The genome of Yoka poxvirus

Abstract

Yoka poxvirus was isolated almost four decades ago from a mosquito pool in the Central African Republic. Its classification as a poxvirus is based solely upon the morphology of virions visualized by electron microscopy. Here we describe sequencing of the Yoka poxvirus genome using a combination of Roche/454 and Illumina next-generation sequencing technologies. A single consensus contig of ∼175 kb in length that encodes 186 predicted genes was generated. Multiple methods were used to show that Yoka poxvirus is most closely related to viruses in the Orthopoxvirus genus, but it is clearly distinct from previously described poxviruses. Collectively, the phylogenetic and genomic sequence analyses suggest that Yoka poxvirus is the prototype member of a new genus in the family Poxviridae.

Fig. 1.

Ultrastructure of Yoka poxvirus. (A) Different stages of assembly and maturation of virions in the cytoplasm of a Vero cell. (B) Mature Yoka poxvirus virions in the cytoplasm of a Vero cell. A fragment of the host cell nucleus can be seen in the lower left corner. Bars, 100 nm.

Fig. 2.

Phylogenetic analysis of Yoka poxvirus. (A) Phylogenetic tree comparing YKV043 to representative sequences of all full-length poxvirus DNA polymerases in the GenBank database as of 25 October 2009. (B) Phylogenetic analysis of the concatenated amino acid sequences of the core 35 ORFs from all species listed in the Chordopoxvirinae subfamily in the ICTV master species list (version 9, 2009) with completely sequenced genomes, as well as the DPV-W84, YLDV, and CMLV-CMS genomes. Multiple sequence alignments were generated using ClustalW. The PHYLIP package (7) was used to generate maximum parsimony phylogenetic trees, and bootstrap values (>90) from 100 replicates are shown.