Rabbit hemorrhagic disease virus - molecular cloning and nucleotide sequencing of a calicivirus genome

The RNA genome of rabbit hemorrhagic disease virus (RHDV) was molecularly cloned. The 5′ terminal sequence of the genomic RNA was determined after PCR amplification of a G-tailed first strand cDNA template. The cloned cDNA allowed determination of the first complete caliciviral sequence encompassing 7437 nucleotides without poly(A) tail. The RHDV genome contains one long open reading frame of 2344 codons which in the 5′ region encodes the nonstructural proteins. Sequence comparison studies revealed significant homology between nonstructural proteins of the feline calicivirus (FCV) and RHDV. In analogy to FCV the deduced RHDV amino acid sequence contains a picornavirus 2C-like sequence, a hypothesized cysteine protease motif, and the conserved polymerase residues GDD. For the protein region containing the GDD motif, alignments of sequences from different viruses including the putative caliciviruses hepatitis E virus and Norwalk virus were performed; concerning the classification of the latter two viruses, a final judgement was not possible. Bacterial expression of sequences derived from the 3′ part of the genomic RHDV RNA showed that this region codes for the viral capsid protein.