Homologous recombination is very rare or absent in human influenza A virus
Homologous recombination is very rare or absent in human influenza A virus
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DOI：
10.1128/jvi.02683-07
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发表时间：
2008-05-01
影响因子：
5.4
通讯作者：
Holmes, Edward C.
中科院分区：
文献类型：
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作者：
Boni, Maciei F.;Zhou, Yang;Holmes, Edward C.
为了确定人类甲型流感病毒中同源重组的程度，我们组装了一个包含13,852个序列的数据集，这些序列代表所有八个片段和两个主要的流通亚型H3N2和H1N1。使用穷举搜索和镶嵌结构的非参数检验，我们在五个不同的RNA片段中鉴定了315个序列(类似于2%)，经过多次比较校正后，这些片段具有统计上显著的马赛克信号，与同源重组兼容。在这些序列中，只有两个含有足够长度的重组区(>；100个核苷酸[NT])，可以用系统发育学方法证实同源重组的发生，其余的涉及非常短的序列区域(15-30个核苷酸)。虽然二次分析揭示了与重组作用相一致的系统发育不一致的模式，但两个候选重组体都没有得到强有力的支持。鉴于我们无法排除扩增过程中混合感染和模板转换的发生，实验室人工制品为这两个案例中发生的系统发育不一致提供了另一种和可能的解释。因此，我们得出结论，如果真的发生了这种情况，同源重组在人类甲型流感病毒的进化中只起到了非常小的作用。
To determine the extent of homologous recombination in human influenza A virus, we assembled a data set of 13,852 sequences representing all eight segments and both major circulating subtypes, H3N2 and H1N1. Using an exhaustive search and a nonparametric test for mosaic structure, we identified 315 sequences (similar to 2%) in five different RNA segments that, after a multiple-comparison correction, had statistically significant mosaic signals compatible with homologous recombination. Of these, only two contained recombinant regions of sufficient length (> 100 nucleotides [nt]) that the occurrence of homologous recombination could be verified using phylogenetic methods, with the rest involving very short sequence regions (15 to 30 nt). Although this secondary analysis revealed patterns of phylogenetic incongruence compatible with the action of recombination, neither candidate recombinant was strongly supported. Given our inability to exclude the occurrence of mixed infection and template switching during amplification, laboratory artifacts provide an alternative and likely explanation for the occurrence of phylogenetic incongruence in these two cases. We therefore conclude that, if it occurs at all, homologous recombination plays only a very minor role in the evolution of human influenza A virus.