The evolutionary biology of poxviruses

Abstract

The poxviruses (family Poxviridae) are a family of double-stranded viruses including several species that infect humans and their domestic animals, most notably Variola virus (VARV), the causative agent of smallpox. The evolutionary biology of these viruses poses numerous questions, for which we have only partial answers at present. Here we review evidence regarding the origin of poxviruses, the frequency of host transfer in poxvirus history, horizontal transfer of host genes to poxviruses, and the population processes accounting for patterns of nucleotide sequence polymorphism.

Figure 1

NJ tree (topology only) of poxviruses based on concatenated amino acid sequences from 29 conserved orthologous proteins (13, 475 aligned sites). The tree was constructed on the basis of the JTT amino acid distance, assuming that rate variation among sites follows a gamma distribution (shape parameter a = 0.86). Numbers on the branches represent percentages of 1000 bootstrap samples supporting each branch; only values ≥ 50 % are shown. For accession numbers of genome sequences, see Supplementary Table S1.

Figure 2

NJ tree (topology only) of smallpox virus isolates based on maximum composite likelihood distance at 132 concatenated orthologous protein-coding genes (118, 992 aligned sites). The tree was constructed on the basis of the maximum composite likelihood distance. Numbers on the branches represent percentages of 1000 bootstrap samples supporting each branch; only values ≥ 95 % are shown.

Figure 3

NJ tree of vertebrate interleukin-10 (IL-10) cytokine family members and homologs from poxviruses of mammals. The tree was based on the Poisson-corrected amino acid distance at 110 aligned sites. Numbers on the branches represent percentages of 1000 bootstrap samples supporting each branch; only values ≥ 50 % are shown.

Figure 4

NJ tree of ankyrin repeat-containing proteins from BPSV and ORFV. The tree was based on the Poisson-corrected amino acid distance at 442 aligned sites. Numbers on the branches represent percentages of 1000 bootstrap samples supporting each branch; only values ≥ 50 % are shown.

Figure 5

Figure 3. NJ tree of vertebrate VEGFA and PDGF and homologs from poxviruses of mammals. The tree was based on the Poisson-corrected amino acid distance at 116 aligned sites. Numbers on the branches represent percentages of 1000 bootstrap samples supporting each branch; only values ≥ 50 % are shown.

Figure 6

(A) Plot of the number of nonsynonymous substitutions per nonsynonymous site (d_N) against the number of synonymous substitutions per synonymous site (d_S) for pairwise comparisons among: (1) 132 orthologous protein-coding genes of Variola virus (VARV; red); and (2) complete polyprotein genes of North American West Nile virus (WNV; green). (B) Mean d_N/d_S in pairwise comparisons of VARV, WNV, and Hepatitis C virus 1a (HCV-1a).