Abstract
Background/AimHepatitis 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.MethodPutative recombinant sequences were identified with the use of SimPlot program. Recombination events were confirmed by bootscaning, using putative recombinant sequence as a query.ResultsTwo crossing over events were identified in the E1/E2 structural region of an intra-typic (1a/1c) recombinant strain.ConclusionOnly 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.
Highlights
Hepatitis C virus (HCV) is estimated to infect 170 million people worldwide and creates a huge disease burden from chronic, progressive liver disease [1]
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
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
Summary
Hepatitis C virus (HCV) is estimated to infect 170 million people worldwide and creates a huge disease burden from chronic, progressive liver disease [1]. HCV has become a major cause of liver cancer and one of the commonest indications of liver transplantation [2,3]. HCV has been classified in the family Flaviviridae, it differs from other members of the family in many details of its genome organization from the original (vector-borne) members of the family [1]. Like most RNA viruses, HCV circulates in vivo as a complex population of different but closely related viral variants, commonly referred to as a quasispecies [4,5,6,7]. Virology Journal 2006, 3:53 Name Genotype Accession number H77 HCV-H COLONEL HC-J1 HCV-1HCV-PT
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