction, sequencing, and data processing. We then detail procedures for HBV expression and genome distribution analysis. This protocol enables detailed analysis of viral expression patterns and HBV-host interactions at single-cell resolution. For complete details on the use and execution of this protocol, please refer to Zhou et al.¹.