Whole genome sequencing of hepatitis B virus genotypes E and A in Zambia reveals limited viral diversity in HIV coinfection

Background The molecular characteristics of hepatitis B virus (HBV) in Africa, including the impact of HIV coinfection, are poorly understood. Methods We performed whole genome sequencing (WGS) on biospecimens collected prior to antiviral therapy in a well-characterized cohort of adults with HBV in Zambia, enriched for HIV coinfection (HBV/HIV). We assessed the frequency of basal core promoter (BCP) and precore variants, substitution frequencies, and the ratio of nonsynonymous to synonymous substitutions (dN/dS ratios), a surrogate for selection pressure. Results Among 215 participants (median age, 33 years, 36% e antigen [HBeAg]-positive, 35% with HBV/HIV), 114 (53.0%) had viral genotype E (gtE) and 101 (47.0%) had genotype A (gtA), subgenotype 1. BCP and precore variants, associated with HBeAg-negativity, were more common with increased age, in the absence of HIV, and with gtE. Distinct from gtA, gtE had dN/dS ratios that were increased in the core versus polymerase region. Low dN/dS ratios were observed in HBV/HIV, especially at the lowest CD4 T cell frequencies. Sequences from acute HBV infection as well as from 5 participants with chronic HBV/HIV who cleared hepatitis B surface antigen early during tenofovir-based antiretroviral therapy showed remarkably low dN/dS ratios. Conclusions HBV gtE exhibited distinct substitution patterns compared to gtA, and HBV/HIV was associated with reduced HBV sequence diversity, consistent with impaired immune pressure.