Protein association and nucleotide sequence similarities among human alpha-papillomaviruses

Human papillomavirus, HPV, is one of the most common sexually transmitted infections in the world, accounting for 50 to 55 percent of all cervical cancers. It is an 8,000 base-pair, latent virus that infects stratified epithelial cells. The Human Papillomavirus Alpha genus strains that contain E5 proteins were compared by E5 protein subtype to depict which E5 proteins are found in cancerous and/or non-cancerous strains. This research also identifies the nucleotide sequence similarity percentages of the cancerous and non-cancerous strains of the Human Papillomavirus Alpha genus. The raw data, which includes the nucleotide sequences and the protein content of the strains, was obtained from the website PaVE: Papillomavirus Genome Database. The E5 Protein Association Network and the Nucleotide Sequence Similarity Percentage Network visualizations were created on ORA, a free network visualization program. The E5 Protein Association Network demonstrates that the E5α protein is the only protein encoded by the cancerous strains, and the majority of the non-cancerous strains contain the E5β protein. The Nucleotide Sequence Similarity Percentage Network illustrates clusters formed after filtering out all links less than 70% similarity, clusters which contain both cancerous and non-cancerous nodes. This indicates that malignancy is not a trait based solely on nucleotide sequence or protein content. This research supports the claim that malignancy of Human Papillomavirus Alpha strains is determined solely by neither protein association nor nucleotide sequence.