Nucleotide sequence of the woodchuck hepatitis virus surface antigen mRNAs and the variability of three overlapping viral genes

A cDNA library was constructed from the liver of a woodchuck chronically infected with woodchuck hepatitis virus (WHV). A clone, pWS23, encompassing the entire surface and X genes of WHV was isolated. Comparison of the complete nucleotide (nt) sequence of pWS23 with those of genomic DNAs from two different WHV isolates showed that it contained a nearly full-length copy of the major mRNA encoding the viral surface antigen (5 mRNA). It was colinear with the WHV genome over 1858 nt and terminated 22 nt downstream from the variant polyadenylation signal within the core gene. Evidence for heterogeneity of the 5′ -terminal region of the S mRNA came from direct sequencing of the 5′ extremities of 20 cDNA inserts, similar to that of pWS23, isolated from a second cDNA library of the same woodchuck liver. In agreement with previous mapping studies of hepadnaviruses, two main initiation regions of S mRNA were localized 27–30 nt upstream and 22–49 nt downstream from the pre-S2 initiation codon. Further analysis of the amino acid sequences of the surface, polymerase and X genes of WHV showed a high conservation among three WHY isolates and a similar distribution of conserved and variable regions in woodchuck and human hepatitis B viruses.