Hepatitis delta virus (HDV) is a defective single-stranded RNA virus. The assembly and transmission of HDV require a supply of hepatitis B surface antigen (HBsAg) from hepatitis B virus (HBV) (21, 25). HDV superinfection can lead to fulminant hepatic failure and also has a high probability of progressing to chronic hepatitis or cirrhosis (8,22,24,27,28). Furthermore, HDV superinfection can increase the risk of hepatocellular carcinoma and mortality in patients with HBVrelated cirrhosis (6). Although the present HBV vaccine is very effective, about 350 million individuals are already chronically infected by HBV worldwide (4). At present, interferon is the only licensed drug for treating chronic hepatitis D, but the relapse rate is high after discontinuation (5). The development of a prophylactic or therapeutic HDV vaccine has a potential use for HBV carriers who are at risk of HDV superinfection and for those who have been infected by HDV already. DNA vaccination is a promising method for preventing and treating persistent viral infections. Previous results suggested that DNA vaccines can produce Th1 immune responses against HDV (11).HDV has two forms of viral proteins, large and small hepatitis D antigens (HDAg). The mRNA encoding large HDAg (L-HDAg) contains a UGG tryptophan codon at the site of the UAG amber termination codon of small HDAg (S-HDAg) because of an RNA editing event (1, 2, 3). Therefore, L-HDAg contains an additional 19 amino acids at the C terminus. LHDAg can be isoprenylated at a unique cysteine located 4 amino acids from the C terminus (7). Mutation of this unique cysteine of L-HDAg to serine can block isoprenylation and HDV assembly (7). Evidence has shown that these additional 19 amino acids of L-HDAg can alter the overall conformation and hydrophobicity of HDAg (12,13,15,18). S-HDAg also contains a unique conformation at the C terminus. This conformation is detectable with a monoclonal antibody (9E4) which is specific for S-HDAg and which does not react with L-HDAg. When isoprenylation is inhibited, this epitope become exposed in L-HDAg (12, 13). Based on this evidence, host immune responses may be different when immunization is carried out with endogenous L-HDAg versus S-HDAg.A previous study demonstrated that an L-HDAg-encoding DNA vaccine could produce low titers of anti-HDV antibodies (11). However, in a subsequent study with the HDV DNA vaccine, no HDAg-specific antibody titers were detectable by a commercial enzyme-linked immunosorbent assay (ELISA) or by a Western blot assay (17). This discrepancy needs further study for clarification.The immunogenic domain of HDV recognized by chronically HDV-infected patients includes amino acids 2 to 7, 63 to 74, 86 to 91, 94 to 100, 159 to 172, 174 to 195, and 197 to 207 (23). It also has been suggested that cytotoxic-T-cell epitopes of HDV may be located at the carboxyl end (amino acids 77 to 195) of . In a longitudinal analysis of the HDV genome at different time points during chronic HDV infection, the emergence of amino acid changes at the c...