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 (59UTR, 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 59UTR-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.
There are eight genotypes A-H of hepatitis B virus (HBV). Most genotypes are further divided into subgenotypes. Genotypes and subgenotypes influence the natural course of infection and therapy. We analysed nine sera from HBV carriers from Peru. Using the small hepatitis B surface protein HBs, all samples could be grouped to genotype F. Sequencing of three complete Peruvian genomes showed that HBV from Peru belongs to subgenotype F1. Two of the genomes from HBeAg positive carriers coded surprisingly for a stop codon in the polymerase-ORF leading to a translational stop after 213 and 214 aa, respectively. The third isolate from an HBe Ag positive carrier had three deletions: aa 1-53 and aa 111-142 in preS. In addition nt. 2002-2087 in the HBc-ORF were deleted, leading to an HBc starting at aa 66.
Hepatitis C virus (HCV) is an important human pathogen that affects 170 million people worldwide. The HCV genome is an RNA molecule that is approximately 9?6 kb in length and encodes a polyprotein that is cleaved proteolytically to generate at least 10 mature viral proteins. Recently, a new HCV protein named F has been described, which is synthesized as a result of a ribosomal frameshift. Little is known about the biological properties of this protein, but the possibility that the F protein may participate in HCV morphology or replication has been raised. In this work, the presence of functional constraints in the F protein was investigated. It was found that the rate of amino acid substitutions along the F protein was significantly higher than the rate of synonymous substitutions, and comparisons involving genes that represented independent phylogenetic lineages yielded very different divergence/conservation patterns. The distribution of stop codons in the F protein across all HCV genotypes was also investigated; genotypes 2 and 3 were found to have more stop codons than genotype 1. The results of this work suggest strongly that the pattern of divergence in the F protein is not affected by functional constraints.
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