Whole genome deep sequencing analysis of viral quasispecies diversity and evolution in HBeAg seroconverters

•Deep sequencing of whole HBV genome uncovers the quasispecies changes in chronic hepatitis B patients.•The nucleotide diversity of HBV negatively correlates with viraemia during HBeAg loss/seroconversion.•Viral quasispecies diversity is greater in spontaneous HBeAg seroconverters before and after seroconversion than in treatment-naïve non-seroconverters.•Responders to IFN have greater viral quasispecies diversity than non-responders at 24 weeks after treatment.•The genome positions of non-synonymous intra-host single nucleotide variants (iSNVs) of HBV tend to be located at possible T cell epitopes.