Microsatellite is an important component of complete hepatitis C virus genomes.

Microsatellites are common and play diverse roles in eukaryotic and prokaryotic genomes. However, to our knowledge, microsatellite distribution remains largely enigmatic in viruses yet is crucial for understanding instability of viral genomes. We have therefore, examined microsatellite distribution in 54 complete genomes of Hepatitis C virus (HCV) from six genotypes, showing microsatellites were an important component of HCV genomes. Our results showed, in all analyzed HCV genomes, genome size and GC content had a weak influence on number, relative abundance and relative density of microsatellites, respectively. For each HCV genome, mono-, di- and trinucleotide repeats were very predominant, whereas other types of repeats rarely occurred. Our results revealed that the occurrence of microsatellites was significantly less than higher prokaryotes and eukaryotes and that all identified microsatellites were very short. The discovery of microsatellites in HCV genomes may become useful for population genetic, evolutionary analysis and strain (isolate) identification.