Spontaneous deletions and duplications of sequences in the genome of cowpox virus.

Abstract

Examination of the genomes of 10 white-pock variants of cowpox virus strain Brighton red (CPV-BR) revealed that 9 of them had lost 32 to 38 kilobase pairs (kbp) from their right-hand ends and that the deleted sequences had been replaced by inverted copies of regions from 21 to 50 kbp long from the left-hand end of the genome. These variants thus possess inverted terminal repeats (ITRs) from 21 to 50 kbp long; all are longer than the ITRs of CPV-BR (10 kbp). The 10th variant is a simple deletion mutant that has lost the sequences between 32 and 12 kbp from the right-hand end of the genome. The limits of the inner ends of the observed deletions (between 32 and 38 kbp from the right-hand end of the CPV-BR genome) appear to be defined by the location of the nearest essential gene on the one hand and the location of the gene that encodes "pock redness" on the other. The genomes of the deletion/duplication white-pock variants appear to have been generated either by single crossover recombinational events between two CPV-BR genomes aligned in opposite directions or by the nonreciprocal transfer of genetic information. The sites where such recombination/transfer occurred were sequenced in four variants. In all of them, the sequences adjacent to such sites show no sequence homology or any other unusual strutural feature. The analogous sites at the internal ends of the two ITRs of CPV-BR also were sequenced and also show no unusual features. It is likely that the ITRs of CPV-BR and of its white-pock variants, and probably those of other orthopoxvirus genomes, arise as a result of nonhomologous recombination or by random nonreciprocal transfer of genetic information.

Hemorrhage in lesions caused by cowpox virus is induced by a viral protein that is related to plasma protein inhibitors of serine proteases.

“…Similar results have been obtained from studies of the DNAs of white-pock variants of rabbitpox virus and monkeypox virus (6)(7)(8). The rearrangements of DNA that generate the white-pock variants of CPV typically involve the replacement of up to 39 kilobases (kb) of one end of the genome with an inverted copy of up to 50 kb of DNA from the other end (4,5). The mechanisms by which these rearrangements proceed are unknown; but it is clear that there are no identifiable homologous sequence elements at the sites of the duplication/deletion end points (5).…”

“…Studies of the structures of the DNAs of these white-pock variants have shown that their genomes are generated from the genome of the wild-type virus by large deletions and duplications of sequences (4,5). Similar results have been obtained from studies of the DNAs of white-pock variants of rabbitpox virus and monkeypox virus (6)(7)(8).…”

“…CPV strain Brighton Red (CPV-BR) and a white-pock variant (CPV-W2), were isolated and cultured as described (5).…”

“…The rearrangements of DNA that generate the white-pock variants of CPV typically involve the replacement of up to 39 kilobases (kb) of one end of the genome with an inverted copy of up to 50 kb of DNA from the other end (4,5). The mechanisms by which these rearrangements proceed are unknown; but it is clear that there are no identifiable homologous sequence elements at the sites of the duplication/deletion end points (5). This result suggests that it is the location of essential genes rather than DNA sequence content that limits where rearrangements may occur.…”

Nucleotide sequence of 42 kbp of vaccinia virus strain WR from near the right inverted terminal repeat

“…The region adjacent to the right ITR is variable in orthopoxviruses and undergoes deletions and terminal transpositions (Mackett & Archard, 1979;Moyer et al, 1980;Lake & Cooper, 1980;Archard et al, 1984;Pickup et al, 1984Pickup et al, , 1986, indicating that many of the ORFs may be nonessential for virus replication in cultured cells. Overall the gene arrangement is similar to that discovered in other regions of the genome; namely the genes are tightly packed, are transcribed from either DNA strand in the genomic centre (Niles et al, 1986) and near the ITR are transcribed outward towards the terminal hairpin Kotwal & Moss, 1988a).…”