Molecular evolutionary analysis of the influenza A(H1N1)pdm, May-September, 2009: temporal and spatial spreading profile of the viruses in Japan.
Molecular evolutionary analysis of the influenza A(H1N1)pdm, May-September, 2009: temporal and spatial spreading profile of the viruses in Japan.
复制标题
DOI：
10.1371/journal.pone.0011057
复制
发表时间：
2010-06-10
期刊：
影响因子：
3.7
通讯作者：
Watanabe H
中科院分区：
文献类型：
--
作者：
Shiino T;Okabe N;Yasui Y;Sunagawa T;Ujike M;Obuchi M;Kishida N;Xu H;Takashita E;Anraku A;Ito R;Doi T;Ejima M;Sugawara H;Horikawa H;Yamazaki S;Kato Y;Oguchi A;Fujita N;Odagiri T;Tashiro M;Watanabe H
2009年3月，墨西哥和美国出现了甲型H1N1流感大流行（A（H1N1）pdm）。在日本，自2009年5月中旬在大坂和兵库县首次爆发甲型H1N1流感以来，截至2009年6月4日，该病毒已蔓延到47个县中的16个。我们分析了日本75株A（H1N1）pdm病毒分离株的全片段连接基因组序列，并将其与世界上163株全基因组序列进行了比较。两种分析方法，基于距离和贝叶斯结合MCMC推理，阐明了在世界和日本的病毒的进化关系。无论采用哪种方法，世界上的病毒都被分为四个不同的集群，只有少数例外。第一组起源于第二组，而第二组在世界范围内传播得更广。另外两个集群（集群1.2和1.3）被认为是不同的reflectants与不同类型的节段扩展。日本的病毒似乎是多源性的，源自约28例转运病例。12例病例与由日本病毒组成的单系群有关，这些单系群被称为微进化枝。虽然大多数微分支属于聚类2，但日本首例感染病例的分支起源于聚类1.2。大坂/科比和福冈病例的微分支都是学校范围内的暴发，已被根除。每个微进化枝的最近共同祖先时间（tMRCA）表明，2009年5月下旬至6月上旬，一些不同的病毒在日本传播，并出现在整个夏季全国范围内传播。我们的研究结果表明，许多病毒在2009年5月下旬从国外传播，而不管对大流行性流感的预防措施，甲型H1N1流感pdm已成为2009年6月在日本的大流行阶段。
In March 2009, pandemic influenza A(H1N1) (A(H1N1)pdm) emerged in Mexico and the United States. In Japan, since the first outbreak of A(H1N1)pdm in Osaka and Hyogo Prefectures occurred in the middle of May 2009, the virus had spread over 16 of 47 prefectures as of June 4, 2009. We analyzed all-segment concatenated genome sequences of 75 isolates of A(H1N1)pdm viruses in Japan, and compared them with 163 full-genome sequences in the world. Two analyzing methods, distance-based and Bayesian coalescent MCMC inferences were adopted to elucidate an evolutionary relationship of the viruses in the world and Japan. Regardless of the method, the viruses in the world were classified into four distinct clusters with a few exceptions. Cluster 1 was originated earlier than cluster 2, while cluster 2 was more widely spread around the world. The other two clusters (clusters 1.2 and 1.3) were suggested to be distinct reassortants with different types of segment assortments. The viruses in Japan seemed to be a multiple origin, which were derived from approximately 28 transported cases. Twelve cases were associated with monophyletic groups consisting of Japanese viruses, which were referred to as micro-clade. While most of the micro-clades belonged to the cluster 2, the clade of the first cases of infection in Japan originated from cluster 1.2. Micro-clades of Osaka/Kobe and the Fukuoka cases, both of which were school-wide outbreaks, were eradicated. Time of most recent common ancestor (tMRCA) for each micro-clade demonstrated that some distinct viruses were transmitted in Japan between late May and early June, 2009, and appeared to spread nation-wide throughout summer. Our results suggest that many viruses were transmitted from abroad in late May 2009 irrespective of preventive actions against the pandemic influenza, and that the influenza A(H1N1)pdm had become a pandemic stage in June 2009 in Japan.
登录
查看更多内容
影响因子：
9.8
作者：
Drummond AJ;Ho SY;Phillips MJ;Rambaut A
通讯作者：
Rambaut A
影响因子：
5.8
作者：
Larkin, M. A.;Blackshields, G.;Higgins, D. G.
通讯作者：
Higgins, D. G.
DOI：
10.1073/pnas.0404206101
发表时间：
2004-07-27
影响因子：
11.1
作者：
Tamura, K;Nei, M;Kumar, S
通讯作者：
Kumar, S
影响因子：
158.5
作者：
Lessler, Justin;Reich, Nicholas G.;Cummings, Derek A. T.
通讯作者：
Cummings, Derek A. T.
影响因子：
10.7
作者：
Tamura, Koichiro;Dudley, Joel;Kumar, Sudhir
通讯作者：
Kumar, Sudhir