The evolutionary patterns of hepatitis C virus subtype 2a and 6a isolates linked to an outbreak in China in 2012

Abstract

An HCV outbreak occurred in 2012 in China, affecting hundreds of patients. We characterized HCV subtype 2a and 6a sequences from 60 and 102 patients, respectively, and co-analyzed them with 82 local controls and 103 calibrating references. The close grouping of the patients׳ sequences contrasted sharply with the diversity of local controls. Scaled by the calibrating references, the emergence of patients׳ isolates was estimated at 2-5 years before sampling. In contrast, the controls intermingled with the calibrating references that were much older. For both subtypes, the major and minor clusters could be defined, with the closeness to indicate linked transmission.

Conclusion: HCV sequences from the study patients grouped into three subtype 2a and two subtype 6a clusters, in addition to three 6a solitary branches, representing descendants of eight earlier strains that were distinct and otherwise sporadic. Due to iatrogenic transmission through reusing needles, five strains were highly selected and preferentially spread.

Keywords: Evolution; Genetic sequence; HCV; Outbreak.

Figure 1

Six MCC trees estimated for subtype 2a sequences in the entire E1 and partial NS5A regions, corresponding to the nucleotides numbered 739–1490 and 6822–7664 in the H77 genome, using the exponential, lognormal and strict clock models. Each tree includes three groups of sequences: 60 from the study patients (blue), 24 local controls (red), and 32 calibrating references (green). Branch length represents the evolutionary ages measured by the grids corresponding to a reverse timescale at the base of each tree, starting from the sampling time (right) to the past (left). Three clusters, a, b, and c, indicate the temporarily classified three subtype 2a lineages determined from the patients exposed in this outbreak. Prior to these three clusters, a common ancestor is indicated with a magenta circle.

Figure 2

The tMRCAs estimated for three clusters (a, b, and c) of subtype 2a sequences and two clusters (L and S) of subtype 6a sequences determined from the study patients and their common ancestors (ANCES) using three clock models, exponential (red), lognormal (green), and strict (yellow). The error bars indicate the 95% highest posterior density credible intervals.

Figure 3

Six MCC trees estimated for subtype 6a sequences in the entire E1 and partial NS5A regions, corresponding to the nucleotides numbered 739–1490 and 6822–7664 in the H77 genome, using the exponential, lognormal and strict models. Each tree contains three groups of sequences: 102 from the study patients (blue or cyan), 58 from the local controls (red), and 71 calibrating references. The latter includes three subgroups: 46 from China (green), 15 from Vietnam (purple), and 10 from Canada (yellow). As a whole, these sequences are divided into four subsets: I, II, III and IV, and many other lineages. Into subset III are classified all the sequences determined from the study patients, of which the majority are divided into clusters S and L. Within cluster L, 3–4 internal nodes are marked, each with a magenta circle and a number, which indicate the ages of the putative earlier 6a strains that had been serially transmitted among patients, likely via the iatrogenic network.