Prediction of directional changes of influenza A virus genome sequences with emphasis on pandemic H1N1/09 as a model case.
Prediction of directional changes of influenza A virus genome sequences with emphasis on pandemic H1N1/09 as a model case.
复制标题
DOI：
10.1093/dnares/dsr005
复制
发表时间：
2011-04
期刊：
影响因子：
--
通讯作者：
Ikemura T
中科院分区：
文献类型：
--
作者：
Iwasaki Y;Abe T;Wada K;Itoh M;Ikemura T
流感病毒对公众健康构成重大威胁，最近将新的大流行毒株H1N1/09引入人群就是一个例证。大流行是由动物来源发生的新变化引起的，这些变化最终适应于人类。病毒基因组研究，特别是流感病毒基因组研究的一个重要问题是预测基因组序列可能发生的危险变化。我们之前建立了一种称为“BLSOM”（批量学习自组织图）的聚类方法，该方法不依赖于序列比对，甚至可以在一次运行中表征和比较100万个基因组序列。由于核苷酸测序的显著进展，同时比较大量基因组序列的策略在基因组研究中变得越来越重要。在这项研究中，我们基于所有甲型流感病毒株的寡核苷酸和密码子组成构建了BLSOMs。在没有关于其宿主的事先信息的情况下，根据宿主成功地聚集了从禽源或人源分离的菌株的序列。值得注意的是，H1N1/09大流行毒株的寡核苷酸和密码子组成与人类季节性甲型流感毒株明显不同。这使我们能够推断甲型流感病毒基因组未来的方向变化。
Influenza virus poses a significant threat to public health, as exemplified by the recent introduction of the new pandemic strain H1N1/09 into human populations. Pandemics have been initiated by the occurrence of novel changes in animal sources that eventually adapt to human. One important issue in studies of viral genomes, particularly those of influenza virus, is to predict possible changes in genomic sequence that will become hazardous. We previously established a clustering method termed ‘BLSOM’ (batch-learning self-organizing map) that does not depend on sequence alignment and can characterize and compare even 1 million genomic sequences in one run. Strategies for comparing a vast number of genomic sequences simultaneously become increasingly important in genome studies because of remarkable progresses in nucleotide sequencing. In this study, we have constructed BLSOMs based on the oligonucleotide and codon composition of all influenza A viral strains available. Without prior information with regard to their hosts, sequences derived from strains isolated from avian or human sources were successfully clustered according to the hosts. Notably, the pandemic H1N1/09 strains have oligonucleotide and codon compositions that are clearly different from those of human seasonal influenza A strains. This enables us to infer future directional changes in the influenza A viral genome.
影响因子：
8.6
作者：
Wang, Xinran;Ouyang, Yijian;Dai, Hongjie
通讯作者：
Dai, Hongjie