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Hepatitis B virus (HBV) DNA clones were propagated from 57 carriers with antibody to hepatitis B e antigen (HBeAg) and sequenced within nucleotides (nt) 1685 to 1926 including the core promoter (nt 1742 to 1849) and the pre-C region (nt 1814 to 1900). Mutations in the core promoter or those in the pre-C region, or both, were detected in 328 (97.9%) of 335 clones from them. Five carriers were infected with HBV mutants with mutations in the core promoter alone, while 20 carriers were infected only with those in the pre-C region to abort the translation of HBeAg precursor; the remaining 32 carriers were infected with HBV mutants with mutations in both the core promoter and pre-C region. Some carriers infected with HBV with mutations in the core promoter exclusively had high HBV DNA titers, comparable with those in carriers infected with wild-type HBV, thereby indicating that such mutations would not affect the transcription of the HBV pregenome extensively. Two point mutations in the core promoter, from A to T at nt 1762 and from G to A at nt 1764, were most prevalent. The other mutations included a point mutation at either of the two nucleotides and their deletion. All of these mutations involved the TTAAA sequence (nt 1758 to 1762) at 28 bp upstream of the initiation site for shorter pre-C mRNAs (nt 1790 +/- 1). The ATAAATT sequence (nt 1789 to 1795) at 23 bp upstream of the initiation site for the pregenome RNA (nt 1818), however, remained intact in all 335 HBV DNA clones. HBV mutants with mutations in the core promoter, unaccompanied by pre-C mutations, prevailed and replaced wild-type HBV in two carriers as they seroconverted from HBeAg to the corresponding antibody. These results indicate that HBV mutants with an HBeAg- phenotype would be generated by mutations in the core promoter which might abort the transcription of pre-C mRNA but do not seriously affect that of pregenome RNA.