Related strains of African swine fever virus with different virulence: genome comparison and analysis.

Two strains of African swine fever virus (ASFV), the high-virulence Lisboa60 (L60) and the low-virulence NH/P68 (NHV), which have previously been used in effective immunization/protection studies, were sequenced. Both were isolated in Portugal during the 11-year period after the introduction of ASFV to the European Continent in 1957. The predicted proteins coded by both strains were compared, and where differences were found these were also compared to other strains of known virulence. This highlighted several genes with significant alterations in low-virulence strains of ASFV that may constitute virulence factors, several of which are still uncharacterized regarding their function. Phylogenetic analysis grouped L60 and NHV closest to other P72 genotype I ASFV strains from Europe and West Africa, consistent with the assumed West African origin of all European strains. Interestingly, a relatively lower genomic identity exists between L60 and NHV, both isolated in a similar geographical location 8 years apart, than with other European and west African strains isolated subsequently and in more distant locations. This may reflect the intensive passage in tissue culture, during the early 1960s, of a Portuguese isolate to obtain an attenuated vaccine, which may have led to NHV. This study contributes to a better understanding of the evolution of ASFV, and defines additional potential virulence genes for future studies of pathogenesis towards the development of effective vaccines.

The genome of Yoka poxvirus.

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.

Prediction of a novel RNA binding domain in crocodilepox Zimbabwe Gene 157.

BACKGROUND: Although the crocodilepox virus (CRV) is currently unclassified, phylogenetic analyses suggest that its closest known relatives are molluscum contagiosum virus (MCV) and the avipox viruses. The CRV genome is approximately 190 kb and contains a large number of unique genes in addition to the set of conserved Chordopoxvirus genes found in all such viruses. Upon sequencing the viral genome, others noted that this virus was also unusual because of the lack of a series of common immuno-suppressive genes. However, the genome contains multiple genes of unknown function that are likely to function in reducing the anti-viral response of the host. RESULTS: By using sensitive database searches for similarity, we observed that gene 157 of CRV-strain Zimbabwe (CRV-ZWE) encodes a protein with a domain that is predicted to bind dsRNA. Domain characterization supported this prediction, therefore, we tested the ability of the Robetta protein structure prediction server to model the amino acid sequence of this protein on a well-characterized RNA binding domain. The model generated by Robetta suggests that CRV-ZWE-157 does indeed contain an RNA binding domain; the model could be overlaid on the template protein structure with high confidence. CONCLUSION: We hypothesize that CRV-ZWE-157 encodes a novel poxvirus RNA binding protein and suggest that as a non-core gene it may play a role in host-range determination or function to dampen host anti-viral responses. Potential targets for this CRV protein include the host interferon response and miRNA pathways.