HETEROGENEITY AND COMMON FEATURES OF DEFECTIVE HEPATITIS-B VIRUS GENOMES DERIVED FROM SPLICED PREGENOMIC RNA

Defective hepatitis B virus (HBV) genomes derived from packaging and r everse transcription of spliced RNA pregenomes were reported to be ass ociated with progression to chronic infection. Since only two types wi th similarly spliced regions were characterized so far we reasoned tha t additional ''spliced'' genome variants may exist. Therefore, we isol ated a large number of defective HBV genomes from sera of seven chroni c carriers by full-length PCR. Forty-eight were found to contain delet ions caused by splicing as identified by cloning, subgenomic PCR, and sequencing. In total, 11 types of spliced genomes derived from excisio n of 10 different introns were present in various combinations in each serum. This diversity resulted from alternative usage of five splice donor and four acceptor sites present in most but not all HBV genotype s. All spliced genomes shared sequence elements essential for replicat ion as well as for transcription of the pre-C and pregenome/C mRNAs an d the X mRNA. Moreover, all contained the coding regions for the X pro tein and for precore/core or precore/core fusion proteins but lacked t he pre-S/S gene promoters. These data demonstrate substantial and HBV genotype-dependent diversity of spliced genomes from which a variety o f aberrant precore/core fusion proteins and normal X protein but no fu nctional envelope and P proteins could be expressed. These genomes and the encoded proteins may play a role in the viral life cycle, persist ence, and pathogenesis. (C) 1997 Academic Press.