Cloning and sequencing of the genome of chicken anaemia virus (CAV) TK-5803 strain and comparison with other CAV strains.

The complete genomic sequence of chicken anaemia virus (CAV) TK-5803 strain was determined. Comparisons of sequence data showed 37 nucleotide differences between TK-5803 and Cux-1, 38 nucleotide differences between TK-5803 and 26P4, and 48 nucleotide differences between TK-5803 and 82-2. There were 65 nucleotide differences in the largest open reading frame (ORF3) between TK-5803 and one Australian isolate. Base changes introduced amino acid changes at 6 positions in the C-terminal half of VP3, at 4 positions in the C-terminal quarter of VP2 and at 17 positions in VP1 among the strains. These indicate that the N-terminal half of VP3 and the N-terminal three quarter of VP2 are well conserved, and might sustain essential function of these proteins. The amino acid changes in VP1 which is thought to be the capsid protein may influence the antigenic character of different VP1s.