Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic
Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic
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DOI：
10.1038/nature08182
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发表时间：
2009-06-25
期刊：
影响因子：
64.8
通讯作者：
Rambaut, Andrew
中科院分区：
文献类型：
--
作者：
Smith, Gavin J. D.;Vijaykrishna, Dhanasekaran;Rambaut, Andrew
2009年3月和4月初，一种新的猪源性甲型H1N1流感病毒（S-OIV）在墨西哥和美国出现（1）。在监测的最初几周内，该病毒通过人与人之间的传播在全球范围内传播到30个国家（截至5月11日），导致世界卫生组织将其大流行警报提高到6级的5级。这种病毒有可能发展成为21世纪的第一次流感大流行。在这里，我们使用进化分析来估计的时间尺度的起源和S-OIV流行病的早期发展。我们表明，它是从几个病毒在猪中传播，并首次传播给人类发生在几个月前承认的爆发。对遗传监测差距的系统发育估计表明，在S-OIV爆发之前有很长一段时间的未采样祖先，这表明猪谱系的重配可能在人类出现之前数年就发生了，并且S-OIV的多个遗传祖先并不表明是人工起源。此外，未采样的流行病历史意味着，基因上最接近的猪病毒的性质和位置几乎不能揭示流行病的直接起源，尽管我们纳入了一组密切相关且以前未发表的猪流感分离株。我们的研究结果强调了对猪流感进行系统监测的必要性，并提供了证据表明，猪中新遗传因子的混合可能导致具有人类大流行潜力的病毒的出现（2）。
In March and early April 2009, a new swine-origin influenza A (H1N1) virus (S-OIV) emerged in Mexico and the United States(1). During the first few weeks of surveillance, the virus spread worldwide to 30 countries (as of May 11) by human-to-human transmission, causing the World Health Organization to raise its pandemic alert to level 5 of 6. This virus has the potential to develop into the first influenza pandemic of the twenty-first century. Here we use evolutionary analysis to estimate the time-scale of the origins and the early development of the S-OIV epidemic. We show that it was derived from several viruses circulating in swine, and that the initial transmission to humans occurred several months before recognition of the outbreak. A phylogenetic estimate of the gaps in genetic surveillance indicates a long period of unsampled ancestry before the S-OIV outbreak, suggesting that the reassortment of swine lineages may have occurred years before emergence in humans, and that the multiple genetic ancestry of S-OIV is not indicative of an artificial origin. Furthermore, the unsampled history of the epidemic means that the nature and location of the genetically closest swine viruses reveal little about the immediate origin of the epidemic, despite the fact that we included a panel of closely related and previously unpublished swine influenza isolates. Our results highlight the need for systematic surveillance of influenza in swine, and provide evidence that the mixing of new genetic elements in swine can result in the emergence of viruses with pandemic potential in humans(2).