Evidence of intratypic recombination in natural populations of hepatitis C virus.
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.
Colina
Rodney
R
Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay.
Casane
Didier
D
Populations, Génétique et Evolution, CNRS, 91198 Gif-sur-Yvette, France.
Vasquez
Silvia
S
Laboratorio de Biología Molecular, Centro Nuclear RACSO, Instituto Peruano de Energía Nuclear IPEN, Av. Canadá 1470, San Borja, Apartado 1687, Lima 41, Peru.
García-Aguirre
Laura
L
Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay.
Chunga
Ausberto
A
Servicio de Inmunología, Hospital Nacional Edgardo Rebagliati Martins HNERN, Domingo Cueto s/n, Jesús María, Lima 11, Peru.
Romero
Héctor
H
Laboratorio de Organización y Evolución del Genoma. Instituto de Biología. Facultad de Ciencias. Iguá 4225, 11400 Montevideo, Uruguay.
Khan
Baldip
B
Division of Human Health, International Atomic Energy Agency, Wagramerstrasse 5, 1400 Vienna, Austria.
Cristina
Juan
J
Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay.
D020121:5' Untranslated Regions / Q000235:genetics; D001483:Base Sequence; D005838:Genotype; D016174:Hepacivirus / Q000145:classification / Q000235:genetics*; D019698:Hepatitis C, Chronic / Q000821:virology*; D006801:Humans; D008969:Molecular Sequence Data; D010568:Peru; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D014758:Viral Core Proteins / Q000235:genetics; D017361:Viral Nonstructural Proteins / Q000737:chemistry / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase
D020121:5' Untranslated Regions; D014758:Viral Core Proteins; D017361:Viral Nonstructural Proteins; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase