Evidence of structural genomic region recombination in Hepatitis C virus

Abstract

Background/aim: Hepatitis C virus (HCV) has been the subject of intense research and clinical investigation as its major role in human disease has emerged. Although homologous recombination has been demonstrated in many members of the family Flaviviridae, to which HCV belongs, there have been few studies reporting recombination on natural populations of HCV. Recombination break-points have been identified in non structural proteins of the HCV genome. Given the implications that recombination has for RNA virus evolution, it is clearly important to determine the extent to which recombination plays a role in HCV evolution. In order to gain insight into these matters, we have performed a phylogenetic analysis of 89 full-length HCV strains from all types and sub-types, isolated all over the world, in order to detect possible recombination events.

Method: Putative recombinant sequences were identified with the use of SimPlot program. Recombination events were confirmed by bootscaning, using putative recombinant sequence as a query.

Results: Two crossing over events were identified in the E1/E2 structural region of an intra-typic (1a/1c) recombinant strain.

Conclusion: Only one of 89 full-length strains studied resulted to be a recombinant HCV strain, revealing that homologous recombination does not play an extensive roll in HCV evolution. Nevertheless, this mechanism can not be denied as a source for generating genetic diversity in natural populations of HCV, since a new intra-typic recombinant strain was found. Moreover, the recombination break-points were found in the structural region of the HCV genome.

Figure 1

Phylogenetic profiles of HCV sequences. In (A) results from SimPlot analysis are shown. The y-axis gives the percentage of identity within a sliding window of 500 bp wide centered on the position plotted, with a step size between plots of 20 bp. Comparison of HCV strain D10749 with strains AF511949 (sub-type 1A), AY651061 (sub-type 1C) and D45172 (sub-type 2B) is shown. The red vertical lines show the recombination points at positions 1407 and 2050. In (B) a schematic representation of the HCV genome is shown. Structural and non-structural regions of the genome are indicated on the top of the figure. Nucleotide positions are shown by numbers on the upper part of the scheme. Amino acid codon positions are shown by numbers in the lower part of the scheme. No coding regions at the 5' and 3' of the genome are shown by a line. Coding region is shown by a yellow rectangle, showing the corresponding proteins by name. Recombination points are shown by red arrows.

Figure 2

Bootscanning of HCV sequences. The y-axis gives the percentage of permutated trees using a sliding window of 500 bp wide centered on the position plotted, with a step size between plots of 20 bp. The rest same as Fig.1A.

Figure 3

Profiles of synonymous and nonsynonymous distances of parental-like versus recombinant. Numbers at the left side of the figure denote distance. Numbers at the bottom of the figure show codon position in the mid point of the window. Comparison AF511949-D10749 is shown in blue and light red for synonymous and nonsynonymous substitutions, respectively. Comparison AY651061-D10749 is shown in yellow and light blue for synonymous and nonsynonymous substitutions, respectively. Vertical red lines show recombination break-points positions.