Phylogenetic Analysis of Papillomavirus E2 Protein and E2BSs. E2 protein amino acid sequences for each of the papillomaviruses were obtained from NCBI and used for COBALT analysis. The resulting multiple alignment was then used to generate a phylogenetic tree to analyze papillomavirus evolution in terms of the E2 protein (a). Clades were identified corresponding to the classical PV genera and indicated on the tree, as well as two subgroups of the alpha-papillomavirus genera (α1 and α2). These were then expanded and examined individually, and the locations of various types of alpha-papillomaviruses (specifically those capable of infecting cutaneous keratinocytes and those possessing a high-risk of progression to cervical cancer) were indicated (b). HPV E2BSs from part one were then reanalyzed using MEME software to identify a consensus E2BS for each of the subgroups identified in 2b, i.e., subgroup α1 and α2, (high and low-risk alpha-papillomaviruses), as well as those capable of infecting cutaneous keratinocytes tissue (c). Alpha E2BSs of were analyzed for changes in the 4-base pair sequence spacer (d). Each of the four E2 binding sites, numbered 1-4 starting from the closest to the p97 promoter, were analyzed for position-specific differences in the 4-base-pair spacer sequence between alpha subgroups (α1 and α2).