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J Gen Virol 85 (2004), 31-37; DOI 10.1099/vir.0.19472-0

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© 2004 Society for General Microbiology

Evidence of intratypic recombination in natural populations of hepatitis C virus

Rodney Colina1, Didier Casane2, Silvia Vasquez3, Laura García-Aguirre1, Ausberto Chunga4, Héctor Romero5, Baldip Khan6 and Juan Cristina1

1 Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
2 Populations, Génétique et Evolution, CNRS, 91198 Gif-sur-Yvette, France
3 Laboratorio de Biología Molecular, Centro Nuclear RACSO, Instituto Peruano de Energía Nuclear IPEN, Av. Canadá 1470, San Borja, Apartado 1687, Lima 41, Peru
4 Servicio de Inmunología, Hospital Nacional Edgardo Rebagliati Martins HNERN, Domingo Cueto s/n, Jesús María, Lima 11, Peru
5 Laboratorio de Organización y Evolución del Genoma. Instituto de Biología. Facultad de Ciencias. Iguá 4225, 11400 Montevideo, Uruguay
6 Division of Human Health, International Atomic Energy Agency, Wagramerstrasse 5, 1400 Vienna, Austria

Correspondence
Juan Cristina
cristina{at}cin1.cin.edu.uy

Hepatitis C virus (HCV) has high genomic variability and, since its discovery, at least six different types and an increasing number of subtypes have been reported. Genotype 1 is the most prevalent genotype found in South America. In the present study, three different genomic regions (5'UTR, core and NS5B) of four HCV strains isolated from Peruvian patients were sequenced in order to investigate the congruence of HCV genotyping for these three genomic regions. Phylogenetic analysis using 5'UTR–core sequences found strain PE22 to be related to subtype 1b. However, the same analysis using the NS5B region found it to be related to subtype 1a. To test the possibility of genetic recombination, phylogenetic studies were carried out, revealing that a crossover event had taken place in the NS5B protein. We discuss the consequences of this observation on HCV genotype classification, laboratory diagnosis and treatment of HCV infection.

The GenBank/EMBL accession numbers of the sequences reported in this work are AJ438618, AJ438622 and AJ582126–AJ582135.




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