Characterization of hepatitis C virus deletion mutants circulating in chronically infected patients

Hepatitis C virus (HCV) has a linear positive-stranded RNA genome of similar to 9,600 nucleotides in length and displays a high level of sequence diversity caused by high mutation rates and recombination. However, when we performed long distance reverse transcription-PCRs on HCV RNA isolated from serum of chronic HCV patients, not only full-length HCV genomes but also HCV RNAs which varied in size from 7,600 to 8,346 nucleotides and contained large in-frame deletions between El and NS2 were amplified. Carefully designed control experiments indicated that these deletion mutants are a bona fide natural RNA species, most likely packaged in virions. Moreover, deletion mutants were detected in sera of patients infected with different HCN genotypes. We observed that 7/37 (18.9%) of genotype 1, 5143 (11.6%) of genotype 3, and 4/13 (30.7%) of genotype 6 samples contained HCV deletion mutant genomes. These observations further exemplify HCVs huge genetic diversity and warrant studies to explore their biological relevance.