Multiple origins of the complementary defective genomes of RF and origin proximal sequences of GS, two human papovavirus isolates.

It has previously been shown that the genome of RF virus, a variant of the human papovavirus, BK, consists of two DNA species, one (R1a) with a deletion corresponding to the early and the other (R2) with a deletion corresponding to the late region of BKV (A. Pater, M.M. Pater, and G. di Mayorca (1980). J. Virol. 36, 480-487; A. Pater, M. M. Pater, R. M. Dougherty, and G. di Mayorca (1981a). Virology 113, 86-94). In this report transfection experiments are used to show that these DNA species are individually defective for infection and that both DNA molecules are required simultaneously for the infection of human embryonic kidney (HEK) cells. DNA fragments containing the origin of replication in each of the DNA species are analyzed to show that R1a contains three and R2 contains two origins of replication. In addition, several changes in the repeat region proximal to the origin of replication are observed. The changes involve deletions and insertions. Examination of the deleted junctions most often reveals involvement of short stretches of repeated sequences (hot spots) in recombination. Another observed change is the insertion into R2 of a 63-bp sequence which contains no homology to either BK or SV40 DNA. This insertion is into the late-promoter region of this late-region coding DNA and appears to replace a poor "TATA" box in BK wild type with a better TATA box with the correct spacing from the "CAAT" box. A 304-bp fragment containing the origin of replication, early and late promoters, and the repeat units proximal to the origin of replication of GS, another variant of human BKV papovaviruses has also been sequenced. Several rearrangements, including deletions and insertions in the repeat region, are observed. Moreover, when homologous regions of this virus are compared to that of BKV, five base changes are detected, one of which is in the 23-bp origin region. This base change gives this 23-bp palindrome of GS a perfect two-fold rotational symmetry.