The genetic diversity and evolutionary history of hepatitis C virus in Vietnam

Abstract

Vietnam has a unique history in association with foreign countries, which may have resulted in multiple introductions of the alien HCV strains to mix with those indigenous ones. In this study, we characterized the HCV sequences in Core-E1 and NS5B regions from 236 Vietnamese individuals. We identified multiple HCV lineages; 6a, 6 e, 6h, 6k, 6l, 6 o, 6p, and two novel variants may represent the indigenous strains; 1a was probably introduced from the US; 1b and 2a possibly originated in East Asia; while 2i, 2j, and 2m were likely brought by French explorers. We inferred the evolutionary history for four major subtypes: 1a, 1b, 6a, and 6 e. The obtained Bayesian Skyline Plots (BSPs) consistently showed the rapid HCV population growth from 1955 to 1963 until 1984 or after, corresponding to the era of the Vietnam War. We also estimated HCV growth rates and reconstructed phylogeographic trees for comparing subtypes 1a, 1b, and HCV-2.

Keywords: BEAST; Evolution; Genotype; HCV; Sequence; Vietnam.

Figure 1

A circular form of phylogenetic tree based on the Core-E1 sequences from 236 study subjects co-analyzed with 13 references for 13 assigned subtypes. Different subtypes are shown in different colors and indicated on the upper right corner of the tree, while clusters in black show minor subtypes with their labels post fixed. All references are shown in purple with their format as: subtype_isolate ID_GenBank number. Close to the internal nodes of each cluster, two digit numbers show the values of bootstrap analysis, of which only those ≥81% are presented. In the center of the tree, a pie chart with its neighboring percentage shows the proportions of the different subtypes of the 236 isolates.

Figure 2

A circle form of phylogenetic tree based on the NS5B sequences from 236 study subjects co-analyzed with 13 references for 13 assigned subtypes. Except that no significant bootstrap supports were shown and the central pie chart was surrounded with the number of sequences each lineage possesses, all other indications are the same as described in Figure 1.

Figure 3

Bayesian Skyline Plots. Four diagrams represent four subtypes 1a, 1b, 6a, 6e. The solid line represents the effective population size through time. The purple area represents the 95% highest posterior density confidence interval. The vertical ruler on the left (Y axis) measures the effective population size while the horizontal scale on the bottom measures time from the present (right) to the past (left).

Figure 4

HCV growth rates. Four simplified diagrams correspond to four BSPs. In each diagram, the median growth curve is shown in red, in which a dot represents a sampling time point. This curve is measured by the vertical ruler for population size on the left and the horizontal time scale on the bottom. The time course of HCV growth is divided into two periods: rapid growth (yellow area) and continuous growth (grey area). For different subtypes, the delimitation of these two periods is dissimilar. Based on the median population sizes exported from the four BSPs within these two periods, simple linear regression analyses were performed and the regression lines are shown separately and appear in each diagram with two discontinued black lines. Accordingly, two regression functions and two R squares are provided in each diagram, in which the slopes indicate the growth rates. In each diagram, a blue curve is also presented, reflecting the changes in the sum of R-squares generated after sliding two regression analyses through all sampling time points within a certain range. Measured by the vertical ruler on the right, this curve identifies the best time point at which the sum of R squares maximizes and two growth periods are thereby divided. Because the BSP for 6e has an additional period of constant population size prior to its rapid growth, three black and two blue curves are shown.