MOLECULAR CHARACTERIZATION OF THE 3'-END OF THE ASTROVIRUS GENOME

We have sequenced the 3'-end of the RNA genomes of 14 serotyped and 12 untyped isolates of human astrovirus. The sequences, which include al l 8 serotypes, were used to predict secondary structures, postulate po ssible functional domains, reveal conserved regions suitable for nucle ic acid amplification and perform phylogenetic analysis. The final nuc leotides of the capsid protein precursor gene and the adjacent 3'-nonc oding region were highly conserved and, except for 35 nucleotides with homology to a sequence in the 3'-end of a coronavirus RNA genome, uni que to astrovirus family. This confirms that the 3'-end is a suitable target for universal and specific detection of astrovirus RNA. For the deduced 72 C-terminal amino acids of the capsid protein precursor, di stances between the serotypes were found to vary from 0.1 substitution per site between serotypes 3 and 7 to more than one substitution per site between serotype 4 and the other serotypes. Different isolates of the same serotype were closely related, which indicates that the pres ently used type-specific antibodies differentiate between phylogenetic ally distinct groups. RNA secondary structures with minimal free energ y were predicted using computer programs. Comparative sequence analysi s verified the significance of certain of the predicted structural ele ments.