Peng Jin, Yang Hao, Jiang Hua, Lin Yi-xiao, Lu Charles Damien, Xu Ya-wei, Zeng Jun
Department of Computational Mathematics and Bio-Statistics, Metabolomics and Multidisciplinary Laboratory for Trauma Research, Institute for Emergency and Disaster Medicine, Sichuan Provincial People's Hospital, Sichuan Academy of Medical Sciences, Chengdu, Sichuan Province, China.
Department of Computational Mathematics and Bio-Statistics, Metabolomics and Multidisciplinary Laboratory for Trauma Research, Institute for Emergency and Disaster Medicine, Sichuan Provincial People's Hospital, Sichuan Academy of Medical Sciences, Chengdu, Sichuan Province, China; Emergency Medicine Center, Sichuan Provincial People's Hospital, Sichuan Academy of Medical Sciences, Chengdu, Sichuan Province, China.
PLoS One. 2014 Mar 26;9(3):e93094. doi: 10.1371/journal.pone.0093094. eCollection 2014.
In February 2013, H7N9 (A/H7N9/2013_China), a novel avian influenza virus, broke out in eastern China and caused human death. It is a global priority to discover its origin and the point in time at which it will become transmittable between humans. We present here an interdisciplinary method to track the origin of H7N9 virus in China and to establish an evolutionary dynamics model for its human-to-human transmission via mutations. After comparing influenza viruses from China since 1983, we established an A/H7N9/2013_China virus evolutionary phylogenetic tree and found that the human instances of virus infection were of avian origin and clustered into an independent line. Comparing hemagglutinin (HA) and neuraminidase (NA) gene sequences of A/H7N9/2013_China viruses with all human-to-human, avian, and swine influenza viruses in China in the past 30 years, we found that A/H7N9/2013_China viruses originated from Baer's Pochard H7N1 virus of Hu Nan Province 2010 (HA gene, EPI: 370846, similarity with H7N9 is 95.5%) and duck influenza viruses of Nanchang city 2000 (NA gene, EPI: 387555, similarity with H7N9 is 97%) through genetic re-assortment. HA and NA gene sequence comparison indicated that A/H7N9/2013_China virus was not similar to human-to-human transmittable influenza viruses. To simulate the evolution dynamics required for human-to-human transmission mutations of H7N9 virus, we employed the Markov model. The result of this calculation indicated that the virus would acquire properties for human-to-human transmission in 11.3 years (95% confidence interval (CI): 11.2-11.3, HA gene).
2013年2月，一种新型禽流感病毒H7N9（A/H7N9/2013_中国）在中国东部爆发并导致人类死亡。发现其起源以及它将在何时变得可在人际间传播是全球优先事项。我们在此提出一种跨学科方法，用于追踪中国H7N9病毒的起源，并建立其通过突变实现人际传播的进化动力学模型。在比较了自1983年以来来自中国的流感病毒后，我们建立了A/H7N9/2013_中国病毒进化系统发育树，发现人类病毒感染实例起源于禽类，并聚集成一个独立的谱系。将A/H7N9/2013_中国病毒的血凝素（HA）和神经氨酸酶（NA）基因序列与过去30年中国所有人际传播、禽类和猪流感病毒进行比较，我们发现A/H7N9/2013_中国病毒通过基因重配起源于2010年湖南省的白眼潜鸭H7N1病毒（HA基因，EPI：370846，与H7N9的相似度为95.5%）和2000年南昌市的鸭流感病毒（NA基因，EPI：387555，与H7N9的相似度为97%）。HA和NA基因序列比较表明，A/H7N9/2013_中国病毒与人际传播的流感病毒不相似。为了模拟H7N9病毒人际传播突变所需的进化动力学，我们采用了马尔可夫模型。该计算结果表明，该病毒将在11.3年内获得人际传播特性（95%置信区间（CI）：11.2 - 11.3，HA基因）。
