PHYLOGENETIC ANALYSIS OF 48 PAPILLOMAVIRUS TYPES AND 28 SUBTYPES AND VARIANTS - A SHOWCASE FOR THE MOLECULAR EVOLUTION OF DNA VIRUSES
PHYLOGENETIC ANALYSIS OF 48 PAPILLOMAVIRUS TYPES AND 28 SUBTYPES AND VARIANTS - A SHOWCASE FOR THE MOLECULAR EVOLUTION OF DNA VIRUSES
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DOI：
10.1128/jvi.66.10.5714-5725.1992
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发表时间：
1992-10-01
影响因子：
5.4
通讯作者：
DELIUS, H
中科院分区：
文献类型：
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作者：
CHAN, SY;BERNARD, HU;DELIUS, H
乳头瘤病毒是研究DNA病毒分子进化的有吸引力的模型，因为大量分离株表现出基因组多样性、宿主物种和组织特异性。为了检验它们之间的关系，我们选择了两个氨基酸序列，一个在早期基因El的52个残基中，另一个在晚期基因L1的44个残基中，这使得所有可获得的乳头瘤病毒序列的插入和无缺失比对成为可能。利用距离矩阵法、最大似然法和简约法，从28个已发表的和20个新确定的动物和人乳头瘤病毒（HPV）基因组序列中提取的氨基酸和相应的核苷酸序列构建了系统发育树。这些树在所有重要的拓扑方面都是一致的。一个主要分支有两个明显分离的簇，包含11种与疣状表皮发育不良相关的HPV类型。第二个主要分支包括所有与生殖器肿瘤有关的乳头瘤病毒，在遥远的关系中，皮肤乳头瘤病毒HPV 2a型（HPV-2a）， HPV-3和HPV-10，以及“屠夫”乳头瘤病毒HPV-7和两种类人猿乳头瘤病毒。四种偶蹄类（偶趾蹄类哺乳动物）乳头瘤病毒、棉尾兔乳头瘤病毒和鸟乳头瘤病毒1型形成了第三个主要分支。最后，四种乳头瘤病毒对这三个分支中的任何一个都没有表现出亲和力；这些是皮肤型HPV-1a， HPV-4， HPV-41和b组牛乳头瘤病毒4型。系统发育表明，乳头瘤病毒的一些分支进化仅限于特定的靶组织，并且发生了乳头瘤病毒与宿主长期共同进化的一般过程。后一种假设仍然是推测性的，因为目前人类类型的数据库存在偏差，而且动物乳头瘤病毒序列的缺乏。与HPV-2、HPV-5、HPV-6、HPV-16和HPV-18的28个亚型和变体的进化距离比较，支持该型是一个自然的分类单位，亚型和变体是类似于所有生物物种自然种群中发现的微小型内基因组多样性的表达。HPV-2c似乎是一个例外，它与HPV-2a在型间量级上有一个进化距离，最终可能不得不被视为一个不同的类型。我们描述了一种实验方法，估计新发现的乳头瘤病毒的分类和系统发育位置，而不需要病毒分离和完整的基因组测序。最后，本文还探讨了自然概念，即基于系统发育的乳头瘤病毒分类学；证明了一种HPV变异簇对其最接近的类型亲属的生根；并提出了一种假设的乳头瘤病毒与其他DNA肿瘤病毒的联合系统发育。
Papillomaviruses are attractive models for studying the molecular evolution of DNA viruses because of the large number of isolates that exhibit genomic diversity and host species and tissue specificity. To examine their relationship, we selected two amino acid sequences, one of 52 residues within the early gene El and the other of 44 residues within the late gene L1, which allowed insertion- and deletion-free alignment of all accessible papillomavirus sequences. We constructed phylogenetic trees from the amino acid and corresponding nucleotide sequences from 28 published and 20 newly determined animal and human papillomavirus (HPV) genomic sequences by using distance matrix, maximum-likelihood, and parsimony methods. The trees agreed in all important topological aspects. One major branch with two clearly separated clusters contained 11 HPV types associated with epidermodysplasia verruciformis. A second major branch had all the papillomaviruses involved in genital neoplasia and, in distant relationship, the cutaneous papillomaviruses HPV type 2a (HPV-2a), HPV-3, and HPV-10 as well as the "butcher's" papillomavirus HPV-7 and two simian papillomaviruses. Four artiodactyl (even-toed hoofed mammal) papillomaviruses, the cottontail rabbit papillomavirus, and avian (chaffinch) papillomavirus type 1 formed a third major branch. Last, four papillomaviruses exhibited little affinity to any of these three branches; these were the cutaneous types HPV-1a, HPV-4, and HPV-41 and B-group bovine papillomavirus type 4. The phylogeny suggests that some branches of papillomavirus evolution are restricted to particular target tissues and that a general process of long-term papillomavirus-host coevolution has occurred. This latter hypothesis is still conjectural because of bias in the current data base for human types and the paucity of animal papillomavirus sequences. The comparison of evolutionary distances for the most closely related types with those of 28 subtypes and variants of HPV-2, HPV-5, HPV-6, HPV-16, and HPV-18 supports the type as a natural taxonomic unit, with subtypes and variants being expressions of minor intratype genomic diversity similar to that found in the natural populations of all biological species. An exception to this seems to be HPV-2c, which has an evolutionary distance from HPV-2a of the intertype magnitude and may eventually have to be regarded as a distinct type. We describe an experimental approach that estimates the taxonomic and phylogenetic positions of newly identified papillomaviruses without viral isolation and complete genomic sequencing. Finally, the paper also explores concepts for a natural, i.e., phylogenetically based, papillomavirus taxonomy; demonstrates the rooting of an HPV variant cluster against its closest type relative; and presents a hypothetical combined phylogeny of the papillomaviruses with other DNA tumor viruses.