Genomic analysis of a transposition-deletion variant of orf virus reveals a 3.3 kbp region of non-essential DNA

Abstract

Restriction endonuclease analysis of the DNA extracted orfvirus strain NZ2, which had been serially passaged in primary bovine testis cells, revealed a population of variants that had over-grown the wild-type virus. At least three distinct mutant forms were identified in which the right end of the genome had been duplicated and translocated to the left end, accompanied by deletions of sequences at the left end. Sequencing of a single variant isolated from the heterogeneous population revealed that recombination had occurred between non-homologous sequences. In this case, 6-6 kb of DNA at the left end of the genome had been replaced by 19-3 kb from the right end. The transposition resulted in the deletion at the left end of 3.3 kb of DNA encoding three genes and the terminal sequence of a fourth gene. The three genes completely deleted were a homologue of dUTPase, a gene that encodes a protein containing ankyrin-like repeats and a homologue of the 5K gene of the vaccinia virus WR strain. Experimental inoculation of sheep showed that the genes are also non-essential in vivo, but that the size of the lesion was reduced, compared with that induced by the wild-type, and resolved more rapidly.

The genome of pseudocowpoxvirus: comparison of a reindeer isolate and a reference strain

“…However, this is most probably due to duplication and translocation of sequence from the right terminus of the genome to the left terminus of the genome, a process which is often accompanied by deletion of sequence at the left terminus of the genome. This is a common phenomenon in poxviruses that have been passaged in cell culture and has been reported previously for ORFV (Fleming et al, 1995;Cottone et al, 1998;McInnes et al, 2001). One open reading frame (ORF) encoding a predicted protein of 150 aa was found entirely within the F00.120R ITR and therefore is repeated at both ends of the genome (ORF 001/ 134).…”

Genomes of the Parapoxviruses Orf Virus and Bovine Papular Stomatitis Virus

“…PPVs, MOCV, and Melanoplus sanguinipes entomopoxvirus are the only poxviruses known to lack a thymidine kinase gene. In contrast, PPV 007, a gene not essential for growth of ORFV in vitro, is a dUTPase gene missing in MOCV (22,43,72,73). Notably, PPVs and MOCV are the only ChPVs lacking homologues of VACV B1R, a Ser/Thr protein kinase similar to cellular VRK1 homologues and giving a temperature-sensitive DNA-negative phenotype (61).…”

“…Hybridization analysis of viral DNA indicates that internal but not terminal genomic regions are conserved between PPVs (26). Data concerning PPV genomics, largely obtained by using ORFV strain NZ2, has revealed (i) colinearity between the ORFV and other poxvirus genera genomes (21,49,50), (ii) the presence of a set of genes mostly located at the termini of the viral genome with putative or known roles in virulence or immunomodulation (15,23,38,42,76), and (iii) the occurrence of genomic rearrangements of the termini upon serial virus passage in vitro (12,22). Less is known about the gene complement and genomic organization of other PPV.…”

Spatial and Temporal Genetic Homogeneity of Orf Viruses Infecting Japanese Serows (Capricornis crispus)

“…All 13 Japanese ORFVs were classified into the same genotype by the differential PCR for the A32L gene. On the other hand, the Taiwanese ORFVs were split into three genotypes by the differential PCR for the A32L gene, indicating sequence variations and deletions in the gene [4], and genome recombination, such as duplication, transposition and deletion, in cultured cells has also been reported [7,10]. Thus, these results suggest that ORFVs that have a genetic character like the S-1/Iwate strain other than the HIS strain, at least in the envelope, VEGF and VIR genes, are highly adapted and maintained in Japanese serows.…”