Intraseasonal dynamics and dominant sequences in H3N2 influenza.
Intraseasonal dynamics and dominant sequences in H3N2 influenza.
复制标题
DOI：
10.1371/journal.pone.0008544
复制
发表时间：
2010-01-01
期刊：
影响因子：
3.7
通讯作者：
Cohen JE
中科院分区：
文献类型：
--
作者：
Creanza N;Schwarz JS;Cohen JE
流感的长期演变已经得到了很好的研究，但季节内序列多样性的模式还不太清楚。从纽约州十年来采集的H3N2流感基因组样本表明，进化动力学存在季节内变化。使用一组氨基酸或核苷酸序列的平均汉明距离作为其多样性的指标，我们发现，流感序列的多样性是显着高于在流感季节的早期流行期间比后期。多样性在流行高峰期最低，很可能是由于流行高峰期单个显性氨基酸序列或极少数显性序列的高流行，与病毒种群的快速扩张相对应。优势序列的频率和持续时间因流感蛋白而异，但在流行高峰期，所有蛋白质都有一个独特序列的丰度。在纽约州，从1995年到2005年，在早期流行期间的高序列多样性表明，季节性抗原漂移可能主要发生在这一时期，其次是典型的一个分支的克隆扩张在流行的高峰期，可能表明中性漂移或纯化选择的转变。
Long-term influenza evolution has been well studied, but the patterns of sequence diversity within seasons are less clear. H3N2 influenza genomes sampled from New York State over ten years indicated intraseasonal changes in evolutionary dynamics. Using the mean Hamming distance of a set of amino acid or nucleotide sequences as an indicator of its diversity, we found that influenza sequence diversity was significantly higher during the early epidemic period than later in the influenza season. Diversity was lowest during the peak of the epidemic, most likely due to the high prevalence of a single dominant amino acid sequence or very few dominant sequences during the peak epidemic period, corresponding with rapid expansion of the viral population. The frequency and duration of dominant sequences varied by influenza protein, but all proteins had an abundance of one distinct sequence during the peak epidemic period. In New York State from 1995 to 2005, high sequence diversity during the early epidemic suggested that seasonal antigenic drift could have occurred primarily in this period, followed by a clonal expansion of typically one clade during the peak of the epidemic, possibly indicating a shift to neutral drift or purifying selection.
登录
查看更多内容
影响因子：
120.7
作者：
Thompson, WW;Shay, DK;Fukuda, K
通讯作者：
Fukuda, K
影响因子：
64.8
作者：
Rambaut, Andrew;Pybus, Oliver G.;Holmes, Edward C.
通讯作者：
Holmes, Edward C.
影响因子：
56.9
作者：
Russell, Colin A.;Jones, Terry C.;Smith, Derek J.
通讯作者：
Smith, Derek J.
影响因子：
64.8
作者：
Ghedin, E;Sengamalay, NA;Salzberg, SL
通讯作者：
Salzberg, SL
影响因子：
9.8
作者：
Holmes EC;Ghedin E;Miller N;Taylor J;Bao Y;St George K;Grenfell BT;Salzberg SL;Fraser CM;Lipman DJ;Taubenberger JK
通讯作者：
Taubenberger JK