Evolutionary rate and genetic drift of hepatitis C virus are not correlated with the host immune response: studies of infected donor-recipient clusters

Abstract

Six donor-recipient clusters of hepatitis C virus (HCV)-infected individuals were studied. For five clusters the period of infection of the donor could be estimated, and for all six clusters the time of infection of the recipients from the donor via blood transfusion was also precisely known. Detailed phylogenetic analyses were carried out to investigate the genomic evolution of the viral quasispecies within infected individuals in each cluster. The molecular clock analysis showed that HCV quasispecies within a patient are evolving at the same rate and that donors that have been infected for longer time tend to have a lower evolutionary rate. Phylogenetic analysis based on the split decomposition method revealed different evolutionary patterns in different donor-recipient clusters. Reactivity of antibody against the first hypervariable region (HVR1) of HCV in donor and recipient sera was evaluated and correlated to the calculated evolutionary rate. Results indicate that anti-HVR1 reactivity was related more to the overall level of humoral immune response of the host than to the HVR1 sequence itself, suggesting that the particular sequence of the HVR1 peptides is not the determinant of reactivity. Moreover, no correlation was found between the evolutionary rate or the heterogeneity of the viral quasispecies in the patients and the strength of the immune response to HVR1 epitopes. Rather, the results seem to imply that genetic drift is less dependent on immune pressure than on the rate of evolution and that the genetic drift of HCV is independent of the host immune pressure.

FIG. 1

Genotyping of six donor-recipient clusters. Unrooted NJ phylogenetic tree of the HCV 258-nt consensus E1/E2 region, including HVR1. Reference sequences of known genotypes are in boldface. Donors and recipients from the six clusters studied are indicated as follows: cluster number (c1 to c6), d for donor, r1 and r2 for recipients 1 and 2, and number of the most representative variants for each quasispecies. Bootstrap percentages of 1,000 bootstrap replicates are given along the appropriate branches. Bootstrap values <50% are not shown. All clades for which the bootstrap values are indicated were also supported by P values of <0.01 in the ML tree, except for the P < 0.05 indicated in the figure.

FIG. 2

SplitsTrees obtained with the split decomposition method for the six donor-recipient clusters studied, designated as for Fig. 1. Squares indicate the different clones sequenced in each patient.

FIG. 3

Correlation between the number of reactive HVR1 peptides from donors and recipients and level of reactivity by enzyme immunoassay expressed as S/CO. CO was defined as the mean of the optical density of eight negative control sera plus 6 SD. The equation of the regression line and the R² value are indicated.

FIG. 4

Evolutionary rate and HVR1 immune response. Absence of correlation between evolutionary rate and anti-HVR1 reactivity. Open squares correspond to the reactivity of patient plasma against autologous HVR1 peptides. When two different peptides derived from a patient's quasispecies, two data points are indicated. Diamonds correspond to the number of reactive peptides of each plasma against all extracluster HVR1 peptides divided by the number of peptides tested.