A Natural Intergenotypic Recombinant of Hepatitis C Virus Identified in St. Petersburg

Abstract

Hepatitis C virus (HCV) evolution is thought to proceed by mutations within the six genotypes. Here, we report on a viable spontaneous HCV recombinant and we show that recombination may play a role in the evolution of this virus. Previously, 149 HCV strains from St. Petersburg had been subtyped by limited sequencing within the NS5B region. In the present study, the core regions of 41 of these strains were sequenced to investigate the concordance of HCV genotyping for these two genomic regions. Two phylogenetically related HCV strains were found to belong to different subtypes, 2k and 1b, according to sequence analysis of the 5 untranslated region (5UTR)-core and the NS5B regions, respectively. By sequencing of the E2-p7-NS2 region, the crossover point was mapped within the NS2 region, probably between positions 3175 and 3176 (according to the numbering system for strain pj6CF). Sequencing of the 5UTR-core regions of four other HCV strains, phylogenetically related to the above-mentioned two strains (based on analysis within the NS5B region), revealed that these four strains were also recombinants. Since a nonrecombinant 2k strain was found in St. Petersburg, the recombination may have taken place there around a decade ago. Since the frequency of this recombinant is now high enough to allow the detection of the recombinant in a fraction of the city's population, it seems to be actively spreading there. The reported recombinant is tentatively designated RF1_2k/1b, in agreement with the nomenclature used for HIV recombinants. Recombination between HCV genotypes must now be considered in the classification, laboratory diagnosis, and treatment of HCV infection.Hepatitis C virus (HCV) is the major agent of parenterally transmitted non-A, non-B hepatitis worldwide (1). HCV is an enveloped virus classified in the family Flaviviridae. It has a single-stranded, positive-sense, nonsegmented RNA genome of approximately 9,500 nucleotides (nt) with a single, long open reading frame encoding a polyprotein of ϳ3,030 amino acids with the gene order C-E1-E2-p7-NS2-NS3-NS4A-NS4B-NS5A-NS5B. The structural proteins are C (core) and E1 and E2 (envelope glycoproteins). The function of the p7 gene product is presently unknown. The NS2 through NS5 regions encode putative nonstructural proteins (2).HCV is characterized by a high degree of genetic heterogeneity. Its variability is, however, distributed unequally within the genome, and some regions, such as NS3 and NS5B, are considerably conserved. HCV is classified into six genotypes and an increasing number of subtypes based on degree of genomic sequence divergence (26,27). Evolution of HCV is believed to be mediated by point, insertion, or deletion mutations. Another mechanism for viral evolution is through recombination. There has so far been little evidence of recombination between HCV strains of different genotypes (38), and it has been suggested that these events are rare in vivo and that the resultant recombinants are usually not viable (26,28,34).Relatively short subgenomic region...

Evidence of intratypic recombination in natural populations of hepatitis C virus

“…However, an infectious HCV chimera comprising the complete open reading frame of a subtype 1b strain and the 59-and 39UTRs of a subtype 1a strain has been constructed and is infectious in vivo (Yagani et al, 1998). Recombination in other flaviviruses has now been demonstrated on a number of occasions (Becher et al, 2001;Worobey & Holmes, 2001;Twiddy & Holmes, 2003), and recently a natural intergenotypic recombinant (2k/1b) of HCV was identified in St Petersburg (Russia) (Kalinina et al, 2002). Our phylogenetic analyses based on two different genomic regions, 59UTR-core and NS5B, demonstrate the existence of natural intragenotypic HCV recombinant strains (1a/1b) circulating in the Peruvian population.…”

“…In the current HCV classification system, HCV strains are divided into genotypes, subtypes and quasispecies, but recombination has not yet been considered in this classification. By analogy with the nomenclature for HIV, we suggest that an HCV recombinant strain be designated a 'recombinant form' (RF), as also suggested by Kalinina et al (2002). RF strains with the same number are progeny resulting from the same recombination event and thus share an identical mosaic structure; for example, the intertypic recombinants among subtypes 2k and 1b observed by Kalinina et al (2002) were described as RF1_2k/1b.…”

“…By analogy with the nomenclature for HIV, we suggest that an HCV recombinant strain be designated a 'recombinant form' (RF), as also suggested by Kalinina et al (2002). RF strains with the same number are progeny resulting from the same recombination event and thus share an identical mosaic structure; for example, the intertypic recombinants among subtypes 2k and 1b observed by Kalinina et al (2002) were described as RF1_2k/1b. Accordingly, we suggest the designation RF2_1a/1b for the Peruvian strain PE22 described herein.…”

“…Tolou et al, 2001;Uzcategui et al, 2001;, hepaciviruses (GB virus C/hepatitis G virus) (Worobey & Holmes, 2001) and Japanese encephalitis or St Louis encephalitis virus (Twiddy & Holmes, 2003). There have been few reports on recombination between HCV strains of different genotypes (Kalinina et al, 2002;Yun et al, 1996) and it has been suggested that these events are rare in vivo and that the resultant recombinants are usually not viable (Simmonds et al, 1994;Smith & Simmonds, 1997).…”

Diversity of Hepatitis C virus in Southern India Based on 5′UTR Sequence

“…The HCV has also been shown to resort to RNA recombination as a means of generating genetic variations. An instance of such inter-genotypic recombination was observed between genotype 2k and 1b in St. Petersburg by Kalinina et al [9]. Colina et al [6] reported intra-typic recombination between genotype 1a and 1b.…”