A NEW CLASS OF DEFECTIVE HEPATITIS-B VIRUS GENOMES WITH AN INTERNAL POLY(DA) SEQUENCE

Sequence heterogeneity of hepatitis B virus (HBV) is increasingly reco gnized to play a role in virus-host interaction. We have used a recent ly established method for HBV full-length genome amplification to sear ch for novel types of HBV variants and to investigate further the sequ ence heterogeneity of HBV genome populations. Using this method, a sub stantial fraction of HBV genomes much shorter than wildtype size was f ound in some sera and liver biopsies from infected patients. Cloning a nd sequencing of a number of these HBV genomes as well as hybridizatio n studies revealed a new minor class of HBV genomes with an internal p oly(dA) sequence approximately 60 to more than 100 nucleotides long in 4 of 10 patients. The 5'-ends of the internal poly(dA) sequences are located at positions corresponding to the authentic processing/polyade nylation sites of the RNA pregenome, whereas the positions of the 3'-e nds are variable due to different sizes of adjacent deletions. These d ata suggest that the poly(A) tail of the pregenomic RNA is occasionall y reverse transcribed by the HBV P-protein and during this process a d eletion seems to be introduced into the DNA minus strand. We propose a mechanism by which this could be accomplished during DNA minus strand synthesis. (C) 1997 Academic Press.