Taylor Jesse E, Korber Bette T
Institute of Cell, Animal, and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK.
Infect Genet Evol. 2005 Jan;5(1):85-95. doi: 10.1016/j.meegid.2004.07.001.
Because recombination between a pair of viral genomes can occur only when both viruses are present in the same host, genealogical evidence of recombination is influenced by the rate of viral migration between infected hosts. If superinfection is rare, then recombining viral genomes will usually be more closely related to each other than to viral genomes present in other hosts and the impact of recombination on the genealogy of a sample of viruses from different hosts may be weak. We used this relationship to estimate the relative rate of intra-subtype HIV-1 superinfection in six urban populations. Comparisons of the population recombination rates estimated from the HIV-1 sequence data with population recombination rates estimated for sets of sequences simulated using a structured coalescent process suggest that intra-subtype superinfection rates in all but one of these populations may be as high as 15% of the corresponding infection rate. However, we caution that these estimates might be upwardly biased if variation in contact and mixing rates between infected hosts causes viral lineages to be concentrated in groups with higher than average superinfection rates.
由于只有当两种病毒同时存在于同一宿主中时，一对病毒基因组之间才会发生重组，因此重组的谱系证据会受到病毒在受感染宿主之间迁移速率的影响。如果双重感染很少见，那么发生重组的病毒基因组通常彼此之间的关系会比与其他宿主中存在的病毒基因组更为密切，并且重组对来自不同宿主的病毒样本谱系的影响可能很小。我们利用这种关系来估计六个城市人群中HIV-1亚型内双重感染的相对速率。将根据HIV-1序列数据估计的群体重组率与使用结构化合并过程模拟的序列集估计的群体重组率进行比较，结果表明，除其中一个人群外，所有这些人群中的亚型内双重感染率可能高达相应感染率的15%。但是，我们提醒，如果受感染宿主之间接触和混合率的差异导致病毒谱系集中在双重感染率高于平均水平的群体中，那么这些估计值可能会偏高。
