Dominant role of host selective pressure in driving hepatitis C virus evolution in perinatal infection

Abstract

The dynamics of the genetic diversification of hepatitis C virus (HCV) populations was addressed in perinatal infection. Clonal sequences of hypervariable region 1 of the putative E2 envelope protein of HCV were obtained from four HCV-infected newborns (sequential samples spanning a period of 6 to 13 months after birth) and from their mothers (all samples collected at delivery). The data show that the variants detected between birth and the third month of life in samples from the four newborns were present in the HCV populations of their mothers at delivery. In the newborns, a unique viral variant (or a small group of closely related variants) remained stable for weeks despite active viral replication. Diversification of the intrahost HCV population was observed 6 to 13 months after birth and was substantially higher in two of the four subjects, as documented by the intersample genetic distance (GD) (P = 0.007). Importantly, a significant correlation between increasing GD and high values for the intersample K(a)/K(s) ratio (the ratio between anoffymous and synonymous substitutions; an index of the action of selective forces) was observed, as documented by the increase of both parameters over time (P = 0.01). These data argue for a dominant role of positive selection for amino acid changes in driving the pattern of genetic diversification of HCV populations, indicate that the intrahost evolution of HCV populations is compatible with a Darwinian model system, and may have implications in the designing of future antiviral strategies.

FIG. 1

HCV RNA copy numbers in plasma fractions obtained by sucrose density gradient. Plasma samples from two transmitter (C and D; subjects m3 and m4 of this work) and two nontransmitter (A and B) mothers were collected at delivery. After collection of the fractions, HCV RNA molecules were quantified in each fraction by quantitative cRT-PCR.

FIG. 2

Deduced amino acid sequence alignments of HVR-1 from four newborns (f1 to f4) and their mothers (m1 to m4; samples were collected at delivery). The initial nucleotide (∗) and amino acid (°) sequences for each mother-infant pair represent the reference sequences. The serial time points are indicated by a number following the subject's identification corresponding to the month after birth; diverging clonal sequences at each time point are indicated by final letters. The sequences from each infant and from the corresponding mother are aligned with the sequence from the first sample. Dashes indicate identity with the reference sequence. Shading indicates amino acids that differ from the reference sequence.

FIG. 3

Phylogenetic reconstruction of the evolutionary relationships within the four HCV-infected infants and their mothers. The deduced amino acid sequences of all clonal sequences were analyzed using the Kimura's formula distance matrix fed into a neighbor-joining tree construction algorithm. Branch lengths are drawn to scale. Different samples are indicated by numbers (as in Fig. 2) and colors: red, mothers' sequences (delivery); black, green, blue, and pink, sequential samples from infants.