We investigated the selection pressures on the haemagglutinin genes of H5N1 avian influenza viruses using fixed effects likelihood models. We found evidence of positive selection in the sequences from isolates from 19...We investigated the selection pressures on the haemagglutinin genes of H5N1 avian influenza viruses using fixed effects likelihood models. We found evidence of positive selection in the sequences from isolates from 1997 to 2007, except viruses from 2000. The haemagglutinin sequences of viruses from southeast Asia, Hong Kong and China's Mainland were the most polymorphic and had similar nonsyn-onymous profiles. Some sites were positively selected in viruses from most regions and a few of these sites displayed different amino acid patterns. Selection appeared to produce different outcomes in vi-ruses from Europe, Africa and Russia and from different host types. One position was found to be positively selected for human isolates only. Although the functions of some positively selected posi-tions are unknown, our analysis provided evidence of different temporal, spatial and host adaptations for H5N1 avian influenza viruses.展开更多
目的分析相关疫苗上市后中国大陆肠道病毒71型(enterovirus type 71,EV71)C4亚型的分子流行特征。方法基于贝叶斯的马尔可夫链蒙特卡罗(markov chain monte carlo,MCMC)分析方法,对EV71疫苗上市前后中国大陆EV71毒株VP1基因相似性进行...目的分析相关疫苗上市后中国大陆肠道病毒71型(enterovirus type 71,EV71)C4亚型的分子流行特征。方法基于贝叶斯的马尔可夫链蒙特卡罗(markov chain monte carlo,MCMC)分析方法,对EV71疫苗上市前后中国大陆EV71毒株VP1基因相似性进行比较。应用贝叶斯天际线模型和SpreaD3 v0.9.6软件对中国大陆C4亚型病毒进行系统发生地理学分析,通过绘制贝叶斯天际线图描绘种群动态历史变化,并应用EasyCodeML软件分析正选择压力位点。结果中国大陆EV71 C4亚型VP1基因序列的平均进化速率为2.25×10-3 site/year,C4a亚型毒株平均进化速率为3.1×10-3 site/year;EV71 C4亚型的起源可追溯至1990年的华东地区,C4a亚型可能起源于1999年。2002—2007年C4亚型经历了种群规模扩张,种群规模于2007年达峰值,且在EV71疫苗上市后仍保持较高水平。C4亚型病毒VP1基因中有5个氨基酸位点承受正选择压力,比对分析EV71疫苗上市后2015—2018年C4亚型病毒序列,筛选到VP1基因第289位点承受正选择压力。结论本研究揭示了EV71 C4亚型的遗传进化信息,为制定手足口病(hand,foot and mouth disease,HFMD)的防控策略提供了科学的数据支持。展开更多
文摘We investigated the selection pressures on the haemagglutinin genes of H5N1 avian influenza viruses using fixed effects likelihood models. We found evidence of positive selection in the sequences from isolates from 1997 to 2007, except viruses from 2000. The haemagglutinin sequences of viruses from southeast Asia, Hong Kong and China's Mainland were the most polymorphic and had similar nonsyn-onymous profiles. Some sites were positively selected in viruses from most regions and a few of these sites displayed different amino acid patterns. Selection appeared to produce different outcomes in vi-ruses from Europe, Africa and Russia and from different host types. One position was found to be positively selected for human isolates only. Although the functions of some positively selected posi-tions are unknown, our analysis provided evidence of different temporal, spatial and host adaptations for H5N1 avian influenza viruses.
文摘目的分析相关疫苗上市后中国大陆肠道病毒71型(enterovirus type 71,EV71)C4亚型的分子流行特征。方法基于贝叶斯的马尔可夫链蒙特卡罗(markov chain monte carlo,MCMC)分析方法,对EV71疫苗上市前后中国大陆EV71毒株VP1基因相似性进行比较。应用贝叶斯天际线模型和SpreaD3 v0.9.6软件对中国大陆C4亚型病毒进行系统发生地理学分析,通过绘制贝叶斯天际线图描绘种群动态历史变化,并应用EasyCodeML软件分析正选择压力位点。结果中国大陆EV71 C4亚型VP1基因序列的平均进化速率为2.25×10-3 site/year,C4a亚型毒株平均进化速率为3.1×10-3 site/year;EV71 C4亚型的起源可追溯至1990年的华东地区,C4a亚型可能起源于1999年。2002—2007年C4亚型经历了种群规模扩张,种群规模于2007年达峰值,且在EV71疫苗上市后仍保持较高水平。C4亚型病毒VP1基因中有5个氨基酸位点承受正选择压力,比对分析EV71疫苗上市后2015—2018年C4亚型病毒序列,筛选到VP1基因第289位点承受正选择压力。结论本研究揭示了EV71 C4亚型的遗传进化信息,为制定手足口病(hand,foot and mouth disease,HFMD)的防控策略提供了科学的数据支持。
