Sakaoka H, Kurita K, Iida Y, Takada S, Umene K, Kim Y T, Ren C S, Nahmias A J
Department of Oral Bacteriology, Hokkaido University, Sapporo, Japan.
J Gen Virol. 1994 Mar;75 ( Pt 3):513-27. doi: 10.1099/0022-1317-75-3-513.
Using the presence or absence of 63 variable restriction endonuclease (RE) sites selected from 225 sites with six REs, genomic polymorphism of 242 herpes simplex virus type 1 (HSV-1) strains from six countries (Japan, Korea, China, Sweden, U.S.A. and Kenya) was quantitatively analysed. Twenty-five of the 63 sites were found to differ between Korean and Kenyan strains. In contrast, only three and six sites were found to differ between isolates from Sweden and the U.S.A. and between those from Korea and China, respectively, suggesting that they are closely related to each other. In this way, characterization of 63 sites enabled us to categorize 186 distinct HSV-1 genotypes from 242 individuals. Some strains from Japan, Korea and China shared the same genotypes, indicating that they are phylogenetically closely related. Many significant correlation coefficients (magnitude of > 0.42; P < 0.01) between pairs of sites were found in isolates from the three Asian countries (Japan, Korea and China) as well as in those from Sweden and the U.S.A., suggesting that HSV-1 strains from within the same ethnic groups are evolutionarily closer. The average number of nucleotide substitutions per nucleotide, as defined by nucleotide diversity (pi), was estimated for HSV-1 genomes within (pi x or pi y) and between (pi xy) countries. On the basis of 225 sites, nucleotide diversity for Kenyan isolates was 0.0056, almost three times higher than that for Korean isolates, implying that Kenyan HSV-1 genomes are much more diverse than those from Korea. In addition, the diversity between HSV-1 isolates from different countries (pi xy) was highest between isolates from the three Asian countries and Kenya (0.0075 to 0.0081) and lowest among those from the three Asian countries (0.0032 to 0.0040). The mutation rate (lambda) for HSV-1 was estimated to be 3.5 x 10(-8)/site/year. All these findings show that the evolution of HSV-1 may be host-dependent and very slow.
利用从225个位点（涉及6种限制性内切酶）中筛选出的63个可变限制性内切酶（RE）位点的有无，对来自六个国家（日本、韩国、中国、瑞典、美国和肯尼亚）的242株单纯疱疹病毒1型（HSV-1）菌株的基因组多态性进行了定量分析。结果发现，韩国和肯尼亚菌株之间有25个位点存在差异。相比之下，瑞典和美国分离株之间以及韩国和中国分离株之间分别只有3个和6个位点存在差异，这表明它们彼此之间关系密切。通过这种方式，对63个位点的特征分析使我们能够将242个个体中的186个不同的HSV-1基因型进行分类。来自日本、韩国和中国的一些菌株具有相同的基因型，这表明它们在系统发育上关系密切。在来自三个亚洲国家（日本、韩国和中国）以及瑞典和美国的分离株中，发现位点对之间存在许多显著的相关系数（幅度>0.42；P<0.01），这表明来自同一族群的HSV-1菌株在进化上更为接近。根据核苷酸多样性（pi）定义，估计了HSV-1基因组在国家内部（pix或piy）和国家之间（pixy）每个核苷酸的平均核苷酸替换数。基于225个位点，肯尼亚分离株的核苷酸多样性为0.0056，几乎是韩国分离株的三倍，这意味着肯尼亚HSV-1基因组的多样性远高于韩国的。此外，不同国家HSV-1分离株之间的多样性（pixy）在三个亚洲国家和肯尼亚的分离株之间最高（0.0075至0.0081），在三个亚洲国家的分离株之间最低（0.0032至0.0040）。HSV-1的突变率（lambda）估计为3.5×10^(-8)/位点/年。所有这些发现表明，HSV-1的进化可能依赖宿主且非常缓慢。
