A sensitive method for the identification of uncharacterized viruses related to known virus groups: hepadnavirus model system

Abstract Amino acid sequence similarity of the reverse transcriptases encoded by retroviruses and hepadnaviruses was first reported by Toh, H., Hayashida, H. & Miyata, T. (1983) Nature (London) 305, 827-829. The regions of similarity extend over a small number of amino acids and require the introduction of gaps through the open reading frame. By using an octapeptide region as the sole criterion for "taxonomic" classification, we have grouped the oncoviruses into two distinct categories and the lentiviruses and hepadnaviruses into two additional groupings. This classification suggests that murine and feline leukemia viruses may be more closely related to the viruses that are associated with leukemia in primates and cattle than had been appreciated. We have exploited a portion of this region because of the minimal translational codon degeneracy of the conserved residues. Unique oligonucleotides from this region have been designed and used in the primer-directed in vitro DNA amplification of the hepadnaviruses as a model system. In addition, mixtures of oligonucleotides with various sequences but of the same length were demonstrated to be efficient primers. The amplification procedure enabled dramatic increases in sensitivity and coincident detection of mammalian and avian genomes. This approach will be a valuable tool to detect and characterize members of viral groups. In addition, since short stretches of similarity have been frequently identified in related but distinct genes, such an approach could prove a valuable asset to molecular studies in general.