HBV deletion mutants complicate the progression of viral liver diseases.This study analyzed HBV sequences from 103 patients including 51 whole genomes and 70 preS clones.Among three hotspots we observed, including core, preS, and BCP regions, most deletions in core and BCP were out of frame, whereas almost all those in preS were in frame.The majority of deletions interrupted epitopes of viral proteins, suggesting possible mechanism for virus to evade immune surveillance.Furthermore, logistic regression analysis of whole genomes showed that among various clinical issues, only antiviral medication appeared to affect the accumulation of deletion mutants (OR =6.81, 95% Cl 1.296~35.817, P=0.023).