Evolution of BK virus based on complete genome data
Evolution of BK virus based on complete genome data
复制标题
DOI：
10.1007/s00239-005-0092-5
复制
发表时间：
2006-09-01
影响因子：
3.9
通讯作者：
Yogo, Yoshiaki
中科院分区：
文献类型：
--
作者：
Nishimoto, Yuriko;Takasaka, Tomokazu;Yogo, Yoshiaki
人类多瘤病毒BK病毒（BKV）在人类中普遍存在，无症状地感染儿童。BKV是唯一一种具有可通过免疫反应性区分的亚型（I-IV）的灵长类多瘤病毒。主要衣壳蛋白（VP 1）基因区（称为表位区）的核苷酸（nt）变异可能导致抗原多样性，已被用于将BKV分离株分类为亚型。在这里，所有的蛋白质编码基因序列，我们试图阐明28 BKV分离株属于亚型I，III和IV之间的进化关系（没有分离属于亚型II，一个次要的，包括在内）。首先，使用GTR + Gamma + I模型，为单个病毒基因以及串联的病毒基因重建最大似然树。在所得到的树，28 BKV分离株一致分为三个分支对应亚型I，III和IV，虽然自助概率并不总是很高。然后，我们使用了更复杂的似然模型，其中一个考虑到密码子结构，以阐明BKV亚型之间的系统发育关系，但深分支的系统发育仍然模糊不清。此外，正选择的可能性，在BKV的演变进行了检查，使用非同义/同义率比作为选择的措施。基于整个基因的分析无法检测到任何阳性选择的强有力证据，但基于表位区域的分析确定了一些可能处于阳性选择的位点（这些位点属于显示亚型相关多态性的位点）。
The human polyomavirus BK virus (BKV) is ubiquitous in humans, infecting children asymptomatically. BKV is the only primate polyomavirus that has subtypes (I-IV) distinguishable by immunological reactivity. Nucleotide (nt) variations in a major capsid protein (VP1) gene region (designated the epitope region), probably responsible for antigenic diversity, have been used to classify BKV isolates into subtypes. Here, with all the protein-encoding gene sequences, we attempted to elucidate the evolutionary relationships among 28 BKV isolates belonging to subtypes I, III, and IV (no isolate belonging to subtype II, a minor one, was included). First, using the GTR + Gamma + I model, maximum likelihood trees were reconstructed for individual viral genes as well as for concatenated viral genes. On the resultant trees, the 28 BKV isolates were consistently divided into three clades corresponding to subtypes I, III, and IV, although bootstrap probabilities are not always high. Then we used more sophisticated likelihood models, one of which takes account of codon structure, to elucidate the phylogenetic relationships among BKV subtypes, but the phylogeny of the deep branchings remained ambiguous. Furthermore, the possibility of positive selection in the evolution of BKV was examined using the nonsynonymous/synonymous rate ratio as a measure of selection. An analysis based on entire genes could not detect any strong evidence for positive selection, but that based on the epitope region identified a few sites potentially under positive selection (these sites were among those showing subtype linked polymorphisms).