Reassortment patterns of avian influenza virus internal segments among different subtypes.
Reassortment patterns of avian influenza virus internal segments among different subtypes.
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DOI：
10.1186/1471-2148-14-16
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发表时间：
2014-01-24
影响因子：
3.4
通讯作者：
Leigh Brown AJ
中科院分区：
文献类型：
--
作者：
Lu L;Lycett SJ;Leigh Brown AJ
禽流感病毒(AIV)的节段性RNA基因组允许共感染病毒之间的基因重组，为产生基因创新提供了一条进化途径。禽流感病毒的遗传多样性(16个血凝素亚型和9个神经氨酸酶亚型)表明，禽流感病毒在鸟类种群中存在广泛的储存库，但亚型之间重新组合的频率仍不清楚。在这里，我们通过将亚型的祖先状态重建为相对于内部蛋白质编码片段的时间尺度系统发育上的离散状态，来量化欧亚禽类病毒库中各亚型之间的重新分类模式。我们进一步分析了寄主种类、推测的进化率和dN/ds比率在不同节段和不同亚型之间的差异，以及这些因素是否可能与亚型间的重排速度有关。除了编码非结构基因的片段8外，五个内部片段之间的一般重排模式相似，它的系统发育更不同。然而，不同亚型之间的发病率存在显著差异。特别是，与H1至H4相比，H5至H9亚型的血凝素编码片段的重排速率较低，而N1和N2亚型的神经氨酸酶编码片段的重排频率低于N3至N9。寄主种类和dN/ds比值与重配率显著相关，而进化率与重配率无关。DN/ds比率与重组率呈负相关，所有片段的阴性选择位点数也呈负相关。这些结果表明，总体选择限制和寄主种类都与重组率有关。这些结果共同确定了野生鸟类种群是新重组物的主要来源，而不是家禽。观察到的H5N1和H9N1较低的重组率可能是由于来自家禽种群的菌株所占比例较大。相比之下，在H1N1、H3N8和H4N6亚型中观察到的较高发病率可能是由于它们的主要来源是感染了大型禽类水库中具有多种低致病性毒株的野鸟。
The segmented RNA genome of avian Influenza viruses (AIV) allows genetic reassortment between co-infecting viruses, providing an evolutionary pathway to generate genetic innovation. The genetic diversity (16 haemagglutinin and 9 neuraminidase subtypes) of AIV indicates an extensive reservoir of influenza viruses exists in bird populations, but how frequently subtypes reassort with each other is still unknown. Here we quantify the reassortment patterns among subtypes in the Eurasian avian viral pool by reconstructing the ancestral states of the subtypes as discrete states on time-scaled phylogenies with respect to the internal protein coding segments. We further analyzed how host species, the inferred evolutionary rates and the dN/dS ratio varied among segments and between discrete subtypes, and whether these factors may be associated with inter-subtype reassortment rate. The general patterns of reassortment are similar among five internal segments with the exception of segment 8, encoding the Non-Structural genes, which has a more divergent phylogeny. However, significant variation in rates between subtypes was observed. In particular, hemagglutinin-encoding segments of subtypes H5 to H9 reassort at a lower rate compared to those of H1 to H4, and Neuraminidase-encoding segments of subtypes N1 and N2 reassort less frequently than N3 to N9. Both host species and dN/dS ratio were significantly associated with reassortment rate, while evolutionary rate was not associated. The dN/dS ratio was negatively correlated with reassortment rate, as was the number of negatively selected sites for all segments. These results indicate that overall selective constraint and host species are both associated with reassortment rate. These results together identify the wild bird population as the major source of new reassortants, rather than domestic poultry. The lower reassortment rates observed for H5N1 and H9N2 may be explained by the large proportion of strains derived from domestic poultry populations. In contrast, the higher rates observed in the H1N1, H3N8 and H4N6 subtypes could be due to their primary origin as infections of wild birds with multiple low pathogenicity strains in the large avian reservoir.
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