Identification of Nucleotide-Level Changes Impacting Gene Content and Genome Evolution in Orthopoxviruses

Abstract

Poxviruses are composed of large double-stranded DNA (dsDNA) genomes coding for several hundred genes whose variation has supported virus adaptation to a wide variety of hosts over their long evolutionary history. Comparative genomics has suggested that the Orthopoxvirus genus in particular has undergone reductive evolution, with the most recent common ancestor likely possessing a gene complement consisting of all genes present in any existing modern-day orthopoxvirus species, similar to the current Cowpox virus species. As orthopoxviruses adapt to new environments, the selection pressure on individual genes may be altered, driving sequence divergence and possible loss of function. This is evidenced by accumulation of mutations and loss of protein-coding open reading frames (ORFs) that progress from individual missense mutations to gene truncation through the introduction of early stop mutations (ESMs), gene fragmentation, and in some cases, a total loss of the ORF. In this study, we have constructed a whole-genome alignment for representative isolates from each Orthopoxvirus species and used it to identify the nucleotide-level changes that have led to gene content variation. By identifying the changes that have led to ESMs, we were able to determine that short indels were the major cause of gene truncations and that the genome length is inversely proportional to the number of ESMs present. We also identified the number and types of protein functional motifs still present in truncated genes to assess their functional significance. IMPORTANCEThis work contributes to our understanding of reductive evolution in poxviruses by identifying genomic remnants such as single nucleotide polymorphisms (SNPs) and indels left behind by evolutionary processes. Our comprehensive analysis of the genomic changes leading to gene truncation and fragmentation was able to detect some of the remnants of these evolutionary processes still present in orthopoxvirus genomes and suggests that these viruses are under continual adaptation due to changes in their environment. These results further our understanding of the evolutionary mechanisms that drive virus variation, allowing orthopoxviruses to adapt to particular environmental niches. Understanding the evolutionary history of these virus pathogens may help predict their future evolutionary potential.

Myxoma Virus and the Leporipoxviruses: An Evolutionary Paradigm

“…The sequence data for RFV and Cal MYXV suggest that in some evolutionary pathways loss of genes is compatible with successful transmission, but whether these genes were actively selected against to enhance transmission by reducing virulence cannot be determined. Similar reductive evolution potentially associated with adaptation to new environments or selection for attenuation has been described in the orthopoxviruses [ 206 , 207 ]. The relatively large number of mutations seen in 50 years of evolution of MYXV in European rabbits potentially provides many pathways by which changes in virulence may occur and, as has occurred in MSW and RFV, it may be that a number of mutations are compatible with increased fitness and that which ones get fixed in the population in the new host species may in part reflect stochastic factors such as local extinction of host populations as much as active selection.…”

Out of the Reservoir: Phenotypic and Genotypic Characterization of a Novel Cowpox Virus Isolated from a Common Vole

“…However, it is clear that FM2292 absolutely and relatively specifies more ORFs (294 in FM2292 versus 289 in RatPox09). The fact that shorter genomes are iso- lated from accidental host species supports the hypothesis of gene loss as a result of adaptation to a new host and may even confirm the hypothesis that CPXV-like genomes represent the phylogenetically oldest representatives of this group of viruses (46,47). Certainly, the functions of the newly annotated ORFs have to be analyzed in more detail.…”

Evolution of and Evolutionary Relationships between Extant Vaccinia Virus Strains

“…The most common differences that are detected by sequencing are single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels), although these mutations accumulate in such great numbers that they provide few insights into the deeper elements of virus phylogenies. Comprehensive analyses of these genomic changes that lead to gene truncation and fragmentation can sometimes detect remnants of the evolutionary process still present in orthopoxvirus genomes (14). Large deletions and other kinds of genome rearrangements are also commonly detected (15,16), especially around the terminal inverted repeats (TIRs) (17), and can significantly affect the lengths of VACV genomes.…”