Department of Biology, Center for Advanced Research in Environmental Genomics, University of Ottawa Ottawa, ON, Canada ; Department of Mathematics and Statistics, University of Ottawa Ottawa, ON, Canada.
Evol Appl. 2014 Mar;7(3):403-12. doi: 10.1111/eva.12138. Epub 2014 Jan 2.
Influenza is one of the most severe respiratory infections affecting humans throughout the world, yet the dynamics of its global transmission network are still contentious. Here, I describe a novel combination of phylogenetics, time series, and graph theory to analyze 14.25 years of data stratified in space and in time, focusing on the main target of the human immune response, the hemagglutinin gene. While bypassing the complete phylogenetic inference of huge data sets, the method still extracts information suggesting that waves of genetic or of nucleotide diversity circulate continuously around the globe for subtypes that undergo sustained transmission over several seasons, such as H3N2 and pandemic H1N1/09, while diversity of prepandemic H1N1 viruses had until 2009 a noncontinuous transmission pattern consistent with a source/sink model. Irrespective of the shift in the structure of H1N1 diversity circulation with the emergence of the pandemic H1N1/09 strain, US prevalence peaks during the winter months when genetic diversity is at its lowest. This suggests that a dominant strain is generally responsible for epidemics and that monitoring genetic and/or nucleotide diversity in real time could provide public health agencies with an indirect estimate of prevalence.
流感是全球范围内影响人类的最严重的呼吸道传染病之一，但流感全球传播网络的动态仍然存在争议。在这里，我描述了一种将系统发生学、时间序列和图论相结合的新方法，以分析 14.25 年的时空分层数据，重点关注人类免疫反应的主要靶标——血凝素基因。该方法绕过了对庞大数据集进行完整的系统发生推断，仍然提取出信息，表明在经历了几个季节持续传播的亚型（如 H3N2 和大流行性 H1N1/09）中，遗传或核苷酸多样性的波连续不断地在全球范围内循环，而大流行性 H1N1/09 出现之前的 H1N1 病毒多样性的传播模式直到 2009 年为止是非连续的，与源/汇模型一致。大流行性 H1N1/09 株的出现并未改变 H1N1 多样性循环结构，美国的流行高峰期仍出现在冬季，此时遗传多样性最低。这表明，一种主要流行株通常会引发流行，实时监测遗传和/或核苷酸多样性可以为公共卫生机构提供流行率的间接估计。
