Accumulation in immunosuppressed patients of hepatitis a virus (HBV) with a deletion in the C gene is associated with severe liver disease. The aim of this study was to determine the phenotype of such genomes in vitro. Four C gene fragments with different types of deletions were inserted in the context of a wild-type genome and tested by transfection into HuH7 cells. The deletions did not influence mRNA and surface protein levels. Truncated C gene translation products were expressed only from variants with in-frame deletions, whereas full-length polymerase was expressed from all variants at a similar or higher level than in wild-type virus. None of the variants was competent for autonomous replication; however, they produced 2- to 4.5-fold more progeny DNA than wild-type HBV when sufficiently complemented with wild-type core protein. Similarly, when variant and wild-type DNA were cotransfected in different ratios, the variants produced 2- to 5-fold more progeny DNA relative to the wild-type; this enrichment required the expression of the viral polymerase in c/s. The mechanism of enrichment depended on the percentage of variant in the transfected DNA mixture. When the transfected DNA contained a small percentage of variant, enhanced replication of the variant accompanied by no or little suppression of wild-type replication was seen. Accordingly, overall production of progeny virus was slightly increased. At a high percentage of variant DNA, replication of both variant and wild-type decreased, probably due to a shortage of wild-type core protein. In conclusion, emergence of C gene deletion variants in vivo may be due to enhanced replication mediated at the level of encapsidation or reverse transcription. If the variants constitute a small part of the ccc DNA, they can be fully trans-complemented by wild-type virus which may increase the overall virus production. (C) 2000 Academic Press.