Distinct hepatitis B virus dynamics in the immunotolerant and early immunoclearance phases

Abstract

Little is known about hepatitis B virus (HBV) diversity changes within a host during the immunotolerant phase of chronic HBV infection. Such knowledge, nevertheless, may help in understanding how host immunity and HBV interact at the early stage of infection. In this study, serial serum samples were collected from a long-term (>17 years) follow-up cohort of seven patients, and multiple copies of the full-length viral genome from serially sampled sera were recovered and analyzed. Viral genetic diversity was positively correlated with host immunity, represented by levels of alanine aminotransferase (ALT), but was negatively correlated with the viral copy number. During the immunotolerant phase, when the host immunity was feeble (ALT < 20 U/liter), viral nucleotide diversity decreased while copy numbers increased. Rates of evolutionary change derived for different patients were in a very narrow range (1.6 x 10(-5) to 5.4 x 10(-5)/site/year). As the disease progressed toward the immunoclearance phase (ALT > 20 U/liter), viral diversity increased but copy numbers decreased. Evolutionary rates varied among patients in accordance with their levels of ALT, ranging from 9.6 x 10(-6) to 3.2 x 10(-4)/site/year. More than half (19/32 sites) of positively selected sites resided in immune epitopes, suggesting their possible role in host immunity. Our results demonstrate that host immunity is a dominant factor in HBV evolution. Different selective forces, including immune-mediated positive selection and virus-mediated negative selection, operate in tandem in shaping viral population dynamics within a host.

FIG. 1.

Profiles of ALT levels (shaded region; left y axis) and nucleotide diversity values (θ) (red line; right y axis) derived for different ages (x axis) of the seven patients in this study.

FIG. 2.

Correlations of average ALT levels and nucleotide diversity values (θ) derived from the entire HBV genome (P = 0.002; tau = 0.604; Kendall's rank sum correlation) (A), nucleotide diversity values for nonsynonymous sites (θ_A) of nonoverlapping regions (P = 0.002; tau = 0.604) (B), and nucleotide diversity values for synonymous sites (θ_S) of nonoverlapping regions (P = 0.101; tau = 0.341) (C).

FIG. 3.

Negative correlation between HBV DNA level (log₁₀ HBV DNA/ml) and nucleotide diversity (P = 0.016; tau = −0.381; Kendall's rank sum correlation).