PDF(Pubmed)
Abstract：
DNA viruses that produce persistent infections have been proposed as potential causes for the extinction of Neanderthals, and, therefore, the identification of viral genome remnants in Neanderthal sequence reads is an initial step to address this hypothesis. Here, as proof of concept, we searched for viral remnants in sequence reads of Neanderthal genome data by mapping to adenovirus, herpesvirus and papillomavirus, which are double-stranded DNA viruses that may establish lifelong latency and can produce persistent infections. The reconstructed ancient viral genomes of adenovirus, herpesvirus and papillomavirus revealed conserved segments, with nucleotide identity to extant viral genomes and variable regions in coding regions with substantial divergence to extant close relatives. Sequence reads mapped to extant viral genomes showed deamination patterns of ancient DNA, and these ancient viral genomes showed divergence consistent with the age of these samples (≈50,000 years) and viral evolutionary rates (10-5 to 10-8 substitutions/site/year). Analysis of random effects showed that the Neanderthal mapping to genomes of extant persistent viruses is above what is expected by random similarities of short reads. Also, negative control with a nonpersistent DNA virus does not yield statistically significant assemblies. This work demonstrates the feasibility of identifying viral genome remnants in archaeological samples with signal-to-noise assessment.
摘要：
产生持续感染的DNA病毒被认为是尼安德特人灭绝的潜在原因，and,因此,尼安德特人序列读段中病毒基因组残留物的鉴定是解决这一假设的第一步.这里,作为概念的证明，我们通过绘制腺病毒来搜索尼安德特人基因组数据序列中的病毒残留物，疱疹病毒和乳头状瘤病毒，它们是双链DNA病毒，可以建立终身潜伏期，并可以产生持续的感染。重建的腺病毒古老的病毒基因组，疱疹病毒和乳头状瘤病毒揭示了保守的片段，与现存的病毒基因组和编码区的可变区具有核苷酸同一性，与现存的近亲有很大的分歧。映射到现有病毒基因组的序列读数显示了古代DNA的脱氨基模式，这些古老的病毒基因组显示出与这些样本的年龄（约50,000年）和病毒进化率（10-5至10-8个替换/位点/年）一致的差异。随机效应的分析表明，尼安德特人对现有持久性病毒基因组的映射高于短读段的随机相似性所预期的。此外，使用非持久性DNA病毒的阴性对照不产生统计学上显著的装配。这项工作证明了通过信噪比评估来识别考古样本中病毒基因组残留物的可行性。
