HPV variants from the same type can be classified into lineages and sublineages based on the complete genome differences and the phylogenetic topologies. We examined nucleotide variations of twelve HPV types within the species Alpha-5 (HPV26, 51, 69, 82), Alpha-6 (HPV30, 53, 56, 66), Alpha-11 (HPV34, 73), Alpha-13 (HPV54) and Alpha-3 (HPV61) by analyzing 1432 partial sequences and 181 complete genomes from multiple geographic populations. The inter-lineage and inter-sublineage mean differences of HPV variants ranged between 0.9–7.3% and 0.3–0.9%, respectively. The heterogeneity and phylogenies of HPV isolates indicate an independent evolutionary history for each type. The noncoding regions were the most variable regions whereas the capsid proteins were relatively conserved. Certain variant lineages and/or sublineages were geographically-associated. These data provide the basis to further classify HPV variants and should foster future studies on the evolution of HPV genomes and the associations of HPV variants with cancer risk.

基于完整的基因组差异和系统发育拓扑，可以将来自同一类型的HPV变体分为谱系和亚谱系。我们检查了 Alpha-5（HPV26、51、69、82）、Alpha-6（HPV30、53、56、66）、Alpha-11（HPV34、73）、Alpha-13（ HPV54) 和 Alpha-3 (HPV61) 通过分析来自多个地理人群的 1432 个部分序列和 181 个完整基因组。HPV变异的谱系间和亚系间平均差异分别在0.9-7.3%和0.3-0.9%之间。HPV 分离株的异质性和系统发育表明每种类型都有独立的进化历史。非编码区是最可变区，而衣壳蛋白相对保守。某些变体谱系和/或亚谱系与地理相关。