A novel sequence found at the 3′-terminus of hepatitis C virus genome

The 3′ end region of positive-strand RNA-virus genomes is implicated in the initiation of genomic replication. We analyzed the extreme 3′ end of the hepatitis C virus (HCV) genome by primer extension of the 5′ end region of the antigenomic strand RNA found in infected liver. We discovered a novel sequence present downstream of the poly(U) stretch that was previously considered to be the 3′ end structure of the HCV genome. The novel sequence was 98 nucleotides long and had no significant homology with any known sequences, viral or nonviral. The discovery of this novel tail on the HCV genome should contribute to the study of HCV replication.