Herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) are ubiquitous human pathogens. Both viruses evolved from simplex viruses infecting African primates and they are thus thought to have left Africa during early human migrations. We analyzed the population structure of HSV-1 and HSV-2 circulating strains. Results indicated that HSV-1 populations have limited geographic structure and the most evident clustering by geography is likely due to recent bottlenecks. For HSV-2, the only level of population structure is accounted for by the so-called "worldwide" and "African" lineages. Analysis of ancestry components and nucleotide diversity, however, did not support the view that the worldwide lineage followed early humans during out-of-Africa dispersal. Although phylogeographic analysis confirmed an African origin for both viruses, molecular dating with a method that corrects for the time-dependent rate phenomenon indicated that HSV-1 and HSV-2 migrated from Africa in relatively recent times. In particular, we estimated that the HSV-2 worldwide lineage left the continent in the 18th century, which corresponds to the height of the transatlantic slave trade, possibly explaining the high prevalence of HSV-2 in the Americas (second highest after Africa). The limited geographic clustering of HSV-1 makes it difficult to date its exit from Africa. The split between the basal clade, containing mostly African sequences, and all other strains was dated at ∼5,000 years ago. Our data do not imply that herpes simplex viruses did not infect early humans but show that the worldwide distribution of circulating strains is the result of relatively recent events.

中文翻译：

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人类单纯疱疹病毒的最近非洲外迁移。

1型和2型单纯疱疹病毒（HSV-1和HSV-2）是普遍存在的人类病原体。两种病毒都是从感染非洲灵长类动物的单纯病毒演变而来的，因此被认为是在人类早期迁徙期间离开非洲的。我们分析了HSV-1和HSV-2循环菌株的种群结构。结果表明，HSV-1人口的地理结构有限，并且根据地理分布，最明显的聚类可能是由于最近的瓶颈。对于HSV-2，人口结构的唯一层次是所谓的“世界范围”和“非洲”血统。然而，对祖先成分和核苷酸多样性的分析并不支持这样的观点，即在非洲以外的传播过程中，世界谱系遵循了早期人类。尽管系统地理分析证实这两种病毒都来自非洲，用校正时间依赖性速率现象的方法进行的分子测年表明，HSV-1和HSV-2在相对较近的时间从非洲迁移。特别是，我们估计，HSV-2的全球血统在18世纪离开了非洲大陆，这与跨大西洋奴隶贸易的高度相对应，这可能解释了HSV-2在美洲的高流行（仅次于非洲）。HSV-1的地理区域有限，因此很难确定其从非洲撤离的时间。基底进化枝（主要包含非洲序列）与所有其他菌株之间的分裂可追溯到大约5,000年前。我们的数据并不意味着单纯疱疹病毒并未感染早期人类，但表明循环菌株的全球分布是相对较新事件的结果。