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Journal of Virology, April 2002, p. 4034-4043, Vol. 76, No. 8
0022-538X/02/$04.00+0     DOI: 10.1128/JVI.76.8.4034-4043.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

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

Olga Kalinina,1,2 Helene Norder,2* Sergey Mukomolov,1 and Lars O. Magnius2

St. Petersburg Pasteur Institute, St. Petersburg 197101, Russia,1 Department of Virology, Swedish Institute for Infectious Disease Control, 171 82 Solna, Sweden2

Received 31 July 2001/ Accepted 21 December 2001

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 (5'UTR)-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 5'UTR-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.

* Corresponding author. Mailing address: Department of Virology, Swedish Institute for Infectious Disease Control, 171 82 Solna, Sweden. Phone: 46 8 457 26 39. Fax: 46 8 337272. E-mail: Helene.Norder{at}smi.ki.se.

Journal of Virology, April 2002, p. 4034-4043, Vol. 76, No. 8
0022-538X/02/$04.00+0     DOI: 10.1128/JVI.76.8.4034-4043.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



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