Evolutionary Dynamics of Local Pandemic H1N1/2009 Influenza Virus Lineages Revealed by Whole-Genome Analysis
Evolutionary Dynamics of Local Pandemic H1N1/2009 Influenza Virus Lineages Revealed by Whole-Genome Analysis
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DOI：
10.1128/jvi.05347-11
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发表时间：
2012-01-01
影响因子：
5.4
通讯作者：
Zambon, Maria
中科院分区：
文献类型：
--
作者：
Baillie, Gregory J.;Galiano, Monica;Zambon, Maria
病毒基因测序和系统发育学可用于研究快速进化病毒的流行病学动态。有了完整的基因组数据，就有可能识别和追踪流行过程中流感病毒等病毒的个别传播链。在这里，我们对来自2009年大流行第一波(127株)和第二波(26株)的153个英国大流行H1N1/09病毒分离株的基因组进行了测序，并使用它们的序列、分离日期和地理位置来推断英国流行的遗传流行病学。我们证明，英国的疫情是由许多循环血统组成的，其中至少有13个是完全或主要是英国聚集性的。其中两个集群的估计偏离时间早于在英国检测到大流行性H1N1/09病毒，这表明在第一个临床病例之前，大流行性H1N1/09病毒已经在联合王国传播。至关重要的是，三个集群包含英国第二波感染的分离物，其中两个代表了似乎在第一波和第二波之间在英国境内持续存在的传播链。这表明，全基因组分析可以详细跟踪单个流感病毒谱系在单一流行病或大流行期间的行为。
Virus gene sequencing and phylogenetics can be used to study the epidemiological dynamics of rapidly evolving viruses. With complete genome data, it becomes possible to identify and trace individual transmission chains of viruses such as influenza virus during the course of an epidemic. Here we sequenced 153 pandemic influenza H1N1/09 virus genomes from United Kingdom isolates from the first (127 isolates) and second (26 isolates) waves of the 2009 pandemic and used their sequences, dates of isolation, and geographical locations to infer the genetic epidemiology of the epidemic in the United Kingdom. We demonstrate that the epidemic in the United Kingdom was composed of many cocirculating lineages, among which at least 13 were exclusively or predominantly United Kingdom clusters. The estimated divergence times of two of the clusters predate the detection of pandemic H1N1/09 virus in the United Kingdom, suggesting that the pandemic H1N1/09 virus was already circulating in the United Kingdom before the first clinical case. Crucially, three clusters contain isolates from the second wave of infections in the United Kingdom, two of which represent chains of transmission that appear to have persisted within the United Kingdom between the first and second waves. This demonstrates that whole-genome analysis can track in fine detail the behavior of individual influenza virus lineages during the course of a single epidemic or pandemic.