The genome of canarypox virus

Abstract

Here we present the genomic sequence, with analysis, of a canarypox virus (CNPV). The 365-kbp CNPV genome contains 328 potential genes in a central region and in 6.5-kbp inverted terminal repeats. Comparison with the previously characterized fowlpox virus (FWPV) genome revealed avipoxvirus-specific genomic features, including large genomic rearrangements relative to other chordopoxviruses and novel cellular homologues and gene families. CNPV also contains many genomic differences with FWPV, including over 75 kbp of additional sequence, 39 genes lacking FWPV homologues, and an average of 47% amino acid divergence between homologues. Differences occur primarily in terminal and, notably, localized internal genomic regions and suggest significant genomic diversity among avipoxviruses. Divergent regions contain gene families, which overall comprise over 49% of the CNPV genome and include genes encoding 51 proteins containing ankyrin repeats, 26 N1R/p28-like proteins, and potential immunomodulatory proteins, including those similar to transforming growth factor beta and beta-nerve growth factor. CNPV genes lacking homologues in FWPV encode proteins similar to ubiquitin, interleukin-10-like proteins, tumor necrosis factor receptor, PIR1 RNA phosphatase, thioredoxin binding protein, MyD116 domain proteins, circovirus Rep proteins, and the nucleotide metabolism proteins thymidylate kinase and ribonucleotide reductase small subunit. These data reveal genomic differences likely affecting differences in avipoxvirus virulence and host range, and they will likely be useful for the design of improved vaccine vectors.

FIG. 1.

Comparative ORF map of CNPV and FWPV genomes. CNPV ORFs (top) are numbered from left to right based on the position of methionine start codons. ORFs transcribed to the right in each virus are located on top relative to those transcribed to the left; CNPV and selected FWPV genome positions are indicated below each virus. CNPV ORFs (top) are manually aligned with FWPV ORFs (bottom). Colored ORFs indicate differences between CNPV and FWPV: ORFs used to introduce gaps or lacking discernible orthologous sequence in the other virus are marked in green; nonhomologous ORFs in similar genomic positions are marked in blue; ORFs severely disrupted in the opposite virus are marked in yellow; and, due to extensive variability, ORFs in terminal regions marked in orange are unaligned. CNPV ORFs lacking discernible homology to any FWPV ORF are marked above with an asterisk; FWPV ORFs lacking discernible homology to any CNPV ORF are marked above with a triangle. Thick black bars at genomic termini represent ITRs. Boxed regions indicate novel coding regions at junction sites of major genome rearrangements previously identified in FWPV (2), with white indicating gaps between grey sequence.