Chan S Y, Delius H, Halpern A L, Bernard H U
Laboratory for Papillomavirus Biology, National University of Singapore.
J Virol. 1995 May;69(5):3074-83. doi: 10.1128/JVI.69.5.3074-3083.1995.
Our aim was to study the phylogenetic relationships of all known papillomaviruses (PVs) and the possibility of establishing a supratype taxonomic classification based on this information. Of the many detectably homologous segments present in PV genomes, a 291-bp segment of the L1 gene is notable because it is flanked by the MY09 and MY11 consensus primers and contains highly conserved amino acid residues which simplify sequence alignment. We determined the MY09-MY11 sequences of human PV type 20 (HPV-20), HPV-21, HPV-22, HPV-23, HPV-24, HPV-36, HPV-37, HPV-38, HPV-48, HPV-50, HPV-60, HPV-70, HPV-72, HPV-73, ovine (sheep) PV, bovine PV type 3 (BPV-3), BPV-5, and BPV-6 and created a database which now encompasses HPV-1 to HPV-70, HPV-72, HPV-73, seven yet untyped HPV genomes, and 15 animal PV types. Three additional animal PVs were analyzed on the basis of other sequence data. We constructed phylogenies based on partial L1 and E6 gene sequences and distinguished five major clades that we call supergroups. One of them unites 54 genital PV types, which can be further divided into eleven groups. The second supergroup has 24 types and unites most PVs that are typically found in epidermodysplasia verruciformis patients but also includes several types typical of other cutaneous lesions, like HPV-4. The third supergroup unites the six known ungulate fibropapillomaviruses, the fourth includes the cutaneous ungulate PVs BPV-3, BPV-4, and BPV-6, and the fifth includes HPV-1, HPV-41, HPV-63, the canine oral PV, and the cottontail rabbit PV. The chaffinch PV and two rodent PVs, Micromys minutus PV and Mastomys natalensis PV, are left ungrouped because of the relative isolation of each of their lineages. Within most supergroups, groups formed on the basis of cladistic principles unite phenotypically similar PV types. We discuss the basis of our classification, the concept of the PV type, speciation, PV-host evolution, and estimates of their rates of evolution.
我们的目标是研究所有已知乳头瘤病毒（PVs）的系统发育关系，以及基于这些信息建立超型分类学分类的可能性。在PV基因组中存在的许多可检测到的同源片段中，L1基因的一个291bp片段值得注意，因为它两侧是MY09和MY11共有引物，并且包含高度保守的氨基酸残基，这简化了序列比对。我们测定了人乳头瘤病毒20型（HPV-20）、HPV-21、HPV-22、HPV-23、HPV-24、HPV-36、HPV-37、HPV-38、HPV-48、HPV-50、HPV-60、HPV-70、HPV-72、HPV-73、绵羊乳头瘤病毒、牛乳头瘤病毒3型（BPV-3）、BPV-5和BPV-6的MY09-MY11序列，并创建了一个数据库，该数据库现在涵盖了HPV-1至HPV-70、HPV-72、HPV-73、7个尚未分型的HPV基因组以及15种动物乳头瘤病毒类型。基于其他序列数据对另外三种动物乳头瘤病毒进行了分析。我们基于部分L1和E6基因序列构建了系统发育树，并区分出五个主要分支，我们将其称为超群。其中一个超群包含54种生殖器乳头瘤病毒类型，可进一步分为11组。第二个超群有24种类型，包含大多数通常在疣状表皮发育不良患者中发现的乳头瘤病毒，但也包括其他皮肤病变典型的几种类型，如HPV-4。第三个超群包含六种已知的有蹄类动物纤维乳头瘤病毒，第四个包括有蹄类动物皮肤乳头瘤病毒BPV-3、BPV-4和BPV-6，第五个包括HPV-1、HPV-41、HPV-63、犬口腔乳头瘤病毒和棉尾兔乳头瘤病毒。金翅雀乳头瘤病毒以及两种啮齿动物乳头瘤病毒，即小家鼠乳头瘤病毒和南非多乳鼠乳头瘤病毒，由于其各自谱系的相对孤立而未分组。在大多数超群中，基于分支分类原则形成的组将表型相似的乳头瘤病毒类型归为一类。我们讨论了我们分类的基础、乳头瘤病毒类型的概念、物种形成、乳头瘤病毒-宿主进化以及它们进化速率的估计。
