Department of Pathology and Laboratory Medicine, University of British Columbia, Canada.
J Bioinform Comput Biol. 2020 Feb;18(1):2050012. doi: 10.1142/S0219720020500122.
Readhead recently reported in the detection and association of human herpesviruses 6A (HHV6A) and 7 (HHV7) with Alzheimer's disease by shotgun sequencing. I was skeptical of the specificity of their modified Viromescan bioinformatics method and subsequent analysis for numerous reasons. Using their supplementary data, the prevalence of variola virus, the etiological agent of the eradicated disease smallpox, can be calculated at 97.5% of their Mount Sinai Brain Bank dataset. Reanalysis of Readhead 's data using highly sensitive and specific alternative methods finds no HHV7 reads in their samples; HHV6A reads were found in only 2 out of their top 15 samples sorted by reported HHV6A abundance. Finally, recreation of Readhead 's modified Viromescan method identifies reasons for its low specificity.
里德黑德（Readhead）最近在通过鸟枪法测序报告了人类疱疹病毒 6A（HHV6A）和 7（HHV7）与阿尔茨海默病的检测和关联。我对他们改进的 Viromescan 生物信息学方法及其后续分析的特异性持怀疑态度，原因有很多。使用他们的补充数据，可以计算出已根除疾病天花的病原体天花病毒在他们的西奈山脑库数据集的流行率为 97.5%。使用高度敏感和特异的替代方法重新分析里德黑德的数据，在他们的样本中没有发现 HHV7 的读取；在按报道的 HHV6A 丰度排序的前 15 个样本中，只有 2 个样本中发现 HHV6A 读取。最后，重新创建里德黑德的改进 Viromescan 方法确定了其低特异性的原因。
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