The hepatitis B virus pregenome: Prediction of RNA structure and implications for the emergence of deletions

The terminally redundant pregenomic RNA of human hepatitis B virus (HBV) co mprises some 3,330 nucleotides and is a replicative intermediate in the pro duction of the circular DNA genome. Deletions are known to arise in the HBV genome during the course of chronic infection and are sometimes associated with interferon therapy. These deletions are limited to small parts of the genome such as the 357-nucleotide pre-S1 region. Long RNA molecules such a s the HBV pregenome have considerable structural flexibility and will under go secondary structure shifts between energetically favourable states in a continuous and semi-random fashion, Since prediction of structure elements that are highly conserved in different forms of one RNA molecule is now fea sible by computer modelling, we have analysed the whole HBV pregenome by tw o different RNA structure prediction algorithms and by new methods that exp loit these algorithms. Significantly, the ends of pregenomic RNA were predi cted to undergo both short-range and long-range interactions, which has rel evance to our knowledge of the virus replicative cycle. By incorporating ph ylogenetic information relating to the 6 recognised genotypes of HBV, it wa s possible to highlight short secondary structures that may be common to ai l HBV strains. For example, although the pre-Si region was predicted to und ergo local folding of a loosely defined nature, most observed pre-S1 deleti ons mapped to all or part of an arm carrying a better-defined structure. Th e loss of such sequences may be mechanistically attributable to polymerase skipping during reverse transcription, and the possible advantages of such deletions are considered. Copyright (C) 2000 S.Karger AG.Basel.